From David.Messina at sbc.su.se  Tue Mar  1 09:02:59 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 1 Mar 2011 15:02:59 +0100
Subject: [Bioperl-l] Plans for the next release (and beyond)
In-Reply-To: <11F5BA8C-D4F4-419B-870B-D4B5180F4D7D@illinois.edu>
References: <11F5BA8C-D4F4-419B-870B-D4B5180F4D7D@illinois.edu>
Message-ID: <AANLkTinSR+RwUrvTeyund+CoxDzgEEqrGP0F2RW0_666@mail.gmail.com>

Hi Chris and everyone,

The plans sound great.

My only concern would be on point 3, moving some of the wiki docs into the
distros.

- In what format would the docs be in the distros?

Would it be POD? There is rich markup (URLs, code blocks, syntax coloring,
font sizes, etc) available on the wiki that I'd hate to lose.


- Are there discordant versions now?

I agree that we shouldn't maintain separate versions of these, but I thought
the tutorial had been moved completely to the wiki a while ago, and AFAIK,
the HOWTOs are only present on the wiki. I admit, though, I haven't looked
into this extensively.


- Tying the docs to the version of the code they came with

This could be beneficial if we expect people to have a (good) reason to be
using different (read: OLD) versions of the code. But in practice we're
pretty much always going to recommend people use the latest version, right?
In which case having the docs on the wiki (in sync with the latest, greatest
version) would be fairly practical.

Even if there is a good case for supporting older versions of the code and
docs, I don't know that that's enough of an asset to outweigh the downsides
such as loss of rich formatting and having to have some POD->wiki bridge and
keep it in sync.


I raise all the above mostly to ask for more information on that part of the
plan ? I suspect you've considered most of my concerns already, so I'm quite
open to seeing a different point of view on this.


Dave








3) I would like to work on moving the HOWTO's and other relevant
> documentation (Tutorial) back into the distributions, maybe in a particular
> namespace (Bio::Manual or similar).  The reason is simple: maintaining
> possibly discordant versions of documentation is unsustainable.  We could
> possibly set up a way of converting POD->wiki for on-line documentation, but
> I would like the documentation be tied to the version of the code it comes
> with, and the only easy way to do so is to package them all together.
>


From awitney at sgul.ac.uk  Tue Mar  1 12:08:12 2011
From: awitney at sgul.ac.uk (Adam Witney)
Date: Tue, 1 Mar 2011 17:08:12 +0000
Subject: [Bioperl-l] building NGS pipeline
In-Reply-To: <0FF71A5D-F5F6-4AAD-9501-4F4911DB40D8@illinois.edu>
References: <86D567CE-1735-4D85-B40F-B67823749FB7@sgul.ac.uk>
	<AANLkTi=eU0f=GuHE=zLfLoc5LhaiHBG_A2mjmMybQeNH@mail.gmail.com>
	<0FF71A5D-F5F6-4AAD-9501-4F4911DB40D8@illinois.edu>
Message-ID: <066A6A2B-05F7-4523-8A22-A91209953BB7@sgul.ac.uk>


On 28 Feb 2011, at 15:03, Chris Fields wrote:

> On Feb 28, 2011, at 6:04 AM, Sean Davis wrote:
> 
>> On Mon, Feb 28, 2011 at 6:06 AM, Adam Witney <awitney at sgul.ac.uk> wrote:
>> 
>>> Hi,
>>> 
>>> I'm trying to put together a set of steps to runs some analysis on NGS data
>>> we have. I have found modules that wrap alignment software such as
>>> bowtie/bwa/maq, but are there any packages to calculate RPKM's etc? what are
>>> people using for this?
>>> 
>>> 
>> scripture, cufflinks/cuffdiff, bioconductor (GenomicFeatures package, for
>> example), ERANGE (wold lab), and several others.  I don't know of perl
>> wrappers for these, but they are all command-line applications, generally
>> speaking.
>> 
>> This is an interesting site to follow for RNA-seq analysis and applications:
>> 
>> http://rna-seqblog.com/
>> 
>> Sean
> 
> BioPerl does have wrappers and interfaces for some packages, particularly Lincoln's Bio::DB::Sam (samtools package) and wrappers for bowtie, tophat, and bwa.  Locally, for comparative gene expression analyses we use bioconductor (many packages to choose from) as well as the command-line tools Sean mentions.
> 
> chris 

Thanks Sean, Chris,

the bowtie/tophat/cufflinks set of tools seem to work well. I have also come across myrna also but I am still getting that setup.

Thanks again

adam



From cjfields at illinois.edu  Tue Mar  1 12:37:29 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 1 Mar 2011 11:37:29 -0600
Subject: [Bioperl-l] Plans for the next release (and beyond)
In-Reply-To: <AANLkTinSR+RwUrvTeyund+CoxDzgEEqrGP0F2RW0_666@mail.gmail.com>
References: <11F5BA8C-D4F4-419B-870B-D4B5180F4D7D@illinois.edu>
	<AANLkTinSR+RwUrvTeyund+CoxDzgEEqrGP0F2RW0_666@mail.gmail.com>
Message-ID: <90D9611F-0DFA-43A6-A3C4-65948DF3F071@illinois.edu>

On Mar 1, 2011, at 8:02 AM, Dave Messina wrote:

> Hi Chris and everyone,
> 
> The plans sound great.
> 
> My only concern would be on point 3, moving some of the wiki docs into the distros.
> 
> - In what format would the docs be in the distros?
> 
> Would it be POD? There is rich markup (URLs, code blocks, syntax coloring, font sizes, etc) available on the wiki that I'd hate to lose.

It would very likely be POD, though I believe there are POD extensions for adding additional markup in CPAN.  We wouldn't necessarily lose the wiki HOWTOs, but they would be only editable via changes to the official docs in github.  My thought is to have wiki pages tied to the latest version in github via POD->wiki, with additional markup added in for syntax highlighting, etc.  Lots of CPAN modules that could help with this, but it needs further investigation.  Might need a HOWTO unto itself :)

One other point: inclusion of docs may also allow easier implementation of inline testing, where synopsis or HOWTO code can be directly tested from POD when specific directives allow for it.  I believe Dist::Zilla has plugins for this, and of course there is Test::Inline:

http://search.cpan.org/dist/Test-Inline/lib/Test/Inline.pm

This pushes the developers a bit to make sure code examples actually pass tests.  In particular I have thought about using this with the eutils cookbook, just to catch any changes on NCBI's end, but then realized it's broadly applicable to other areas as well.  

> - Are there discordant versions now?
> 
> I agree that we shouldn't maintain separate versions of these, but I thought the tutorial had been moved completely to the wiki a while ago, and AFAIK, the HOWTOs are only present on the wiki. I admit, though, I haven't looked into this extensively.

The original intent on moving docs to the wiki was somewhat correct: we wanted dynamic documentation that could be marked up for easier reading, better annotation, etc.  Wiki markup and templates has proved more useful than simple POD (HOWTO for Bio::Graphics, for example).  

However, at least to me there seems to be a fundamental disconnect between the code being developed in one repository (github) and the documentation being maintained elsewhere (wiki).  In many cases, once docs are placed on the wiki they seem to be largely forgotten by the devs once they have reached 'completeness'.  Our focus tends to be the code itself, not the documentation.  I'm basically looking for ways to resolve that and have documentation evolve along with the code, if possible making it testable.

Lastly, access to critical documentation is now reliant on access to the wiki, which may not always be possible.  We've had several wiki outages over the years and have recently talked about (off-list) migrating some resource away from open bio servers, wikis being one due to maintenance overhead and spam.  We'll always have a centralized website of some sort, I just want to make sure that one has means to access good documentation all the time.  Installing it with the code seems the best way currently, but I'm open to suggestions.

> - Tying the docs to the version of the code they came with
> 
> This could be beneficial if we expect people to have a (good) reason to be using different (read: OLD) versions of the code. But in practice we're pretty much always going to recommend people use the latest version, right? In which case having the docs on the wiki (in sync with the latest, greatest version) would be fairly practical.

Right, I agree, and I believe the wikis should only contain a very specific version of the docs, probably either the latest CPAN release or master.  However, I'm thinking of cases where users might not be able to get the latest/greatest, perhaps b/c they are constrained in using a specific version: with Ensembl (v. 1.2.3) or via sysadmin restrictions. 

If we consistently point to the official documentation as being on the wiki, we're not tying it to any specific version (unless it's explicitly stated), only what should work with the current version.    The only history is via the edits on the wiki page, which is not associated with anything, just the edits made.  

We should be able to demonstrate via tests that code and examples released with a specific version of BioPerl, including those in the HOWTOs and the tutorial, should work with that version of the software; anything else is a documentation error or a bug.  We can't do that currently.

> Even if there is a good case for supporting older versions of the code and docs, I don't know that that's enough of an asset to outweigh the downsides such as loss of rich formatting and having to have some POD->wiki bridge and keep it in sync.

The actual process of including documentation with the code works as the archival process itself (v 1.7 docs go with v 1.7 code, v 2 with v2 code, etc).  And I think there are ways around the lack of rich formatting with POD, just need to look into it more.

> I raise all the above mostly to ask for more information on that part of the plan ? I suspect you've considered most of my concerns already, so I'm quite open to seeing a different point of view on this.
> 
> 
> Dave

I've thought about it (as you can probably tell) but I think thought is needed about how to approach it.  It might require testing things out a bit first.

chris



From moitrayee at mbu.iisc.ernet.in  Tue Mar  1 06:22:54 2011
From: moitrayee at mbu.iisc.ernet.in (moitrayee at mbu.iisc.ernet.in)
Date: Tue, 1 Mar 2011 16:52:54 +0530 (IST)
Subject: [Bioperl-l] clustering trees obtained from phylip neighbor
Message-ID: <57675.10.128.10.17.1298978574.squirrel@mbu.iisc.ernet.in>

Dear BioPerl Users/Developers,

I have obtained a tree using a very large number of nodes
(1000 nodes) using the neighbor joining in PHYLIP. A small
test output looks like the following:

  +------------------------------------------------Bovine
--6
  !    +-------------------------------------------Mouse
  +----5
       !                        +------------------Gibbon
       +------------------------4
                                !    +-------------Orang
                                +----3
                                     !   +---------Gorilla
                                     +---2
                                         ! +-------Chimp
                                         +-1
                                           +-------Human

The outtree in Newick format is:

(Bovine:0.81551,(Mouse:0.73556,(Gibbon:0.31044,(Orang:0.24003,
(Gorilla:0.16418,(Chimp:0.13460,Human:0.13460):0.02958):0.07586):0.07040):0.42512):0.07995);


I am trying to obtain the cluster at different fork level of this tree.

The fork level goes as an user input. I looked into the link

http://www.bioperl.org/wiki/HOWTO:Trees#Related_Modules

But the Node connectivity methods described there does not apply
to the tree I have pasted above.

Any help / suggestions would be thankfully appreciated.

Thanks a lot in advance and looking forward to hear from you.

Sincere Regards,
Moitrayee Bhattacharyya
Molecular Biophysics Unit,
Indian Institute of Science
Bangalore-560012
India



-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.


From lskatz at gmail.com  Wed Mar  2 09:32:24 2011
From: lskatz at gmail.com (Lee Katz)
Date: Wed, 2 Mar 2011 09:32:24 -0500
Subject: [Bioperl-l] GuessSeqFormat
Message-ID: <AANLkTi=Aa=a-gs4shAM3yxk7w=h5MVqPy0VKKhLYoDah@mail.gmail.com>

Hi,
I noticed that even though there is a GuessSeqFormat module, SeqIO and
probably other modules first rely on the extension of a filename rather than
the content.  Could the behavior be altered so that it first checks the
content of the file, and if it turns up nothing then check the file
extension?

From daniel.standage at gmail.com  Wed Mar  2 11:01:12 2011
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 2 Mar 2011 10:01:12 -0600
Subject: [Bioperl-l] BioPerl POD
Message-ID: <AANLkTi=tfUzD78O-mA0tq84sFrtsCnaN4ZYD7Y0T+xnk@mail.gmail.com>

BioPerl,

I've been writing Perl (and BioPerl) for several years now, but I have
little to know experience using POD. I've added some POD to a module I wrote
and now I am trying to create an HTML page from it. I was able to do so with
*pod2html*, but the output is...underwhelming. The docs at
http://doc.bioperl.org aren't the essence of beauty themselves, but they do
have a bit of color and really nice features (like links to the code, etc).

Which tool(s) was/were used to generate the BioPerl HTML docs?

--
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University

From cjfields at illinois.edu  Wed Mar  2 11:26:58 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 2 Mar 2011 10:26:58 -0600
Subject: [Bioperl-l] GuessSeqFormat
In-Reply-To: <AANLkTi=Aa=a-gs4shAM3yxk7w=h5MVqPy0VKKhLYoDah@mail.gmail.com>
References: <AANLkTi=Aa=a-gs4shAM3yxk7w=h5MVqPy0VKKhLYoDah@mail.gmail.com>
Message-ID: <4F41B8DA-93D6-4442-95DC-D0EA24322351@illinois.edu>

On Mar 2, 2011, at 8:32 AM, Lee Katz wrote:

> Hi,
> I noticed that even though there is a GuessSeqFormat module, SeqIO and
> probably other modules first rely on the extension of a filename rather than
> the content.  Could the behavior be altered so that it first checks the
> content of the file, and if it turns up nothing then check the file
> extension?

The current behavior is the most common use case; stipulating the format with the file extension is pretty common and a surer way to get the correct format beyond explicitly setting it.  

If you want the opposite you can manually run the file through GuessSeqFormat and then (using the guess) use SeqIO with the guessed format, but I'm curious as to why you would want this behavior.  If it's for validation, I would highly recommend NOT using that module for validation purposes...

chris



From cjfields at illinois.edu  Wed Mar  2 11:40:22 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 2 Mar 2011 10:40:22 -0600
Subject: [Bioperl-l] BioPerl POD
In-Reply-To: <AANLkTi=tfUzD78O-mA0tq84sFrtsCnaN4ZYD7Y0T+xnk@mail.gmail.com>
References: <AANLkTi=tfUzD78O-mA0tq84sFrtsCnaN4ZYD7Y0T+xnk@mail.gmail.com>
Message-ID: <26289423-6B39-418C-B16B-1CECA73B5983@illinois.edu>

pdoc, I believe, is used for the doc.bioperl.org site:

http://pdoc.sourceforge.net/

Most POD->HTML converters are simple for a reason, sites generally use CSS to deal with formatting.  You could get around that with a few tools that embed the formatting with the HTML elements (see below link for examples), but I highly suggest using CSS if possible.  

Here's a stackoverflow article on the search.cpan.org HTML output:

http://stackoverflow.com/questions/4996684/modern-pod-to-html-converter-to-produce-results-like-search-cpan-org

Also, ActiveState has another one that generates their custom HTML (pretty nice), it comes with their perl dist I think.

chris

On Mar 2, 2011, at 10:01 AM, Daniel Standage wrote:

> BioPerl,
> 
> I've been writing Perl (and BioPerl) for several years now, but I have
> little to know experience using POD. I've added some POD to a module I wrote
> and now I am trying to create an HTML page from it. I was able to do so with
> *pod2html*, but the output is...underwhelming. The docs at
> http://doc.bioperl.org aren't the essence of beauty themselves, but they do
> have a bit of color and really nice features (like links to the code, etc).
> 
> Which tool(s) was/were used to generate the BioPerl HTML docs?
> 
> --
> Daniel S. Standage
> Graduate Research Assistant
> Bioinformatics and Computational Biology Program
> Iowa State University
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From lskatz at gmail.com  Wed Mar  2 11:53:52 2011
From: lskatz at gmail.com (Lee Katz)
Date: Wed, 2 Mar 2011 11:53:52 -0500
Subject: [Bioperl-l] GuessSeqFormat
In-Reply-To: <4F41B8DA-93D6-4442-95DC-D0EA24322351@illinois.edu>
References: <AANLkTi=Aa=a-gs4shAM3yxk7w=h5MVqPy0VKKhLYoDah@mail.gmail.com>
	<4F41B8DA-93D6-4442-95DC-D0EA24322351@illinois.edu>
Message-ID: <AANLkTimNeG4+n21mAVQfN3PS10snVStD6WTwAqT1EMhm@mail.gmail.com>

>
> The current behavior is the most common use case; stipulating the format
> with the file extension is pretty common and a surer way to get the correct
> format beyond explicitly setting it.
>
> If you want the opposite you can manually run the file through
> GuessSeqFormat and then (using the guess) use SeqIO with the guessed format,
> but I'm curious as to why you would want this behavior.  If it's for
> validation, I would highly recommend NOT using that module for validation
> purposes...
>
> chris
>


I understand your reasoning that checking a file extension is almost like a
user setting for providing the correct format.  Also I understand that I can
use the guessing module to discover the format on my own if I should choose
to do so.

However for your curiosity I'll try to explain why I would want this.
 Occasionally I get an error that I gave the wrong format for an input file.
 This could be quickly remedied by BioPerl figuring out the format by the
contents of the file rather than the extension.

Although now that I think about it--perhaps it is not a very fast method for
discovering the format and that it only looks at the first numbers of lines
before making a decision.  This would make it error-prone and slow I
suppose.

From daniel.standage at gmail.com  Wed Mar  2 11:55:46 2011
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 2 Mar 2011 10:55:46 -0600
Subject: [Bioperl-l] BioPerl POD
In-Reply-To: <26289423-6B39-418C-B16B-1CECA73B5983@illinois.edu>
References: <AANLkTi=tfUzD78O-mA0tq84sFrtsCnaN4ZYD7Y0T+xnk@mail.gmail.com>
	<26289423-6B39-418C-B16B-1CECA73B5983@illinois.edu>
Message-ID: <AANLkTikyhzULFY9foc5rOQ4yxMEpwS-4=RxFSBjfSioD@mail.gmail.com>

Great! Thanks!

--
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University



On Wed, Mar 2, 2011 at 10:40 AM, Chris Fields <cjfields at illinois.edu> wrote:

> pdoc, I believe, is used for the doc.bioperl.org site:
>
> http://pdoc.sourceforge.net/
>
> Most POD->HTML converters are simple for a reason, sites generally use CSS
> to deal with formatting.  You could get around that with a few tools that
> embed the formatting with the HTML elements (see below link for examples),
> but I highly suggest using CSS if possible.
>
> Here's a stackoverflow article on the search.cpan.org HTML output:
>
>
> http://stackoverflow.com/questions/4996684/modern-pod-to-html-converter-to-produce-results-like-search-cpan-org
>
> Also, ActiveState has another one that generates their custom HTML (pretty
> nice), it comes with their perl dist I think.
>
> chris
>
> On Mar 2, 2011, at 10:01 AM, Daniel Standage wrote:
>
> > BioPerl,
> >
> > I've been writing Perl (and BioPerl) for several years now, but I have
> > little to know experience using POD. I've added some POD to a module I
> wrote
> > and now I am trying to create an HTML page from it. I was able to do so
> with
> > *pod2html*, but the output is...underwhelming. The docs at
> > http://doc.bioperl.org aren't the essence of beauty themselves, but they
> do
> > have a bit of color and really nice features (like links to the code,
> etc).
> >
> > Which tool(s) was/were used to generate the BioPerl HTML docs?
> >
> > --
> > Daniel S. Standage
> > Graduate Research Assistant
> > Bioinformatics and Computational Biology Program
> > Iowa State University
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>

From roy.chaudhuri at gmail.com  Wed Mar  2 13:06:48 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Wed, 02 Mar 2011 18:06:48 +0000
Subject: [Bioperl-l] clustering trees obtained from phylip neighbor
In-Reply-To: <57675.10.128.10.17.1298978574.squirrel@mbu.iisc.ernet.in>
References: <57675.10.128.10.17.1298978574.squirrel@mbu.iisc.ernet.in>
Message-ID: <4D6E8738.7010103@gmail.com>

Hi Moitrayee,

I know a fair amount about phylogenetics, but I have no idea what you 
mean by the "fork level" of a tree. Perhaps you could use your example 
tree to explain what input you want the user to specify, and what output 
you want to produce?

Roy.

On 01/03/2011 11:22, moitrayee at mbu.iisc.ernet.in wrote:
> Dear BioPerl Users/Developers,
>
> I have obtained a tree using a very large number of nodes
> (1000 nodes) using the neighbor joining in PHYLIP. A small
> test output looks like the following:
>
>    +------------------------------------------------Bovine
> --6
>    !    +-------------------------------------------Mouse
>    +----5
>         !                        +------------------Gibbon
>         +------------------------4
>                                  !    +-------------Orang
>                                  +----3
>                                       !   +---------Gorilla
>                                       +---2
>                                           ! +-------Chimp
>                                           +-1
>                                             +-------Human
>
> The outtree in Newick format is:
>
> (Bovine:0.81551,(Mouse:0.73556,(Gibbon:0.31044,(Orang:0.24003,
> (Gorilla:0.16418,(Chimp:0.13460,Human:0.13460):0.02958):0.07586):0.07040):0.42512):0.07995);
>
>
> I am trying to obtain the cluster at different fork level of this tree.
>
> The fork level goes as an user input. I looked into the link
>
> http://www.bioperl.org/wiki/HOWTO:Trees#Related_Modules
>
> But the Node connectivity methods described there does not apply
> to the tree I have pasted above.
>
> Any help / suggestions would be thankfully appreciated.
>
> Thanks a lot in advance and looking forward to hear from you.
>
> Sincere Regards,
> Moitrayee Bhattacharyya
> Molecular Biophysics Unit,
> Indian Institute of Science
> Bangalore-560012
> India
>
>
>


From David.Messina at sbc.su.se  Thu Mar  3 10:52:44 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 3 Mar 2011 16:52:44 +0100
Subject: [Bioperl-l] Plans for the next release (and beyond)
In-Reply-To: <90D9611F-0DFA-43A6-A3C4-65948DF3F071@illinois.edu>
References: <11F5BA8C-D4F4-419B-870B-D4B5180F4D7D@illinois.edu>
	<AANLkTinSR+RwUrvTeyund+CoxDzgEEqrGP0F2RW0_666@mail.gmail.com>
	<90D9611F-0DFA-43A6-A3C4-65948DF3F071@illinois.edu>
Message-ID: <AANLkTikiWXv9yhVDYiPcAZ9D_12=d5TrKWcCMvsir0P4@mail.gmail.com>

Thanks, Chris.


> [re inline testing]
>


> This pushes the developers a bit to make sure code examples actually pass
> tests.  In particular I have thought about using this with the eutils
> cookbook, just to catch any changes on NCBI's end, but then realized it's
> broadly applicable to other areas as well.


This is a great idea, and goes well with the docs being version controlled
(your point below) along with the code itself.



> However, at least to me there seems to be a fundamental disconnect between
> the code being developed in one repository (github) and the documentation
> being maintained elsewhere (wiki).  In many cases, once docs are placed on
> the wiki they seem to be largely forgotten by the devs once they have
> reached 'completeness'.  Our focus tends to be the code itself, not the
> documentation.  I'm basically looking for ways to resolve that and have
> documentation evolve along with the code, if possible making it testable.
>

Yes, I can't argue. This has been a problem.



>   We should be able to demonstrate via tests that code and examples
> released with a specific version of BioPerl, including those in the HOWTOs
> and the tutorial, should work with that version of the software; anything
> else is a documentation error or a bug.  We can't do that currently.


That would be great.

In the end I'd have to say correct, up-to-date, and testable documentation
is the most important thing. Hopefully, we can find a way to keep the
readability/usability high ? which I think pretty much requires richer
formatting ? at the same time. Certainly worth trying in any case!


Dave


From p.j.a.cock at googlemail.com  Thu Mar  3 15:35:29 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 3 Mar 2011 20:35:29 +0000
Subject: [Bioperl-l] Fwd: [Bosc] Bioinformatics Open Source Conference (BOSC
 2011)--Call for Abstracts
In-Reply-To: <3922D2BE-5A99-4CDE-91AB-B311C42E10CE@lbl.gov>
References: <3922D2BE-5A99-4CDE-91AB-B311C42E10CE@lbl.gov>
Message-ID: <AANLkTinwgazvb5WPV-tiS41tO8wVkQ65NT0m75TPUVVw@mail.gmail.com>

Dear all,

I hope some of you will consider coming to BOSC 2011 in Vienna, and
maybe even submitting a talk or poster abstract.

Thank you,

Peter
(Biopython)


---------- Forwarded message ----------
From: Nomi Harris <nlharris at lbl.gov>
Date: Thu, Mar 3, 2011 at 7:37 PM
Subject: [Bosc] Bioinformatics Open Source Conference (BOSC
2011)--Call for Abstracts
To: bosc-announce at lists.open-bio.org, members at open-bio.org, GMOD
Announcements List <gmod-announce at lists.sourceforge.net>, GMOD
Developers List <gmod-devel at lists.sourceforge.net>
Cc: Nomi Harris <nlharris at lbl.gov>


We invite you to submit an abstract to BOSC 2011! ?Please forward this
message as appropriate, and forgive multiple postings.

Call for Abstracts for the 12th Annual Bioinformatics Open Source
Conference (BOSC 2011)
An ISMB 2011 Special Interest Group (SIG)

Dates: July 15-16, 2011
Location: Vienna, Austria
Web site: http://www.open-bio.org/wiki/BOSC_2011
Email: bosc at open-bio.org
BOSC announcements mailing list:
http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:
April 18, 2011: Deadline for submitting abstracts to BOSC 2011
May 9, 2011: Notifications of accepted abstracts emailed to
corresponding authors
July 13-14, 2011: Codefest 2011 programming session (see
http://www.open-bio.org/wiki/Codefest_2011 for details)
July 15-16, 2011: BOSC 2011
July 17-19, 2011: ISMB 2011

The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.

We invite you to submit abstracts for talks and posters. ?Sessions include:
- Approaches to parallel processing
- Cloud-based approaches to improving software and data accessibility
- The Semantic Web in open source bioinformatics
- Data visualization
- Tools for next-generation sequencing
- Other Open Source software

In addition to the above sessions, there will be a panel discussion
about "Meeting the challenges of inter-institutional collaboration".
We are also working to arrange a joint session with one of the other
ISMB SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student
Travel Awards for BOSC 2011. Each winner will be awarded $250 to
defray the costs of travel to BOSC 2011.

For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee:
Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock,
Erwin Frise, Darin London, Ron Taylor


_______________________________________________
BOSC mailing list
BOSC at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bosc


From sac at bioperl.org  Thu Mar  3 16:45:27 2011
From: sac at bioperl.org (Steve Chervitz)
Date: Thu, 3 Mar 2011 13:45:27 -0800
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
Message-ID: <AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>

Good catch, Elia. Looks like an legitimate edge case. Your fix looks
reasonable to me, but I haven't tried running it through the regression
tests to see if it breaks anything else.

Would be good to get this fix into the upcoming release.

Cheers,
Steve


On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:

> Hi Steve and Rob,
>
> it's been sometime since I last plunged my head into the code, but today we
> nailed a bug in Bio::Restriction::Analysis.
>
> Basically if a sequence has a restriction site which is exactly at the
> start of the sequence, it fails to produce any sites. The  culprits is this
> line (536 of Analysis.pm)
>
> unless ($cut_positions[0]) {
>
> where if the position is zero, it will fail to execute the rest of the
> code, so I changed it to:
>
> unless (defined($cut_positions[0])) {
>
> Also, for similar reasons a bit further down this line:
>
> my $start=1; my $stop; my %seq; my %stop;
>
> needs to change to:
> my $start=0; my $stop; my %seq; my %stop;
>
> I didn't commit the changes because I wanted to check if it makes sense,
> etc.
>
> The bug seems reproducible also in older, stable versions of bioperl, such
> as 1.4 and 1.6...
>
> best
>
> Elia
>
>
>
> ---
> Scientific Director - Bioinformatics, UCL Genomics
> Senior Lecturer, Bioinformatics
>
> UCL Cancer Institute
> Paul O' Gorman Building
> University College London
> 72, Huntley Street
> WC1E 6BT
> London
> UK
>
> Institute of Cell and Molecular Science
> Barts and The London School of Medicine and Dentistry
> 4 Newark Street
> Whitechapel
> London
> E1 2AT
>
> Office (UCL): +44 207 679 6493
> Fax: +44 0207 6796817
> Office (ICMS): +44 0207 8822374
>
> Mobile: +44 787 6478912
>
>
>
>
-- 
Steve Chervitz, Ph.D.
Omicia Inc. |  Senior Computational Biologist
2200 Powell Street, Ste 525, Emeryville CA 94608
T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com

Omicia.com: Unlocking Individualized Medicine.

From cjfields at illinois.edu  Thu Mar  3 17:42:41 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 3 Mar 2011 16:42:41 -0600
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
Message-ID: <E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>

Elia, Steve,

Any tests we can add for this?  I ran tests with the changes below and had several failing ones, but when only implementing the first fix ('unless (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate issue (string-based positions are 0-based, bioperl coords are 1-based).

chris

On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:

> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
> reasonable to me, but I haven't tried running it through the regression
> tests to see if it breaks anything else.
> 
> Would be good to get this fix into the upcoming release.
> 
> Cheers,
> Steve
> 
> 
> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
> 
>> Hi Steve and Rob,
>> 
>> it's been sometime since I last plunged my head into the code, but today we
>> nailed a bug in Bio::Restriction::Analysis.
>> 
>> Basically if a sequence has a restriction site which is exactly at the
>> start of the sequence, it fails to produce any sites. The  culprits is this
>> line (536 of Analysis.pm)
>> 
>> unless ($cut_positions[0]) {
>> 
>> where if the position is zero, it will fail to execute the rest of the
>> code, so I changed it to:
>> 
>> unless (defined($cut_positions[0])) {
>> 
>> Also, for similar reasons a bit further down this line:
>> 
>> my $start=1; my $stop; my %seq; my %stop;
>> 
>> needs to change to:
>> my $start=0; my $stop; my %seq; my %stop;
>> 
>> I didn't commit the changes because I wanted to check if it makes sense,
>> etc.
>> 
>> The bug seems reproducible also in older, stable versions of bioperl, such
>> as 1.4 and 1.6...
>> 
>> best
>> 
>> Elia
>> 
>> 
>> 
>> ---
>> Scientific Director - Bioinformatics, UCL Genomics
>> Senior Lecturer, Bioinformatics
>> 
>> UCL Cancer Institute
>> Paul O' Gorman Building
>> University College London
>> 72, Huntley Street
>> WC1E 6BT
>> London
>> UK
>> 
>> Institute of Cell and Molecular Science
>> Barts and The London School of Medicine and Dentistry
>> 4 Newark Street
>> Whitechapel
>> London
>> E1 2AT
>> 
>> Office (UCL): +44 207 679 6493
>> Fax: +44 0207 6796817
>> Office (ICMS): +44 0207 8822374
>> 
>> Mobile: +44 787 6478912
>> 
>> 
>> 
>> 
> -- 
> Steve Chervitz, Ph.D.
> Omicia Inc. |  Senior Computational Biologist
> 2200 Powell Street, Ste 525, Emeryville CA 94608
> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
> 
> Omicia.com: Unlocking Individualized Medicine.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Thu Mar  3 17:57:57 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 3 Mar 2011 16:57:57 -0600
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
	<E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
Message-ID: <CADBF252-9F51-4C7C-8062-C98B0E8E3B13@illinois.edu>

Forgot to add the summary, just for completeness. lots of errors like this that are halting tests:

------------- EXCEPTION -------------
MSG: Bad start parameter (0). Start must be positive.
STACK Bio::PrimarySeq::subseq /Users/cjfields/bioperl/bioperl-live/blib/lib/Bio/PrimarySeq.pm:400
STACK Bio::Restriction::Analysis::fragment_maps Bio/Restriction/Analysis.pm:556
STACK toplevel t/Restriction/Analysis-refac.t:143
-------------------------------------

Test Summary Report
-------------------
t/Restriction/Analysis-refac.t (Wstat: 65280 Tests: 26 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 91 tests but ran 26.
t/Restriction/Analysis.t      (Wstat: 65280 Tests: 118 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 177 tests but ran 118.
t/Restriction/Gel.t           (Wstat: 65280 Tests: 3 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 9 tests but ran 3.
Files=4, Tests=165, 29 wallclock secs ( 0.05 usr  0.03 sys +  3.44 cusr  0.21 csys =  3.73 CPU)
Result: FAIL
Failed 3/4 test programs. 0/165 subtests failed.

-c

On Mar 3, 2011, at 4:42 PM, Chris Fields wrote:

> Elia, Steve,
> 
> Any tests we can add for this?  I ran tests with the changes below and had several failing ones, but when only implementing the first fix ('unless (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate issue (string-based positions are 0-based, bioperl coords are 1-based).
> 
> chris
> 
> On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:
> 
>> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
>> reasonable to me, but I haven't tried running it through the regression
>> tests to see if it breaks anything else.
>> 
>> Would be good to get this fix into the upcoming release.
>> 
>> Cheers,
>> Steve
>> 
>> 
>> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
>> 
>>> Hi Steve and Rob,
>>> 
>>> it's been sometime since I last plunged my head into the code, but today we
>>> nailed a bug in Bio::Restriction::Analysis.
>>> 
>>> Basically if a sequence has a restriction site which is exactly at the
>>> start of the sequence, it fails to produce any sites. The  culprits is this
>>> line (536 of Analysis.pm)
>>> 
>>> unless ($cut_positions[0]) {
>>> 
>>> where if the position is zero, it will fail to execute the rest of the
>>> code, so I changed it to:
>>> 
>>> unless (defined($cut_positions[0])) {
>>> 
>>> Also, for similar reasons a bit further down this line:
>>> 
>>> my $start=1; my $stop; my %seq; my %stop;
>>> 
>>> needs to change to:
>>> my $start=0; my $stop; my %seq; my %stop;
>>> 
>>> I didn't commit the changes because I wanted to check if it makes sense,
>>> etc.
>>> 
>>> The bug seems reproducible also in older, stable versions of bioperl, such
>>> as 1.4 and 1.6...
>>> 
>>> best
>>> 
>>> Elia
>>> 
>>> 
>>> 
>>> ---
>>> Scientific Director - Bioinformatics, UCL Genomics
>>> Senior Lecturer, Bioinformatics
>>> 
>>> UCL Cancer Institute
>>> Paul O' Gorman Building
>>> University College London
>>> 72, Huntley Street
>>> WC1E 6BT
>>> London
>>> UK
>>> 
>>> Institute of Cell and Molecular Science
>>> Barts and The London School of Medicine and Dentistry
>>> 4 Newark Street
>>> Whitechapel
>>> London
>>> E1 2AT
>>> 
>>> Office (UCL): +44 207 679 6493
>>> Fax: +44 0207 6796817
>>> Office (ICMS): +44 0207 8822374
>>> 
>>> Mobile: +44 787 6478912
>>> 
>>> 
>>> 
>>> 
>> -- 
>> Steve Chervitz, Ph.D.
>> Omicia Inc. |  Senior Computational Biologist
>> 2200 Powell Street, Ste 525, Emeryville CA 94608
>> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
>> 
>> Omicia.com: Unlocking Individualized Medicine.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From sac at bioperl.org  Thu Mar  3 18:07:52 2011
From: sac at bioperl.org (Steve Chervitz)
Date: Thu, 3 Mar 2011 15:07:52 -0800
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <CADBF252-9F51-4C7C-8062-C98B0E8E3B13@illinois.edu>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
	<E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
	<CADBF252-9F51-4C7C-8062-C98B0E8E3B13@illinois.edu>
Message-ID: <AANLkTik7CGWADGzJvenQt7kbmOoMGij4u6Q5U9NOP_rd@mail.gmail.com>

Chris: Thanks or checking. I'm not sure about this.

Elia: Can you send an example sequence + enzyme name that causes the issue
you found?

Steve

On Thu, Mar 3, 2011 at 2:57 PM, Chris Fields <cjfields at illinois.edu> wrote:

> Forgot to add the summary, just for completeness. lots of errors like this
> that are halting tests:
>
> ------------- EXCEPTION -------------
> MSG: Bad start parameter (0). Start must be positive.
> STACK Bio::PrimarySeq::subseq
> /Users/cjfields/bioperl/bioperl-live/blib/lib/Bio/PrimarySeq.pm:400
> STACK Bio::Restriction::Analysis::fragment_maps
> Bio/Restriction/Analysis.pm:556
> STACK toplevel t/Restriction/Analysis-refac.t:143
> -------------------------------------
>
> Test Summary Report
> -------------------
> t/Restriction/Analysis-refac.t (Wstat: 65280 Tests: 26 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 91 tests but ran 26.
> t/Restriction/Analysis.t      (Wstat: 65280 Tests: 118 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 177 tests but ran 118.
> t/Restriction/Gel.t           (Wstat: 65280 Tests: 3 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 9 tests but ran 3.
> Files=4, Tests=165, 29 wallclock secs ( 0.05 usr  0.03 sys +  3.44 cusr
>  0.21 csys =  3.73 CPU)
> Result: FAIL
> Failed 3/4 test programs. 0/165 subtests failed.
>
> -c
>
> On Mar 3, 2011, at 4:42 PM, Chris Fields wrote:
>
> > Elia, Steve,
> >
> > Any tests we can add for this?  I ran tests with the changes below and
> had several failing ones, but when only implementing the first fix ('unless
> (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate
> issue (string-based positions are 0-based, bioperl coords are 1-based).
> >
> > chris
> >
> > On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:
> >
> >> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
> >> reasonable to me, but I haven't tried running it through the regression
> >> tests to see if it breaks anything else.
> >>
> >> Would be good to get this fix into the upcoming release.
> >>
> >> Cheers,
> >> Steve
> >>
> >>
> >> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
> >>
> >>> Hi Steve and Rob,
> >>>
> >>> it's been sometime since I last plunged my head into the code, but
> today we
> >>> nailed a bug in Bio::Restriction::Analysis.
> >>>
> >>> Basically if a sequence has a restriction site which is exactly at the
> >>> start of the sequence, it fails to produce any sites. The  culprits is
> this
> >>> line (536 of Analysis.pm)
> >>>
> >>> unless ($cut_positions[0]) {
> >>>
> >>> where if the position is zero, it will fail to execute the rest of the
> >>> code, so I changed it to:
> >>>
> >>> unless (defined($cut_positions[0])) {
> >>>
> >>> Also, for similar reasons a bit further down this line:
> >>>
> >>> my $start=1; my $stop; my %seq; my %stop;
> >>>
> >>> needs to change to:
> >>> my $start=0; my $stop; my %seq; my %stop;
> >>>
> >>> I didn't commit the changes because I wanted to check if it makes
> sense,
> >>> etc.
> >>>
> >>> The bug seems reproducible also in older, stable versions of bioperl,
> such
> >>> as 1.4 and 1.6...
> >>>
> >>> best
> >>>
> >>> Elia
> >>>
> >>>
> >>>
> >>> ---
> >>> Scientific Director - Bioinformatics, UCL Genomics
> >>> Senior Lecturer, Bioinformatics
> >>>
> >>> UCL Cancer Institute
> >>> Paul O' Gorman Building
> >>> University College London
> >>> 72, Huntley Street
> >>> WC1E 6BT
> >>> London
> >>> UK
> >>>
> >>> Institute of Cell and Molecular Science
> >>> Barts and The London School of Medicine and Dentistry
> >>> 4 Newark Street
> >>> Whitechapel
> >>> London
> >>> E1 2AT
> >>>
> >>> Office (UCL): +44 207 679 6493
> >>> Fax: +44 0207 6796817
> >>> Office (ICMS): +44 0207 8822374
> >>>
> >>> Mobile: +44 787 6478912
> >>>
> >>>
> >>>
> >>>
> >> --
> >> Steve Chervitz, Ph.D.
> >> Omicia Inc. |  Senior Computational Biologist
> >> 2200 Powell Street, Ste 525, Emeryville CA 94608
> >> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
> >>
> >> Omicia.com: Unlocking Individualized Medicine.
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>

From hartzell at alerce.com  Thu Mar  3 18:04:34 2011
From: hartzell at alerce.com (George Hartzell)
Date: Thu, 3 Mar 2011 15:04:34 -0800
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
Message-ID: <19824.7810.437300.584113@gargle.gargle.HOWL>


Hi all,

I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
seems to have it.  The only tarballs that end up in Chris' directory
are these:

/Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
/Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
/Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz

It is listed in the 02packages.details.txt.gz file that is mirrored.

Thoughts, suggestions?

Thanks,

g.

From cjfields at illinois.edu  Thu Mar  3 21:24:05 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 3 Mar 2011 20:24:05 -0600
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <19824.7810.437300.584113@gargle.gargle.HOWL>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
Message-ID: <5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>

On Mar 3, 2011, at 5:04 PM, George Hartzell wrote:

> Hi all,
> 
> I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
> does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
> seems to have it.  The only tarballs that end up in Chris' directory
> are these:
> 
> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
> 
> It is listed in the 02packages.details.txt.gz file that is mirrored.
> 
> Thoughts, suggestions?
> 
> Thanks,
> 
> g.

That's odd; could it be the repo you created the mirror from?

This is my PAUSE account:

 BioPerl-1.6.0.meta                                   78518  Sun, 25 Jan 2009 05:19:20 GMT
 BioPerl-1.6.0.readme                                 12174  Sun, 25 Jan 2009 05:19:41 GMT
 BioPerl-1.6.0.tar.gz                               6813396  Sun, 25 Jan 2009 17:14:12 GMT
 BioPerl-1.6.1.meta                                   82231  Tue, 29 Sep 2009 16:33:52 GMT
 BioPerl-1.6.1.readme                                 12174  Tue, 29 Sep 2009 16:33:49 GMT
 BioPerl-1.6.1.tar.gz                               10462526  Tue, 29 Sep 2009 16:43:11 GMT
 BioPerl-DB-1.6.0_001.tar.gz                         494106  Wed, 30 Sep 2009 20:49:59 GMT
 BioPerl-Network-1.6.0_001.tar.gz                   2198338  Wed, 30 Sep 2009 20:50:18 GMT
 BioPerl-Run-1.6.1_001.tar.gz                       4289239  Wed, 30 Sep 2009 21:07:38 GMT
 BioPerl-db-1.6.0.meta                                 7728  Tue, 24 Feb 2009 02:58:05 GMT
 BioPerl-db-1.6.0.readme                               7066  Tue, 24 Feb 2009 02:58:05 GMT
 BioPerl-db-1.6.0.tar.gz                             392773  Tue, 24 Feb 2009 15:33:05 GMT
 BioPerl-network-1.6.0.meta                            1268  Tue, 24 Feb 2009 03:00:26 GMT
 BioPerl-network-1.6.0.readme                          3669  Tue, 24 Feb 2009 03:00:28 GMT
 BioPerl-network-1.6.0.tar.gz                       1410782  Tue, 24 Feb 2009 15:33:16 GMT
 BioPerl-run-1.6.0.meta                               10289  Tue, 24 Feb 2009 02:59:26 GMT
 BioPerl-run-1.6.0.readme                               576  Tue, 24 Feb 2009 02:59:26 GMT
 BioPerl-run-1.6.0.tar.gz                           4082430  Tue, 24 Feb 2009 15:34:43 GMT
 BioPerl-run-1.6.1.meta                               10289  Wed, 25 Feb 2009 16:07:06 GMT
 BioPerl-run-1.6.1.readme                               576  Wed, 25 Feb 2009 16:07:06 GMT
 BioPerl-run-1.6.1.tar.gz                           4082463  Wed, 25 Feb 2009 16:14:37 GMT
 CHECKSUMS                                             5035  Sun, 03 Oct 2010 19:21:56 GMT

chris

From hartzell at alerce.com  Fri Mar  4 00:50:49 2011
From: hartzell at alerce.com (George Hartzell)
Date: Thu, 3 Mar 2011 21:50:49 -0800
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
	<5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
Message-ID: <19824.32185.570232.624286@gargle.gargle.HOWL>

Chris Fields writes:
 > On Mar 3, 2011, at 5:04 PM, George Hartzell wrote:
 > 
 > > Hi all,
 > > 
 > > I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
 > > does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
 > > seems to have it.  The only tarballs that end up in Chris' directory
 > > are these:
 > > 
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
 > > 
 > > It is listed in the 02packages.details.txt.gz file that is mirrored.
 > > 
 > > Thoughts, suggestions?
 > > 
 > > Thanks,
 > > 
 > > g.
 > 
 > That's odd; could it be the repo you created the mirror from?
 > 
 > This is my PAUSE account:
 > 
 >  BioPerl-1.6.0.meta                                   78518  Sun, 25 Jan 2009 05:19:20 GMT
 >  BioPerl-1.6.0.readme                                 12174  Sun, 25 Jan 2009 05:19:41 GMT
 >  BioPerl-1.6.0.tar.gz                               6813396  Sun, 25 Jan 2009 17:14:12 GMT
 >  BioPerl-1.6.1.meta                                   82231  Tue, 29 Sep 2009 16:33:52 GMT
 >  BioPerl-1.6.1.readme                                 12174  Tue, 29 Sep 2009 16:33:49 GMT
 >  BioPerl-1.6.1.tar.gz                               10462526  Tue, 29 Sep 2009 16:43:11 GMT
 >  BioPerl-DB-1.6.0_001.tar.gz                         494106  Wed, 30 Sep 2009 20:49:59 GMT
 >  BioPerl-Network-1.6.0_001.tar.gz                   2198338  Wed, 30 Sep 2009 20:50:18 GMT
 >  BioPerl-Run-1.6.1_001.tar.gz                       4289239  Wed, 30 Sep 2009 21:07:38 GMT
 >  BioPerl-db-1.6.0.meta                                 7728  Tue, 24 Feb 2009 02:58:05 GMT
 >  BioPerl-db-1.6.0.readme                               7066  Tue, 24 Feb 2009 02:58:05 GMT
 >  BioPerl-db-1.6.0.tar.gz                             392773  Tue, 24 Feb 2009 15:33:05 GMT
 >  BioPerl-network-1.6.0.meta                            1268  Tue, 24 Feb 2009 03:00:26 GMT
 >  BioPerl-network-1.6.0.readme                          3669  Tue, 24 Feb 2009 03:00:28 GMT
 >  BioPerl-network-1.6.0.tar.gz                       1410782  Tue, 24 Feb 2009 15:33:16 GMT
 >  BioPerl-run-1.6.0.meta                               10289  Tue, 24 Feb 2009 02:59:26 GMT
 >  BioPerl-run-1.6.0.readme                               576  Tue, 24 Feb 2009 02:59:26 GMT
 >  BioPerl-run-1.6.0.tar.gz                           4082430  Tue, 24 Feb 2009 15:34:43 GMT
 >  BioPerl-run-1.6.1.meta                               10289  Wed, 25 Feb 2009 16:07:06 GMT
 >  BioPerl-run-1.6.1.readme                               576  Wed, 25 Feb 2009 16:07:06 GMT
 >  BioPerl-run-1.6.1.tar.gz                           4082463  Wed, 25 Feb 2009 16:14:37 GMT
 >  CHECKSUMS                                             5035  Sun, 03 Oct 2010 19:21:56 GMT
 > 
 > chris
 > 
 > 

I've tried a couple of them, a couple of times.  Wouldn't surprise me
if it's something on my end.  I'll peek under the minicpan kilt over
the weekend and see if I can see what's going on.

g.

From e.stupka at ucl.ac.uk  Fri Mar  4 04:30:17 2011
From: e.stupka at ucl.ac.uk (Elia Stupka)
Date: Fri, 4 Mar 2011 09:30:17 +0000
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
	<E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
Message-ID: <535DCA0E-A74D-483B-96FB-544387EF08C3@ucl.ac.uk>

Ignore the second fix, the first one is the useful and correct one. The 2nd one was an oversight.

Elia


---
Scientific Director - Bioinformatics, UCL Genomics
Senior Lecturer, Bioinformatics

UCL Cancer Institute
Paul O' Gorman Building
University College London
Gower Street
WC1E 6BT
London
UK

Institute of Cell and Molecular Science
Barts and The London School of Medicine and Dentistry
4 Newark Street
Whitechapel
London
E1 2AT

Office (UCL): +44 207 679 6493
Fax: +44 0207 6796817 
Office (ICMS): +44 0207 8822374

On 3 Mar 2011, at 22:42, Chris Fields <cjfields at illinois.edu> wrote:

> Elia, Steve,
> 
> Any tests we can add for this?  I ran tests with the changes below and had several failing ones, but when only implementing the first fix ('unless (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate issue (string-based positions are 0-based, bioperl coords are 1-based).
> 
> chris
> 
> On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:
> 
>> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
>> reasonable to me, but I haven't tried running it through the regression
>> tests to see if it breaks anything else.
>> 
>> Would be good to get this fix into the upcoming release.
>> 
>> Cheers,
>> Steve
>> 
>> 
>> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
>> 
>>> Hi Steve and Rob,
>>> 
>>> it's been sometime since I last plunged my head into the code, but today we
>>> nailed a bug in Bio::Restriction::Analysis.
>>> 
>>> Basically if a sequence has a restriction site which is exactly at the
>>> start of the sequence, it fails to produce any sites. The  culprits is this
>>> line (536 of Analysis.pm)
>>> 
>>> unless ($cut_positions[0]) {
>>> 
>>> where if the position is zero, it will fail to execute the rest of the
>>> code, so I changed it to:
>>> 
>>> unless (defined($cut_positions[0])) {
>>> 
>>> Also, for similar reasons a bit further down this line:
>>> 
>>> my $start=1; my $stop; my %seq; my %stop;
>>> 
>>> needs to change to:
>>> my $start=0; my $stop; my %seq; my %stop;
>>> 
>>> I didn't commit the changes because I wanted to check if it makes sense,
>>> etc.
>>> 
>>> The bug seems reproducible also in older, stable versions of bioperl, such
>>> as 1.4 and 1.6...
>>> 
>>> best
>>> 
>>> Elia
>>> 
>>> 
>>> 
>>> ---
>>> Scientific Director - Bioinformatics, UCL Genomics
>>> Senior Lecturer, Bioinformatics
>>> 
>>> UCL Cancer Institute
>>> Paul O' Gorman Building
>>> University College London
>>> 72, Huntley Street
>>> WC1E 6BT
>>> London
>>> UK
>>> 
>>> Institute of Cell and Molecular Science
>>> Barts and The London School of Medicine and Dentistry
>>> 4 Newark Street
>>> Whitechapel
>>> London
>>> E1 2AT
>>> 
>>> Office (UCL): +44 207 679 6493
>>> Fax: +44 0207 6796817
>>> Office (ICMS): +44 0207 8822374
>>> 
>>> Mobile: +44 787 6478912
>>> 
>>> 
>>> 
>>> 
>> -- 
>> Steve Chervitz, Ph.D.
>> Omicia Inc. |  Senior Computational Biologist
>> 2200 Powell Street, Ste 525, Emeryville CA 94608
>> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
>> 
>> Omicia.com: Unlocking Individualized Medicine.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From cjfields at illinois.edu  Fri Mar  4 11:09:42 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 4 Mar 2011 10:09:42 -0600
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <535DCA0E-A74D-483B-96FB-544387EF08C3@ucl.ac.uk>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
	<E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
	<535DCA0E-A74D-483B-96FB-544387EF08C3@ucl.ac.uk>
Message-ID: <243A2900-C5D3-4772-AC88-69A3ABF238E6@illinois.edu>

Committed to github, should be in the next release.  I'll see if I can add a simple test for this.

chris


On Mar 4, 2011, at 3:30 AM, Elia Stupka wrote:

> Ignore the second fix, the first one is the useful and correct one. The 2nd one was an oversight.
> 
> Elia
> 
> 
> ---
> Scientific Director - Bioinformatics, UCL Genomics
> Senior Lecturer, Bioinformatics
> 
> UCL Cancer Institute
> Paul O' Gorman Building
> University College London
> Gower Street
> WC1E 6BT
> London
> UK
> 
> Institute of Cell and Molecular Science
> Barts and The London School of Medicine and Dentistry
> 4 Newark Street
> Whitechapel
> London
> E1 2AT
> 
> Office (UCL): +44 207 679 6493
> Fax: +44 0207 6796817 
> Office (ICMS): +44 0207 8822374
> 
> On 3 Mar 2011, at 22:42, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Elia, Steve,
>> 
>> Any tests we can add for this?  I ran tests with the changes below and had several failing ones, but when only implementing the first fix ('unless (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate issue (string-based positions are 0-based, bioperl coords are 1-based).
>> 
>> chris
>> 
>> On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:
>> 
>>> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
>>> reasonable to me, but I haven't tried running it through the regression
>>> tests to see if it breaks anything else.
>>> 
>>> Would be good to get this fix into the upcoming release.
>>> 
>>> Cheers,
>>> Steve
>>> 
>>> 
>>> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
>>> 
>>>> Hi Steve and Rob,
>>>> 
>>>> it's been sometime since I last plunged my head into the code, but today we
>>>> nailed a bug in Bio::Restriction::Analysis.
>>>> 
>>>> Basically if a sequence has a restriction site which is exactly at the
>>>> start of the sequence, it fails to produce any sites. The  culprits is this
>>>> line (536 of Analysis.pm)
>>>> 
>>>> unless ($cut_positions[0]) {
>>>> 
>>>> where if the position is zero, it will fail to execute the rest of the
>>>> code, so I changed it to:
>>>> 
>>>> unless (defined($cut_positions[0])) {
>>>> 
>>>> Also, for similar reasons a bit further down this line:
>>>> 
>>>> my $start=1; my $stop; my %seq; my %stop;
>>>> 
>>>> needs to change to:
>>>> my $start=0; my $stop; my %seq; my %stop;
>>>> 
>>>> I didn't commit the changes because I wanted to check if it makes sense,
>>>> etc.
>>>> 
>>>> The bug seems reproducible also in older, stable versions of bioperl, such
>>>> as 1.4 and 1.6...
>>>> 
>>>> best
>>>> 
>>>> Elia
>>>> 
>>>> 
>>>> 
>>>> ---
>>>> Scientific Director - Bioinformatics, UCL Genomics
>>>> Senior Lecturer, Bioinformatics
>>>> 
>>>> UCL Cancer Institute
>>>> Paul O' Gorman Building
>>>> University College London
>>>> 72, Huntley Street
>>>> WC1E 6BT
>>>> London
>>>> UK
>>>> 
>>>> Institute of Cell and Molecular Science
>>>> Barts and The London School of Medicine and Dentistry
>>>> 4 Newark Street
>>>> Whitechapel
>>>> London
>>>> E1 2AT
>>>> 
>>>> Office (UCL): +44 207 679 6493
>>>> Fax: +44 0207 6796817
>>>> Office (ICMS): +44 0207 8822374
>>>> 
>>>> Mobile: +44 787 6478912
>>>> 
>>>> 
>>>> 
>>>> 
>>> -- 
>>> Steve Chervitz, Ph.D.
>>> Omicia Inc. |  Senior Computational Biologist
>>> 2200 Powell Street, Ste 525, Emeryville CA 94608
>>> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
>>> 
>>> Omicia.com: Unlocking Individualized Medicine.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 



From hartzell at alerce.com  Fri Mar  4 13:16:03 2011
From: hartzell at alerce.com (George Hartzell)
Date: Fri, 4 Mar 2011 10:16:03 -0800
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
	<5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
Message-ID: <19825.11363.446731.724414@gargle.gargle.HOWL>

Chris Fields writes:
 > On Mar 3, 2011, at 5:04 PM, George Hartzell wrote:
 > 
 > > Hi all,
 > > 
 > > I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
 > > does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
 > > seems to have it.  The only tarballs that end up in Chris' directory
 > > are these:
 > > 
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
 > > 
 > > It is listed in the 02packages.details.txt.gz file that is mirrored.
 > > 
 > > Thoughts, suggestions?
 > > 
 > > Thanks,
 > > 
 > > g.
 > 
 > That's odd; could it be the repo you created the mirror from?
 > 
 > This is my PAUSE account:
 > 
 >  BioPerl-1.6.0.meta                                   78518  Sun, 25 Jan 2009 05:19:20 GMT
 >  BioPerl-1.6.0.readme                                 12174  Sun, 25 Jan 2009 05:19:41 GMT
 >  BioPerl-1.6.0.tar.gz                               6813396  Sun, 25 Jan 2009 17:14:12 GMT
 >  BioPerl-1.6.1.meta                                   82231  Tue, 29 Sep 2009 16:33:52 GMT
 >  BioPerl-1.6.1.readme                                 12174  Tue, 29 Sep 2009 16:33:49 GMT
 >  BioPerl-1.6.1.tar.gz                               10462526  Tue, 29 Sep 2009 16:43:11 GMT
 >  BioPerl-DB-1.6.0_001.tar.gz                         494106  Wed, 30 Sep 2009 20:49:59 GMT
 >  BioPerl-Network-1.6.0_001.tar.gz                   2198338  Wed, 30 Sep 2009 20:50:18 GMT
 >  BioPerl-Run-1.6.1_001.tar.gz                       4289239  Wed, 30 Sep 2009 21:07:38 GMT
 >  BioPerl-db-1.6.0.meta                                 7728  Tue, 24 Feb 2009 02:58:05 GMT
 >  BioPerl-db-1.6.0.readme                               7066  Tue, 24 Feb 2009 02:58:05 GMT
 >  BioPerl-db-1.6.0.tar.gz                             392773  Tue, 24 Feb 2009 15:33:05 GMT
 >  BioPerl-network-1.6.0.meta                            1268  Tue, 24 Feb 2009 03:00:26 GMT
 >  BioPerl-network-1.6.0.readme                          3669  Tue, 24 Feb 2009 03:00:28 GMT
 >  BioPerl-network-1.6.0.tar.gz                       1410782  Tue, 24 Feb 2009 15:33:16 GMT
 >  BioPerl-run-1.6.0.meta                               10289  Tue, 24 Feb 2009 02:59:26 GMT
 >  BioPerl-run-1.6.0.readme                               576  Tue, 24 Feb 2009 02:59:26 GMT
 >  BioPerl-run-1.6.0.tar.gz                           4082430  Tue, 24 Feb 2009 15:34:43 GMT
 >  BioPerl-run-1.6.1.meta                               10289  Wed, 25 Feb 2009 16:07:06 GMT
 >  BioPerl-run-1.6.1.readme                               576  Wed, 25 Feb 2009 16:07:06 GMT
 >  BioPerl-run-1.6.1.tar.gz                           4082463  Wed, 25 Feb 2009 16:14:37 GMT
 >  CHECKSUMS                                             5035  Sun, 03 Oct 2010 19:21:56 GMT
 > 
 > chris
 > 
 > 

Ok, apparently we've earned a reputation, and it has preceeded us....
Here's the code that Ricardo uses to filter the list of things to mirror:

  sub _filter_module {
    my $self = shift;
    my $args = shift;
  
    if ($self->{skip_perl}) {
      return 1 if $args->{path} =~ m{/(?:emb|syb|bio)?perl-\d}i;
      return 1 if $args->{path} =~ m{/(?:parrot|ponie)-\d}i;
      return 1 if $args->{path} =~ m{/(?:kurila)-\d}i;
      return 1 if $args->{path} =~ m{/\bperl-?5\.004}i;
      return 1 if $args->{path} =~ m{/\bperl_mlb\.zip}i;
    }
  
    return 1 if $self->__do_filter($self->{path_filters},   $args->{path});
    return 1 if $self->__do_filter($self->{module_filters}, $args->{module});
    return 0;
  }

I'll ask him why he's filtering bioperl out and we can see if we can
fix it.  I'm hoping that it's just an over-eager cut-n-paste of stuff
that he thinks of as the "perl" source (which is why it's within the
skip_perl test) and not that we've done something egregious.

g.

From cjfields at illinois.edu  Fri Mar  4 13:24:05 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 4 Mar 2011 12:24:05 -0600
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <19825.11363.446731.724414@gargle.gargle.HOWL>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
	<5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
	<19825.11363.446731.724414@gargle.gargle.HOWL>
Message-ID: <F8DFAE16-FE59-4EDF-80D0-4FE60620FFF8@illinois.edu>

On Mar 4, 2011, at 12:16 PM, George Hartzell wrote:

> Chris Fields writes:
>> On Mar 3, 2011, at 5:04 PM, George Hartzell wrote:
>> 
>>> Hi all,
>>> 
>>> I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
>>> does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
>>> seems to have it.  The only tarballs that end up in Chris' directory
>>> are these:
>>> 
>>> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
>>> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
>>> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
>>> 
>>> It is listed in the 02packages.details.txt.gz file that is mirrored.
>>> 
>>> Thoughts, suggestions?
>>> 
>>> Thanks,
>>> 
>>> g.
>> 
>> That's odd; could it be the repo you created the mirror from?
>> 
>> This is my PAUSE account:
>> 
>> BioPerl-1.6.0.meta                                   78518  Sun, 25 Jan 2009 05:19:20 GMT
>> BioPerl-1.6.0.readme                                 12174  Sun, 25 Jan 2009 05:19:41 GMT
>> BioPerl-1.6.0.tar.gz                               6813396  Sun, 25 Jan 2009 17:14:12 GMT
>> BioPerl-1.6.1.meta                                   82231  Tue, 29 Sep 2009 16:33:52 GMT
>> BioPerl-1.6.1.readme                                 12174  Tue, 29 Sep 2009 16:33:49 GMT
>> BioPerl-1.6.1.tar.gz                               10462526  Tue, 29 Sep 2009 16:43:11 GMT
>> BioPerl-DB-1.6.0_001.tar.gz                         494106  Wed, 30 Sep 2009 20:49:59 GMT
>> BioPerl-Network-1.6.0_001.tar.gz                   2198338  Wed, 30 Sep 2009 20:50:18 GMT
>> BioPerl-Run-1.6.1_001.tar.gz                       4289239  Wed, 30 Sep 2009 21:07:38 GMT
>> BioPerl-db-1.6.0.meta                                 7728  Tue, 24 Feb 2009 02:58:05 GMT
>> BioPerl-db-1.6.0.readme                               7066  Tue, 24 Feb 2009 02:58:05 GMT
>> BioPerl-db-1.6.0.tar.gz                             392773  Tue, 24 Feb 2009 15:33:05 GMT
>> BioPerl-network-1.6.0.meta                            1268  Tue, 24 Feb 2009 03:00:26 GMT
>> BioPerl-network-1.6.0.readme                          3669  Tue, 24 Feb 2009 03:00:28 GMT
>> BioPerl-network-1.6.0.tar.gz                       1410782  Tue, 24 Feb 2009 15:33:16 GMT
>> BioPerl-run-1.6.0.meta                               10289  Tue, 24 Feb 2009 02:59:26 GMT
>> BioPerl-run-1.6.0.readme                               576  Tue, 24 Feb 2009 02:59:26 GMT
>> BioPerl-run-1.6.0.tar.gz                           4082430  Tue, 24 Feb 2009 15:34:43 GMT
>> BioPerl-run-1.6.1.meta                               10289  Wed, 25 Feb 2009 16:07:06 GMT
>> BioPerl-run-1.6.1.readme                               576  Wed, 25 Feb 2009 16:07:06 GMT
>> BioPerl-run-1.6.1.tar.gz                           4082463  Wed, 25 Feb 2009 16:14:37 GMT
>> CHECKSUMS                                             5035  Sun, 03 Oct 2010 19:21:56 GMT
>> 
>> chris
>> 
>> 
> 
> Ok, apparently we've earned a reputation, and it has preceeded us....
> Here's the code that Ricardo uses to filter the list of things to mirror:
> 
>  sub _filter_module {
>    my $self = shift;
>    my $args = shift;
> 
>    if ($self->{skip_perl}) {
>      return 1 if $args->{path} =~ m{/(?:emb|syb|bio)?perl-\d}i;
>      return 1 if $args->{path} =~ m{/(?:parrot|ponie)-\d}i;
>      return 1 if $args->{path} =~ m{/(?:kurila)-\d}i;
>      return 1 if $args->{path} =~ m{/\bperl-?5\.004}i;
>      return 1 if $args->{path} =~ m{/\bperl_mlb\.zip}i;
>    }
> 
>    return 1 if $self->__do_filter($self->{path_filters},   $args->{path});
>    return 1 if $self->__do_filter($self->{module_filters}, $args->{module});
>    return 0;
>  }
> 
> I'll ask him why he's filtering bioperl out and we can see if we can
> fix it.  I'm hoping that it's just an over-eager cut-n-paste of stuff
> that he thinks of as the "perl" source (which is why it's within the
> skip_perl test) and not that we've done something egregious.
> 
> g.

Could be the size of the distribution was considered egregious (we're at 10 MB compressed I think).  Most of the other dists that appear to be filtered are fairly large as well.  That's nothing really these days; would be interested to hear what Ricardo says.

chris



From hlapp at drycafe.net  Fri Mar  4 18:26:25 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Fri, 4 Mar 2011 18:26:25 -0500
Subject: [Bioperl-l] Informatics job opportunity at NESCent
Message-ID: <1878F27F-000D-4C80-B9EA-A83F7887828F@drycafe.net>

(Apologies if you receive multiple copies, and also if you are not  
interested in job opportunities.  In my defense, quite a few people on  
Bio* lists might qualify for (let alone enjoy) the position. And if  
you know someone who might be interested please forward.)

===================================================
User Interface Design and Web Application Developer
===================================================

The National Evolutionary Synthesis Center (NESCent) seeks a creative  
and enthusiastic individual to design user interfaces and web  
applications for scientific applications. The incumbent will work as  
part of a small informatics team in close collaboration with domain  
scientists.

NESCent is an NSF-funded center dedicated to cross-disciplinary  
research in evolutionary science. Our informatics team works closely  
with visiting and resident scientists to support their custom software  
and database development needs. All NESCent software products are open- 
source, and the Center has a number of initiatives to actively promote  
collaborative development of community software resources  
(informatics.nescent.org). Above all, we are enthusiastic about our  
work, about the mission of the Center, and about the contribution of  
informatics to that mission.

Job description: The incumbent will design and develop user interfaces  
and web applications for databases and other software tools for  
sponsored scientists and staff. The job responsibilities include all  
stages of the software development process, including requirements  
gathering, design, implementation, release packaging and  
documentation, as part of a small team (typically 2-3 individuals)  
following project management best practices. We expect the incumbent  
to present their work at conferences and contribute to publications  
with scientific collaborators; interact regularly with visiting and  
resident scientists, other members of the informatics team and Center  
staff; and generally serve as an expert resource for Center personnel.  
The position provides opportunities for professional development. Most  
informatics staff work at our Durham NC offices, located adjacent to  
Duke University, but we do support a wide range of technologies for  
virtual communication with off-site staff and collaborators.

Required Qualifications:
* Demonstrated success collaborating with clients on custom software  
solutions
* Experience with various stages of the software development cycle
* Expertise in development and testing of user interface designs
* Excellent communication skills, both virtual and face-to-face
* A four-year college degree in Computer Science, Bioinformatics or a  
related field

Preferred Qualifications:
* M.S. or Ph.D. in Computer Science, Bioinformatics or related field  
along with demonstrated interest in science, particularly biology
* Expertise in rapid application development and respective  
programming technologies and languages (e.g., modern scripting  
languages and web-application frameworks such as Python/Django, Ruby/ 
Ruby-on-Rails, and Perl/Catalyst), fluency in Java programming, and  
prior experience in relational database programming (PostgreSQL or  
MySQL)
* Expertise in dynamic and interactive web technologies (JavaScript,  
CGI), web service (SOAP, REST, XML, JSON) and semantic web technologies
* Experience with open-source, and collaborative, software  
development, software usability design and assessment
* Expertise in graphic design, data visualization and/or scientific  
data integration

How to apply: Please send cover letter, resume and contact information  
for three references to Dr. Karen Cranston, Training Coordinator and  
Bioinformatics Project Manager (karen.cranston at nescent.org). Review of  
applications will begin March 21, 2011. Informal inquires or requests  
for additional information may be directed to Dr. Cranston by email or  
phone (+1-919-613-2275).

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================





From hartzell at alerce.com  Sat Mar  5 16:18:50 2011
From: hartzell at alerce.com (George Hartzell)
Date: Sat, 5 Mar 2011 13:18:50 -0800
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <19824.7810.437300.584113@gargle.gargle.HOWL>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
Message-ID: <19826.43194.173739.594355@gargle.gargle.HOWL>

George Hartzell writes:
 > 
 > Hi all,
 > 
 > I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
 > does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
 > seems to have it.  The only tarballs that end up in Chris' directory
 > are these:
 > 
 > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
 > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
 > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
 > 
 > It is listed in the 02packages.details.txt.gz file that is mirrored.
 > 

Here's the conclusion, for the list and posterity.

CPAN::Mini is excluding the BioPerl modules, as well as the perl
source distributions, because they're "too big".

You can get minicpan to mirror all this stuff by adding

 perl: 1

to your .minicpan, which causes the app to set its internal skip_perl
flag to 0, which in turn causes it to mirror the big stuff.

I'm running a few experiments to figure out how much add'l space gets
used if one allows bioperl without all of the other perl source
releases.  Maybe I can convince Ricard to do something less heavy
handed for us.

g.

From hlapp at drycafe.net  Sat Mar  5 21:58:04 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 5 Mar 2011 21:58:04 -0500
Subject: [Bioperl-l] Job opening for GMOD User Support Specialist
Message-ID: <814155D1-1CD5-4E66-B726-2CF7E33EF3CE@drycafe.net>

(Apologies if you receive multiple copies, and also if you are not  
interested in job opportunities. If you know someone who might be  
interested please forward.)

============================
GMOD User Support Specialist
============================

Are you fascinated by genomics and bioinformatics? Are you passionate  
about collaborative open-source software? Do you enjoy teaching and  
working with scientists?  If so, then this position is for you.

The Generic Model Organism Database project (GMOD) is a collection of  
open source software tools for creating and managing biological, and  
particularly genomic, databases.  GMOD has a large, highly  
distributed, and dynamic community of software users and developers.   
The University of North Carolina at Chapel Hill has an opening for a  
GMOD user support specialist, to be based at the US National  
Evolutionary Synthesis Center (NESCent, www.nescent.org) in Durham,  
North Carolina, while serving the international community of GMOD users.

Job Description:

The GMOD user support specialist will maintain online documentation;  
respond to mailing list help requests; present tutorials; organize  
short courses, conference sessions and other community building  
activities; survey user needs, and recruit members of the community to  
assist with these functions.   The incumbent will collaborate closely  
with the GMOD Coordinator (Scott Cain, The Ontario Institute for  
Cancer Research) and other distributed personnel.  See http://gmod.org/wiki/GMOD_Help_Desk 
  for more background on the activities of the user support  
specialist.  The salary range is $68,906 to $82,687, depending on  
qualifications, and the incumbent will receive a comprehensive  
benefits package as an SPA employee within the UNC system.

Qualifications:

Required qualifications include: excellent written and verbal  
communication skills; team orientation with strong interpersonal  
skills. Preferred qualifications include: an MS or PhD in biology,  
computer science or related field; three or more years of experience  
with web programming and relational database management systems; three  
or more years of experience with genome database administration or  
curation, preferably in a GMOD environment; at least one year of  
experience with web content management, ideally using MediaWiki;  
freedom to travel 5-15 weeks/yr.

To Apply:

Please provide a cover letter and CV, including contact information  
for three references, to Hilmar Lapp, Assistant Director of  
Informatics, NESCent, at hlapp at nescent.org, and submit materials  
through http://bit.ly/h9l74r.  Inquiries may be addressed to H. Lapp  
by email or by phone at 919.668.5288.

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================





From eigenrosen at gmail.com  Sun Mar  6 18:34:09 2011
From: eigenrosen at gmail.com (Michael Rosen)
Date: Sun, 6 Mar 2011 15:34:09 -0800
Subject: [Bioperl-l] bioperl-ext installation
Message-ID: <AANLkTinuaavEU4RwxZu=bmFpUVxpYBAisOv9wgKmQ9+9@mail.gmail.com>

Hi all,
Sorry in advance for a most likely trivial question: I did the standard
make/make test/make install of the bioperl-ext packages with no problems (I
can post the full output if useful). But when I try to run a simple program
that has no trouble on a different machine w bioperl-ext I get:

"The C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has
not been installed.
 Please install the bioperl-ext package"

Any ideas what might be happening? I don't know if the problem was with
installation (but I got "all tests successful during make test") or if I may
need to add the installed packages to some path variable? I'm relatively new
to both bioperl and perl generally so not sure where to start

Thanks

From rmb32 at cornell.edu  Mon Mar  7 11:26:28 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Mon, 07 Mar 2011 11:26:28 -0500
Subject: [Bioperl-l] call for project ideas - Google Summer of Code
Message-ID: <4D750734.4020002@cornell.edu>

Hi all,

Google's Summer of Code is coming round again, very soon now (mentoring 
organization applications are due this week).  We need to update our 
project ideas for prospective Summer of Code interns.  The rest of the 
page also needs updates, changing dates and such.

There's a page on the BioPerl wiki, please have a look and add your 
ideas for intern projects.

For more on Google Summer of Code, what it is and how it works, see 
their FAQ at 
http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2011/faqs

One of the summer intern ideas I have on the page so far is to help with 
the tough grunt work of breaking BioPerl into smaller, more easily 
managed distributions.  I'm sure you all can think of plenty more!

Here's the page: http://www.bioperl.org/wiki/Google_Summer_of_Code

Please have a look, add your project ideas, and delete ones that have 
already been done or are no longer relevant.

Rob


From tzhu at mail.bnu.edu.cn  Tue Mar  8 01:45:11 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Tue, 08 Mar 2011 14:45:11 +0800
Subject: [Bioperl-l] locate introns in a protein sequence
Message-ID: <1299566711.5243.11.camel@ubuntu>

Hello, everyone. For example, I have a GTF file annotating like this,

Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 start_codon 25009
25011 . + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 stop_codon 26003
26005 . + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 24828
25172 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25009 25172 .
+ 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 25245
25364 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25245 25364 .
+ 1 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 25414
26178 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25414 26002 .
+ 1 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";

Obviously this transcript "SPOG_00008T0" has two introns.

Also I have a corresponding protein sequence file like this( in fasta
format),

>SPOG_00008T0 | SPOG_00008 | Schizosaccharomyces cryophilus OY26 exosome
subunit Rrp45 (292 aa)
MSKSLEPSANNKGFIVNALKKELRLDGRSLTDFRDLKIEFGEDYGQVDISLGSTRVMARI
SAEITKPYSDRPFDGIFAITTELTPLASPAFETGRVSEQEVIISRLIEQAIRRSNALDTE
SLCIISGQKCWSVRASVHFINHDGNLVDAACIAVITGLCHFRRPEITVLGDEVTVHSIEE
RVPVPLSVLHTPICVTFSFFEDGSLSAIDASLEEEELRTGSMTVTLNKNREICQIFKAGG
VTIEASSVVACAHTAFQKTTSIISEIQRALDEDLSKKETQFFGGSAENQRS*

I hope to precisely locate these two introns into the protein
sequence(find their location among the amino acids). Please recommend a
relatively convenient method. Thank you!



-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)


From jason at bioperl.org  Tue Mar  8 02:42:54 2011
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 07 Mar 2011 23:42:54 -0800
Subject: [Bioperl-l] locate introns in a protein sequence
In-Reply-To: <1299566711.5243.11.camel@ubuntu>
References: <1299566711.5243.11.camel@ubuntu>
Message-ID: <4D75DDFE.9090602@bioperl.org>

I think there are several ways to do this, the easiest is to walk 
through each exon, and count up the codons, and print out the 
translation of the codons so far when you get to the end of an exon, 
keeping the overhang for the next exon.

That's basically what I do here in terms of counting, though I'm mapping 
introns into an alignment not a single peptide (though undocumented so 
it is a bit impenetrable)
  https://github.com/hyphaltip/thesis/blob/master/src/intron/map_introns_aln.pl

Use Bio::DB::SeqFeature::Store will make this much easier.  You will 
want to convert this Broad GTF to GFF3 with this script
https://github.com/hyphaltip/genome-scripts/blob/master/data_format/gtf2gff3_3level.pl

Then load the annotation along with a scaffold GFF3 (like one from this 
script run on your FASTA genome file
  https://github.com/hyphaltip/genome-scripts/blob/master/gbrowse_tools/fasta_to_gbrowse_scaffold.pl
  - just watch out -- the Broad is capitalizing the contig name 
(Supercontig_3.1) while the FASTA file will have it uncapped and 
truncated name (supercont_3.1) so you need to fix that in either of the 
files so it is consistent - a perl one liner will work here;
perl -i -p -e 's/^>supercont3\./>Supercontig_3./' GENOME.fasta

and load this in and you'll then be able to use the Bio::DB::SeqFeature 
to get all genes, walk through them a CDS for each gene, one a time, and 
then just keep count of the frame you are in and the exon length and 
you'll know where the introns go in the protein.

for my $gene ( $dbh->features(-type => 
"gene:S_cryophilus_OY26_V3_CALLGENES_FINAL_2
") ) {
  for my $mRNA ( $gene->get_SeqFeatures('mRNA') ) {
   for my $CDS ( $mRNA->get_SeqFeatures('CDS') ) {
    my $length = $CDS->length;
    # do some stuff to keep count or whatever you need to figure out 
where you are to put the intron
   }
  }
}

you can also see this code which converts folders of GFF3 + genomes into 
coding seqs, translated peps, etc.
  https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/gff3_to_cdspep.pl

It all depends on what you want to report from this type of query.

Tao Zhu wrote:
> Hello, everyone. For example, I have a GTF file annotating like this,
>
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 start_codon 25009
> 25011 . + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 stop_codon 26003
> 26005 . + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 24828
> 25172 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25009 25172 .
> + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 25245
> 25364 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25245 25364 .
> + 1 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 25414
> 26178 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25414 26002 .
> + 1 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
>
> Obviously this transcript "SPOG_00008T0" has two introns.
>
> Also I have a corresponding protein sequence file like this( in fasta
> format),
>
>> SPOG_00008T0 | SPOG_00008 | Schizosaccharomyces cryophilus OY26 exosome
> subunit Rrp45 (292 aa)
> MSKSLEPSANNKGFIVNALKKELRLDGRSLTDFRDLKIEFGEDYGQVDISLGSTRVMARI
> SAEITKPYSDRPFDGIFAITTELTPLASPAFETGRVSEQEVIISRLIEQAIRRSNALDTE
> SLCIISGQKCWSVRASVHFINHDGNLVDAACIAVITGLCHFRRPEITVLGDEVTVHSIEE
> RVPVPLSVLHTPICVTFSFFEDGSLSAIDASLEEEELRTGSMTVTLNKNREICQIFKAGG
> VTIEASSVVACAHTAFQKTTSIISEIQRALDEDLSKKETQFFGGSAENQRS*
>
> I hope to precisely locate these two introns into the protein
> sequence(find their location among the amino acids). Please recommend a
> relatively convenient method. Thank you!
>
>
>

-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki


From bio.justin100 at gmail.com  Tue Mar  8 17:31:42 2011
From: bio.justin100 at gmail.com (Justin Li)
Date: Tue, 8 Mar 2011 17:31:42 -0500
Subject: [Bioperl-l] Bio::Phylo vs Bio:TreeIO; interface to Fitch
Message-ID: <AANLkTik+HwSQNN3WCkaqQRPz3xqheaa0khmzdD5nndJa@mail.gmail.com>

Hi,

Both Bio::Phylo and Bio:TreeIO seem to be able to parse phylogenetic trees.

Could anyone having experience with both of them please comment on their
capability/robustness/ease of use?

Where can I find the documentation for
"Bio::Tools::Run::PiseApplication::fitch"?

Thanks,

Justin

From abhishek.vit at gmail.com  Tue Mar  8 17:42:03 2011
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Tue, 8 Mar 2011 14:42:03 -0800
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
	Sequences (reads)
Message-ID: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>

Hi All

I have results from different megablast of short reads(DNA sequences)
and after extracting the tophit for each read I want to bin them by
their lineage creating a tree.

For example.

If blast query hits the reference ->
gi|196110604|gb|CP001103.1|__Alteromonas_macleodii_'Deep_ecotype',_complete_genome

I want to get the lineage for this specie.

Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Alteromonas;Alteromona

The final goal is to do the above mapping as efficiently as possible.
Any pointers will be appreciated.


Thanks!
-Abhi

From miguel.pignatelli at uv.es  Wed Mar  9 04:20:47 2011
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Wed, 09 Mar 2011 09:20:47 +0000
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
Message-ID: <4D77466F.4040604@uv.es>

Hi Abhishek,

For a non bioperl related solution, take a look at Bio::LITE::Taxonomy.
It has been design to deal with great number of sequences (it is fast 
and efficient).

You may also find interesting the Blast2lca tool,

https://github.com/emepyc/Blast2lca

It currently works with the best hits for each query (calculates the 
lower common ancestor), but if you want to use only the best hit, please 
drop me a line.

Please, let me know if you need further help with any of these,

Cheers,

M;



On 08/03/11 22:42, Abhishek Pratap wrote:
> Hi All
>
> I have results from different megablast of short reads(DNA sequences)
> and after extracting the tophit for each read I want to bin them by
> their lineage creating a tree.
>
> For example.
>
> If blast query hits the reference ->
> gi|196110604|gb|CP001103.1|__Alteromonas_macleodii_'Deep_ecotype',_complete_genome
>
> I want to get the lineage for this specie.
>
> Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Alteromonas;Alteromona
>
> The final goal is to do the above mapping as efficiently as possible.
> Any pointers will be appreciated.
>
>
> Thanks!
> -Abhi
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From shalabh.sharma7 at gmail.com  Wed Mar  9 12:34:57 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 9 Mar 2011 12:34:57 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <4D77466F.4040604@uv.es>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
Message-ID: <AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>

Hey Abhishek:
                    The other way to deal with this that you can download
the gi_taxaid file from ncbi.
Convert all your GI's to taxaid and use Bio::DB:Taxanomy.
http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Taxon.html

I think there are lot of other options too, if you are interested you can
search for the thread which i started long time back.

Hope this helps.

-Shalabh Sharma
-----------------------------------------------
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636

On Wed, Mar 9, 2011 at 4:20 AM, Miguel Pignatelli
<miguel.pignatelli at uv.es>wrote:

> Hi Abhishek,
>
> For a non bioperl related solution, take a look at Bio::LITE::Taxonomy.
> It has been design to deal with great number of sequences (it is fast and
> efficient).
>
> You may also find interesting the Blast2lca tool,
>
> https://github.com/emepyc/Blast2lca
>
> It currently works with the best hits for each query (calculates the lower
> common ancestor), but if you want to use only the best hit, please drop me a
> line.
>
> Please, let me know if you need further help with any of these,
>
> Cheers,
>
> M;
>
>
>
>
> On 08/03/11 22:42, Abhishek Pratap wrote:
>
>> Hi All
>>
>> I have results from different megablast of short reads(DNA sequences)
>> and after extracting the tophit for each read I want to bin them by
>> their lineage creating a tree.
>>
>> For example.
>>
>> If blast query hits the reference ->
>>
>> gi|196110604|gb|CP001103.1|__Alteromonas_macleodii_'Deep_ecotype',_complete_genome
>>
>> I want to get the lineage for this specie.
>>
>>
>> Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Alteromonas;Alteromona
>>
>> The final goal is to do the above mapping as efficiently as possible.
>> Any pointers will be appreciated.
>>
>>
>> Thanks!
>> -Abhi
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From abhishek.vit at gmail.com  Wed Mar  9 22:25:58 2011
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Wed, 9 Mar 2011 19:25:58 -0800
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
Message-ID: <AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>

Thanks guys. I could not try either method today but will get back to
you if I face problem.

Best,
-Abhi

On Wed, Mar 9, 2011 at 9:34 AM, shalabh sharma
<shalabh.sharma7 at gmail.com> wrote:
> Hey Abhishek:
> ?? ? ? ? ? ? ? ? ? ?The other way to deal with this that you can download
> the gi_taxaid file from ncbi.
> Convert all your GI's to taxaid and use Bio::DB:Taxanomy.
> http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy
> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Taxon.html
> I think there are lot of other options too, if you are interested you can
> search for the thread which i started long time back.
> Hope this helps.
> -Shalabh Sharma
> -----------------------------------------------
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
>
> On Wed, Mar 9, 2011 at 4:20 AM, Miguel Pignatelli <miguel.pignatelli at uv.es>
> wrote:
>>
>> Hi Abhishek,
>>
>> For a non bioperl related solution, take a look at Bio::LITE::Taxonomy.
>> It has been design to deal with great number of sequences (it is fast and
>> efficient).
>>
>> You may also find interesting the Blast2lca tool,
>>
>> https://github.com/emepyc/Blast2lca
>>
>> It currently works with the best hits for each query (calculates the lower
>> common ancestor), but if you want to use only the best hit, please drop me a
>> line.
>>
>> Please, let me know if you need further help with any of these,
>>
>> Cheers,
>>
>> M;
>>
>>
>>
>> On 08/03/11 22:42, Abhishek Pratap wrote:
>>>
>>> Hi All
>>>
>>> I have results from different megablast of short reads(DNA sequences)
>>> and after extracting the tophit for each read I want to bin them by
>>> their lineage creating a tree.
>>>
>>> For example.
>>>
>>> If blast query hits the reference ->
>>>
>>> gi|196110604|gb|CP001103.1|__Alteromonas_macleodii_'Deep_ecotype',_complete_genome
>>>
>>> I want to get the lineage for this specie.
>>>
>>>
>>> Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Alteromonas;Alteromona
>>>
>>> The final goal is to do the above mapping as efficiently as possible.
>>> Any pointers will be appreciated.
>>>
>>>
>>> Thanks!
>>> -Abhi
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From ian.mcdowell at gmail.com  Thu Mar 10 12:11:50 2011
From: ian.mcdowell at gmail.com (Ian Mc Dowell)
Date: Thu, 10 Mar 2011 12:11:50 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
	<AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
Message-ID: <AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>

Hi all,

I would like to take local blast hit sequences, i.e. hsp_hseq, and extract
the full sequences of those hits from the original fasta file and put them
in a fasta file of all hits that I can use later.

This should be a widely performed task but I can't find any scripts that
directly address this issue.  I have not acquired the skills to make my own
scripts for this task.

Thanks so much if you have anything that can help me out,

Ian McDowell
Aquatic Pathology
University of Rhode Island

From ian.mcdowell at gmail.com  Thu Mar 10 12:13:01 2011
From: ian.mcdowell at gmail.com (Ian Mc Dowell)
Date: Thu, 10 Mar 2011 12:13:01 -0500
Subject: [Bioperl-l] Local blast hit (hsp_hseq) extracted from fasta file
Message-ID: <AANLkTinF-Ai-AvTPG6ET9xWW0NaeMQugYJpumm4g-7NH@mail.gmail.com>

Hi all,

I would like to take local blast hit sequences, i.e. hsp_hseq in blast xml
format, and extract the full sequences of those hits from the original fasta
file and put them in a fasta file of all hits that I can use later.

This should be a widely performed task but I can't find any scripts that
directly address this issue.  I have not acquired the skills to make my own
scripts for this task.

Thanks so much if you have anything that can help me out,

Ian McDowell
Aquatic Pathology
University of Rhode Island

From rmb32 at cornell.edu  Thu Mar 10 12:22:51 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 10 Mar 2011 12:22:51 -0500
Subject: [Bioperl-l] update Google Summer of Code project ideas
Message-ID: <4D7908EB.6050003@cornell.edu>

Hi all,

Please make sure the BioPerl information is up to date for 2011 on both 
the OBF and BioPerl wikis.  The current page looks pretty good, just be 
aware that Google will be looking at it in the next few days to evaluate 
whether OBF will be accepted again this year to GSoC.

OBF wiki page: http://www.open-bio.org/wiki/Google_Summer_of_Code
BioPerl wiki: http://bioperl.org/wiki/Google_Summer_of_Code

Rob

----
Robert Buels
(prospective) 2011 OBF GSoC Organization Admin

From shalabh.sharma7 at gmail.com  Thu Mar 10 12:24:04 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Thu, 10 Mar 2011 12:24:04 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
	<AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
	<AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>
Message-ID: <AANLkTik9jt9Pkrgng4zv4nRhDmK0_bRpnbGJe+i9Dark@mail.gmail.com>

Hey Ian,
            I am not sure if i understood your problem completely.
But if you have ids of blast hits you can use 'fastacmd' to fetch sequences
from the database you used for blast.

-Shalabh Sharma
-----------------------------------------
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636

On Thu, Mar 10, 2011 at 12:11 PM, Ian Mc Dowell <ian.mcdowell at gmail.com>wrote:

> Hi all,
>
> I would like to take local blast hit sequences, i.e. hsp_hseq, and extract
> the full sequences of those hits from the original fasta file and put them
> in a fasta file of all hits that I can use later.
>
> This should be a widely performed task but I can't find any scripts that
> directly address this issue.  I have not acquired the skills to make my own
> scripts for this task.
>
> Thanks so much if you have anything that can help me out,
>
> Ian McDowell
> Aquatic Pathology
> University of Rhode Island
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From ian.mcdowell at gmail.com  Thu Mar 10 12:31:29 2011
From: ian.mcdowell at gmail.com (Ian Mc Dowell)
Date: Thu, 10 Mar 2011 12:31:29 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTik9jt9Pkrgng4zv4nRhDmK0_bRpnbGJe+i9Dark@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
	<AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
	<AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>
	<AANLkTik9jt9Pkrgng4zv4nRhDmK0_bRpnbGJe+i9Dark@mail.gmail.com>
Message-ID: <AANLkTi=-12y0LWzV2gRgriE=z3=d_-OKwDRe2wSWkmwr@mail.gmail.com>

I have a deeply sequenced transcriptome so when I look for a gene of
interest in my short reads (108bp) I get thousands of hits, at very low E
values.  And I want to do this for many sequences of interest. That's why I
want a script to automate the process of grabbing the accession numbers from
the blast xml output, then searching in the fasta file which is equivalent
to my local database and pulling those relevant reads.

On Thu, Mar 10, 2011 at 12:24 PM, shalabh sharma
<shalabh.sharma7 at gmail.com>wrote:

> Hey Ian,
>             I am not sure if i understood your problem completely.
> But if you have ids of blast hits you can use 'fastacmd' to fetch sequences
> from the database you used for blast.
>
> -Shalabh Sharma
> -----------------------------------------
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
>
> On Thu, Mar 10, 2011 at 12:11 PM, Ian Mc Dowell <ian.mcdowell at gmail.com>wrote:
>
>> Hi all,
>>
>> I would like to take local blast hit sequences, i.e. hsp_hseq, and extract
>> the full sequences of those hits from the original fasta file and put them
>> in a fasta file of all hits that I can use later.
>>
>> This should be a widely performed task but I can't find any scripts that
>> directly address this issue.  I have not acquired the skills to make my
>> own
>> scripts for this task.
>>
>> Thanks so much if you have anything that can help me out,
>>
>> Ian McDowell
>> Aquatic Pathology
>> University of Rhode Island
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>

From hrh at fmi.ch  Thu Mar 10 12:37:07 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Thu, 10 Mar 2011 18:37:07 +0100
Subject: [Bioperl-l] Local blast hit (hsp_hseq) extracted from fasta file
In-Reply-To: <AANLkTinF-Ai-AvTPG6ET9xWW0NaeMQugYJpumm4g-7NH@mail.gmail.com>
References: <AANLkTinF-Ai-AvTPG6ET9xWW0NaeMQugYJpumm4g-7NH@mail.gmail.com>
Message-ID: <4D790C43.5080801@fmi.ch>



On 03/10/2011 06:13 PM, Ian Mc Dowell wrote:
> Hi all,
>
> I would like to take local blast hit sequences, i.e. hsp_hseq in blast xml
> format, and extract the full sequences of those hits from the original fasta
> file and put them in a fasta file of all hits that I can use later.
>
> This should be a widely performed task but I can't find any scripts that
> directly address this issue.  I have not acquired the skills to make my own
> scripts for this task.


Hi Ian

It is not a Bioperl solution, but a simple one:

Assuming, you are using the NCBI blast+ tools, make sure you create the 
BLAST indices with the "-parse_seqids" option. This will allow you to 
extract individual sequences (in fasta format) from the BLAST database 
with the command 'blastdbcmd' by providing a comma-delimited search 
string of sequence identifiers. Fore more details see:

http://tinyurl.com/5sq2ehg


Regards, Hans


> Thanks so much if you have anything that can help me out,
>
> Ian McDowell
> Aquatic Pathology
> University of Rhode Island
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

From shalabh.sharma7 at gmail.com  Thu Mar 10 12:42:51 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Thu, 10 Mar 2011 12:42:51 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTi=-12y0LWzV2gRgriE=z3=d_-OKwDRe2wSWkmwr@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
	<AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
	<AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>
	<AANLkTik9jt9Pkrgng4zv4nRhDmK0_bRpnbGJe+i9Dark@mail.gmail.com>
	<AANLkTi=-12y0LWzV2gRgriE=z3=d_-OKwDRe2wSWkmwr@mail.gmail.com>
Message-ID: <AANLkTin13Uhj8ZgQ1-+c0SjXbRBvU8VHdGhUXyqea1FV@mail.gmail.com>

Hey Ian,
             Writing that kind of script would not take that much time. But
i am not very much familiar with xml format.
But still you can do without writing a complicated script.

once you get the output you can get all the ids (use grep or simple perl
script to parse ids).
Then use that list of ids to fetch sequences from your database by using
"fastacmd" .

-Shalabh


On Thu, Mar 10, 2011 at 12:31 PM, Ian Mc Dowell <ian.mcdowell at gmail.com>wrote:

> I have a deeply sequenced transcriptome so when I look for a gene of
> interest in my short reads (108bp) I get thousands of hits, at very low E
> values.  And I want to do this for many sequences of interest. That's why I
> want a script to automate the process of grabbing the accession numbers from
> the blast xml output, then searching in the fasta file which is equivalent
> to my local database and pulling those relevant reads.
>
> On Thu, Mar 10, 2011 at 12:24 PM, shalabh sharma <
> shalabh.sharma7 at gmail.com> wrote:
>
>> Hey Ian,
>>             I am not sure if i understood your problem completely.
>> But if you have ids of blast hits you can use 'fastacmd' to fetch
>> sequences from the database you used for blast.
>>
>> -Shalabh Sharma
>> -----------------------------------------
>> Shalabh Sharma
>> Scientific Computing Professional Associate (Bioinformatics Specialist)
>> Department of Marine Sciences
>> University of Georgia
>> Athens, GA 30602-3636
>>
>> On Thu, Mar 10, 2011 at 12:11 PM, Ian Mc Dowell <ian.mcdowell at gmail.com>wrote:
>>
>>> Hi all,
>>>
>>> I would like to take local blast hit sequences, i.e. hsp_hseq, and
>>> extract
>>> the full sequences of those hits from the original fasta file and put
>>> them
>>> in a fasta file of all hits that I can use later.
>>>
>>> This should be a widely performed task but I can't find any scripts that
>>> directly address this issue.  I have not acquired the skills to make my
>>> own
>>> scripts for this task.
>>>
>>> Thanks so much if you have anything that can help me out,
>>>
>>> Ian McDowell
>>> Aquatic Pathology
>>> University of Rhode Island
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636

From cjfields at illinois.edu  Mon Mar 14 13:44:44 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 12:44:44 -0500
Subject: [Bioperl-l] bioperl wiki spam
Message-ID: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>

All,

We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:

http://www.mediawiki.org/wiki/Extension:ConfirmAccount

I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.  

Any thoughts?

chris

From cjfields at illinois.edu  Mon Mar 14 13:51:51 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 12:51:51 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Google Summer of Code
Message-ID: <42CCFB33-B9FC-41C2-987D-BF969F5111EC@illinois.edu>

All,

As Rob Buels previously mentioned, the Open Bioinformatics Foundation has again applied for the Google Summer of Code (GSoC).  BioPerl has been involved with GSoC over the last several years, most recently when Jun Yin refactored the alignment subsystem, code that will be incorporated into BioPerl after the 1.6.2 release:

http://www.bioperl.org/wiki/Google_Summer_of_Code#2010

We have several ideas for projects for the upcoming GSoC 2011 on the wiki, but we are open to just about anything BioPerl-related.  We are also looking for more potential mentors!  If you have ideas or would like to be a mentor, free to submit to the web page, discuss it on this list, or join us on IRC (#obf-soc on freenode).

chris

Christopher Fields
IGB Postdoctoral Fellow
Genomics of Neural & Behavioral Plasticity
University of Illinois Urbana-Champaign
Institute for Genomic Biology
1206 W. Gregory Dr. , MC-195
Urbana, IL 61801



From scott at scottcain.net  Mon Mar 14 14:12:55 2011
From: scott at scottcain.net (Scott Cain)
Date: Mon, 14 Mar 2011 14:12:55 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
Message-ID: <AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>

Hi Chris,

The GMOD wiki has been getting hit similarly.  I've been thinking
about the "vampire" model that EcoliWiki uses: once you have an
account, you have the ability to approve other people's accounts.  The
hope being to distribute the load.  I'm not thrilled about it though:
I want the barrier to entry to be as low as possible.  We already make
it so that you have to have an account to edit, passing a recaptcha on
the way.  Apparently that barrier is already a little too low :-/

Scott


On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
> All,
>
> We have been getting inundated on the wiki with spam lately. ?In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>
> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>
> I wanted to get everyone's opinion on this prior to enforcing it. ?The queue is pretty configurable, and one can set this to auto-delete old requests.
>
> Any thoughts?
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research


From cjfields at illinois.edu  Mon Mar 14 14:25:05 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 13:25:05 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
Message-ID: <5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>

On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):

"Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."

I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.

chris

On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:

> Hi Chris,
> 
> The GMOD wiki has been getting hit similarly.  I've been thinking
> about the "vampire" model that EcoliWiki uses: once you have an
> account, you have the ability to approve other people's accounts.  The
> hope being to distribute the load.  I'm not thrilled about it though:
> I want the barrier to entry to be as low as possible.  We already make
> it so that you have to have an account to edit, passing a recaptcha on
> the way.  Apparently that barrier is already a little too low :-/
> 
> Scott
> 
> 
> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> All,
>> 
>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>> 
>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>> 
>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>> 
>> Any thoughts?
>> 
>> chris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research



From David.Messina at sbc.su.se  Mon Mar 14 14:25:10 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 14 Mar 2011 19:25:10 +0100
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
Message-ID: <5650D7D3-11ED-4ABF-89E8-BE9175848196@sbc.su.se>

> Any thoughts?

Do it.


From hlapp at drycafe.net  Mon Mar 14 14:48:55 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Mon, 14 Mar 2011 14:48:55 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
Message-ID: <6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>

Any update on the OpenID extension?

	-hilmar

On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:

> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit 
> ):
>
> "Unfortunately, reCAPTCHA might be a victim of its own success - as  
> of 2011, some spammers appear to have figured out a way to bypass  
> it, either through character recognition or by using humans. For  
> that reason, it is not necessarily recommended."
>
> I agree about the barrier to entry issue, but unfortunately with the  
> wiki we're facing a reality check re: spam attacks.  We can probably  
> set up a new group for users that allows account approval, though,  
> which might alleviate the process somewhat.
>
> chris
>
> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>
>> Hi Chris,
>>
>> The GMOD wiki has been getting hit similarly.  I've been thinking
>> about the "vampire" model that EcoliWiki uses: once you have an
>> account, you have the ability to approve other people's accounts.   
>> The
>> hope being to distribute the load.  I'm not thrilled about it though:
>> I want the barrier to entry to be as low as possible.  We already  
>> make
>> it so that you have to have an account to edit, passing a recaptcha  
>> on
>> the way.  Apparently that barrier is already a little too low :-/
>>
>> Scott
>>
>>
>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields  
>> <cjfields at illinois.edu> wrote:
>>> All,
>>>
>>> We have been getting inundated on the wiki with spam lately.  In  
>>> order to get on top of this, I'm thinking about having the wiki  
>>> set up so wiki admins approve new user accounts, using the  
>>> ConfirmAccount plugin:
>>>
>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>
>>> I wanted to get everyone's opinion on this prior to enforcing it.   
>>> The queue is pretty configurable, and one can set this to auto- 
>>> delete old requests.
>>>
>>> Any thoughts?
>>>
>>> chris
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>>
>> -- 
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at  
>> scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================





From cjfields at illinois.edu  Mon Mar 14 14:55:31 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 13:55:31 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
Message-ID: <2EB73F6E-AAD3-46BD-BB57-AAB3AA1063F7@illinois.edu>

We can test that one out first.  Maybe that will help.

chris

On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:

> Any update on the OpenID extension?
> 
> 	-hilmar
> 
> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
> 
>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>> 
>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>> 
>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>> 
>> chris
>> 
>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>> 
>>> Hi Chris,
>>> 
>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>> about the "vampire" model that EcoliWiki uses: once you have an
>>> account, you have the ability to approve other people's accounts.  The
>>> hope being to distribute the load.  I'm not thrilled about it though:
>>> I want the barrier to entry to be as low as possible.  We already make
>>> it so that you have to have an account to edit, passing a recaptcha on
>>> the way.  Apparently that barrier is already a little too low :-/
>>> 
>>> Scott
>>> 
>>> 
>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>> All,
>>>> 
>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>> 
>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>> 
>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>> 
>>>> Any thoughts?
>>>> 
>>>> chris
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From hartzell at alerce.com  Mon Mar 14 20:37:36 2011
From: hartzell at alerce.com (George Hartzell)
Date: Mon, 14 Mar 2011 17:37:36 -0700
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <5650D7D3-11ED-4ABF-89E8-BE9175848196@sbc.su.se>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<5650D7D3-11ED-4ABF-89E8-BE9175848196@sbc.su.se>
Message-ID: <19838.46288.715397.413627@gargle.gargle.HOWL>

Dave Messina writes:
 > > Any thoughts?
 > 
 > Do it.

Do it^2.  You have better things to do than waste time on spammers.

It's nice to not have the bar too high for new folks, but in this age
of spam I think people understand.

g.

From cjfields at illinois.edu  Mon Mar 14 23:01:45 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 22:01:45 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
Message-ID: <84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>

Okay, we have bioperl.org set up to use OpenID, works well:  

http://www.bioperl.org/wiki/Special:OpenIDLogin

I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.

chris

On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:

> Any update on the OpenID extension?
> 
> 	-hilmar
> 
> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
> 
>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>> 
>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>> 
>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>> 
>> chris
>> 
>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>> 
>>> Hi Chris,
>>> 
>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>> about the "vampire" model that EcoliWiki uses: once you have an
>>> account, you have the ability to approve other people's accounts.  The
>>> hope being to distribute the load.  I'm not thrilled about it though:
>>> I want the barrier to entry to be as low as possible.  We already make
>>> it so that you have to have an account to edit, passing a recaptcha on
>>> the way.  Apparently that barrier is already a little too low :-/
>>> 
>>> Scott
>>> 
>>> 
>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>> All,
>>>> 
>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>> 
>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>> 
>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>> 
>>>> Any thoughts?
>>>> 
>>>> chris
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Mon Mar 14 23:12:16 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 22:12:16 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <19838.46288.715397.413627@gargle.gargle.HOWL>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<5650D7D3-11ED-4ABF-89E8-BE9175848196@sbc.su.se>
	<19838.46288.715397.413627@gargle.gargle.HOWL>
Message-ID: <D49A790C-E30D-4587-B9B6-0D5E99B84D97@illinois.edu>

On Mar 14, 2011, at 7:37 PM, George Hartzell wrote:

> Dave Messina writes:
>>> Any thoughts?
>> 
>> Do it.
> 
> Do it^2.  You have better things to do than waste time on spammers.
> 
> It's nice to not have the bar too high for new folks, but in this age
> of spam I think people understand.
> 
> g.

I've disabled new account creation unless OpenID is used; apparently this has worked elsewhere to cut down on spam.  All old accounts are still active, but I think new users will be prompted to tie an OpenID to the account.  

Anyway, if that doesn't work we'll go to the next step (account verification).

chris



From ross at cuhk.edu.hk  Tue Mar 15 01:54:35 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Tue, 15 Mar 2011 13:54:35 +0800
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
Message-ID: <004001cbe2d5$76598200$630c8600$@edu.hk>

$gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
'Fasta');            
$allseqobj = $gb->get_Stream_by_acc("A3ZI37");        
                l
print "HEELO";                                           
while ($seqobj = $allseqobj->next_seq) {             
                        #$seqobj = $allseqobj->next_seq;

                        $seq=$seqobj->seq;

                        }

                    print "222   HEELO";



I find that the 1st HEELO can be printed while the 2nd one can't. Google
does not return checking success/failure or null/exist of the Seq Object. As
the 1st HEELO can be executed, so no throw/exception occurs for the
get_Stream_by_acc. So what can I do? The real case is not hard-coding this
A3ZI37 but reading a file that may contain a lot of these "illegitimate"
accession numbers.


From David.Messina at sbc.su.se  Tue Mar 15 05:02:05 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 15 Mar 2011 10:02:05 +0100
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <004001cbe2d5$76598200$630c8600$@edu.hk>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
Message-ID: <AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>

Hi Ross,

Your code is incomplete and you didn't provide the output from running it,
so it's not easy to figure out where you're going wrong.

Try copying the example code directly from here


http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html

and making sure that works first before modifying it.


More documentation and examples here:
http://www.bioperl.org/wiki/HOWTO:Beginners
http://www.bioperl.org/wiki/Bioperl_scripts


Dave




On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:

> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
> 'Fasta');
> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>                l
> print "HEELO";
> while ($seqobj = $allseqobj->next_seq) {
>                        #$seqobj = $allseqobj->next_seq;
>
>                        $seq=$seqobj->seq;
>
>                        }
>
>                    print "222   HEELO";
>
>
>
> I find that the 1st HEELO can be printed while the 2nd one can't. Google
> does not return checking success/failure or null/exist of the Seq Object.
> As
> the 1st HEELO can be executed, so no throw/exception occurs for the
> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
> accession numbers.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From ross at cuhk.edu.hk  Tue Mar 15 10:16:56 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Tue, 15 Mar 2011 22:16:56 +0800
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
Message-ID: <005301cbe31b$a3bee550$eb3caff0$@edu.hk>

While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...

 

 

#!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   

use Bio::DB::GenBank;

 

$gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');


$allseqobj = $gb->get_Stream_by_acc("A3ZI37");


 print "HEELO";

while ($seqobj = $allseqobj->next_seq) {
                       #$seqobj = $allseqobj->next_seq;
                       $seq=$seqobj->seq;
}
print "222   HEELO";




 

 

From: Dave Messina [mailto:David.Messina at sbc.su.se] 
Sent: 2011?3?15? 17:02
To: Ross KK Leung
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] how to prevent forced exit?

 

Hi Ross,

 

Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.

 

Try copying the example code directly from here

 

    http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html

 

and making sure that works first before modifying it.

 

 

More documentation and examples here:

http://www.bioperl.org/wiki/HOWTO:Beginners

http://www.bioperl.org/wiki/Bioperl_scripts

 

 

Dave

 

 

 

On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:

$gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
'Fasta');
$allseqobj = $gb->get_Stream_by_acc("A3ZI37");
               l
print "HEELO";
while ($seqobj = $allseqobj->next_seq) {
                       #$seqobj = $allseqobj->next_seq;

                       $seq=$seqobj->seq;

                       }

                   print "222   HEELO";



I find that the 1st HEELO can be printed while the 2nd one can't. Google
does not return checking success/failure or null/exist of the Seq Object. As
the 1st HEELO can be executed, so no throw/exception occurs for the
get_Stream_by_acc. So what can I do? The real case is not hard-coding this
A3ZI37 but reading a file that may contain a lot of these "illegitimate"
accession numbers.

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

 



From cjfields at illinois.edu  Tue Mar 15 10:44:23 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 15 Mar 2011 09:44:23 -0500
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <005301cbe31b$a3bee550$eb3caff0$@edu.hk>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
Message-ID: <DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>

Ross,

Hope you're exaggerating, you really shouldn't use this service for retrieving 1 million records as you'll likely find your IP banned by NCBI; they are starting to enforce stricter web-based access to their  server now.  Bio::DB::GenBank uses a GET HTTP request using URI-based parameters which effectively limits the length of the query to around 200-300 IDs per request, so you would have to split single one large request many.  Thousands of repeated requests, even with a timeout, may flag your IP as 'spam'.  You can use something like Bio::DB::EUtilities to grab larger groups of seqs (~1000 IDs) b/c the latest EUtilities uses POST requests vs GET for a large number of IDs, but you are still effectively limited by the number of requests.

Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?

chris

On Mar 15, 2011, at 9:16 AM, Ross KK Leung wrote:

> While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...
> 
> 
> 
> 
> 
> #!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   
> 
> use Bio::DB::GenBank;
> 
> 
> 
> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');
> 
> 
> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
> 
> 
> print "HEELO";
> 
> while ($seqobj = $allseqobj->next_seq) {
>                       #$seqobj = $allseqobj->next_seq;
>                       $seq=$seqobj->seq;
> }
> print "222   HEELO";
> 
> 
> 
> 
> 
> 
> 
> 
> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
> Sent: 2011?3?15? 17:02
> To: Ross KK Leung
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] how to prevent forced exit?
> 
> 
> 
> Hi Ross,
> 
> 
> 
> Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.
> 
> 
> 
> Try copying the example code directly from here
> 
> 
> 
>    http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html
> 
> 
> 
> and making sure that works first before modifying it.
> 
> 
> 
> 
> 
> More documentation and examples here:
> 
> http://www.bioperl.org/wiki/HOWTO:Beginners
> 
> http://www.bioperl.org/wiki/Bioperl_scripts
> 
> 
> 
> 
> 
> Dave
> 
> 
> 
> 
> 
> 
> 
> On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:
> 
> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
> 'Fasta');
> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>               l
> print "HEELO";
> while ($seqobj = $allseqobj->next_seq) {
>                       #$seqobj = $allseqobj->next_seq;
> 
>                       $seq=$seqobj->seq;
> 
>                       }
> 
>                   print "222   HEELO";
> 
> 
> 
> I find that the 1st HEELO can be printed while the 2nd one can't. Google
> does not return checking success/failure or null/exist of the Seq Object. As
> the 1st HEELO can be executed, so no throw/exception occurs for the
> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
> accession numbers.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From dvadell at clustering.com.ar  Tue Mar 15 10:59:20 2011
From: dvadell at clustering.com.ar (Diego M. Vadell)
Date: Tue, 15 Mar 2011 11:59:20 -0300
Subject: [Bioperl-l] advice about bioperl-ext -- defunct?
Message-ID: <38be317a0815ba7276d56e5a6c93d116@webmail.clustering.com.ar>

Hi,

 I have just downloaded bioperl-ext from github, and it says "XS-based
BioPerl extensions to C libraries (defunct) ? [Read more ->
https://github.com/bioperl/bioperl-ext#readme]" . I read the readme but it
looks alive ( i.e. no mention of an ending of the project ). 

 I installed it ( adding "-fPIC" in the 3 Makefile.PLs ) and I'm about to
start using it. But, does is it still maintained? Is it still in use?
Recommended for a new project? I don't mind fixing compilation errors, but
maybe there is a new package that superseded it. Maybe I'm downloading it
from the wrong place.

 Regards,
 -- Diego




From jimhu at tamu.edu  Tue Mar 15 11:25:36 2011
From: jimhu at tamu.edu (Jim Hu)
Date: Tue, 15 Mar 2011 10:25:36 -0500
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
	<DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
Message-ID: <9CD1455E-88B4-4E2A-B3BC-398C10D5AAA9@tamu.edu>

Hi Chris,

A version of this admonition should be on every wiki HOWTO that involves retrieving records from external sources, and in the docs for the relevant modules.  Speaking as someone who has used BioPerl intermittently for years, and who has Sysiphus-like relationship with the learning curve, I think the docs could use more discussion of when to use particular modules in addition to the details of how to use them provided in the perldocs. I realize this is hard, given the perl "more than one way to do it" world view, but that's my $0.02.

Since BioPerl.org is a wiki, I suppose I should do that admonition edit myself... especially since I already know the wiki markup to transclude the same text into multiple pages.

Jim

Sent from my iPad

On Mar 15, 2011, at 9:44 AM, Chris Fields <cjfields at illinois.edu> wrote:

> Ross,
> 
> Hope you're exaggerating, you really shouldn't use this service for retrieving 1 million records as you'll likely find your IP banned by NCBI; they are starting to enforce stricter web-based access to their  server now.  Bio::DB::GenBank uses a GET HTTP request using URI-based parameters which effectively limits the length of the query to around 200-300 IDs per request, so you would have to split single one large request many.  Thousands of repeated requests, even with a timeout, may flag your IP as 'spam'.  You can use something like Bio::DB::EUtilities to grab larger groups of seqs (~1000 IDs) b/c the latest EUtilities uses POST requests vs GET for a large number of IDs, but you are still effectively limited by the number of requests.
> 
> Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?
> 
> chris
> 
> On Mar 15, 2011, at 9:16 AM, Ross KK Leung wrote:
> 
>> While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...
>> 
>> 
>> 
>> 
>> 
>> #!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   
>> 
>> use Bio::DB::GenBank;
>> 
>> 
>> 
>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');
>> 
>> 
>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>> 
>> 
>> print "HEELO";
>> 
>> while ($seqobj = $allseqobj->next_seq) {
>>                      #$seqobj = $allseqobj->next_seq;
>>                      $seq=$seqobj->seq;
>> }
>> print "222   HEELO";
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
>> Sent: 2011?3?15? 17:02
>> To: Ross KK Leung
>> Cc: bioperl-l at lists.open-bio.org
>> Subject: Re: [Bioperl-l] how to prevent forced exit?
>> 
>> 
>> 
>> Hi Ross,
>> 
>> 
>> 
>> Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.
>> 
>> 
>> 
>> Try copying the example code directly from here
>> 
>> 
>> 
>>   http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html
>> 
>> 
>> 
>> and making sure that works first before modifying it.
>> 
>> 
>> 
>> 
>> 
>> More documentation and examples here:
>> 
>> http://www.bioperl.org/wiki/HOWTO:Beginners
>> 
>> http://www.bioperl.org/wiki/Bioperl_scripts
>> 
>> 
>> 
>> 
>> 
>> Dave
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:
>> 
>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
>> 'Fasta');
>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>              l
>> print "HEELO";
>> while ($seqobj = $allseqobj->next_seq) {
>>                      #$seqobj = $allseqobj->next_seq;
>> 
>>                      $seq=$seqobj->seq;
>> 
>>                      }
>> 
>>                  print "222   HEELO";
>> 
>> 
>> 
>> I find that the 1st HEELO can be printed while the 2nd one can't. Google
>> does not return checking success/failure or null/exist of the Seq Object. As
>> the 1st HEELO can be executed, so no throw/exception occurs for the
>> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
>> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
>> accession numbers.
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From cjfields at illinois.edu  Tue Mar 15 11:45:20 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 15 Mar 2011 10:45:20 -0500
Subject: [Bioperl-l] advice about bioperl-ext -- defunct?
In-Reply-To: <38be317a0815ba7276d56e5a6c93d116@webmail.clustering.com.ar>
References: <38be317a0815ba7276d56e5a6c93d116@webmail.clustering.com.ar>
Message-ID: <3892F905-2D1F-43CF-8968-055C9F902504@illinois.edu>

On Mar 15, 2011, at 9:59 AM, Diego M. Vadell wrote:

> Hi,
> 
> I have just downloaded bioperl-ext from github, and it says "XS-based
> BioPerl extensions to C libraries (defunct) ? [Read more ->
> https://github.com/bioperl/bioperl-ext#readme]" . I read the readme but it
> looks alive ( i.e. no mention of an ending of the project ). 
> 
> I installed it ( adding "-fPIC" in the 3 Makefile.PLs ) and I'm about to
> start using it. But, does is it still maintained? Is it still in use?

Re: being maintained: No, except Bio::Tools::HMM (https://github.com/bioperl/Bio-Tools-HMM)

Re: in use: somewhat.  I think some still use Bio::SeqIO::staden::read and Bio::Ext::Align, but they haven't actively maintained in quite some time.

> Recommended for a new project? I don't mind fixing compilation errors, but
> maybe there is a new package that superseded it. Maybe I'm downloading it
> from the wrong place.
> 
> Regards,
> -- Diego

The code still works in some cases but is somewhat bit-rotted (I recall getting very inconsistent results from Bio::SearchUtils, not sure why).  

We (Bio* projects) are starting to consolidate around using BioLib for consistent bindings to C/C++ libraries, though that project is undergoing some changes:

http://biolib.open-bio.org/wiki/Main_Page

Pjotr Prins is the lead on that, worth talking to.  The next big step is to interface with EMBOSS libraries, which is very promising.

chris

From cjfields at illinois.edu  Tue Mar 15 11:54:38 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 15 Mar 2011 10:54:38 -0500
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <9CD1455E-88B4-4E2A-B3BC-398C10D5AAA9@tamu.edu>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
	<DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
	<9CD1455E-88B4-4E2A-B3BC-398C10D5AAA9@tamu.edu>
Message-ID: <3E73745F-A687-4229-B71E-5C56B2D1FBAE@illinois.edu>

Jim,

It's worth noting in something more prominent, like the tutorial, FAQ, and appropriate HOWTO's.  We've long considered whether it would be worth setting up a cookbook-like section that includes simple workflows, that would also be appropriate for something like this.

Also, I do think this is mentioned in the POD for several modules, but worth adding a prominent section on it if it's not present.  In Bio::DB::GenBank:

  WARNING: Please do NOT spam the Entrez web server with multiple requests.  NCBI offers Batch Entrez for this purpose.

That could be placed somewhere that is a bit more helpful.

chris


On Mar 15, 2011, at 10:25 AM, Jim Hu wrote:

> Hi Chris,
> 
> A version of this admonition should be on every wiki HOWTO that involves retrieving records from external sources, and in the docs for the relevant modules.  Speaking as someone who has used BioPerl intermittently for years, and who has Sysiphus-like relationship with the learning curve, I think the docs could use more discussion of when to use particular modules in addition to the details of how to use them provided in the perldocs. I realize this is hard, given the perl "more than one way to do it" world view, but that's my $0.02.
> 
> Since BioPerl.org is a wiki, I suppose I should do that admonition edit myself... especially since I already know the wiki markup to transclude the same text into multiple pages.
> 
> Jim
> 
> Sent from my iPad
> 
> On Mar 15, 2011, at 9:44 AM, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Ross,
>> 
>> Hope you're exaggerating, you really shouldn't use this service for retrieving 1 million records as you'll likely find your IP banned by NCBI; they are starting to enforce stricter web-based access to their  server now.  Bio::DB::GenBank uses a GET HTTP request using URI-based parameters which effectively limits the length of the query to around 200-300 IDs per request, so you would have to split single one large request many.  Thousands of repeated requests, even with a timeout, may flag your IP as 'spam'.  You can use something like Bio::DB::EUtilities to grab larger groups of seqs (~1000 IDs) b/c the latest EUtilities uses POST requests vs GET for a large number of IDs, but you are still effectively limited by the number of requests.
>> 
>> Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?
>> 
>> chris
>> 
>> On Mar 15, 2011, at 9:16 AM, Ross KK Leung wrote:
>> 
>>> While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...
>>> 
>>> 
>>> 
>>> 
>>> 
>>> #!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   
>>> 
>>> use Bio::DB::GenBank;
>>> 
>>> 
>>> 
>>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');
>>> 
>>> 
>>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>> 
>>> 
>>> print "HEELO";
>>> 
>>> while ($seqobj = $allseqobj->next_seq) {
>>>                     #$seqobj = $allseqobj->next_seq;
>>>                     $seq=$seqobj->seq;
>>> }
>>> print "222   HEELO";
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
>>> Sent: 2011?3?15? 17:02
>>> To: Ross KK Leung
>>> Cc: bioperl-l at lists.open-bio.org
>>> Subject: Re: [Bioperl-l] how to prevent forced exit?
>>> 
>>> 
>>> 
>>> Hi Ross,
>>> 
>>> 
>>> 
>>> Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.
>>> 
>>> 
>>> 
>>> Try copying the example code directly from here
>>> 
>>> 
>>> 
>>>  http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html
>>> 
>>> 
>>> 
>>> and making sure that works first before modifying it.
>>> 
>>> 
>>> 
>>> 
>>> 
>>> More documentation and examples here:
>>> 
>>> http://www.bioperl.org/wiki/HOWTO:Beginners
>>> 
>>> http://www.bioperl.org/wiki/Bioperl_scripts
>>> 
>>> 
>>> 
>>> 
>>> 
>>> Dave
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:
>>> 
>>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
>>> 'Fasta');
>>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>>             l
>>> print "HEELO";
>>> while ($seqobj = $allseqobj->next_seq) {
>>>                     #$seqobj = $allseqobj->next_seq;
>>> 
>>>                     $seq=$seqobj->seq;
>>> 
>>>                     }
>>> 
>>>                 print "222   HEELO";
>>> 
>>> 
>>> 
>>> I find that the 1st HEELO can be printed while the 2nd one can't. Google
>>> does not return checking success/failure or null/exist of the Seq Object. As
>>> the 1st HEELO can be executed, so no throw/exception occurs for the
>>> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
>>> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
>>> accession numbers.
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From dvadell at clustering.com.ar  Tue Mar 15 12:01:22 2011
From: dvadell at clustering.com.ar (Diego M. Vadell)
Date: Tue, 15 Mar 2011 13:01:22 -0300
Subject: [Bioperl-l] advice about bioperl-ext -- defunct?
In-Reply-To: <3892F905-2D1F-43CF-8968-055C9F902504@illinois.edu>
Message-ID: <218950b508a0e4a8ad07227974989e5f@webmail.clustering.com.ar>

Hi Chris,

 Thank you! I will align with bioperl-run then, and keep an eye on biolib.

Cheers,
 -- Diego


 
----------------original message-----------------
From: "Chris Fields" cjfields at illinois.edu
To: "Diego M. Vadell" dvadell at clustering.com.ar
CC: bioperl-l at lists.open-bio.org
Date: Tue, 15 Mar 2011 10:45:20 -0500
-------------------------------------------------
 
 
> On Mar 15, 2011, at 9:59 AM, Diego M. Vadell wrote:
> 
>> Hi,
>> 
>> I have just downloaded bioperl-ext from github, and it says "XS-based
>> BioPerl extensions to C libraries (defunct) ? [Read more ->
>> https://github.com/bioperl/bioperl-ext#readme]" . I read the readme but 
>> it
>> looks alive ( i.e. no mention of an ending of the project ). 
>> 
>> I installed it ( adding "-fPIC" in the 3 Makefile.PLs ) and I'm about to
>> start using it. But, does is it still maintained? Is it still in use?
> 
> Re: being maintained: No, except Bio::Tools::HMM 
> (https://github.com/bioperl/Bio-Tools-HMM)
> 
> Re: in use: somewhat. I think some still use Bio::SeqIO::staden::read and 
> Bio::Ext::Align, but they haven't actively maintained in quite some time.
> 
>> Recommended for a new project? I don't mind fixing compilation errors,
but
>> maybe there is a new package that superseded it. Maybe I'm downloading it
>> from the wrong place.
>> 
>> Regards,
>> -- Diego
> 
> The code still works in some cases but is somewhat bit-rotted (I recall
getting 
> very inconsistent results from Bio::SearchUtils, not sure why). 
> 
> We (Bio* projects) are starting to consolidate around using BioLib for 
> consistent bindings to C/C++ libraries, though that project is undergoing
some 
> changes:
> 
> http://biolib.open-bio.org/wiki/Main_Page
> 
> Pjotr Prins is the lead on that, worth talking to. The next big step is to
interface 
> with EMBOSS libraries, which is very promising.
> 
> chris
> 




From ross at cuhk.edu.hk  Tue Mar 15 20:55:42 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Wed, 16 Mar 2011 08:55:42 +0800
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
	<DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
Message-ID: <007201cbe374$dffa5eb0$9fef1c10$@edu.hk>

-----Original Message-----
From: Chris Fields [mailto:cjfields at illinois.edu] 
Sent: 2011?3?15? 22:44
To: Ross KK Leung
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] how to prevent forced exit?

Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?

chris


Dear Chris,

Thanks for your suggestion. The problem we encounter is that we don't know what database/genbank files we have to retrieve in order to accomplish the job. It seems that the nr database does not include all the records, and we don't know whether we have to concatenate all the genbank files into a very big one so to parse one by one. Any advice?

Gratefully, Ross



From jimhu at tamu.edu  Wed Mar 16 02:22:23 2011
From: jimhu at tamu.edu (Jim Hu)
Date: Wed, 16 Mar 2011 01:22:23 -0500
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <3E73745F-A687-4229-B71E-5C56B2D1FBAE@illinois.edu>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
	<DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
	<9CD1455E-88B4-4E2A-B3BC-398C10D5AAA9@tamu.edu>
	<3E73745F-A687-4229-B71E-5C56B2D1FBAE@illinois.edu>
Message-ID: <D714889D-D73C-4E45-87E3-FE921BFEBA48@tamu.edu>

I put a snippet at the end of:

	http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database

The snippet is on an independent page, and is included via 

	{{:Remote_database_admonition}}
 
which allows people to put it into other pages, and to edit it and have the changes update on all the pages where it's included.  So if someone wants to reword it, make it red text, put it in a box div or whatever, it just has to be done once.  Or, since it's a wiki,  others can just kill it altogether. ;)

Jim

On Mar 15, 2011, at 10:54 AM, Chris Fields wrote:

> Jim,
> 
> It's worth noting in something more prominent, like the tutorial, FAQ, and appropriate HOWTO's.  We've long considered whether it would be worth setting up a cookbook-like section that includes simple workflows, that would also be appropriate for something like this.
> 
> Also, I do think this is mentioned in the POD for several modules, but worth adding a prominent section on it if it's not present.  In Bio::DB::GenBank:
> 
>  WARNING: Please do NOT spam the Entrez web server with multiple requests.  NCBI offers Batch Entrez for this purpose.
> 
> That could be placed somewhere that is a bit more helpful.
> 
> chris
> 
> 
> On Mar 15, 2011, at 10:25 AM, Jim Hu wrote:
> 
>> Hi Chris,
>> 
>> A version of this admonition should be on every wiki HOWTO that involves retrieving records from external sources, and in the docs for the relevant modules.  Speaking as someone who has used BioPerl intermittently for years, and who has Sysiphus-like relationship with the learning curve, I think the docs could use more discussion of when to use particular modules in addition to the details of how to use them provided in the perldocs. I realize this is hard, given the perl "more than one way to do it" world view, but that's my $0.02.
>> 
>> Since BioPerl.org is a wiki, I suppose I should do that admonition edit myself... especially since I already know the wiki markup to transclude the same text into multiple pages.
>> 
>> Jim
>> 
>> Sent from my iPad
>> 
>> On Mar 15, 2011, at 9:44 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> 
>>> Ross,
>>> 
>>> Hope you're exaggerating, you really shouldn't use this service for retrieving 1 million records as you'll likely find your IP banned by NCBI; they are starting to enforce stricter web-based access to their  server now.  Bio::DB::GenBank uses a GET HTTP request using URI-based parameters which effectively limits the length of the query to around 200-300 IDs per request, so you would have to split single one large request many.  Thousands of repeated requests, even with a timeout, may flag your IP as 'spam'.  You can use something like Bio::DB::EUtilities to grab larger groups of seqs (~1000 IDs) b/c the latest EUtilities uses POST requests vs GET for a large number of IDs, but you are still effectively limited by the number of requests.
>>> 
>>> Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?
>>> 
>>> chris
>>> 
>>> On Mar 15, 2011, at 9:16 AM, Ross KK Leung wrote:
>>> 
>>>> While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> #!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   
>>>> 
>>>> use Bio::DB::GenBank;
>>>> 
>>>> 
>>>> 
>>>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');
>>>> 
>>>> 
>>>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>>> 
>>>> 
>>>> print "HEELO";
>>>> 
>>>> while ($seqobj = $allseqobj->next_seq) {
>>>>                    #$seqobj = $allseqobj->next_seq;
>>>>                    $seq=$seqobj->seq;
>>>> }
>>>> print "222   HEELO";
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
>>>> Sent: 2011?3?15? 17:02
>>>> To: Ross KK Leung
>>>> Cc: bioperl-l at lists.open-bio.org
>>>> Subject: Re: [Bioperl-l] how to prevent forced exit?
>>>> 
>>>> 
>>>> 
>>>> Hi Ross,
>>>> 
>>>> 
>>>> 
>>>> Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.
>>>> 
>>>> 
>>>> 
>>>> Try copying the example code directly from here
>>>> 
>>>> 
>>>> 
>>>> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html
>>>> 
>>>> 
>>>> 
>>>> and making sure that works first before modifying it.
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> More documentation and examples here:
>>>> 
>>>> http://www.bioperl.org/wiki/HOWTO:Beginners
>>>> 
>>>> http://www.bioperl.org/wiki/Bioperl_scripts
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> Dave
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:
>>>> 
>>>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
>>>> 'Fasta');
>>>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>>>            l
>>>> print "HEELO";
>>>> while ($seqobj = $allseqobj->next_seq) {
>>>>                    #$seqobj = $allseqobj->next_seq;
>>>> 
>>>>                    $seq=$seqobj->seq;
>>>> 
>>>>                    }
>>>> 
>>>>                print "222   HEELO";
>>>> 
>>>> 
>>>> 
>>>> I find that the 1st HEELO can be printed while the 2nd one can't. Google
>>>> does not return checking success/failure or null/exist of the Seq Object. As
>>>> the 1st HEELO can be executed, so no throw/exception occurs for the
>>>> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
>>>> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
>>>> accession numbers.
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054




From cjfields at illinois.edu  Wed Mar 16 13:58:23 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 12:58:23 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
Message-ID: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>

(apologies if you receive multiple copies of this)

All,

We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:

http://redmine.open-bio.org/

All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.

For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:

1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.

2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.

Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.

Let us know if you have any questions.  

chris

Christopher Fields
IGB Postdoctoral Fellow
Genomics of Neural & Behavioral Plasticity
University of Illinois Urbana-Champaign
Institute for Genomic Biology
1206 W. Gregory Dr. , MC-195
Urbana, IL 61801

From simon.noel.2 at ulaval.ca  Wed Mar 16 15:40:09 2011
From: simon.noel.2 at ulaval.ca (=?iso-8859-1?Q?Simon_No=EBl?=)
Date: Wed, 16 Mar 2011 15:40:09 -0400
Subject: [Bioperl-l]  Perl/BioPerl
Message-ID: <1C970CA8E580A84394CE5CF42FEC0046DF67A4FA81@EXCH-MBX-E.ulaval.ca>

 Hi, 
 
I don't know if I am on the right mailling list for this.
 
My director say that I should have a class of Perl or BioPerl.  Witch one should be better?  Do you know where I can find such class?


Simon No?l
CdeC

From cjfields at illinois.edu  Wed Mar 16 18:30:40 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 17:30:40 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
	<AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
Message-ID: <D6A1291F-898A-4563-8C19-FA2E92D48767@illinois.edu>

Huh, Dave Messina reported something similar earlier.  I actually tested this myself and couldn't reproduce it, maybe I'll try it on Firefox (I was using Chrome).

chris

On Mar 16, 2011, at 3:48 PM, Jonathan Duke Leto wrote:

> Howdy,
> 
> Thanks for working on this Chris!
> 
> I am not sure the password reset works properly.
> 
> Attached is a screenshot of it giving odd errors.
> 
> This was on Firefox 3.6.
> 
> Duke
> 
> On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> (apologies if you receive multiple copies of this)
>> 
>> All,
>> 
>> We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:
>> 
>> http://redmine.open-bio.org/
>> 
>> All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.
>> 
>> For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:
>> 
>> 1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.
>> 
>> 2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.
>> 
>> Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
>> 
>> Let us know if you have any questions.
>> 
>> chris
>> 
>> Christopher Fields
>> IGB Postdoctoral Fellow
>> Genomics of Neural & Behavioral Plasticity
>> University of Illinois Urbana-Champaign
>> Institute for Genomic Biology
>> 1206 W. Gregory Dr. , MC-195
>> Urbana, IL 61801
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> Jonathan "Duke" Leto
> jonathan at leto.net
> http://leto.net
> <obf_redmine.png>



From cjfields at illinois.edu  Wed Mar 16 18:50:18 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 17:50:18 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
	<AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
Message-ID: <F380825D-8F8B-4766-99C3-36FDD8E9C99D@illinois.edu>

I reset the plugins and reloaded the database.  Does that help?  I tested it out again using a test user (using the 'Lost password' link) and it seemed to work.

If not, I can manually reset and send the password to you.

chris

On Mar 16, 2011, at 3:48 PM, Jonathan Duke Leto wrote:

> Howdy,
> 
> Thanks for working on this Chris!
> 
> I am not sure the password reset works properly.
> 
> Attached is a screenshot of it giving odd errors.
> 
> This was on Firefox 3.6.
> 
> Duke
> 
> On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> (apologies if you receive multiple copies of this)
>> 
>> All,
>> 
>> We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:
>> 
>> http://redmine.open-bio.org/
>> 
>> All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.
>> 
>> For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:
>> 
>> 1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.
>> 
>> 2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.
>> 
>> Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
>> 
>> Let us know if you have any questions.
>> 
>> chris
>> 
>> Christopher Fields
>> IGB Postdoctoral Fellow
>> Genomics of Neural & Behavioral Plasticity
>> University of Illinois Urbana-Champaign
>> Institute for Genomic Biology
>> 1206 W. Gregory Dr. , MC-195
>> Urbana, IL 61801
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> Jonathan "Duke" Leto
> jonathan at leto.net
> http://leto.net
> <obf_redmine.png>



From hlapp at drycafe.net  Wed Mar 16 23:05:15 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 16 Mar 2011 23:05:15 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
Message-ID: <1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>


On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:

> Okay, we have bioperl.org set up to use OpenID, works well:

Seems to work mostly - there seems to be some odd small problem with  
ClaimID: typing in my username leads to an OpenID error, whereas  
entering my full ClaimID OpenID works.  Not sure why that would be.

Any chance this can be enabled for BioSQL too (and accordingly account  
creation disabled there, too)?

	-hilmar

>
>
> http://www.bioperl.org/wiki/Special:OpenIDLogin
>
> I have also temporarily shut down new user account creation (new  
> users must now use OpenID); old users can still use the login, but  
> they can also tie their account to an OpenID.  Let's see if it cuts  
> down on the spam.
>
> chris
>
> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>
>> Any update on the OpenID extension?
>>
>> 	-hilmar
>>
>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>
>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit 
>>> ):
>>>
>>> "Unfortunately, reCAPTCHA might be a victim of its own success -  
>>> as of 2011, some spammers appear to have figured out a way to  
>>> bypass it, either through character recognition or by using  
>>> humans. For that reason, it is not necessarily recommended."
>>>
>>> I agree about the barrier to entry issue, but unfortunately with  
>>> the wiki we're facing a reality check re: spam attacks.  We can  
>>> probably set up a new group for users that allows account  
>>> approval, though, which might alleviate the process somewhat.
>>>
>>> chris
>>>
>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>
>>>> Hi Chris,
>>>>
>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>> account, you have the ability to approve other people's  
>>>> accounts.  The
>>>> hope being to distribute the load.  I'm not thrilled about it  
>>>> though:
>>>> I want the barrier to entry to be as low as possible.  We already  
>>>> make
>>>> it so that you have to have an account to edit, passing a  
>>>> recaptcha on
>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu 
>>>> > wrote:
>>>>> All,
>>>>>
>>>>> We have been getting inundated on the wiki with spam lately.  In  
>>>>> order to get on top of this, I'm thinking about having the wiki  
>>>>> set up so wiki admins approve new user accounts, using the  
>>>>> ConfirmAccount plugin:
>>>>>
>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>
>>>>> I wanted to get everyone's opinion on this prior to enforcing  
>>>>> it.  The queue is pretty configurable, and one can set this to  
>>>>> auto-delete old requests.
>>>>>
>>>>> Any thoughts?
>>>>>
>>>>> chris
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>
>>>>
>>>>
>>>> -- 
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at  
>>>> scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                      
>>>> 216-392-3087
>>>> Ontario Institute for Cancer Research
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>> ===========================================================
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================





From cjfields at illinois.edu  Wed Mar 16 23:08:11 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 22:08:11 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
Message-ID: <E0AD66F8-13FE-4940-A0F5-2E4CC0C02755@illinois.edu>

I can work on that.  Peter, need this for biopython?

chris

On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:

> 
> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
> 
>> Okay, we have bioperl.org set up to use OpenID, works well:
> 
> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works.  Not sure why that would be.
> 
> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
> 
> 	-hilmar
> 
>> 
>> 
>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>> 
>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.
>> 
>> chris
>> 
>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>> 
>>> Any update on the OpenID extension?
>>> 
>>> 	-hilmar
>>> 
>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>> 
>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>> 
>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>> 
>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>> 
>>>> chris
>>>> 
>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>> 
>>>>> Hi Chris,
>>>>> 
>>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>> account, you have the ability to approve other people's accounts.  The
>>>>> hope being to distribute the load.  I'm not thrilled about it though:
>>>>> I want the barrier to entry to be as low as possible.  We already make
>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>> 
>>>>> Scott
>>>>> 
>>>>> 
>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>> All,
>>>>>> 
>>>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>> 
>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>> 
>>>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>> 
>>>>>> Any thoughts?
>>>>>> 
>>>>>> chris
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> -- 
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>> ===========================================================
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 



From cjfields at illinois.edu  Wed Mar 16 23:59:17 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 22:59:17 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
Message-ID: <B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>

Done, for BioSQL.  Let me know about Biopython and the others.

-c 

On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:

> 
> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
> 
>> Okay, we have bioperl.org set up to use OpenID, works well:
> 
> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works.  Not sure why that would be.
> 
> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
> 
> 	-hilmar
> 
>> 
>> 
>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>> 
>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.
>> 
>> chris
>> 
>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>> 
>>> Any update on the OpenID extension?
>>> 
>>> 	-hilmar
>>> 
>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>> 
>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>> 
>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>> 
>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>> 
>>>> chris
>>>> 
>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>> 
>>>>> Hi Chris,
>>>>> 
>>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>> account, you have the ability to approve other people's accounts.  The
>>>>> hope being to distribute the load.  I'm not thrilled about it though:
>>>>> I want the barrier to entry to be as low as possible.  We already make
>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>> 
>>>>> Scott
>>>>> 
>>>>> 
>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>> All,
>>>>>> 
>>>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>> 
>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>> 
>>>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>> 
>>>>>> Any thoughts?
>>>>>> 
>>>>>> chris
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> -- 
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>> ===========================================================
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 



From hlapp at drycafe.net  Thu Mar 17 00:07:45 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Thu, 17 Mar 2011 00:07:45 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
Message-ID: <6747C6EA-27BC-43C1-89B4-0F3AEF18BFA4@drycafe.net>


On Mar 16, 2011, at 11:59 PM, Chris Fields wrote:

> Done, for BioSQL.  Let me know about Biopython and the others.

Great, works! -hilmar


-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================





From p.j.a.cock at googlemail.com  Thu Mar 17 04:27:22 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 17 Mar 2011 08:27:22 +0000
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
Message-ID: <AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>

Yes please - thanks Chris!

Peter

On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu> wrote:
> Done, for BioSQL. ?Let me know about Biopython and the others.
>
> -c
>
> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>
>>
>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>
>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>
>> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works. ?Not sure why that would be.
>>
>> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
>>
>> ? ? ? -hilmar
>>
>>>
>>>
>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>
>>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID. ?Let's see if it cuts down on the spam.
>>>
>>> chris
>>>
>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>
>>>> Any update on the OpenID extension?
>>>>
>>>> ? ? -hilmar
>>>>
>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>
>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>>>
>>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>>>
>>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks. ?We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>>>
>>>>> chris
>>>>>
>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>
>>>>>> Hi Chris,
>>>>>>
>>>>>> The GMOD wiki has been getting hit similarly. ?I've been thinking
>>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>>> account, you have the ability to approve other people's accounts. ?The
>>>>>> hope being to distribute the load. ?I'm not thrilled about it though:
>>>>>> I want the barrier to entry to be as low as possible. ?We already make
>>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>>> the way. ?Apparently that barrier is already a little too low :-/
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>>> All,
>>>>>>>
>>>>>>> We have been getting inundated on the wiki with spam lately. ?In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>>>
>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>
>>>>>>> I wanted to get everyone's opinion on this prior to enforcing it. ?The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>>>
>>>>>>> Any thoughts?
>>>>>>>
>>>>>>> chris
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> ------------------------------------------------------------------------
>>>>>> Scott Cain, Ph. D.


From David.Messina at sbc.su.se  Thu Mar 17 04:51:21 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 17 Mar 2011 09:51:21 +0100
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <F380825D-8F8B-4766-99C3-36FDD8E9C99D@illinois.edu>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
	<AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
	<F380825D-8F8B-4766-99C3-36FDD8E9C99D@illinois.edu>
Message-ID: <AANLkTik8oYG1yJ7HdV119K08NsbqpDTUpDAtKUPSKUMF@mail.gmail.com>

Works for me now ? I was able to reset the password and log in.

Thanks, Chris!

Dave




On Wed, Mar 16, 2011 at 23:50, Chris Fields <cjfields at illinois.edu> wrote:

> I reset the plugins and reloaded the database.  Does that help?  I tested
> it out again using a test user (using the 'Lost password' link) and it
> seemed to work.
>
> If not, I can manually reset and send the password to you.
>
> chris
>
> On Mar 16, 2011, at 3:48 PM, Jonathan Duke Leto wrote:
>
> > Howdy,
> >
> > Thanks for working on this Chris!
> >
> > I am not sure the password reset works properly.
> >
> > Attached is a screenshot of it giving odd errors.
> >
> > This was on Firefox 3.6.
> >
> > Duke
> >
> > On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu>
> wrote:
> >> (apologies if you receive multiple copies of this)
> >>
> >> All,
> >>
> >> We are currently about 95% done with a transition over to our new
> Redmine tracking system, to the point where we feel comfortable in going
> ahead with opening it to developers:
> >>
> >> http://redmine.open-bio.org/
> >>
> >> All edits to bugzilla reports on our old system (
> http://bugzilla.open-bio.org/) are now disabled and the system is now
> read-only.  Any new bugs and comments to old ones should be reported on the
> new Redmine server.
> >>
> >> For current Bugzilla users, we have migrated login IDs to Redmine (this
> is normally an email address), but we have reset user passwords for security
> reasons.  There are two ways to access your account:
> >>
> >> 1) When logging in (http://redmine.open-bio.org/login), click on the
> 'Lost password' link.  You will be prompted for your email address (this
> should be the same as your bugzilla login).  An new email will be sent out
> containing directions for resetting your password and logging in.
> >>
> >> 2) It is possible the above may be automatically detected as spam.  If
> the above doesn't work or the reset email isn't received within a day,
> contact support at helpdesk.open-bio.org to receive your new password.
> >>
> >> Also, note that Redmine has a different syntax for those who want to add
> links to their reports; see
> http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
> >>
> >> Let us know if you have any questions.
> >>
> >> chris
> >>
> >> Christopher Fields
> >> IGB Postdoctoral Fellow
> >> Genomics of Neural & Behavioral Plasticity
> >> University of Illinois Urbana-Champaign
> >> Institute for Genomic Biology
> >> 1206 W. Gregory Dr. , MC-195
> >> Urbana, IL 61801
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> >
> >
> > --
> > Jonathan "Duke" Leto
> > jonathan at leto.net
> > http://leto.net
> > <obf_redmine.png>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From cjfields at illinois.edu  Thu Mar 17 07:36:05 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Mar 2011 06:36:05 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <AANLkTik8oYG1yJ7HdV119K08NsbqpDTUpDAtKUPSKUMF@mail.gmail.com>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
	<AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
	<F380825D-8F8B-4766-99C3-36FDD8E9C99D@illinois.edu>
	<AANLkTik8oYG1yJ7HdV119K08NsbqpDTUpDAtKUPSKUMF@mail.gmail.com>
Message-ID: <B8AB68C4-0DD8-408E-8C49-D33339E6C6ED@illinois.edu>

I did a little database cleansing; the email notification settings were screwy (why the warnings popped up).

chris

On Mar 17, 2011, at 3:51 AM, Dave Messina wrote:

> Works for me now ? I was able to reset the password and log in.
> 
> Thanks, Chris!
> 
> Dave
> 
> 
> 
> 
> On Wed, Mar 16, 2011 at 23:50, Chris Fields <cjfields at illinois.edu> wrote:
> I reset the plugins and reloaded the database.  Does that help?  I tested it out again using a test user (using the 'Lost password' link) and it seemed to work.
> 
> If not, I can manually reset and send the password to you.
> 
> chris
> 
> On Mar 16, 2011, at 3:48 PM, Jonathan Duke Leto wrote:
> 
> > Howdy,
> >
> > Thanks for working on this Chris!
> >
> > I am not sure the password reset works properly.
> >
> > Attached is a screenshot of it giving odd errors.
> >
> > This was on Firefox 3.6.
> >
> > Duke
> >
> > On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
> >> (apologies if you receive multiple copies of this)
> >>
> >> All,
> >>
> >> We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:
> >>
> >> http://redmine.open-bio.org/
> >>
> >> All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.
> >>
> >> For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:
> >>
> >> 1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.
> >>
> >> 2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.
> >>
> >> Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
> >>
> >> Let us know if you have any questions.
> >>
> >> chris
> >>
> >> Christopher Fields
> >> IGB Postdoctoral Fellow
> >> Genomics of Neural & Behavioral Plasticity
> >> University of Illinois Urbana-Champaign
> >> Institute for Genomic Biology
> >> 1206 W. Gregory Dr. , MC-195
> >> Urbana, IL 61801
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> >
> >
> > --
> > Jonathan "Duke" Leto
> > jonathan at leto.net
> > http://leto.net
> > <obf_redmine.png>
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From cjfields at illinois.edu  Thu Mar 17 12:16:19 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Mar 2011 11:16:19 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
	<AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
Message-ID: <B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>

Peter, 

It's set up for biopython.  Will make an announcement on open-bio-l and post something on the blog when I catch my breath (redmine and this in one week is a little tiring!).

Will also ping biojava and the other wiki groups about switching over.

chris

On Mar 17, 2011, at 3:27 AM, Peter Cock wrote:

> Yes please - thanks Chris!
> 
> Peter
> 
> On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu> wrote:
>> Done, for BioSQL.  Let me know about Biopython and the others.
>> 
>> -c
>> 
>> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>> 
>>> 
>>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>> 
>>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>> 
>>> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works.  Not sure why that would be.
>>> 
>>> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
>>> 
>>>       -hilmar
>>> 
>>>> 
>>>> 
>>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>> 
>>>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.
>>>> 
>>>> chris
>>>> 
>>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>> 
>>>>> Any update on the OpenID extension?
>>>>> 
>>>>>     -hilmar
>>>>> 
>>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>> 
>>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>>>> 
>>>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>>>> 
>>>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>>>> 
>>>>>> chris
>>>>>> 
>>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>> 
>>>>>>> Hi Chris,
>>>>>>> 
>>>>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>>>> account, you have the ability to approve other people's accounts.  The
>>>>>>> hope being to distribute the load.  I'm not thrilled about it though:
>>>>>>> I want the barrier to entry to be as low as possible.  We already make
>>>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>>>> 
>>>>>>> Scott
>>>>>>> 
>>>>>>> 
>>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>>>> All,
>>>>>>>> 
>>>>>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>>>> 
>>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>> 
>>>>>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>>>> 
>>>>>>>> Any thoughts?
>>>>>>>> 
>>>>>>>> chris
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> --
>>>>>>> ------------------------------------------------------------------------
>>>>>>> Scott Cain, Ph. D.



From adam at retchless.us  Thu Mar 17 12:32:37 2011
From: adam at retchless.us (Adam Retchless)
Date: Thu, 17 Mar 2011 12:32:37 -0400
Subject: [Bioperl-l] Wiki login with OpenId
Message-ID: <4D8237A5.4050706@retchless.us>

Greetings all,

First: A "thank you" to everyone who has developed BioPerl and the 
BioPerl Wiki -- I'm new to BioPerl, but have already benefited from its 
ability to simplify tasks that would otherwise be very tedious.

Anyway, I noticed some outdated information on the Wiki, and wanted to 
change it, but had a little trouble figuring out how to do so. 
Basically, it wasn't clear that the way to create an account was to 
click on the "Login with OpenId" button. As someone who doesn't use 
OpenID, I immediately went to the traditional "Login" page, but got 
stumped there. It did not occur to me that the OpenID page would be any 
different. Only after looking at the recent discussion on the mailing 
list did I figure out what I needed to do.

In the interest of eliminating any obstacle to participation, I think it 
would be helpful for the Wiki itself to clearly indicate how to create a 
new account. Either by changing the wording of the "login with OpenID 
link", or placing a message on the traditional "Log In" page telling 
people what they need to do to make an account.

Thanks, and I look forward to participating here.

-Adam

-- 

Adam Retchless
Center for Genomic Sciences
Allegheny-Singer Research Institute


From cjfields at illinois.edu  Thu Mar 17 13:13:14 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Mar 2011 12:13:14 -0500
Subject: [Bioperl-l] Wiki login with OpenId
In-Reply-To: <4D8237A5.4050706@retchless.us>
References: <4D8237A5.4050706@retchless.us>
Message-ID: <62E050E8-E567-4117-B14C-1F613CC81016@illinois.edu>

Adam, 

We're in the process of doing so; the addition of OpenID logins is a few days old.  I'm actually writing a blog post right now on the problems we've had and the use of OpenID, and will add a few things to the wiki pages so the login is clearer (including adding text to the normal login page).

chris

On Mar 17, 2011, at 11:32 AM, Adam Retchless wrote:

> Greetings all,
> 
> First: A "thank you" to everyone who has developed BioPerl and the BioPerl Wiki -- I'm new to BioPerl, but have already benefited from its ability to simplify tasks that would otherwise be very tedious.
> 
> Anyway, I noticed some outdated information on the Wiki, and wanted to change it, but had a little trouble figuring out how to do so. Basically, it wasn't clear that the way to create an account was to click on the "Login with OpenId" button. As someone who doesn't use OpenID, I immediately went to the traditional "Login" page, but got stumped there. It did not occur to me that the OpenID page would be any different. Only after looking at the recent discussion on the mailing list did I figure out what I needed to do.
> 
> In the interest of eliminating any obstacle to participation, I think it would be helpful for the Wiki itself to clearly indicate how to create a new account. Either by changing the wording of the "login with OpenID link", or placing a message on the traditional "Log In" page telling people what they need to do to make an account.
> 
> Thanks, and I look forward to participating here.
> 
> -Adam
> 
> -- 
> 
> Adam Retchless
> Center for Genomic Sciences
> Allegheny-Singer Research Institute
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From hlapp at drycafe.net  Thu Mar 17 15:38:01 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Thu, 17 Mar 2011 15:38:01 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
	<AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
	<B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>
Message-ID: <A95A687E-25DD-4325-983D-BE9A5F45FA23@drycafe.net>

Just a thought towards the future - OpenIDs are so easy to obtain that  
the way it is right now (any OpenID will do) is built on the premise  
that it's not used widely enough (yet!) to make it worth the spammers'  
time.  Same story as with reCaptcha, probably. So once OpenID is used  
widely, we'll probably have to restrict the OpenID providers that we  
permit.

	-hilmar

On Mar 17, 2011, at 12:16 PM, Chris Fields wrote:

> Peter,
>
> It's set up for biopython.  Will make an announcement on open-bio-l  
> and post something on the blog when I catch my breath (redmine and  
> this in one week is a little tiring!).
>
> Will also ping biojava and the other wiki groups about switching over.
>
> chris
>
> On Mar 17, 2011, at 3:27 AM, Peter Cock wrote:
>
>> Yes please - thanks Chris!
>>
>> Peter
>>
>> On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu>  
>> wrote:
>>> Done, for BioSQL.  Let me know about Biopython and the others.
>>>
>>> -c
>>>
>>> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>>>
>>>>
>>>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>>>
>>>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>>>
>>>> Seems to work mostly - there seems to be some odd small problem  
>>>> with ClaimID: typing in my username leads to an OpenID error,  
>>>> whereas entering my full ClaimID OpenID works.  Not sure why that  
>>>> would be.
>>>>
>>>> Any chance this can be enabled for BioSQL too (and accordingly  
>>>> account creation disabled there, too)?
>>>>
>>>>      -hilmar
>>>>
>>>>>
>>>>>
>>>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>>>
>>>>> I have also temporarily shut down new user account creation (new  
>>>>> users must now use OpenID); old users can still use the login,  
>>>>> but they can also tie their account to an OpenID.  Let's see if  
>>>>> it cuts down on the spam.
>>>>>
>>>>> chris
>>>>>
>>>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>>>
>>>>>> Any update on the OpenID extension?
>>>>>>
>>>>>>    -hilmar
>>>>>>
>>>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>>>
>>>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit 
>>>>>>> ):
>>>>>>>
>>>>>>> "Unfortunately, reCAPTCHA might be a victim of its own success  
>>>>>>> - as of 2011, some spammers appear to have figured out a way  
>>>>>>> to bypass it, either through character recognition or by using  
>>>>>>> humans. For that reason, it is not necessarily recommended."
>>>>>>>
>>>>>>> I agree about the barrier to entry issue, but unfortunately  
>>>>>>> with the wiki we're facing a reality check re: spam attacks.   
>>>>>>> We can probably set up a new group for users that allows  
>>>>>>> account approval, though, which might alleviate the process  
>>>>>>> somewhat.
>>>>>>>
>>>>>>> chris
>>>>>>>
>>>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>>>
>>>>>>>> Hi Chris,
>>>>>>>>
>>>>>>>> The GMOD wiki has been getting hit similarly.  I've been  
>>>>>>>> thinking
>>>>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>>>>> account, you have the ability to approve other people's  
>>>>>>>> accounts.  The
>>>>>>>> hope being to distribute the load.  I'm not thrilled about it  
>>>>>>>> though:
>>>>>>>> I want the barrier to entry to be as low as possible.  We  
>>>>>>>> already make
>>>>>>>> it so that you have to have an account to edit, passing a  
>>>>>>>> recaptcha on
>>>>>>>> the way.  Apparently that barrier is already a little too  
>>>>>>>> low :-/
>>>>>>>>
>>>>>>>> Scott
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu 
>>>>>>>> > wrote:
>>>>>>>>> All,
>>>>>>>>>
>>>>>>>>> We have been getting inundated on the wiki with spam  
>>>>>>>>> lately.  In order to get on top of this, I'm thinking about  
>>>>>>>>> having the wiki set up so wiki admins approve new user  
>>>>>>>>> accounts, using the ConfirmAccount plugin:
>>>>>>>>>
>>>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>>>
>>>>>>>>> I wanted to get everyone's opinion on this prior to  
>>>>>>>>> enforcing it.  The queue is pretty configurable, and one can  
>>>>>>>>> set this to auto-delete old requests.
>>>>>>>>>
>>>>>>>>> Any thoughts?
>>>>>>>>>
>>>>>>>>> chris
>>>>>>>>> _______________________________________________
>>>>>>>>> Bioperl-l mailing list
>>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> Scott Cain, Ph. D.
>

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================





From cjfields at illinois.edu  Thu Mar 17 15:40:47 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Mar 2011 14:40:47 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <A95A687E-25DD-4325-983D-BE9A5F45FA23@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
	<AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
	<B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>
	<A95A687E-25DD-4325-983D-BE9A5F45FA23@drycafe.net>
Message-ID: <2E6327AD-4CD3-45CE-A105-66FA3A474294@illinois.edu>

That's easy enough to do with the OpenID plugin settings:

$wgOpenIDConsumerAllow
an array of regular expressions that match OpenIDs you want to allow to log in. For example, "@^(http://)?wikitravel.org/@" will allow OpenIDs from the Wikitravel domain.
$wgOpenIDConsumerDeny
an array of regular expressions that match OpenIDs you want to deny access to. This is mostly useful for servers that are known to be bad. Example: "#^(http://)?example.com/#".

chris

On Mar 17, 2011, at 2:38 PM, Hilmar Lapp wrote:

> Just a thought towards the future - OpenIDs are so easy to obtain that the way it is right now (any OpenID will do) is built on the premise that it's not used widely enough (yet!) to make it worth the spammers' time.  Same story as with reCaptcha, probably. So once OpenID is used widely, we'll probably have to restrict the OpenID providers that we permit.
> 
> 	-hilmar
> 
> On Mar 17, 2011, at 12:16 PM, Chris Fields wrote:
> 
>> Peter,
>> 
>> It's set up for biopython.  Will make an announcement on open-bio-l and post something on the blog when I catch my breath (redmine and this in one week is a little tiring!).
>> 
>> Will also ping biojava and the other wiki groups about switching over.
>> 
>> chris
>> 
>> On Mar 17, 2011, at 3:27 AM, Peter Cock wrote:
>> 
>>> Yes please - thanks Chris!
>>> 
>>> Peter
>>> 
>>> On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu> wrote:
>>>> Done, for BioSQL.  Let me know about Biopython and the others.
>>>> 
>>>> -c
>>>> 
>>>> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>>>> 
>>>>> 
>>>>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>>>> 
>>>>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>>>> 
>>>>> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works.  Not sure why that would be.
>>>>> 
>>>>> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
>>>>> 
>>>>>     -hilmar
>>>>> 
>>>>>> 
>>>>>> 
>>>>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>>>> 
>>>>>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.
>>>>>> 
>>>>>> chris
>>>>>> 
>>>>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>>>> 
>>>>>>> Any update on the OpenID extension?
>>>>>>> 
>>>>>>>   -hilmar
>>>>>>> 
>>>>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>>>> 
>>>>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>>>>>> 
>>>>>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>>>>>> 
>>>>>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>>>>>> 
>>>>>>>> chris
>>>>>>>> 
>>>>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>>>> 
>>>>>>>>> Hi Chris,
>>>>>>>>> 
>>>>>>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>>>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>>>>>> account, you have the ability to approve other people's accounts.  The
>>>>>>>>> hope being to distribute the load.  I'm not thrilled about it though:
>>>>>>>>> I want the barrier to entry to be as low as possible.  We already make
>>>>>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>>>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>>>>>> 
>>>>>>>>> Scott
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>>>>>> All,
>>>>>>>>>> 
>>>>>>>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>>>>>> 
>>>>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>>>> 
>>>>>>>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>>>>>> 
>>>>>>>>>> Any thoughts?
>>>>>>>>>> 
>>>>>>>>>> chris
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Bioperl-l mailing list
>>>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> --
>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>> Scott Cain, Ph. D.
>> 
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 



From hlapp at drycafe.net  Thu Mar 17 16:01:42 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Thu, 17 Mar 2011 16:01:42 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <2E6327AD-4CD3-45CE-A105-66FA3A474294@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
	<AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
	<B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>
	<A95A687E-25DD-4325-983D-BE9A5F45FA23@drycafe.net>
	<2E6327AD-4CD3-45CE-A105-66FA3A474294@illinois.edu>
Message-ID: <14304AC6-1AAA-44C3-A169-F0111BA59AC2@drycafe.net>

Indeed. And I guess we can add "bad" providers incrementally as we  
spam from them trickle in. I can imagine that at some point there'll  
also be a blacklist of spam OpenID providers.

	-hilmar

On Mar 17, 2011, at 3:40 PM, Chris Fields wrote:

> That's easy enough to do with the OpenID plugin settings:
>
> $wgOpenIDConsumerAllow
> an array of regular expressions that match OpenIDs you want to allow  
> to log in. For example, "@^(http://)?wikitravel.org/@" will allow  
> OpenIDs from the Wikitravel domain.
> $wgOpenIDConsumerDeny
> an array of regular expressions that match OpenIDs you want to deny  
> access to. This is mostly useful for servers that are known to be  
> bad. Example: "#^(http://)?example.com/#".
>
> chris
>
> On Mar 17, 2011, at 2:38 PM, Hilmar Lapp wrote:
>
>> Just a thought towards the future - OpenIDs are so easy to obtain  
>> that the way it is right now (any OpenID will do) is built on the  
>> premise that it's not used widely enough (yet!) to make it worth  
>> the spammers' time.  Same story as with reCaptcha, probably. So  
>> once OpenID is used widely, we'll probably have to restrict the  
>> OpenID providers that we permit.
>>
>> 	-hilmar
>>
>> On Mar 17, 2011, at 12:16 PM, Chris Fields wrote:
>>
>>> Peter,
>>>
>>> It's set up for biopython.  Will make an announcement on open-bio- 
>>> l and post something on the blog when I catch my breath (redmine  
>>> and this in one week is a little tiring!).
>>>
>>> Will also ping biojava and the other wiki groups about switching  
>>> over.
>>>
>>> chris
>>>
>>> On Mar 17, 2011, at 3:27 AM, Peter Cock wrote:
>>>
>>>> Yes please - thanks Chris!
>>>>
>>>> Peter
>>>>
>>>> On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu>  
>>>> wrote:
>>>>> Done, for BioSQL.  Let me know about Biopython and the others.
>>>>>
>>>>> -c
>>>>>
>>>>> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>>>>>
>>>>>>
>>>>>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>>>>>
>>>>>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>>>>>
>>>>>> Seems to work mostly - there seems to be some odd small problem  
>>>>>> with ClaimID: typing in my username leads to an OpenID error,  
>>>>>> whereas entering my full ClaimID OpenID works.  Not sure why  
>>>>>> that would be.
>>>>>>
>>>>>> Any chance this can be enabled for BioSQL too (and accordingly  
>>>>>> account creation disabled there, too)?
>>>>>>
>>>>>>    -hilmar
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>>>>>
>>>>>>> I have also temporarily shut down new user account creation  
>>>>>>> (new users must now use OpenID); old users can still use the  
>>>>>>> login, but they can also tie their account to an OpenID.   
>>>>>>> Let's see if it cuts down on the spam.
>>>>>>>
>>>>>>> chris
>>>>>>>
>>>>>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>>>>>
>>>>>>>> Any update on the OpenID extension?
>>>>>>>>
>>>>>>>>  -hilmar
>>>>>>>>
>>>>>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>>>>>
>>>>>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit 
>>>>>>>>> ):
>>>>>>>>>
>>>>>>>>> "Unfortunately, reCAPTCHA might be a victim of its own  
>>>>>>>>> success - as of 2011, some spammers appear to have figured  
>>>>>>>>> out a way to bypass it, either through character recognition  
>>>>>>>>> or by using humans. For that reason, it is not necessarily  
>>>>>>>>> recommended."
>>>>>>>>>
>>>>>>>>> I agree about the barrier to entry issue, but unfortunately  
>>>>>>>>> with the wiki we're facing a reality check re: spam  
>>>>>>>>> attacks.  We can probably set up a new group for users that  
>>>>>>>>> allows account approval, though, which might alleviate the  
>>>>>>>>> process somewhat.
>>>>>>>>>
>>>>>>>>> chris
>>>>>>>>>
>>>>>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>>>>>
>>>>>>>>>> Hi Chris,
>>>>>>>>>>
>>>>>>>>>> The GMOD wiki has been getting hit similarly.  I've been  
>>>>>>>>>> thinking
>>>>>>>>>> about the "vampire" model that EcoliWiki uses: once you  
>>>>>>>>>> have an
>>>>>>>>>> account, you have the ability to approve other people's  
>>>>>>>>>> accounts.  The
>>>>>>>>>> hope being to distribute the load.  I'm not thrilled about  
>>>>>>>>>> it though:
>>>>>>>>>> I want the barrier to entry to be as low as possible.  We  
>>>>>>>>>> already make
>>>>>>>>>> it so that you have to have an account to edit, passing a  
>>>>>>>>>> recaptcha on
>>>>>>>>>> the way.  Apparently that barrier is already a little too  
>>>>>>>>>> low :-/
>>>>>>>>>>
>>>>>>>>>> Scott
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu 
>>>>>>>>>> > wrote:
>>>>>>>>>>> All,
>>>>>>>>>>>
>>>>>>>>>>> We have been getting inundated on the wiki with spam  
>>>>>>>>>>> lately.  In order to get on top of this, I'm thinking  
>>>>>>>>>>> about having the wiki set up so wiki admins approve new  
>>>>>>>>>>> user accounts, using the ConfirmAccount plugin:
>>>>>>>>>>>
>>>>>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>>>>>
>>>>>>>>>>> I wanted to get everyone's opinion on this prior to  
>>>>>>>>>>> enforcing it.  The queue is pretty configurable, and one  
>>>>>>>>>>> can set this to auto-delete old requests.
>>>>>>>>>>>
>>>>>>>>>>> Any thoughts?
>>>>>>>>>>>
>>>>>>>>>>> chris
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Bioperl-l mailing list
>>>>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>> Scott Cain, Ph. D.
>>>
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>> ===========================================================
>>
>>
>>
>>
>

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================





From tzhu at mail.bnu.edu.cn  Fri Mar 18 00:33:32 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Fri, 18 Mar 2011 12:33:32 +0800
Subject: [Bioperl-l] What's wrong with the script about module
 Bio::SeqFeature::Gene::GeneStructure
Message-ID: <1300422812.12949.5.camel@ubuntu>

I wrote my script like this,

#!/usr/bin/perl -w
use Bio::SeqIO;
my $catch_seq = Bio::SeqIO -> new(-file => 'test.gbk',-format=>
'genbank');
while( my $seq_obj = $catch_seq -> next_seq)
{
	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
get_SeqFeatures;
	for my $mRNA_feature (@all_mRNA_features)
	{
			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
		{
			@exons=$mRNA_feature->exons;
			$exon_number = scalar(@exons);
			print "$exon_number\n";
		}
	}
}

I hope to count exon number in every mRNA. But it print nothing(You can
arbitrarily get a genbank file to test it). What's wrong?


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)



From hrh at fmi.ch  Fri Mar 18 05:17:30 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Fri, 18 Mar 2011 10:17:30 +0100
Subject: [Bioperl-l] What's wrong with the script about module
	Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300422812.12949.5.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu>
Message-ID: <4D83232A.9050502@fmi.ch>

Hi Tao

I don't fully understand your script, but I do see a major problem:

why do you select for "primary_tag eq 'mRNA'" first?


this simple loop will probably do what you want:

while( my $seq_obj = $catch_seq -> next_seq) {

	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
$seq_obj ->get_SeqFeatures;
	$exon_number = scalar(@all_exon_features);
	print "$exon_number\n";
}


Alternatively, I recommend to read the HOWTO page:

http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

which has a nice example to print out all 'primary_tag' (ie the 'feature 
keys' in a GenBank formated file)

I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
definition:
http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html


Regards, Hans



On 03/18/2011 05:33 AM, Tao Zhu wrote:
> I wrote my script like this,
>
> #!/usr/bin/perl -w
> use Bio::SeqIO;
> my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
> 'genbank');
> while( my $seq_obj = $catch_seq ->  next_seq)
> {
> 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
> get_SeqFeatures;
> 	for my $mRNA_feature (@all_mRNA_features)
> 	{
> 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
> 		{
> 			@exons=$mRNA_feature->exons;
> 			$exon_number = scalar(@exons);
> 			print "$exon_number\n";
> 		}
> 	}
> }
>
> I hope to count exon number in every mRNA. But it print nothing(You can
> arbitrarily get a genbank file to test it). What's wrong?
>
>

From tzhu at mail.bnu.edu.cn  Fri Mar 18 07:32:00 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Fri, 18 Mar 2011 19:32:00 +0800
Subject: [Bioperl-l] What's wrong with the script about module
 Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <4D83232A.9050502@fmi.ch>
References: <1300422812.12949.5.camel@ubuntu>  <4D83232A.9050502@fmi.ch>
Message-ID: <1300447920.16670.2.camel@ubuntu>

Of course that's OK. But what I really want to know is how to use module
Bio::SeqFeature::Gene::GeneStructure. 

? 2011-03-18?? 10:17 +0100?Hans-Rudolf Hotz???
> Hi Tao
> 
> I don't fully understand your script, but I do see a major problem:
> 
> why do you select for "primary_tag eq 'mRNA'" first?
> 
> 
> this simple loop will probably do what you want:
> 
> while( my $seq_obj = $catch_seq -> next_seq) {
> 
> 	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
> $seq_obj ->get_SeqFeatures;
> 	$exon_number = scalar(@all_exon_features);
> 	print "$exon_number\n";
> }
> 
> 
> Alternatively, I recommend to read the HOWTO page:
> 
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> 
> which has a nice example to print out all 'primary_tag' (ie the 'feature 
> keys' in a GenBank formated file)
> 
> I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
> definition:
> http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
> 
> 
> Regards, Hans
> 
> 
> 
> On 03/18/2011 05:33 AM, Tao Zhu wrote:
> > I wrote my script like this,
> >
> > #!/usr/bin/perl -w
> > use Bio::SeqIO;
> > my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
> > 'genbank');
> > while( my $seq_obj = $catch_seq ->  next_seq)
> > {
> > 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
> > get_SeqFeatures;
> > 	for my $mRNA_feature (@all_mRNA_features)
> > 	{
> > 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
> > 		{
> > 			@exons=$mRNA_feature->exons;
> > 			$exon_number = scalar(@exons);
> > 			print "$exon_number\n";
> > 		}
> > 	}
> > }
> >
> > I hope to count exon number in every mRNA. But it print nothing(You can
> > arbitrarily get a genbank file to test it). What's wrong?
> >
> >

-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)



From cjfields at illinois.edu  Fri Mar 18 09:04:34 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 18 Mar 2011 08:04:34 -0500
Subject: [Bioperl-l] What's wrong with the script about module
	Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300447920.16670.2.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu> <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
Message-ID: <2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>

The SeqFeatures derived from a GenBank file are simple Bio::SeqFeature::Generic instances.  I don't think there is a straightforward way to have the parser return Bio::SeqFeature::Gene::GeneStructure instances.

chris

On Mar 18, 2011, at 6:32 AM, Tao Zhu wrote:

> Of course that's OK. But what I really want to know is how to use module
> Bio::SeqFeature::Gene::GeneStructure. 
> 
> ? 2011-03-18?? 10:17 +0100?Hans-Rudolf Hotz???
>> Hi Tao
>> 
>> I don't fully understand your script, but I do see a major problem:
>> 
>> why do you select for "primary_tag eq 'mRNA'" first?
>> 
>> 
>> this simple loop will probably do what you want:
>> 
>> while( my $seq_obj = $catch_seq -> next_seq) {
>> 
>> 	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
>> $seq_obj ->get_SeqFeatures;
>> 	$exon_number = scalar(@all_exon_features);
>> 	print "$exon_number\n";
>> }
>> 
>> 
>> Alternatively, I recommend to read the HOWTO page:
>> 
>> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
>> 
>> which has a nice example to print out all 'primary_tag' (ie the 'feature 
>> keys' in a GenBank formated file)
>> 
>> I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
>> definition:
>> http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
>> 
>> 
>> Regards, Hans
>> 
>> 
>> 
>> On 03/18/2011 05:33 AM, Tao Zhu wrote:
>>> I wrote my script like this,
>>> 
>>> #!/usr/bin/perl -w
>>> use Bio::SeqIO;
>>> my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
>>> 'genbank');
>>> while( my $seq_obj = $catch_seq ->  next_seq)
>>> {
>>> 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
>>> get_SeqFeatures;
>>> 	for my $mRNA_feature (@all_mRNA_features)
>>> 	{
>>> 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
>>> 		{
>>> 			@exons=$mRNA_feature->exons;
>>> 			$exon_number = scalar(@exons);
>>> 			print "$exon_number\n";
>>> 		}
>>> 	}
>>> }
>>> 
>>> I hope to count exon number in every mRNA. But it print nothing(You can
>>> arbitrarily get a genbank file to test it). What's wrong?
>>> 
>>> 
> 
> -- 
> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> 100875, China
> Email: tzhu at mail.bnu.edu.cn
> Website: http://bnuzt.org (mainly written in Chinese)
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From ross at cuhk.edu.hk  Fri Mar 18 09:22:40 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Fri, 18 Mar 2011 21:22:40 +0800
Subject: [Bioperl-l]  failure in unsubscription
In-Reply-To: <1300447920.16670.2.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu> <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
Message-ID: <018101cbe56f$8ec755f0$ac5601d0$@edu.hk>

unable to unsubscribe bioperl mailing list, anybody can help? the web link, after clicking "unsubscribe", there is no confirmation email sent to my email account and I keep receiving emails from bioperl mailing list.



From tzhu at mail.bnu.edu.cn  Fri Mar 18 09:57:21 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Fri, 18 Mar 2011 21:57:21 +0800
Subject: [Bioperl-l] What's wrong with the script about module
 Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
References: <1300422812.12949.5.camel@ubuntu>  <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
	<2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
Message-ID: <1300456641.18688.4.camel@ubuntu>

Yes. But in the document
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
Bio::SeqFeature::Generic. I wonder how to do such inheritance.

? 2011-03-18?? 08:04 -0500?Chris Fields???
> The SeqFeatures derived from a GenBank file are simple Bio::SeqFeature::Generic instances.  I don't think there is a straightforward way to have the parser return Bio::SeqFeature::Gene::GeneStructure instances.
> 
> chris
> 
> On Mar 18, 2011, at 6:32 AM, Tao Zhu wrote:
> 
> > Of course that's OK. But what I really want to know is how to use module
> > Bio::SeqFeature::Gene::GeneStructure. 
> > 
> > ? 2011-03-18?? 10:17 +0100?Hans-Rudolf Hotz???
> >> Hi Tao
> >> 
> >> I don't fully understand your script, but I do see a major problem:
> >> 
> >> why do you select for "primary_tag eq 'mRNA'" first?
> >> 
> >> 
> >> this simple loop will probably do what you want:
> >> 
> >> while( my $seq_obj = $catch_seq -> next_seq) {
> >> 
> >> 	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
> >> $seq_obj ->get_SeqFeatures;
> >> 	$exon_number = scalar(@all_exon_features);
> >> 	print "$exon_number\n";
> >> }
> >> 
> >> 
> >> Alternatively, I recommend to read the HOWTO page:
> >> 
> >> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> >> 
> >> which has a nice example to print out all 'primary_tag' (ie the 'feature 
> >> keys' in a GenBank formated file)
> >> 
> >> I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
> >> definition:
> >> http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
> >> 
> >> 
> >> Regards, Hans
> >> 
> >> 
> >> 
> >> On 03/18/2011 05:33 AM, Tao Zhu wrote:
> >>> I wrote my script like this,
> >>> 
> >>> #!/usr/bin/perl -w
> >>> use Bio::SeqIO;
> >>> my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
> >>> 'genbank');
> >>> while( my $seq_obj = $catch_seq ->  next_seq)
> >>> {
> >>> 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
> >>> get_SeqFeatures;
> >>> 	for my $mRNA_feature (@all_mRNA_features)
> >>> 	{
> >>> 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
> >>> 		{
> >>> 			@exons=$mRNA_feature->exons;
> >>> 			$exon_number = scalar(@exons);
> >>> 			print "$exon_number\n";
> >>> 		}
> >>> 	}
> >>> }
> >>> 
> >>> I hope to count exon number in every mRNA. But it print nothing(You can
> >>> arbitrarily get a genbank file to test it). What's wrong?
> >>> 
> >>> 
> > 
> > -- 
> > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> > 100875, China
> > Email: tzhu at mail.bnu.edu.cn
> > Website: http://bnuzt.org (mainly written in Chinese)
> > 
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From fs5 at sanger.ac.uk  Fri Mar 18 11:05:29 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Fri, 18 Mar 2011 15:05:29 +0000
Subject: [Bioperl-l] What's wrong with the script about
	module	Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300456641.18688.4.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu>  <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
	<2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
	<1300456641.18688.4.camel@ubuntu>
Message-ID: <1300460730.12411.50.camel@deskpro15336.internal.sanger.ac.uk>

maybe I'm missing the point here but I think an "mRNA" feature should
not be a Bio::SeqFeature::Gene::GeneStructure and it should not have
exons - it would not make sense biologically.

Frank


On Fri, 2011-03-18 at 21:57 +0800, Tao Zhu wrote:
> Yes. But in the document
> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
> It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
> Bio::SeqFeature::Generic. I wonder how to do such inheritance.
> 
> ? 2011-03-18?? 08:04 -0500?Chris Fields???
> > The SeqFeatures derived from a GenBank file are simple Bio::SeqFeature::Generic instances.  I don't think there is a straightforward way to have the parser return Bio::SeqFeature::Gene::GeneStructure instances.
> > 
> > chris
> > 
> > On Mar 18, 2011, at 6:32 AM, Tao Zhu wrote:
> > 
> > > Of course that's OK. But what I really want to know is how to use module
> > > Bio::SeqFeature::Gene::GeneStructure. 
> > > 
> > > ? 2011-03-18?? 10:17 +0100?Hans-Rudolf Hotz???
> > >> Hi Tao
> > >> 
> > >> I don't fully understand your script, but I do see a major problem:
> > >> 
> > >> why do you select for "primary_tag eq 'mRNA'" first?
> > >> 
> > >> 
> > >> this simple loop will probably do what you want:
> > >> 
> > >> while( my $seq_obj = $catch_seq -> next_seq) {
> > >> 
> > >> 	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
> > >> $seq_obj ->get_SeqFeatures;
> > >> 	$exon_number = scalar(@all_exon_features);
> > >> 	print "$exon_number\n";
> > >> }
> > >> 
> > >> 
> > >> Alternatively, I recommend to read the HOWTO page:
> > >> 
> > >> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> > >> 
> > >> which has a nice example to print out all 'primary_tag' (ie the 'feature 
> > >> keys' in a GenBank formated file)
> > >> 
> > >> I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
> > >> definition:
> > >> http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
> > >> 
> > >> 
> > >> Regards, Hans
> > >> 
> > >> 
> > >> 
> > >> On 03/18/2011 05:33 AM, Tao Zhu wrote:
> > >>> I wrote my script like this,
> > >>> 
> > >>> #!/usr/bin/perl -w
> > >>> use Bio::SeqIO;
> > >>> my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
> > >>> 'genbank');
> > >>> while( my $seq_obj = $catch_seq ->  next_seq)
> > >>> {
> > >>> 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
> > >>> get_SeqFeatures;
> > >>> 	for my $mRNA_feature (@all_mRNA_features)
> > >>> 	{
> > >>> 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
> > >>> 		{
> > >>> 			@exons=$mRNA_feature->exons;
> > >>> 			$exon_number = scalar(@exons);
> > >>> 			print "$exon_number\n";
> > >>> 		}
> > >>> 	}
> > >>> }
> > >>> 
> > >>> I hope to count exon number in every mRNA. But it print nothing(You can
> > >>> arbitrarily get a genbank file to test it). What's wrong?
> > >>> 
> > >>> 
> > > 
> > > -- 
> > > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> > > 100875, China
> > > Email: tzhu at mail.bnu.edu.cn
> > > Website: http://bnuzt.org (mainly written in Chinese)
> > > 
> > > 
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From chapmanb at 50mail.com  Fri Mar  4 07:37:28 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Fri, 4 Mar 2011 07:37:28 -0500
Subject: [Bioperl-l] Bioinformatics Open Source Conference (BOSC 2011)--Call
 for Abstracts
Message-ID: <20110304123728.GD27839@sobchak>

We invite you to submit an abstract to BOSC 2011! Please forward this
message as appropriate, and forgive multiple postings.

Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference (BOSC 2011)
An ISMB 2011 Special Interest Group (SIG)

Dates: July 15-16, 2011
Location: Vienna, Austria
Web site: http://www.open-bio.org/wiki/BOSC_2011
Email: bosc at open-bio.org
BOSC announcements mailing list:  http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:
April 18, 2011: Deadline for submitting abstracts to BOSC 2011
May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors
July 13-14, 2011: Codefest 2011 programming session (see http://www.open-bio.org/wiki/Codefest_2011 for details)
July 15-16, 2011: BOSC 2011
July 17-19, 2011: ISMB 2011

The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.

We invite you to submit abstracts for talks and posters.  Sessions include:
- Approaches to parallel processing
- Cloud-based approaches to improving software and data accessibility
- The Semantic Web in open source bioinformatics
- Data visualization
- Tools for next-generation sequencing
- Other Open Source software

In addition to the above sessions, there will be a panel discussion
about "Meeting the challenges of inter-institutional collaboration". We
are also working to arrange a joint session with one of the other ISMB
SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student Travel
Awards for BOSC 2011. Each winner will be awarded $250 to defray the
costs of travel to BOSC 2011.
 
For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee:
Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor 

From bill_zt at sina.com  Thu Mar 17 20:48:19 2011
From: bill_zt at sina.com (Tao Zhu)
Date: Fri, 18 Mar 2011 08:48:19 +0800
Subject: [Bioperl-l] Perl/BioPerl (Simon No?l)
Message-ID: <1300409299.2349.5.camel@ubuntu>

In order to learn BioPerl, you should first learn and master Perl. If
you are not majoring in Bioinformatics, learning Perl is just OK.
Otherwise you should learn both Perl and BioPerl.


> Message: 2
> Date: Wed, 16 Mar 2011 15:40:09 -0400
> From: Simon No?l <simon.noel.2 at ulaval.ca>
> Subject: [Bioperl-l]  Perl/BioPerl
> To: "bioperl-l at lists.open-bio.org" <bioperl-l at lists.open-bio.org>
> Message-ID:
>         <1C970CA8E580A84394CE5CF42FEC0046DF67A4FA81 at EXCH-MBX-E.ulaval.ca>
> Content-Type: text/plain; charset="iso-8859-1"
> 
>  Hi, 
>  
> I don't know if I am on the right mailling list for this.
>  
> My director say that I should have a class of Perl or BioPerl.  Witch
> one should be better?  Do you know where I can find such class?
> 
> 
> Simon No?l
> CdeC
> 


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)


From bio.justin100 at gmail.com  Fri Mar  4 15:24:51 2011
From: bio.justin100 at gmail.com (justin100)
Date: Fri, 4 Mar 2011 12:24:51 -0800 (PST)
Subject: [Bioperl-l] Please recommend Perl module to parse phylogentic trees
Message-ID: <2e94f0bb-0282-4d53-b205-56ff895665de@w7g2000pre.googlegroups.com>

Hi,

I am writing a script to parse phylogenetic trees. The input will be
trees in Newick format for now (maybe NEXUS in the future).

Quite a few Perl modules can parse phylogenetic trees. For Newick
format, there are Bio::TreeIO and  Bio::Phylo::Parsers. For NEXUS
format, there is Bio::NEXUS. From my understanding, it's not difficult
to convert from Newick to NEXUS or vice versa, if only for the purpose
of parsing trees.

I'd to know the advantages and disadvantages of these modules when
compared with each other. Please recommend one that you think is the
most capable parser (and hopefully has the least bugs).

Thanks.

Justin

From jonathan at leto.net  Wed Mar 16 16:48:24 2011
From: jonathan at leto.net (Jonathan "Duke" Leto)
Date: Wed, 16 Mar 2011 13:48:24 -0700
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
Message-ID: <AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>

Howdy,

Thanks for working on this Chris!

I am not sure the password reset works properly.

Attached is a screenshot of it giving odd errors.

This was on Firefox 3.6.

Duke

On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
> (apologies if you receive multiple copies of this)
>
> All,
>
> We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:
>
> http://redmine.open-bio.org/
>
> All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only. ?Any new bugs and comments to old ones should be reported on the new Redmine server.
>
> For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons. ?There are two ways to access your account:
>
> 1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link. ?You will be prompted for your email address (this should be the same as your bugzilla login). ?An new email will be sent out containing directions for resetting your password and logging in.
>
> 2) It is possible the above may be automatically detected as spam. ?If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.
>
> Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
>
> Let us know if you have any questions.
>
> chris
>
> Christopher Fields
> IGB Postdoctoral Fellow
> Genomics of Neural & Behavioral Plasticity
> University of Illinois Urbana-Champaign
> Institute for Genomic Biology
> 1206 W. Gregory Dr. , MC-195
> Urbana, IL 61801
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Jonathan "Duke" Leto
jonathan at leto.net
http://leto.net
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From rutgeraldo at gmail.com  Fri Mar 18 10:16:25 2011
From: rutgeraldo at gmail.com (Rutger Vos)
Date: Fri, 18 Mar 2011 14:16:25 +0000
Subject: [Bioperl-l] Please forward: collecting support for Japanese
	scientists
Message-ID: <AANLkTiksWdna1MLpbBWk2nDv0LAyrXdU7xV3Fs5gSHkF@mail.gmail.com>

Dear colleagues,

A web page has been launched to collect support for Japanese
(bio-)scientists: http://biohelpathon.org - please forward this
address widely.

The purpose of the web page is to establish a knowledge base of
available support for our colleagues in Japan. You are invited to
submit any tips, ideas and offers including accommodation, funding
resources, exchange schemes, lab space, server space and open
positions for visiting students and research personnel from Japan.

We will collect your suggestions and offers and will share them with
whoever is best placed to disseminate them. This initiative originates
with the attendees of the BioHackathons (the Japanese website
http://hackathon.dbcls.jp is offline due to the earthquake), but
anyone is very welcome to contribute. To get in touch, join
http://groups.google.com/group/biohelpathon.

This initiative is no alternative to first responders who are helping
out in Japan right now. The rescue operation and food and shelter
support comes first. If you can only do one thing, it should be a
donation to something like the Red Cross. This comes later.

See also:
A different initiative, with which we're in touch:
http://www.nipponsciencesupport.net/
More info on Nature blogs:
http://blogs.nature.com/news/thegreatbeyond/2011/03/helping_hand_for_scientistrefu.html

PLEASE NOTE: WE ARE NOT HANDLING MONEY. This is simply a way to
crowdsource information about available resources.

Thank you.

Rutger Vos

From spotforever at tiscali.it  Sun Mar 13 14:15:54 2011
From: spotforever at tiscali.it (marcocirilli)
Date: Sun, 13 Mar 2011 11:15:54 -0700 (PDT)
Subject: [Bioperl-l]  slit sequence with BioPerl by ID-query
Message-ID: <31138653.post@talk.nabble.com>


Hello, I have 2 fasta file with similar sequences and I want to compare them
and eliminate sequences with the same IDquery (or extract only different
ID-query). How can I do it with BioPerl? Thanks 
-- 
View this message in context: http://old.nabble.com/slit-sequence-with-BioPerl-by-ID-query-tp31138653p31138653.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From suhail.mn12 at yahoo.co.uk  Fri Mar 18 12:18:49 2011
From: suhail.mn12 at yahoo.co.uk (Suhail M)
Date: Fri, 18 Mar 2011 16:18:49 +0000 (GMT)
Subject: [Bioperl-l] RemoteBlast
Message-ID: <988359.99459.qm@web132309.mail.ird.yahoo.com>

Dear Sir or Madam,
I am using a remote blast and encounter either a too many hsp or CPU overload 
problem with my specific gene. The gene itself is not that big so I was 
wondering is there a parameter I can pass when using the submit option to 
restrict number of hsp and to avoid the cpu and too many hsp problem? (I know I 
can use repeat masking and change the e-value but I need something that does not 
require those changes)

my $prog = 'blastn';
#my $db   = 'swissprot';
my $e_val= '1e-10';

my @params = ( '-prog'       => $prog,
#       '-data'       => $db,
               '-expect'     => $e_val,
               '-readmethod' => 'SearchIO'
            );

my $factory = Bio::Tools::Run::RemoteBlast->new(@params);

$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens [ORGN]';

delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};

my $str = Bio::SeqIO->new(-file            =>'temporary.fa' , 
 '-format'         => 'fasta');

my $r = $factory->submit_blast('temporary.fa');

Thank you for your help.
Suhail


      

From shalabh.sharma7 at gmail.com  Fri Mar 18 12:41:42 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Fri, 18 Mar 2011 12:41:42 -0400
Subject: [Bioperl-l] RemoteBlast
In-Reply-To: <988359.99459.qm@web132309.mail.ird.yahoo.com>
References: <988359.99459.qm@web132309.mail.ird.yahoo.com>
Message-ID: <AANLkTikLD+A9o0Nujg9ThGbFL3HvtaAGXaihoEX5OmTE@mail.gmail.com>

Suhail,
         You can restrict the number of hits by using "-v" and "-b"
parameters.

-Shalabh


On Fri, Mar 18, 2011 at 12:18 PM, Suhail M <suhail.mn12 at yahoo.co.uk> wrote:

> Dear Sir or Madam,
> I am using a remote blast and encounter either a too many hsp or CPU
> overload
> problem with my specific gene. The gene itself is not that big so I was
> wondering is there a parameter I can pass when using the submit option to
> restrict number of hsp and to avoid the cpu and too many hsp problem? (I
> know I
> can use repeat masking and change the e-value but I need something that
> does not
> require those changes)
>
> my $prog = 'blastn';
> #my $db   = 'swissprot';
> my $e_val= '1e-10';
>
> my @params = ( '-prog'       => $prog,
> #       '-data'       => $db,
>               '-expect'     => $e_val,
>               '-readmethod' => 'SearchIO'
>            );
>
> my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
>
> $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens
> [ORGN]';
>
> delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};
>
> my $str = Bio::SeqIO->new(-file            =>'temporary.fa' ,
>  '-format'         => 'fasta');
>
> my $r = $factory->submit_blast('temporary.fa');
>
> Thank you for your help.
> Suhail
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636

From rmb32 at cornell.edu  Fri Mar 18 15:24:03 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Fri, 18 Mar 2011 15:24:03 -0400
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
Message-ID: <4D83B153.6010006@cornell.edu>

Hi all,

Great news: Google announced today that the Open Bioinformatics
Foundation has been accepted as a mentoring organization for this
summer's Google Summer of Code!

GSoC is a Google-sponsored student internship program for open-source
projects, open to students from around the world (not just US
residents).   Students are paid a $5000 USD stipend to work as a
developer on an open-source project for the summer. For more on GSoC,
see GSoC 2011 FAQ at http://bit.ly/hpoz8W

Student applications are due April 8, 2011 at 19:00 UTC.  Students who
are interested in participating should look at the OBF's GSoC page at
http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
ideas, and whom to contact about applying.

For current developers on OBF projects, please consider volunteering to
be a mentor if you have not already, and contribute project ideas.  Just
list your name and project ideas on OBF wiki and on the relevant
project's GSoC wiki page.

Thanks to all who helped make OBF's application to GSoC a success, and
let's have a great, productive summer of code!

Rob Buels
OBF GSoC 2011 Administrator



From cjfields at illinois.edu  Fri Mar 18 16:06:36 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 18 Mar 2011 15:06:36 -0500
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <4D83B153.6010006@cornell.edu>
References: <4D83B153.6010006@cornell.edu>
Message-ID: <AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>

Congrats Rob!

chris

On Mar 18, 2011, at 2:24 PM, Robert Buels wrote:

> Hi all,
> 
> Great news: Google announced today that the Open Bioinformatics
> Foundation has been accepted as a mentoring organization for this
> summer's Google Summer of Code!
> 
> GSoC is a Google-sponsored student internship program for open-source
> projects, open to students from around the world (not just US
> residents).   Students are paid a $5000 USD stipend to work as a
> developer on an open-source project for the summer. For more on GSoC,
> see GSoC 2011 FAQ at http://bit.ly/hpoz8W
> 
> Student applications are due April 8, 2011 at 19:00 UTC.  Students who
> are interested in participating should look at the OBF's GSoC page at
> http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
> ideas, and whom to contact about applying.
> 
> For current developers on OBF projects, please consider volunteering to
> be a mentor if you have not already, and contribute project ideas.  Just
> list your name and project ideas on OBF wiki and on the relevant
> project's GSoC wiki page.
> 
> Thanks to all who helped make OBF's application to GSoC a success, and
> let's have a great, productive summer of code!
> 
> Rob Buels
> OBF GSoC 2011 Administrator
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From ross at cuhk.edu.hk  Fri Mar 18 19:28:51 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Sat, 19 Mar 2011 07:28:51 +0800
Subject: [Bioperl-l]  failure in unsubscription
In-Reply-To: <AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
Message-ID: <018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>

unable to unsubscribe bioperl mailing list, can anybody help? the web link,
after clicking "unsubscribe" at
http://lists.open-bio.org/mailman/options/bioperl-announce-l, there is no
confirmation email sent to my email account and I keep receiving emails from
bioperl mailing list.


From Kevin.M.Brown at asu.edu  Fri Mar 18 19:35:37 2011
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Fri, 18 Mar 2011 16:35:37 -0700
Subject: [Bioperl-l] failure in unsubscription
In-Reply-To: <018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>
References: <4D83B153.6010006@cornell.edu><AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
	<018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>
Message-ID: <1A4207F8295607498283FE9E93B775B407816AC4@EX02.asurite.ad.asu.edu>

Looks like you're unsubscribing to the wrong list. That is for the
Bioperl ANNOUNCE list. See the signature at the bottom of the emails for
the correct link to remove yourself from the Bioperl-l list.

Kevin Brown
Center for Innovations in Medicine
Biodesign Institute
Arizona State University 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Ross KK Leung
> Sent: Friday, March 18, 2011 4:29 PM
> To: 'Chris Fields'; 'Robert Buels'
> Cc: 'BioPerl List'
> Subject: [Bioperl-l] failure in unsubscription
> 
> unable to unsubscribe bioperl mailing list, can anybody help? the web
> link,
> after clicking "unsubscribe" at
> http://lists.open-bio.org/mailman/options/bioperl-announce-l, there is
> no
> confirmation email sent to my email account and I keep receiving
emails
> from
> bioperl mailing list.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From David.Messina at sbc.su.se  Fri Mar 18 19:55:08 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Sat, 19 Mar 2011 00:55:08 +0100
Subject: [Bioperl-l] failure in unsubscription
In-Reply-To: <018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
	<018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>
Message-ID: <AANLkTin6k3AfwYFxgRKLGWbL5BhqxkQr7Vv6MebhObzY@mail.gmail.com>

Looks like you accidentally found the page for the wrong email list. This is
bioperl-l, not bioperl-announce-l.

Try clicking unsubscribe on this page:
http://lists.open-bio.org/mailman/listinfo/bioperl-l



On Sat, Mar 19, 2011 at 00:28, Ross KK Leung <ross at cuhk.edu.hk> wrote:

> unable to unsubscribe bioperl mailing list, can anybody help? the web link,
> after clicking "unsubscribe" at
> http://lists.open-bio.org/mailman/options/bioperl-announce-l, there is no
> confirmation email sent to my email account and I keep receiving emails
> from
> bioperl mailing list.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From David.Messina at sbc.su.se  Fri Mar 18 19:56:12 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Sat, 19 Mar 2011 00:56:12 +0100
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
Message-ID: <AANLkTikTsPeJvs0StBPzicxM55XgfvGbjrZMrwX9mwNo@mail.gmail.com>

Hear, hear! Thanks again Rob for leading this effort. You rock!

Dave



On Fri, Mar 18, 2011 at 21:06, Chris Fields <cjfields at illinois.edu> wrote:

> Congrats Rob!
>
> chris
>
> On Mar 18, 2011, at 2:24 PM, Robert Buels wrote:
>
> > Hi all,
> >
> > Great news: Google announced today that the Open Bioinformatics
> > Foundation has been accepted as a mentoring organization for this
> > summer's Google Summer of Code!
> >
> > GSoC is a Google-sponsored student internship program for open-source
> > projects, open to students from around the world (not just US
> > residents).   Students are paid a $5000 USD stipend to work as a
> > developer on an open-source project for the summer. For more on GSoC,
> > see GSoC 2011 FAQ at http://bit.ly/hpoz8W
> >
> > Student applications are due April 8, 2011 at 19:00 UTC.  Students who
> > are interested in participating should look at the OBF's GSoC page at
> > http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
> > ideas, and whom to contact about applying.
> >
> > For current developers on OBF projects, please consider volunteering to
> > be a mentor if you have not already, and contribute project ideas.  Just
> > list your name and project ideas on OBF wiki and on the relevant
> > project's GSoC wiki page.
> >
> > Thanks to all who helped make OBF's application to GSoC a success, and
> > let's have a great, productive summer of code!
> >
> > Rob Buels
> > OBF GSoC 2011 Administrator
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From hlapp at drycafe.net  Fri Mar 18 22:04:28 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Fri, 18 Mar 2011 22:04:28 -0400
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <AANLkTikTsPeJvs0StBPzicxM55XgfvGbjrZMrwX9mwNo@mail.gmail.com>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
	<AANLkTikTsPeJvs0StBPzicxM55XgfvGbjrZMrwX9mwNo@mail.gmail.com>
Message-ID: <19636599-D2B1-49E5-B557-3E406B405523@drycafe.net>

Yes! -hilmar

On Mar 18, 2011, at 7:56 PM, Dave Messina wrote:

> Hear, hear! Thanks again Rob for leading this effort. You rock!
>
> Dave
>
>
>
> On Fri, Mar 18, 2011 at 21:06, Chris Fields <cjfields at illinois.edu>  
> wrote:
>
>> Congrats Rob!
>>
>> chris
>>
>> On Mar 18, 2011, at 2:24 PM, Robert Buels wrote:
>>
>>> Hi all,
>>>
>>> Great news: Google announced today that the Open Bioinformatics
>>> Foundation has been accepted as a mentoring organization for this
>>> summer's Google Summer of Code!
>>>
>>> GSoC is a Google-sponsored student internship program for open- 
>>> source
>>> projects, open to students from around the world (not just US
>>> residents).   Students are paid a $5000 USD stipend to work as a
>>> developer on an open-source project for the summer. For more on  
>>> GSoC,
>>> see GSoC 2011 FAQ at http://bit.ly/hpoz8W
>>>
>>> Student applications are due April 8, 2011 at 19:00 UTC.  Students  
>>> who
>>> are interested in participating should look at the OBF's GSoC page  
>>> at
>>> http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
>>> ideas, and whom to contact about applying.
>>>
>>> For current developers on OBF projects, please consider  
>>> volunteering to
>>> be a mentor if you have not already, and contribute project  
>>> ideas.  Just
>>> list your name and project ideas on OBF wiki and on the relevant
>>> project's GSoC wiki page.
>>>
>>> Thanks to all who helped make OBF's application to GSoC a success,  
>>> and
>>> let's have a great, productive summer of code!
>>>
>>> Rob Buels
>>> OBF GSoC 2011 Administrator
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================





From chiragmatkarbioinfo at gmail.com  Fri Mar 18 23:44:32 2011
From: chiragmatkarbioinfo at gmail.com (Chirag Matkar)
Date: Sat, 19 Mar 2011 10:44:32 +0700
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <19636599-D2B1-49E5-B557-3E406B405523@drycafe.net>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
	<AANLkTikTsPeJvs0StBPzicxM55XgfvGbjrZMrwX9mwNo@mail.gmail.com>
	<19636599-D2B1-49E5-B557-3E406B405523@drycafe.net>
Message-ID: <AANLkTin6_H-T7Eq2jxU-SM4CuMF=nBZpXoM_n6joFfmn@mail.gmail.com>

Great News

On Sat, Mar 19, 2011 at 9:04 AM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> Yes! -hilmar
>
>
> On Mar 18, 2011, at 7:56 PM, Dave Messina wrote:
>
>  Hear, hear! Thanks again Rob for leading this effort. You rock!
>>
>> Dave
>>
>>
>>
>> On Fri, Mar 18, 2011 at 21:06, Chris Fields <cjfields at illinois.edu>
>> wrote:
>>
>>  Congrats Rob!
>>>
>>> chris
>>>
>>> On Mar 18, 2011, at 2:24 PM, Robert Buels wrote:
>>>
>>>  Hi all,
>>>>
>>>> Great news: Google announced today that the Open Bioinformatics
>>>> Foundation has been accepted as a mentoring organization for this
>>>> summer's Google Summer of Code!
>>>>
>>>> GSoC is a Google-sponsored student internship program for open-source
>>>> projects, open to students from around the world (not just US
>>>> residents).   Students are paid a $5000 USD stipend to work as a
>>>> developer on an open-source project for the summer. For more on GSoC,
>>>> see GSoC 2011 FAQ at http://bit.ly/hpoz8W
>>>>
>>>> Student applications are due April 8, 2011 at 19:00 UTC.  Students who
>>>> are interested in participating should look at the OBF's GSoC page at
>>>> http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
>>>> ideas, and whom to contact about applying.
>>>>
>>>> For current developers on OBF projects, please consider volunteering to
>>>> be a mentor if you have not already, and contribute project ideas.  Just
>>>> list your name and project ideas on OBF wiki and on the relevant
>>>> project's GSoC wiki page.
>>>>
>>>> Thanks to all who helped make OBF's application to GSoC a success, and
>>>> let's have a great, productive summer of code!
>>>>
>>>> Rob Buels
>>>> OBF GSoC 2011 Administrator
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>  _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Regards,
Chirag Matkar

From tzhu at mail.bnu.edu.cn  Sat Mar 19 05:49:22 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Sat, 19 Mar 2011 17:49:22 +0800
Subject: [Bioperl-l] What's wrong with the script about module
 Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300460730.12411.50.camel@deskpro15336.internal.sanger.ac.uk>
References: <1300422812.12949.5.camel@ubuntu>  <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
	<2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
	<1300456641.18688.4.camel@ubuntu>
	<1300460730.12411.50.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <1300528162.5998.4.camel@ubuntu>

But I think an "mRNA" feature should have exons. For example:


     mRNA            complement(join(1031434..1031901,1031940..1032269,
                     1032329..1032418,1032472..1032489))
                     /locus_tag="SPCC825.05c"
                     /transcript_id="NM_001023047.1"
                     /db_xref="GI:68021105"
                     /db_xref="GeneID:2539459"

Such mRNA should have 4 exons and 3 introns, right? And I just want to
calculate the lengths of every exons and introns quickly.

Besides, in the document of module Bio::SeqFeature::Gene::GeneStructure,
it writes like these:

@exons = $gene->exons();
@introns = $gene->introns();
@utr_sites = $gene->utrs();

Then where does the object "$gene" come from? I've searched through all
the google sites but found nothing.

? 2011-03-18?? 15:05 +0000?Frank Schwach??? 
> maybe I'm missing the point here but I think an "mRNA" feature should
> not be a Bio::SeqFeature::Gene::GeneStructure and it should not have
> exons - it would not make sense biologically.
> 
> Frank
> 
> 
> On Fri, 2011-03-18 at 21:57 +0800, Tao Zhu wrote:
> > Yes. But in the document
> > http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
> > It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
> > Bio::SeqFeature::Generic. I wonder how to do such inheritance.


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)




From manju.rawat2 at gmail.com  Sat Mar 19 06:29:32 2011
From: manju.rawat2 at gmail.com (manju rawat)
Date: Sat, 19 Mar 2011 15:59:32 +0530
Subject: [Bioperl-l] bio-scf installation error
Message-ID: <AANLkTikQwcqs0YyaHvddq9yjowOpoe_YDRj4Z03zXRdv@mail.gmail.com>

Hello ,

I want to install Bio-SCF module on windows..But i am unable to do this bcs
to install bio-scf i have to install io_lib oe zlib on windows..
I download both from the described url in install file of bio-scf....i also
indtalled MinGW ..but now i dont know how to install it???
pls help to install it..

Thanks in Advance
Manju Rawat

From jason.stajich at gmail.com  Sat Mar 19 14:19:23 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 19 Mar 2011 11:19:23 -0700
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <4D83B153.6010006@cornell.edu>
References: <4D83B153.6010006@cornell.edu>
Message-ID: <6387373A-E17F-4CE2-9B19-E296A2668018@gmail.com>

Nice work Rob. Thanks for leading the effort and thanks to those who agreed to mentor. 

Sent from my iPhone-please excuse typos

--
Jason Stajich

On Mar 18, 2011, at 12:24 PM, Robert Buels <rmb32 at cornell.edu> wrote:

> Hi all,
> 
> Great news: Google announced today that the Open Bioinformatics
> Foundation has been accepted as a mentoring organization for this
> summer's Google Summer of Code!
> 
> GSoC is a Google-sponsored student internship program for open-source
> projects, open to students from around the world (not just US
> residents).   Students are paid a $5000 USD stipend to work as a
> developer on an open-source project for the summer. For more on GSoC,
> see GSoC 2011 FAQ at http://bit.ly/hpoz8W
> 
> Student applications are due April 8, 2011 at 19:00 UTC.  Students who
> are interested in participating should look at the OBF's GSoC page at
> http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
> ideas, and whom to contact about applying.
> 
> For current developers on OBF projects, please consider volunteering to
> be a mentor if you have not already, and contribute project ideas.  Just
> list your name and project ideas on OBF wiki and on the relevant
> project's GSoC wiki page.
> 
> Thanks to all who helped make OBF's application to GSoC a success, and
> let's have a great, productive summer of code!
> 
> Rob Buels
> OBF GSoC 2011 Administrator
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From jason.stajich at gmail.com  Sat Mar 19 14:31:17 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 19 Mar 2011 11:31:17 -0700
Subject: [Bioperl-l] What's wrong with the script about module
	Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300528162.5998.4.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu> <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
	<2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
	<1300456641.18688.4.camel@ubuntu>
	<1300460730.12411.50.camel@deskpro15336.internal.sanger.ac.uk>
	<1300528162.5998.4.camel@ubuntu>
Message-ID: <093660B8-458E-4617-8D12-228985CA88CD@gmail.com>

You have to instantiate the gene structure and copy the exon objects into the substructure. Unless you have specific methods in the GeneStructure I would just pull out the data from the generic objects. 

See the genbank to gff script and the Unflattener for ways to more simply destruct the mRNA feature into gene->mRNA->CDS,Exons 

If you are just wanting to count Exons 
You can see example on slide 27 or so. 

http://jason.open-bio.org/Bioperl_Tutorials/ProgrammingBiology2008/ProgBiology_BioPerl_I.pdf

Sent from my iPhone-please excuse typos

--
Jason Stajich

On Mar 19, 2011, at 2:49 AM, Tao Zhu <tzhu at mail.bnu.edu.cn> wrote:

> But I think an "mRNA" feature should have exons. For example:
> 
> 
>     mRNA            complement(join(1031434..1031901,1031940..1032269,
>                     1032329..1032418,1032472..1032489))
>                     /locus_tag="SPCC825.05c"
>                     /transcript_id="NM_001023047.1"
>                     /db_xref="GI:68021105"
>                     /db_xref="GeneID:2539459"
> 
> Such mRNA should have 4 exons and 3 introns, right? And I just want to
> calculate the lengths of every exons and introns quickly.
> 
> Besides, in the document of module Bio::SeqFeature::Gene::GeneStructure,
> it writes like these:
> 
> @exons = $gene->exons();
> @introns = $gene->introns();
> @utr_sites = $gene->utrs();
> 
> Then where does the object "$gene" come from? I've searched through all
> the google sites but found nothing.
> 
> ? 2011-03-18?? 15:05 +0000?Frank Schwach??? 
>> maybe I'm missing the point here but I think an "mRNA" feature should
>> not be a Bio::SeqFeature::Gene::GeneStructure and it should not have
>> exons - it would not make sense biologically.
>> 
>> Frank
>> 
>> 
>> On Fri, 2011-03-18 at 21:57 +0800, Tao Zhu wrote:
>>> Yes. But in the document
>>> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
>>> It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
>>> Bio::SeqFeature::Generic. I wonder how to do such inheritance.
> 
> 
> -- 
> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> 100875, China
> Email: tzhu at mail.bnu.edu.cn
> Website: http://bnuzt.org (mainly written in Chinese)
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From jason.stajich at gmail.com  Sat Mar 19 14:36:49 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 19 Mar 2011 11:36:49 -0700
Subject: [Bioperl-l] Please recommend Perl module to parse phylogentic
	trees
In-Reply-To: <2e94f0bb-0282-4d53-b205-56ff895665de@w7g2000pre.googlegroups.com>
References: <2e94f0bb-0282-4d53-b205-56ff895665de@w7g2000pre.googlegroups.com>
Message-ID: <447BFFD2-06E6-41E0-81BF-B03EB919316C@gmail.com>

Nexus is richer and we only parse the trees from that format. Since the format is a newick tree embedded within it relies on the same code in the newick parser. 

Knowing what you want to do would more likely lead to better answer.  As for bugs - you can search the redmine big tracker to see whether they are reported issues that are unresolved and you can examine the tests in the t directory to see what compliance is tested. 

Jason
Sent from my iPhone-please excuse typos

--
Jason Stajich

On Mar 4, 2011, at 12:24 PM, justin100 <bio.justin100 at gmail.com> wrote:

> Hi,
> 
> I am writing a script to parse phylogenetic trees. The input will be
> trees in Newick format for now (maybe NEXUS in the future).
> 
> Quite a few Perl modules can parse phylogenetic trees. For Newick
> format, there are Bio::TreeIO and  Bio::Phylo::Parsers. For NEXUS
> format, there is Bio::NEXUS. From my understanding, it's not difficult
> to convert from Newick to NEXUS or vice versa, if only for the purpose
> of parsing trees.
> 
> I'd to know the advantages and disadvantages of these modules when
> compared with each other. Please recommend one that you think is the
> most capable parser (and hopefully has the least bugs).
> 
> Thanks.
> 
> Justin
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From veer_lovepune at yahoo.co.in  Sat Mar 19 16:56:06 2011
From: veer_lovepune at yahoo.co.in (virendra patil)
Date: Sun, 20 Mar 2011 02:26:06 +0530 (IST)
Subject: [Bioperl-l] Bioperl-l Digest, Vol 95, Issue 19
In-Reply-To: <mailman.21.1300550405.26148.bioperl-l@lists.open-bio.org>
Message-ID: <790813.91588.qm@web137312.mail.in.yahoo.com>

hi can some one help me i tried to install ?bioperl many time but it show message likeCan't locate Bio/Seq.pm in @INC (@INC contains: E:/JAVA1/.metadata/.plugins/org.epic.debug E:/JAVA1/PERL EXAM D:/Perl/site/lib D:/Perl/lib .) at E:/JAVA1/PERL EXAM/PERLEXAM.pl line 2.BEGIN failed--compilation aborted at E:/JAVA1/PERL EXAM/PERLEXAM.pl line 2.?

---i try with java perl intgration my perl is working but bioperl show upper message



From ngoodman at systemsbiology.org  Tue Mar 22 09:57:50 2011
From: ngoodman at systemsbiology.org (Nathan (Nat) Goodman)
Date: Tue, 22 Mar 2011 06:57:50 -0700
Subject: [Bioperl-l] Ensembl stable_id_event table
Message-ID: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>

With apologies, this is not technically a bioperl question, but hopefully close enough.  I'm trying to map old Ensembl IDs to current ones.  Table stable_id_event on their ftp site seems to be the place to get this information, but the data in that table (for human build 61) is cyclic, meaning that old IDs are sometimes mapped to new ones which in turn are mapped back to the old one.  This seems wrong...  And, it's not a rare occurrence: 18% of IDs in the table lie on cycles, the largest of which contains more than 6000 IDs!

To see one short cycle, run this query (against human build 61).

mysql> select * from stable_id_event where 
    ->     (old_stable_id='ENSP00000399673' or new_stable_id='ENSP00000399673')
    -> and (old_stable_id='ENSP00000365536' or new_stable_id='ENSP00000365536');

The results are

+-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
| old_stable_id   | old_version | new_stable_id   | new_version | mapping_session_id | type        | score |
+-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
| ENSP00000399673 |           2 | ENSP00000365536 |           3 |                380 | translation |     1 | 
| ENSP00000399673 |           2 | ENSP00000365536 |           3 |                381 | translation |     1 | 
| ENSP00000365536 |           3 | ENSP00000399673 |           2 |                381 | translation |     1 | 
| ENSP00000399673 |           2 | ENSP00000365536 |           3 |                382 | translation |     1 | 
| ENSP00000365536 |           3 | ENSP00000399673 |           2 |                382 | translation |     1 | 
+-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+

The first and last lines reveal the cycle:

line 1) ENSP00000399673-> ENSP00000365536
line 5) ENSP00000365536-> ENSP00000399673

If anyone can shed some light, I would be most grateful.

Thanks very much,
Nat Goodman



From molecules at cpan.org  Wed Mar 23 14:44:15 2011
From: molecules at cpan.org (Christopher Bottoms)
Date: Wed, 23 Mar 2011 13:44:15 -0500
Subject: [Bioperl-l] Ensembl stable_id_event table
In-Reply-To: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>
References: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>
Message-ID: <AANLkTi=acb_oG6-PiDLeh373LkYUz9K=XDhUimv922qz@mail.gmail.com>

Hi Nat,

Have you tried contacting someone at Ensembl about it? That is the
first place I would try.

--Christopher Bottoms


On Tue, Mar 22, 2011 at 8:57 AM, Nathan (Nat) Goodman
<ngoodman at systemsbiology.org> wrote:
> With apologies, this is not technically a bioperl question, but hopefully close enough. ?I'm trying to map old Ensembl IDs to current ones. ?Table stable_id_event on their ftp site seems to be the place to get this information, but the data in that table (for human build 61) is cyclic, meaning that old IDs are sometimes mapped to new ones which in turn are mapped back to the old one. ?This seems wrong... ?And, it's not a rare occurrence: 18% of IDs in the table lie on cycles, the largest of which contains more than 6000 IDs!
>
> To see one short cycle, run this query (against human build 61).
>
> mysql> select * from stable_id_event where
> ? ?-> ? ? (old_stable_id='ENSP00000399673' or new_stable_id='ENSP00000399673')
> ? ?-> and (old_stable_id='ENSP00000365536' or new_stable_id='ENSP00000365536');
>
> The results are
>
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> | old_stable_id ? | old_version | new_stable_id ? | new_version | mapping_session_id | type ? ? ? ?| score |
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> | ENSP00000399673 | ? ? ? ? ? 2 | ENSP00000365536 | ? ? ? ? ? 3 | ? ? ? ? ? ? ? ?380 | translation | ? ? 1 |
> | ENSP00000399673 | ? ? ? ? ? 2 | ENSP00000365536 | ? ? ? ? ? 3 | ? ? ? ? ? ? ? ?381 | translation | ? ? 1 |
> | ENSP00000365536 | ? ? ? ? ? 3 | ENSP00000399673 | ? ? ? ? ? 2 | ? ? ? ? ? ? ? ?381 | translation | ? ? 1 |
> | ENSP00000399673 | ? ? ? ? ? 2 | ENSP00000365536 | ? ? ? ? ? 3 | ? ? ? ? ? ? ? ?382 | translation | ? ? 1 |
> | ENSP00000365536 | ? ? ? ? ? 3 | ENSP00000399673 | ? ? ? ? ? 2 | ? ? ? ? ? ? ? ?382 | translation | ? ? 1 |
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
>
> The first and last lines reveal the cycle:
>
> line 1) ENSP00000399673-> ENSP00000365536
> line 5) ENSP00000365536-> ENSP00000399673
>
> If anyone can shed some light, I would be most grateful.
>
> Thanks very much,
> Nat Goodman
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From cjfields at illinois.edu  Wed Mar 23 18:23:47 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 23 Mar 2011 17:23:47 -0500
Subject: [Bioperl-l] Ensembl stable_id_event table
In-Reply-To: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>
References: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>
Message-ID: <890FA151-63D4-4EAF-8141-8975911126E4@illinois.edu>

Odd, wonder what the ensembl folks have to say about it.  Have you asked them?

chris

On Mar 22, 2011, at 8:57 AM, Nathan (Nat) Goodman wrote:

> With apologies, this is not technically a bioperl question, but hopefully close enough.  I'm trying to map old Ensembl IDs to current ones.  Table stable_id_event on their ftp site seems to be the place to get this information, but the data in that table (for human build 61) is cyclic, meaning that old IDs are sometimes mapped to new ones which in turn are mapped back to the old one.  This seems wrong...  And, it's not a rare occurrence: 18% of IDs in the table lie on cycles, the largest of which contains more than 6000 IDs!
> 
> To see one short cycle, run this query (against human build 61).
> 
> mysql> select * from stable_id_event where 
>    ->     (old_stable_id='ENSP00000399673' or new_stable_id='ENSP00000399673')
>    -> and (old_stable_id='ENSP00000365536' or new_stable_id='ENSP00000365536');
> 
> The results are
> 
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> | old_stable_id   | old_version | new_stable_id   | new_version | mapping_session_id | type        | score |
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> | ENSP00000399673 |           2 | ENSP00000365536 |           3 |                380 | translation |     1 | 
> | ENSP00000399673 |           2 | ENSP00000365536 |           3 |                381 | translation |     1 | 
> | ENSP00000365536 |           3 | ENSP00000399673 |           2 |                381 | translation |     1 | 
> | ENSP00000399673 |           2 | ENSP00000365536 |           3 |                382 | translation |     1 | 
> | ENSP00000365536 |           3 | ENSP00000399673 |           2 |                382 | translation |     1 | 
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> 
> The first and last lines reveal the cycle:
> 
> line 1) ENSP00000399673-> ENSP00000365536
> line 5) ENSP00000365536-> ENSP00000399673
> 
> If anyone can shed some light, I would be most grateful.
> 
> Thanks very much,
> Nat Goodman
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From roy.chaudhuri at gmail.com  Thu Mar 24 09:47:27 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Thu, 24 Mar 2011 13:47:27 +0000
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
Message-ID: <4D8B4B6F.7010407@gmail.com>

Hi all,

I have discovered a possible bug in Bioperl, although maybe it's my 
expectations that are wrong, not the code.

I noticed that when calculating molecular weights for a bunch of protein 
sequences using Bio::Tools::SeqStats->get_mol_wt, the values I was 
getting were slightly different from the ones given by Emboss pepstats. 
This was due to my protein sequences ending with *, since they were 
derived from translating annotated genes including the stop codon. 
Surprisingly (to me, at least) Bio::Seq->length gives a value that 
counts the terminal *, so one greater than the number of amino acids. 
SeqStats->get_mol_wt calls Bio::Seq->length to determine the number of 
water molecules to subtract from the total molecular weight, so the 
reported weights for my sequence were the weight of one water molecule 
less than they should have been. I'm not sure if this is a bug in 
get_mol_wt, in Bio::Seq->length, or if it's bad practice to use protein 
sequences with a terminal asterisk (I've never had a problem doing so 
before).

Cheers,
Roy.

From adsj at novozymes.com  Thu Mar 24 11:01:25 2011
From: adsj at novozymes.com (Adam =?utf-8?Q?Sj=C3=B8gren?=)
Date: Thu, 24 Mar 2011 16:01:25 +0100
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
In-Reply-To: <4D8B4B6F.7010407@gmail.com> (Roy Chaudhuri's message of "Thu, 24
	Mar 2011 13:47:27 +0000")
References: <4D8B4B6F.7010407@gmail.com>
Message-ID: <87mxkkbm0q.fsf@topper.koldfront.dk>

On Thu, 24 Mar 2011 13:47:27 +0000, Roy wrote:

> This was due to my protein sequences ending with *, since they were
> derived from translating annotated genes including the stop codon.

If you give ->translate() the -complete=>1 option, the stop codon will
not be included in the resulting protein sequence.

 * http://bioperl.org/cgi-bin/deob_detail.cgi?method=Bio::PrimarySeqI::translate


  Best regards,

    Adam

-- 
                                                          Adam Sj?gren
                                                    adsj at novozymes.com


From roy.chaudhuri at gmail.com  Thu Mar 24 11:27:36 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Thu, 24 Mar 2011 15:27:36 +0000
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
In-Reply-To: <87mxkkbm0q.fsf@topper.koldfront.dk>
References: <4D8B4B6F.7010407@gmail.com> <87mxkkbm0q.fsf@topper.koldfront.dk>
Message-ID: <4D8B62E8.2050902@gmail.com>

On 24/03/2011 15:01, Adam Sj?gren wrote:
> If you give ->translate() the -complete=>1 option, the stop codon will
> not be included in the resulting protein sequence.

Ah, that's useful to know, thanks Adam. I still think that get_mol_wt 
should deal with such sequences without giving an incorrect weight, though.

From cjfields at illinois.edu  Thu Mar 24 11:47:29 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 24 Mar 2011 10:47:29 -0500
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
In-Reply-To: <4D8B4B6F.7010407@gmail.com>
References: <4D8B4B6F.7010407@gmail.com>
Message-ID: <2F1303AE-4678-4901-A33C-A7811FF8F309@illinois.edu>


On Mar 24, 2011, at 8:47 AM, Roy Chaudhuri wrote:

> Hi all,
> 
> I have discovered a possible bug in Bioperl, although maybe it's my expectations that are wrong, not the code.
> 
> I noticed that when calculating molecular weights for a bunch of protein sequences using Bio::Tools::SeqStats->get_mol_wt, the values I was getting were slightly different from the ones given by Emboss pepstats. This was due to my protein sequences ending with *, since they were derived from translating annotated genes including the stop codon. Surprisingly (to me, at least) Bio::Seq->length gives a value that counts the terminal *, so one greater than the number of amino acids. SeqStats->get_mol_wt calls Bio::Seq->length to determine the number of water molecules to subtract from the total molecular weight, so the reported weights for my sequence were the weight of one water molecule less than they should have been. I'm not sure if this is a bug in get_mol_wt, in Bio::Seq->length, or if it's bad practice to use protein sequences with a terminal asterisk (I've never had a problem doing so before).

The method should account for the possibility that '*' is present; should be easy enough to fix with something like:

my $len = $seq =~ tr/A-Za-z/A-Za-z/;

I'm not able to do this right away (on fam vacation), can you file this on our new bug server?

http://redmine.open-bio.org

> Cheers,
> Roy.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

chris

From roy.chaudhuri at gmail.com  Thu Mar 24 12:08:22 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Thu, 24 Mar 2011 16:08:22 +0000
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
In-Reply-To: <2F1303AE-4678-4901-A33C-A7811FF8F309@illinois.edu>
References: <4D8B4B6F.7010407@gmail.com>
	<2F1303AE-4678-4901-A33C-A7811FF8F309@illinois.edu>
Message-ID: <4D8B6C76.6090401@gmail.com>

Done:
http://redmine.open-bio.org/issues/3185

Have a good break,
Roy.

On 24/03/2011 15:47, Chris Fields wrote:
>
> On Mar 24, 2011, at 8:47 AM, Roy Chaudhuri wrote:
>
>> Hi all,
>>
>> I have discovered a possible bug in Bioperl, although maybe it's my
>> expectations that are wrong, not the code.
>>
>> I noticed that when calculating molecular weights for a bunch of
>> protein sequences using Bio::Tools::SeqStats->get_mol_wt, the
>> values I was getting were slightly different from the ones given by
>> Emboss pepstats. This was due to my protein sequences ending with
>> *, since they were derived from translating annotated genes
>> including the stop codon. Surprisingly (to me, at least)
>> Bio::Seq->length gives a value that counts the terminal *, so one
>> greater than the number of amino acids. SeqStats->get_mol_wt calls
>> Bio::Seq->length to determine the number of water molecules to
>> subtract from the total molecular weight, so the reported weights
>> for my sequence were the weight of one water molecule less than
>> they should have been. I'm not sure if this is a bug in get_mol_wt,
>> in Bio::Seq->length, or if it's bad practice to use protein
>> sequences with a terminal asterisk (I've never had a problem doing
>> so before).
>
> The method should account for the possibility that '*' is present;
> should be easy enough to fix with something like:
>
> my $len = $seq =~ tr/A-Za-z/A-Za-z/;
>
> I'm not able to do this right away (on fam vacation), can you file
> this on our new bug server?
>
> http://redmine.open-bio.org
>
>> Cheers, Roy. _______________________________________________
>> Bioperl-l mailing list Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> chris


From rachitasharma at gmail.com  Thu Mar 24 13:12:43 2011
From: rachitasharma at gmail.com (Rachita Sharma)
Date: Thu, 24 Mar 2011 11:12:43 -0600
Subject: [Bioperl-l] Genbank to gff3 format
Message-ID: <AANLkTimarbmi3XnFZ9VjT2GMHUoS6COkVGnbtawYh2a+@mail.gmail.com>

I am having trouble using the perl script bp_genbank2gff3.pl for
converting my genbank file into gff3 format. Unique IDs are not
created by the Bioperl converter so I cannot get the gff3 file
validated on the official GFF validator I want to use the final gff3
file on Gbrowse without errors. Will appreciate your suggestions.

Thanks!
Rachita

From dan.bolser at gmail.com  Fri Mar 25 07:21:57 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Fri, 25 Mar 2011 11:21:57 +0000
Subject: [Bioperl-l] from SimpleAlign to SAM/BAM
In-Reply-To: <AANLkTinEo3Ac8h5Gh-l4aqiKE0C1-iPiP96XilazQ4Hd@mail.gmail.com>
References: <AANLkTilHpBojt1AoAR6qe8YgqXrt8vp_dl64GOblTH3h@mail.gmail.com>
	<CF66A9BB040D49189BB80C9E057422AC@NewLife>
	<AANLkTinEo3Ac8h5Gh-l4aqiKE0C1-iPiP96XilazQ4Hd@mail.gmail.com>
Message-ID: <AANLkTikk4jNjG203Lw764Exdb9VBoZPVkXki8n8jVwLO@mail.gmail.com>

On 19 May 2010 17:40, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Bio::Samtools, which is separate from bioperl but compatible with it,
> provides read/write access to SAM and BAM via Heng's C library.

If I understand correctly, Bio::Samtools is a meta package that
encompasses Bio::DB::Sam and friends. However, when I look at
Bio::DB::Sam, I only see "Read SAM/BAM database files", not write, and
I don't see how to write SAM files from the docs there.

I just looked at the pod for Bio::Assembly::IO::sam (how come this
isn't documented in CPAN?), and I read:

This is a (currently) read-only IO module designed to convert
Sequence/Alignment Map (SAM) ...

I guess this is what was being discussed on in this thread (the fact
that IO doesn't yet write, but XS can be used to get it writing).

Did I understand correctly, or is there some way to write SAM from BioPerl?


Cheers,
Dan..

> Lincoln
>
> On Wed, May 19, 2010 at 9:34 AM, Mark A. Jensen <maj at fortinbras.us> wrote:
>
>> Albert-- have a look at Bio::Tools::Run::Samtools which incorporates the
>> use of Bio::Assembly::IO::sam (I think). I know there is only read
>> capability for B:A:I:sam, but Samtools may give you the appropriate wrapper
>> for doing writes (some assembly (so to speak) required...)-- cheers MAJ
>> ----- Original Message ----- From: "Albert Vilella" <avilella at gmail.com>
>>
>> To: <bioperl-l at bioperl.org>
>> Sent: Wednesday, May 19, 2010 4:36 AM
>>
>> Subject: [Bioperl-l] from SimpleAlign to SAM/BAM
>>
>>
>> ?Hi,
>>>
>>> I would like to know what would be the best way to generate a SAM/BAM file
>>> with cDNA alignments against the human reference from a bunch of
>>> Bio::SimpleAlign
>>> cDNA multiple sequence alignment objects.
>>>
>>> Considering I've got a way to map the cDNAs to chromosome coordinates,
>>> how can I generate a SAM/BAM file with ~1,000,000 entries against ~23.000
>>> human
>>> coordinates?
>>>
>>> As far as I can see, there is an Bio::Assembly::IO::sam.pm which loads
>>> assemblies.
>>> Should I be using some other tool existing not in bioperl?
>>>
>>> Cheers,
>>>
>>> Albert.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From dan.bolser at gmail.com  Sat Mar 26 20:11:27 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Sun, 27 Mar 2011 00:11:27 +0000
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
Message-ID: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>

Hi all,

I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm uses:
    if (length $source_tag) {

within the '_types_sql' function to test if $source_tag is defined
(and has a length). This obviously fails when $source_tag it isn't
defined, and I see the above error message from my script when I call
the 'features' function (as shown below).

>From tests (thanks to rbuels in #bioperl) it seems the value of $type
is simply 'fwd link intensity', so:
      ($primary_tag,$source_tag) = split ':',$type,2;

on line 1047 leaves $source_tag undefined.

Here is my proposed fix:

diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
index 00103c2..dfc70c0 100644
--- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
+++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
@@ -1057,8 +1057,8 @@ sub _types_sql {
       ($primary_tag,$source_tag) = split ':',$type,2;
     }

-    if (length $source_tag) {
-      if (length($primary_tag)) {
+    if (defined $source_tag && length $source_tag) {
+      if (defined $primary_tag && length($primary_tag)) {
         push @matches,"tl.tag=?";
         push @args,"$primary_tag:$source_tag";
       }


which seems to work. I'd write some tests, but an old bug that I can't
track down prevents me from running tests on this package
(http://bugzilla.open-bio.org/show_bug.cgi?id=2899).

Cheers,
Dan.


Here are some snippets of code to give context:

my $intensities = Bio::DB::SeqFeature::Store->
  new( -adaptor => 'DBI::mysql',
	-dsn => 'db:mysql.server.ac.uk',
	-user => 'me',
	-pass => 'secret',
       -verbose => $verbose,
     );

my @fwd_intensity = $intensities->
    features( -seqid => 'some-id', -type => 'fwd link intensity',
              -start => 10,
              -end   => 200,
    );

From hufeiyc at gmail.com  Tue Mar 22 15:14:54 2011
From: hufeiyc at gmail.com (Fei Hu)
Date: Tue, 22 Mar 2011 15:14:54 -0400
Subject: [Bioperl-l] GSoC 2011
Message-ID: <AANLkTim6o3bJ6NkBRmoUC5e76GaGzpjP5+xE+ZrWcEdc@mail.gmail.com>

Hi, All.

My name is Fei Hu from U. of South Carolina. I am currently a second-year
Ph.D student in computer science focusing on gene order and sequence(DNA &
AA) phylogeny as well as whole genome alignment. I am instreseted in joining
bioperl project of GSoC 2011. I have two ideas that would like to share.

My first idea is to extend the bioperl so that it can process and analysis
gene order data using published package such as MGR, GRAPPA and distance
estimator. This is a relatively new type of data and many great researchers
have contributed to this type of phylogeny reconstruction (Dr. Pavel Penzer,
Dr. Bernard Moret and Dr. David Sankoff).

Secondly as maximum likelihood becomes more and more popular, especially
RAxML has been widely recognized and used(over 1000 citations). I think it's
time to integrate that as well as GARLI into the Bio::Tools. I extensively
used and explored RAxML in my last publication on gene order phylogeny.

Those are just my preliminary thoughts, not even a plan and any suggestion
is greatly appreciated!!! I use perl on daily bases for data processing and
composing testing scripts, but not much OOP involved.

PS: Rest api for CIPRES is no longer available. So this following task can't
be finished right now:
Development of a
Bio::Tools::Run::RemoteBlast<http://bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast>-like
interface to CIPRES remote analyses; for more see this
thread<http://thread.gmane.org/gmane.comp.lang.perl.bio.general/16524>
.

And Thank you all.
Best

Fei

-- 
*Fei Hu
Bioinformatics Lab
3D-11 Swearingen Building
U of South Carolina
Tel: 803-397-5240*

From Dallas.Thomas at AGR.GC.CA  Wed Mar 23 13:08:12 2011
From: Dallas.Thomas at AGR.GC.CA (Thomas, Dallas)
Date: Wed, 23 Mar 2011 11:08:12 -0600
Subject: [Bioperl-l] Bio::Tools::Protparam
Message-ID: <DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>

Need help.  I am trying to use the Bio::Tools::Protparam perl module.

 

For testing purposes I have copied and pasted the example in the module,
I have set:

 

use strict;

use Bio::Tools::Protparam;

use Bio::DB::GenBank;

 

Every time I try and run the script I get the following error:

                        

                              Can't locate object method "new" via
package "Protparam" (perhaps you forgot to load "Protparam"?) at ...

 

Do you have any ideas?  Any help would be very much appreciated.

 

Sincerely

Dallas Thomas

 



From ravimbt at gmail.com  Thu Mar 24 08:33:55 2011
From: ravimbt at gmail.com (=?UTF-8?B?wrbigKLil4/guYvigKLgrofgrrDgrrXgrr/Rj86xzr3OueKXj+C5i+KAouKAosK2?=)
Date: Thu, 24 Mar 2011 18:03:55 +0530
Subject: [Bioperl-l] Bioperl installation doubt
Message-ID: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>

Hi,

Could you please help me installing bioperl-db, bioperl-run & other packages
using ppm on windows 7? Please find the attachment for the error message I
get. I would really appreciate if you help me fix this issue.

Thanks,

With regards,
Ravi.
-------------- next part --------------
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From abualiga at gmail.com  Sun Mar 27 09:34:05 2011
From: abualiga at gmail.com (Galeb Abu-Ali)
Date: Sun, 27 Mar 2011 06:34:05 -0700 (PDT)
Subject: [Bioperl-l] CDS complement statements from GenBank
Message-ID: <cdf62961-ac89-4274-91ed-9a233d2de15c@k10g2000prh.googlegroups.com>

Hi,

I'm trying to parse CDS complement statements from GenBank files of
bacterial genomes. I know it works for 'join' statements with
Bio::Location::SplitLocationI, but there is no spliced genes in
bacterial annotations and therefore no 'join()' statements. When I
replace 'complement' with 'join' in the bacterial GenBank file,
Bio::Location::SplitLocationI gets the coordinates. I took a look at
SplitLocationI.pm and Split.pm to see if I could replace 'join' with
'complement' to get it to work but no luck. At your convenience,
please advise.

cheers,

galeb

From drinmontana at gmail.com  Sun Mar 27 10:37:17 2011
From: drinmontana at gmail.com (Drin)
Date: Sun, 27 Mar 2011 07:37:17 -0700 (PDT)
Subject: [Bioperl-l] Various bioperl build test errors
Message-ID: <799d8933-c2de-4c88-ac2c-03bb1b32dd78@z27g2000prz.googlegroups.com>

Hello BioPerl mailing list!

So I have been successfully building BioPerl (though I thought I was
failing), but have been getting some errors during said builds. I'm
running ubuntu 9.04 and I ran 'perl Build.PL', then './Build test'
using bash. If any other information is desired, please let me know.
And here are some gists to help with some context:
perl Build.PL - https://gist.github.com/e4be0891635463b07812
./Build test - https://gist.github.com/3e9a1cba10ca0e9b087d

From cjfields at illinois.edu  Sun Mar 27 12:43:11 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 27 Mar 2011 11:43:11 -0500
Subject: [Bioperl-l] Bio::Tools::Protparam
In-Reply-To: <DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>
References: <DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>
Message-ID: <851BC032-98F0-441D-9185-5079527CDA3E@illinois.edu>

Dallas,

Can you send a script example?  Hard to judge what is going wrong w/o code.

chris
 
On Mar 23, 2011, at 12:08 PM, Thomas, Dallas wrote:

> Need help.  I am trying to use the Bio::Tools::Protparam perl module.
> 
> 
> 
> For testing purposes I have copied and pasted the example in the module,
> I have set:
> 
> 
> 
> use strict;
> 
> use Bio::Tools::Protparam;
> 
> use Bio::DB::GenBank;
> 
> 
> 
> Every time I try and run the script I get the following error:
> 
> 
> 
>                              Can't locate object method "new" via
> package "Protparam" (perhaps you forgot to load "Protparam"?) at ...
> 
> 
> 
> Do you have any ideas?  Any help would be very much appreciated.
> 
> 
> 
> Sincerely
> 
> Dallas Thomas
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From David.Messina at sbc.su.se  Sun Mar 27 13:05:05 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Sun, 27 Mar 2011 19:05:05 +0200
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
Message-ID: <AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>

Hi Ravi,

The get_sequence and write_sequence methods are in the Bio::Perl module, not
Bio::Seq. So your first line

use Bio::Seq;

should be replaced with

use Bio::Perl;


More examples in the BioPerl Tutorial here:
http://www.bioperl.org/wiki/BioPerl_Tutorial


Dve



2011/3/24 ?????????????????? <ravimbt at gmail.com>

> Hi,
>
> Could you please help me installing bioperl-db, bioperl-run & other
> packages
> using ppm on windows 7? Please find the attachment for the error message I
> get. I would really appreciate if you help me fix this issue.
>
> Thanks,
>
> With regards,
> Ravi.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From jason at bioperl.org  Sun Mar 27 13:28:04 2011
From: jason at bioperl.org (Jason Stajich)
Date: Sun, 27 Mar 2011 10:28:04 -0700
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
Message-ID: <4D8F73A4.8050408@bioperl.org>

Dan - not sure why you would need to do this as length on an undef 
should still return false (an undef).

$ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} 
print "\n"'
no
$ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"} 
print "\n"'
no

Also, having no 'source' is probably not proper GFF3.

BTW bugzilla is dead so the bug that you refer to is here
   http://redmine.open-bio.org/issues/2899
I've assigned the bug to Lincoln to help figure out what should be done 
with it.

Thanks,
jason

Dan Bolser wrote:
> Hi all,
>
> I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm uses:
>      if (length $source_tag) {
>
> within the '_types_sql' function to test if $source_tag is defined
> (and has a length). This obviously fails when $source_tag it isn't
> defined, and I see the above error message from my script when I call
> the 'features' function (as shown below).
>
> > From tests (thanks to rbuels in #bioperl) it seems the value of $type
> is simply 'fwd link intensity', so:
>        ($primary_tag,$source_tag) = split ':',$type,2;
>
> on line 1047 leaves $source_tag undefined.
>
> Here is my proposed fix:
>
> diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
> index 00103c2..dfc70c0 100644
> --- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
> +++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
> @@ -1057,8 +1057,8 @@ sub _types_sql {
>         ($primary_tag,$source_tag) = split ':',$type,2;
>       }
>
> -    if (length $source_tag) {
> -      if (length($primary_tag)) {
> +    if (defined $source_tag&&  length $source_tag) {
> +      if (defined $primary_tag&&  length($primary_tag)) {
>           push @matches,"tl.tag=?";
>           push @args,"$primary_tag:$source_tag";
>         }
>
>
> which seems to work. I'd write some tests, but an old bug that I can't
> track down prevents me from running tests on this package
> (http://bugzilla.open-bio.org/show_bug.cgi?id=2899).
>
> Cheers,
> Dan.
>
>
> Here are some snippets of code to give context:
>
> my $intensities = Bio::DB::SeqFeature::Store->
>    new( -adaptor =>  'DBI::mysql',
> 	-dsn =>  'db:mysql.server.ac.uk',
> 	-user =>  'me',
> 	-pass =>  'secret',
>         -verbose =>  $verbose,
>       );
>
> my @fwd_intensity = $intensities->
>      features( -seqid =>  'some-id', -type =>  'fwd link intensity',
>                -start =>  10,
>                -end   =>  200,
>      );
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki


From dan.bolser at gmail.com  Sun Mar 27 13:55:02 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Sun, 27 Mar 2011 18:55:02 +0100
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <4D8F73A4.8050408@bioperl.org>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
	<4D8F73A4.8050408@bioperl.org>
Message-ID: <AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>

On 27 March 2011 18:28, Jason Stajich <jason at bioperl.org> wrote:
> Dan - not sure why you would need to do this as length on an undef should
> still return false (an undef).
>
> $ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} print
> "\n"'
> no
> $ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"}
> print "\n"'
> no

Doesn't the latter spew a warning? (The output before / after my 'bug
fix' is the same, I just don't see 100s of warnings about undefined
values).


> Also, having no 'source' is probably not proper GFF3.

I'm quite sure it is, but by GFF does have a source. I'm just calling
'features' with only a feature type and not a feature type and a
source (because I only care about source). My call is pretty similar
to the example here:

http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/DB/SeqFeature/Store.pm#features

 @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');


> BTW bugzilla is dead so the bug that you refer to is here
> ?http://redmine.open-bio.org/issues/2899
> I've assigned the bug to Lincoln to help figure out what should be done with
> it.
>
> Thanks,
> jason

Cheers Jason,
Dan.


> Dan Bolser wrote:
>>
>> Hi all,
>>
>> I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm
>> uses:
>> ? ? if (length $source_tag) {
>>
>> within the '_types_sql' function to test if $source_tag is defined
>> (and has a length). This obviously fails when $source_tag it isn't
>> defined, and I see the above error message from my script when I call
>> the 'features' function (as shown below).
>>
>> > From tests (thanks to rbuels in #bioperl) it seems the value of $type
>> is simply 'fwd link intensity', so:
>> ? ? ? ($primary_tag,$source_tag) = split ':',$type,2;
>>
>> on line 1047 leaves $source_tag undefined.
>>
>> Here is my proposed fix:
>>
>> diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
>> index 00103c2..dfc70c0 100644
>> --- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>> +++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>> @@ -1057,8 +1057,8 @@ sub _types_sql {
>> ? ? ? ?($primary_tag,$source_tag) = split ':',$type,2;
>> ? ? ?}
>>
>> - ? ?if (length $source_tag) {
>> - ? ? ?if (length($primary_tag)) {
>> + ? ?if (defined $source_tag&& ?length $source_tag) {
>> + ? ? ?if (defined $primary_tag&& ?length($primary_tag)) {
>> ? ? ? ? ?push @matches,"tl.tag=?";
>> ? ? ? ? ?push @args,"$primary_tag:$source_tag";
>> ? ? ? ?}
>>
>>
>> which seems to work. I'd write some tests, but an old bug that I can't
>> track down prevents me from running tests on this package
>> (http://bugzilla.open-bio.org/show_bug.cgi?id=2899).
>>
>> Cheers,
>> Dan.
>>
>>
>> Here are some snippets of code to give context:
>>
>> my $intensities = Bio::DB::SeqFeature::Store->
>> ? new( -adaptor => ?'DBI::mysql',
>> ? ? ? ?-dsn => ?'db:mysql.server.ac.uk',
>> ? ? ? ?-user => ?'me',
>> ? ? ? ?-pass => ?'secret',
>> ? ? ? ?-verbose => ?$verbose,
>> ? ? ?);
>>
>> my @fwd_intensity = $intensities->
>> ? ? features( -seqid => ?'some-id', -type => ?'fwd link intensity',
>> ? ? ? ? ? ? ? -start => ?10,
>> ? ? ? ? ? ? ? -end ? => ?200,
>> ? ? );
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> jason at bioperl.org
> http://bioperl.org/wiki
>
>


From jason at bioperl.org  Sun Mar 27 13:59:09 2011
From: jason at bioperl.org (Jason Stajich)
Date: Sun, 27 Mar 2011 10:59:09 -0700
Subject: [Bioperl-l] CDS complement statements from GenBank
In-Reply-To: <cdf62961-ac89-4274-91ed-9a233d2de15c@k10g2000prh.googlegroups.com>
References: <cdf62961-ac89-4274-91ed-9a233d2de15c@k10g2000prh.googlegroups.com>
Message-ID: <4D8F7AED.1070705@bioperl.org>

they won't be split locations they will be Bio::Location::Simple 
locations then - I don't understand if that is causing you problems?



Galeb Abu-Ali wrote:
> Hi,
>
> I'm trying to parse CDS complement statements from GenBank files of
> bacterial genomes. I know it works for 'join' statements with
> Bio::Location::SplitLocationI, but there is no spliced genes in
> bacterial annotations and therefore no 'join()' statements. When I
> replace 'complement' with 'join' in the bacterial GenBank file,
> Bio::Location::SplitLocationI gets the coordinates. I took a look at
> SplitLocationI.pm and Split.pm to see if I could replace 'join' with
> 'complement' to get it to work but no luck. At your convenience,
> please advise.
>
> cheers,
>
> galeb
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki


From dan.bolser at gmail.com  Sun Mar 27 14:00:40 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Sun, 27 Mar 2011 19:00:40 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
Message-ID: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>

Hello,

I'm trying to get Bio::DB::BigWig installed again, this time on a different box.

I installed kent from git as described here:
http://genome.ucsc.edu/admin/git.html


I made the following changes, similar to those described previously:

git diff
diff --git a/src/inc/common.mk b/src/inc/common.mk
index c7fc557..5187901 100644
--- a/src/inc/common.mk
+++ b/src/inc/common.mk
@@ -3,7 +3,7 @@ CC=gcc
 ifeq (${COPT},)
     COPT=-O -g
 endif
-CFLAGS=
+CFLAGS=-fPIC
 HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
-DMACHTYPE_${MACHTYPE}
 HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
-I../../../../../inc

diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
index fa2292b..acb97d2 100644
--- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
+++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
@@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
     /* Parse current line. */
     wordCount = chopLine(line, row);
     if (wordCount == ArraySize(row))
-         errAbort("Too many fields (%d max is %lu) line %d of %s",
wordCount, ArraySize(row),
+         errAbort("Too many fields (%d max is %u) line %d of %s",
wordCount, ArraySize(row),
             lf->lineIx, lf->fileName);
     char *chrom = row[0];
     unsigned int start = lineFileNeedNum(lf, row, 1);


After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
-lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
correctly after typing 'make' in kent/src (should I be building it
differently?)



Now when I try to install Bio::DB::BigWig via cpan, things look like this:

cpan

cpan shell -- CPAN exploration and modules installation (v1.9600)
Enter 'h' for help.

cpan[1]> install Bio::DB::BigWig
CPAN: Storable loaded ok (v2.25)
Going to read '/homes/dbolser/.cpan/Metadata'
  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
Running install for module 'Bio::DB::BigWig'
Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
CPAN: Digest::SHA loaded ok (v5.61)
CPAN: Compress::Zlib loaded ok (v2.03)
Checksum for /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
ok
CPAN: Archive::Tar loaded ok (v1.76)
Bio-BigFile-1.05
Bio-BigFile-1.05/Changes
Bio-BigFile-1.05/LICENSE
Bio-BigFile-1.05/DISCLAIMER
Bio-BigFile-1.05/Build.PL
Bio-BigFile-1.05/typemap
Bio-BigFile-1.05/META.yml
Bio-BigFile-1.05/README
Bio-BigFile-1.05/MANIFEST
Bio-BigFile-1.05/ExampleData
Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
Bio-BigFile-1.05/ExampleData/refSeqTest.as
Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
Bio-BigFile-1.05/bin
Bio-BigFile-1.05/bin/bigWigToWig.pl
Bio-BigFile-1.05/bin/wigToBigWig.pl
Bio-BigFile-1.05/bin/index_bigwigset.pl
Bio-BigFile-1.05/lib
Bio-BigFile-1.05/lib/Bio
Bio-BigFile-1.05/lib/Bio/DB
Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
Bio-BigFile-1.05/lib/Bio/DB/BigFile
Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
Bio-BigFile-1.05/t
Bio-BigFile-1.05/t/02.bigbed.t
Bio-BigFile-1.05/t/03.bigwig_high.t
Bio-BigFile-1.05/t/04.bigbed_high.t
Bio-BigFile-1.05/t/05.bigwig_set.t
/bin/tar: Read 9216 bytes from -
Bio-BigFile-1.05/t/01.bigwig.t
Bio-BigFile-1.05/patches
Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
CPAN: File::Temp loaded ok (v0.22)
CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
CPAN: CPAN::Meta loaded ok (v2.110580)
CPAN: Module::CoreList loaded ok (v2.46)
CPAN: Time::HiRes loaded ok (v1.9717)

  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz


This module requires the compiled jkweb.a library from Jim Kent's source tree.
If you haven't already done so, please download the source from
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
contents of the "kent/src/lib" subdirectory as directed in the README. Then
enter the location of the "kent/src" subdirectory at the prompt below.
To prevent
this message from appearing in the future, set the environment
variable KENT_SRC
to point to the "kent/src" subdirectory.

Please enter the location of Kent source tree: /homes/dbolser/build/src/kent/src

Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-BigFile' version '1.05'
Building Bio-BigFile
gcc -I/homes/dbolser/build/src/kent/src/inc
-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
-DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
-c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
-Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
lib/Bio/DB/BigFile.c
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be undefined
lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be undefined
lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be undefined
lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be undefined
lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
lib/Bio/DB/BigFile.xs: In function
?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be undefined
lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
lib/Bio/DB/BigFile.xs: In function
?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be undefined
lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
-mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
/homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
  LDS/Bio-BigFile-1.05.tar.gz
  ./Build -- OK
CPAN: YAML loaded ok (v0.72)
Running Build test
t/01.bigwig.t ....... Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at t/01.bigwig.t line 28
Compilation failed in require at t/01.bigwig.t line 28.
BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
Failed 29/29 subtests
t/02.bigbed.t ....... Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at t/02.bigbed.t line 28
Compilation failed in require at t/02.bigbed.t line 28.
BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
Failed 15/15 subtests
t/03.bigwig_high.t .. Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
Compilation failed in require at t/03.bigwig_high.t line 28.
BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 32/32 subtests
t/04.bigbed_high.t .. Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
line 7.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
line 7.
Compilation failed in require at t/04.bigbed_high.t line 28.
BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 35/35 subtests
t/05.bigwig_set.t ... Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
line 177.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
line 177.
Compilation failed in require at t/05.bigwig_set.t line 19.
BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
No subtests run

Test Summary Report
-------------------
t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 29 tests but ran 0.
t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 15 tests but ran 0.
t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 32 tests but ran 0.
t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 35 tests but ran 0.
t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
0.11 csys =  1.09 CPU)
Result: FAIL
Failed 5/5 test programs. 0/0 subtests failed.
  LDS/Bio-BigFile-1.05.tar.gz
  ./Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports LDS/Bio-BigFile-1.05.tar.gz
Running Build install
  make test had returned bad status, won't install without force
Failed during this command:
 LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO

cpan[2]>






Any hints?

Cheers,
Dan.


From roy.chaudhuri at gmail.com  Sun Mar 27 14:26:55 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Sun, 27 Mar 2011 19:26:55 +0100
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>	<4D8F73A4.8050408@bioperl.org>
	<AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
Message-ID: <4D8F816F.5010809@gmail.com>

Hi Dan,

I think your problem is that you are using the outdated -w flag, which 
reports warnings from inside modules that may not have been designed 
with warnings in mind. The "use warnings" pragma is preferred. See:
http://perldoc.perl.org/perllexwarn.html#What%27s-wrong-with-*-w*-and-$^W

Cheers,
Roy.

On 27/03/2011 18:55, Dan Bolser wrote:
> On 27 March 2011 18:28, Jason Stajich<jason at bioperl.org>  wrote:
>> Dan - not sure why you would need to do this as length on an undef should
>> still return false (an undef).
>>
>> $ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} print
>> "\n"'
>> no
>> $ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"}
>> print "\n"'
>> no
>
> Doesn't the latter spew a warning? (The output before / after my 'bug
> fix' is the same, I just don't see 100s of warnings about undefined
> values).
>
>
>> Also, having no 'source' is probably not proper GFF3.
>
> I'm quite sure it is, but by GFF does have a source. I'm just calling
> 'features' with only a feature type and not a feature type and a
> source (because I only care about source). My call is pretty similar
> to the example here:
>
> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/DB/SeqFeature/Store.pm#features
>
>   @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');
>
>
>> BTW bugzilla is dead so the bug that you refer to is here
>>   http://redmine.open-bio.org/issues/2899
>> I've assigned the bug to Lincoln to help figure out what should be done with
>> it.
>>
>> Thanks,
>> jason
>
> Cheers Jason,
> Dan.
>
>
>> Dan Bolser wrote:
>>>
>>> Hi all,
>>>
>>> I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> uses:
>>>      if (length $source_tag) {
>>>
>>> within the '_types_sql' function to test if $source_tag is defined
>>> (and has a length). This obviously fails when $source_tag it isn't
>>> defined, and I see the above error message from my script when I call
>>> the 'features' function (as shown below).
>>>
>>>>  From tests (thanks to rbuels in #bioperl) it seems the value of $type
>>> is simply 'fwd link intensity', so:
>>>        ($primary_tag,$source_tag) = split ':',$type,2;
>>>
>>> on line 1047 leaves $source_tag undefined.
>>>
>>> Here is my proposed fix:
>>>
>>> diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
>>> index 00103c2..dfc70c0 100644
>>> --- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> +++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> @@ -1057,8 +1057,8 @@ sub _types_sql {
>>>         ($primary_tag,$source_tag) = split ':',$type,2;
>>>       }
>>>
>>> -    if (length $source_tag) {
>>> -      if (length($primary_tag)) {
>>> +    if (defined $source_tag&&    length $source_tag) {
>>> +      if (defined $primary_tag&&    length($primary_tag)) {
>>>           push @matches,"tl.tag=?";
>>>           push @args,"$primary_tag:$source_tag";
>>>         }
>>>
>>>
>>> which seems to work. I'd write some tests, but an old bug that I can't
>>> track down prevents me from running tests on this package
>>> (http://bugzilla.open-bio.org/show_bug.cgi?id=2899).
>>>
>>> Cheers,
>>> Dan.
>>>
>>>
>>> Here are some snippets of code to give context:
>>>
>>> my $intensities = Bio::DB::SeqFeature::Store->
>>>    new( -adaptor =>    'DBI::mysql',
>>>         -dsn =>    'db:mysql.server.ac.uk',
>>>         -user =>    'me',
>>>         -pass =>    'secret',
>>>         -verbose =>    $verbose,
>>>       );
>>>
>>> my @fwd_intensity = $intensities->
>>>      features( -seqid =>    'some-id', -type =>    'fwd link intensity',
>>>                -start =>    10,
>>>                -end   =>    200,
>>>      );
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> --
>> Jason Stajich
>> jason at bioperl.org
>> http://bioperl.org/wiki
>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From cjfields at illinois.edu  Sun Mar 27 16:13:14 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 27 Mar 2011 15:13:14 -0500
Subject: [Bioperl-l] Use of uninitialized value in length at
	Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
	<4D8F73A4.8050408@bioperl.org>
	<AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
Message-ID: <4960971A-8C61-49F2-B43A-E32BAFC4C59E@illinois.edu>

On Mar 27, 2011, at 12:55 PM, Dan Bolser wrote:

> On 27 March 2011 18:28, Jason Stajich <jason at bioperl.org> wrote:
>> Dan - not sure why you would need to do this as length on an undef should
>> still return false (an undef).
>> 
>> $ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} print
>> "\n"'
>> no
>> $ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"}
>> print "\n"'
>> no
> 
> Doesn't the latter spew a warning? (The output before / after my 'bug
> fix' is the same, I just don't see 100s of warnings about undefined
> values).

Only with later versions of perl (I think perl 5.12).

>> Also, having no 'source' is probably not proper GFF3.
> 
> I'm quite sure it is, but by GFF does have a source. I'm just calling
> 'features' with only a feature type and not a feature type and a
> source (because I only care about source). My call is pretty similar
> to the example here:
> 
> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/DB/SeqFeature/Store.pm#features
> 
> @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');

I think Jason is inferring that the GFF3 is invalid from your statement below re: $source_tag not being defined, which to me means the source attribute for the feature is not defined.

Note: b/c something works with SF::Store does NOT mean the source is proper GFF3; it is quite possible to have invalid GFF3 loaded into the database w/o a hiccup.  I think the loader assumes the data loaded has already been validated; IIRC there is very little validation done on GFF3 loaded into SF::Store, particularly the 'type'.

chris

>> BTW bugzilla is dead so the bug that you refer to is here
>>  http://redmine.open-bio.org/issues/2899
>> I've assigned the bug to Lincoln to help figure out what should be done with
>> it.
>> 
>> Thanks,
>> jason
> 
> Cheers Jason,
> Dan.
> 
> 
>> Dan Bolser wrote:
>>> 
>>> Hi all,
>>> 
>>> I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> uses:
>>>     if (length $source_tag) {
>>> 
>>> within the '_types_sql' function to test if $source_tag is defined
>>> (and has a length). This obviously fails when $source_tag it isn't
>>> defined, and I see the above error message from my script when I call
>>> the 'features' function (as shown below).
>>> 
>>>> From tests (thanks to rbuels in #bioperl) it seems the value of $type
>>> is simply 'fwd link intensity', so:
>>>       ($primary_tag,$source_tag) = split ':',$type,2;
>>> 
>>> on line 1047 leaves $source_tag undefined.
>>> 
>>> Here is my proposed fix:
>>> 
>>> diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
>>> index 00103c2..dfc70c0 100644
>>> --- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> +++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> @@ -1057,8 +1057,8 @@ sub _types_sql {
>>>        ($primary_tag,$source_tag) = split ':',$type,2;
>>>      }
>>> 
>>> -    if (length $source_tag) {
>>> -      if (length($primary_tag)) {
>>> +    if (defined $source_tag&&  length $source_tag) {
>>> +      if (defined $primary_tag&&  length($primary_tag)) {
>>>          push @matches,"tl.tag=?";
>>>          push @args,"$primary_tag:$source_tag";
>>>        }
>>> 
>>> 
>>> which seems to work. I'd write some tests, but an old bug that I can't
>>> track down prevents me from running tests on this package
>>> (http://bugzilla.open-bio.org/show_bug.cgi?id=2899).
>>> 
>>> Cheers,
>>> Dan.
>>> 
>>> 
>>> Here are some snippets of code to give context:
>>> 
>>> my $intensities = Bio::DB::SeqFeature::Store->
>>>   new( -adaptor =>  'DBI::mysql',
>>>        -dsn =>  'db:mysql.server.ac.uk',
>>>        -user =>  'me',
>>>        -pass =>  'secret',
>>>        -verbose =>  $verbose,
>>>      );
>>> 
>>> my @fwd_intensity = $intensities->
>>>     features( -seqid =>  'some-id', -type =>  'fwd link intensity',
>>>               -start =>  10,
>>>               -end   =>  200,
>>>     );
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> --
>> Jason Stajich
>> jason at bioperl.org
>> http://bioperl.org/wiki
>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Sun Mar 27 16:13:56 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 27 Mar 2011 15:13:56 -0500
Subject: [Bioperl-l] Various bioperl build test errors
In-Reply-To: <799d8933-c2de-4c88-ac2c-03bb1b32dd78@z27g2000prz.googlegroups.com>
References: <799d8933-c2de-4c88-ac2c-03bb1b32dd78@z27g2000prz.googlegroups.com>
Message-ID: <FFAB293A-555E-4F4B-90C4-A50458AB2B8C@illinois.edu>

Re: the two problems:

1) The build failures are a new one, haven't seen that before.  

2) The failed tests are all related to NeXML and Bio::Phylo; it appears that Bio::Phylo is having versioning problems.  

Feel free to report these on our bug tracker:

http://redmine.open-bio.org/

chris


On Mar 27, 2011, at 9:37 AM, Drin wrote:

> Hello BioPerl mailing list!
> 
> So I have been successfully building BioPerl (though I thought I was
> failing), but have been getting some errors during said builds. I'm
> running ubuntu 9.04 and I ran 'perl Build.PL', then './Build test'
> using bash. If any other information is desired, please let me know.
> And here are some gists to help with some context:
> perl Build.PL - https://gist.github.com/e4be0891635463b07812
> ./Build test - https://gist.github.com/3e9a1cba10ca0e9b087d
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From heikki.lehvaslaiho at gmail.com  Mon Mar 28 02:11:12 2011
From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho)
Date: Mon, 28 Mar 2011 09:11:12 +0300
Subject: [Bioperl-l] Bio::Tools::Protparam
In-Reply-To: <DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>
References: <AcvpfORY7lvf7BT4TLGDgl1oKgOEwg==>
	<DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>
Message-ID: <AANLkTi=3wtG+7HO4O8vUbdrnVEu-NXofwmZfVHvRLeVH@mail.gmail.com>

The synopsis code should read:

	my $pp = Bio::Tools::Protparam->new(seq=>$seq->seq);

Fixed in the repository.

? ?? -Heikki

Heikki Lehvaslaiho - skype:heikki_lehvaslaiho http://about.me/heikki
cell: +966 545 595 849? office: +966 2 808 2429

Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
4700 King Abdullah University of Science and Technology (KAUST)
Thuwal 23955-6900, Kingdom of Saudi Arabia




On 23 March 2011 20:08, Thomas, Dallas <Dallas.Thomas at agr.gc.ca> wrote:
> Need help. ?I am trying to use the Bio::Tools::Protparam perl module.
>
>
>
> For testing purposes I have copied and pasted the example in the module,
> I have set:
>
>
>
> use strict;
>
> use Bio::Tools::Protparam;
>
> use Bio::DB::GenBank;
>
>
>
> Every time I try and run the script I get the following error:
>
>
>
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?Can't locate object method "new" via
> package "Protparam" (perhaps you forgot to load "Protparam"?) at ...
>
>
>
> Do you have any ideas? ?Any help would be very much appreciated.
>
>
>
> Sincerely
>
> Dallas Thomas
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From David.Messina at sbc.su.se  Mon Mar 28 03:33:25 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 28 Mar 2011 09:33:25 +0200
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
Message-ID: <AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>

Hi Ravi,

Please make sure to "Reply All" so that everyone on the mailing list can
follow (and add to) the discussion.

If you read the first line of the exception, you'll see it states what the
error is:
"WebDBSeqI Error ? check query sequences!"

You'd have no way of knowing this, but that ID and database combination is
not functioning anymore, so that's why in this case you're getting an error.
Please try using the example in the tutorial here:

  http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts

which has been updated to a different ID which should work.

Sorry for the confusion! So that we can prevent other people from having the
same issue, could you tell me where you got that example code?

Dave






2011/3/28 ?????????????????? <ravimbt at gmail.com>

> Hi Dave,
>
> Thanks a lot for your reply. It is really helpful. Please find the
> screenshot after making the change you pointed out. But I am getting
> "Exception: Bio::Root::Exception" error. I think I have to set the
> environment variables but I am not sure how to do that. Could you please
> guide me on this too.
>
> I can go to the "Environment Variable" Window in my pc. But I dont know
> what to enter once I click "New" on that window.
>
> Thanks in advance.
>
> With regards,
> Ravi.
>
>
> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>
>> Hi Ravi,
>>
>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>> not Bio::Seq. So your first line
>>
>> use Bio::Seq;
>>
>> should be replaced with
>>
>> use Bio::Perl;
>>
>>
>> More examples in the BioPerl Tutorial here:
>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>
>>
>> Dve
>>
>>
>>
>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>
>>> Hi,
>>>
>>> Could you please help me installing bioperl-db, bioperl-run & other
>>> packages
>>> using ppm on windows 7? Please find the attachment for the error message
>>> I
>>> get. I would really appreciate if you help me fix this issue.
>>>
>>> Thanks,
>>>
>>> With regards,
>>> Ravi.
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>


From David.Messina at sbc.su.se  Mon Mar 28 07:51:41 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 28 Mar 2011 13:51:41 +0200
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
Message-ID: <AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>

>
> Thank you very much. It is working. I got the program code from the
> following link.
>
> http://www.bioperl.org/Core/Latest/bptutorial.html


Aha, okay. You got there from Google, I guess? That is *way* out of date.

To the other core devs, in order to prevent this confusion in the future,
I'd like to delete the Core/ directory from our website since it's been
superseded at this point by other docs and is not current. I intend to put
up a ticket at Redmine, but I will wait a bit before doing so to allow time
for people to see this and comment ? please do speak up if there's good
reason to keep it.


Could you please give me the link to join this forum to see other
> discussions, which would be more helpful to me?
>

Sure, you can sign up for the mailing list here:

 <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


And the archives are also searchable:

    http://news.gmane.org/gmane.comp.lang.perl.bio.general


Please let me know if you have any suggestion for me to keep learning the
> bioperl.


I would also suggest reading the (current) tutorial and HOWTOs at
www.bioperl.org . Lots of good links on the main page there, particularly
under the Documentation heading.


Dave





> With regards,
> Ravi.
>
>
> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>
>> Hi Ravi,
>>
>> Please make sure to "Reply All" so that everyone on the mailing list can
>> follow (and add to) the discussion.
>>
>> If you read the first line of the exception, you'll see it states what the
>> error is:
>> "WebDBSeqI Error ? check query sequences!"
>>
>> You'd have no way of knowing this, but that ID and database combination is
>> not functioning anymore, so that's why in this case you're getting an error.
>> Please try using the example in the tutorial here:
>>
>>
>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>
>> which has been updated to a different ID which should work.
>>
>> Sorry for the confusion! So that we can prevent other people from having
>> the same issue, could you tell me where you got that example code?
>>
>> Dave
>>
>>
>>
>>
>>
>>
>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>
>>> Hi Dave,
>>>
>>> Thanks a lot for your reply. It is really helpful. Please find the
>>> screenshot after making the change you pointed out. But I am getting
>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>> environment variables but I am not sure how to do that. Could you please
>>> guide me on this too.
>>>
>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>> what to enter once I click "New" on that window.
>>>
>>> Thanks in advance.
>>>
>>> With regards,
>>> Ravi.
>>>
>>>
>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>
>>>> Hi Ravi,
>>>>
>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>> not Bio::Seq. So your first line
>>>>
>>>> use Bio::Seq;
>>>>
>>>> should be replaced with
>>>>
>>>> use Bio::Perl;
>>>>
>>>>
>>>> More examples in the BioPerl Tutorial here:
>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>
>>>>
>>>> Dve
>>>>
>>>>
>>>>
>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>
>>>>> Hi,
>>>>>
>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>> packages
>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>> message I
>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> With regards,
>>>>> Ravi.
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>
>>>>
>>>
>>
>


From David.Messina at sbc.su.se  Mon Mar 28 08:45:34 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 28 Mar 2011 14:45:34 +0200
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTinhqidOd7VBDT+hr6E-VNKwOobtyZ1Zn=A1uPfy@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
	<AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
	<AANLkTinhqidOd7VBDT+hr6E-VNKwOobtyZ1Zn=A1uPfy@mail.gmail.com>
Message-ID: <AANLkTikiN9J28oNWWnQ5hJSWYB_DKTPHPegj+7wZ-ELr@mail.gmail.com>

Again, please "Reply All" so that your messages go to the mailing list.

Ravi, PLEASE read the documentation on the website first and try to figure
out how to solve your problem on your own. BioPerl is a complex system and
requires some effort to learn how to use. I and everyone on this list
volunteers our time answering questions, and we are happy to do so, but you
have to meet us halfway.


Dave




2011/3/28 ?????????????????? <ravimbt at gmail.com>

> Hi Dave,
>
> Thanks for the information. I have also signed up to join the forum.
>
> I could not retrieve the sequence from other databases other than Genbank.
> Could you please do the changes on the below programme to make it working so
> that I can try in my system.
> --------------------
> use Bio::Perl;
>
> $seq_object = get_sequence('genbank',"ECORHO");
>
> write_sequence(">ael.fasta",'fasta',$seq_object);
> ------------------
>
> Thanks once again.
>
> With regards,
> Ravi.
>
>
> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>
>> Thank you very much. It is working. I got the program code from the
>>> following link.
>>>
>>> http://www.bioperl.org/Core/Latest/bptutorial.html
>>
>>
>> Aha, okay. You got there from Google, I guess? That is *way* out of date.
>>
>> To the other core devs, in order to prevent this confusion in the future,
>> I'd like to delete the Core/ directory from our website since it's been
>> superseded at this point by other docs and is not current. I intend to put
>> up a ticket at Redmine, but I will wait a bit before doing so to allow time
>> for people to see this and comment ? please do speak up if there's good
>> reason to keep it.
>>
>>
>> Could you please give me the link to join this forum to see other
>>> discussions, which would be more helpful to me?
>>>
>>
>> Sure, you can sign up for the mailing list here:
>>
>>  <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> And the archives are also searchable:
>>
>>     http://news.gmane.org/gmane.comp.lang.perl.bio.general
>>
>>
>> Please let me know if you have any suggestion for me to keep learning the
>>> bioperl.
>>
>>
>> I would also suggest reading the (current) tutorial and HOWTOs at
>> www.bioperl.org . Lots of good links on the main page there, particularly
>> under the Documentation heading.
>>
>>
>> Dave
>>
>>
>>
>>
>>
>>> With regards,
>>> Ravi.
>>>
>>>
>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>>>
>>>> Hi Ravi,
>>>>
>>>> Please make sure to "Reply All" so that everyone on the mailing list can
>>>> follow (and add to) the discussion.
>>>>
>>>> If you read the first line of the exception, you'll see it states what
>>>> the error is:
>>>> "WebDBSeqI Error ? check query sequences!"
>>>>
>>>> You'd have no way of knowing this, but that ID and database combination
>>>> is not functioning anymore, so that's why in this case you're getting an
>>>> error. Please try using the example in the tutorial here:
>>>>
>>>>
>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>>>
>>>> which has been updated to a different ID which should work.
>>>>
>>>> Sorry for the confusion! So that we can prevent other people from having
>>>> the same issue, could you tell me where you got that example code?
>>>>
>>>> Dave
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>>>
>>>>> Hi Dave,
>>>>>
>>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>>> screenshot after making the change you pointed out. But I am getting
>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>>> environment variables but I am not sure how to do that. Could you please
>>>>> guide me on this too.
>>>>>
>>>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>>>> what to enter once I click "New" on that window.
>>>>>
>>>>> Thanks in advance.
>>>>>
>>>>> With regards,
>>>>> Ravi.
>>>>>
>>>>>
>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>>>
>>>>>> Hi Ravi,
>>>>>>
>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl
>>>>>> module, not Bio::Seq. So your first line
>>>>>>
>>>>>> use Bio::Seq;
>>>>>>
>>>>>> should be replaced with
>>>>>>
>>>>>> use Bio::Perl;
>>>>>>
>>>>>>
>>>>>> More examples in the BioPerl Tutorial here:
>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>>>
>>>>>>
>>>>>> Dve
>>>>>>
>>>>>>
>>>>>>
>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>>>> packages
>>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>>> message I
>>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> With regards,
>>>>>>> Ravi.
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>


From abualiga at gmail.com  Mon Mar 28 09:19:00 2011
From: abualiga at gmail.com (Galeb Abu-Ali)
Date: Mon, 28 Mar 2011 09:19:00 -0400
Subject: [Bioperl-l] CDS complement statements from GenBank
In-Reply-To: <4D8F7AED.1070705@bioperl.org>
References: <cdf62961-ac89-4274-91ed-9a233d2de15c@k10g2000prh.googlegroups.com>
	<4D8F7AED.1070705@bioperl.org>
Message-ID: <AANLkTimpN2sRvrkn86Ges7100ssRizHr5GU7rPhDvyUS@mail.gmail.com>

I was using the wrong module, Bio::Location::Simple was what I needed.
thanks much!

galeb

On Sun, Mar 27, 2011 at 1:59 PM, Jason Stajich <jason at bioperl.org> wrote:

> they won't be split locations they will be Bio::Location::Simple locations
> then - I don't understand if that is causing you problems?
>
>
>
> Galeb Abu-Ali wrote:
>
>> Hi,
>>
>> I'm trying to parse CDS complement statements from GenBank files of
>> bacterial genomes. I know it works for 'join' statements with
>> Bio::Location::SplitLocationI, but there is no spliced genes in
>> bacterial annotations and therefore no 'join()' statements. When I
>> replace 'complement' with 'join' in the bacterial GenBank file,
>> Bio::Location::SplitLocationI gets the coordinates. I took a look at
>> SplitLocationI.pm and Split.pm to see if I could replace 'join' with
>> 'complement' to get it to work but no luck. At your convenience,
>> please advise.
>>
>> cheers,
>>
>> galeb
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> --
> Jason Stajich
> jason at bioperl.org
> http://bioperl.org/wiki
>
>

From cjfields at illinois.edu  Mon Mar 28 09:27:38 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 28 Mar 2011 08:27:38 -0500
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
	<AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
Message-ID: <6CE8AACF-0D78-4BBA-8094-CC189B0FF872@illinois.edu>

Dave,

+1 on removing old docs to prevent confusion.  Or, alternatively, +1 to syncing those to current docs (though I think decreasing the replication effort in keeping docs up-to-date is probably the best tact).

chris

On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:

>> 
>> Thank you very much. It is working. I got the program code from the
>> following link.
>> 
>> http://www.bioperl.org/Core/Latest/bptutorial.html
> 
> 
> Aha, okay. You got there from Google, I guess? That is *way* out of date.
> 
> To the other core devs, in order to prevent this confusion in the future,
> I'd like to delete the Core/ directory from our website since it's been
> superseded at this point by other docs and is not current. I intend to put
> up a ticket at Redmine, but I will wait a bit before doing so to allow time
> for people to see this and comment ? please do speak up if there's good
> reason to keep it.
> 
> 
> Could you please give me the link to join this forum to see other
>> discussions, which would be more helpful to me?
>> 
> 
> Sure, you can sign up for the mailing list here:
> 
> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> And the archives are also searchable:
> 
>    http://news.gmane.org/gmane.comp.lang.perl.bio.general
> 
> 
> Please let me know if you have any suggestion for me to keep learning the
>> bioperl.
> 
> 
> I would also suggest reading the (current) tutorial and HOWTOs at
> www.bioperl.org . Lots of good links on the main page there, particularly
> under the Documentation heading.
> 
> 
> Dave
> 
> 
> 
> 
> 
>> With regards,
>> Ravi.
>> 
>> 
>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>> 
>>> Hi Ravi,
>>> 
>>> Please make sure to "Reply All" so that everyone on the mailing list can
>>> follow (and add to) the discussion.
>>> 
>>> If you read the first line of the exception, you'll see it states what the
>>> error is:
>>> "WebDBSeqI Error ? check query sequences!"
>>> 
>>> You'd have no way of knowing this, but that ID and database combination is
>>> not functioning anymore, so that's why in this case you're getting an error.
>>> Please try using the example in the tutorial here:
>>> 
>>> 
>>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>> 
>>> which has been updated to a different ID which should work.
>>> 
>>> Sorry for the confusion! So that we can prevent other people from having
>>> the same issue, could you tell me where you got that example code?
>>> 
>>> Dave
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>> 
>>>> Hi Dave,
>>>> 
>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>> screenshot after making the change you pointed out. But I am getting
>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>> environment variables but I am not sure how to do that. Could you please
>>>> guide me on this too.
>>>> 
>>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>>> what to enter once I click "New" on that window.
>>>> 
>>>> Thanks in advance.
>>>> 
>>>> With regards,
>>>> Ravi.
>>>> 
>>>> 
>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>> 
>>>>> Hi Ravi,
>>>>> 
>>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>>> not Bio::Seq. So your first line
>>>>> 
>>>>> use Bio::Seq;
>>>>> 
>>>>> should be replaced with
>>>>> 
>>>>> use Bio::Perl;
>>>>> 
>>>>> 
>>>>> More examples in the BioPerl Tutorial here:
>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>> 
>>>>> 
>>>>> Dve
>>>>> 
>>>>> 
>>>>> 
>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>>> packages
>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>> message I
>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>> 
>>>>>> Thanks,
>>>>>> 
>>>>>> With regards,
>>>>>> Ravi.
>>>>>> 
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>> 
>>>>> 
>>>>> 
>>>> 
>>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From dan.bolser at gmail.com  Mon Mar 28 13:15:32 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 28 Mar 2011 18:15:32 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
Message-ID: <AANLkTikQgn2-YU4-4JBdLkSopFFihhJ-=2KG25P0Ugv6@mail.gmail.com>

--- Build.PL~   2011-03-14 20:27:57.000000000 +0000
+++ Build.PL    2011-03-28 18:06:45.503757000 +0100
@@ -16,7 +16,7 @@
     dist_abstract      => "Manipulate Jim Kent's BigWig and BigBed
index files for genomic features.",
     license            => 'perl',
     include_dirs       => [$jk_include],
-    extra_linker_flags => ["$jk_lib/$LibFile",'-lz'],
+    extra_linker_flags => ["$jk_lib/$LibFile",'-lz','-lssl'],

     extra_compiler_flags=>[
        # turn off warnings originating in Perl's Newx* calls

On 27 March 2011 19:00, Dan Bolser <dan.bolser at gmail.com> wrote:
> Hello,
>
> I'm trying to get Bio::DB::BigWig installed again, this time on a different box.
>
> I installed kent from git as described here:
> http://genome.ucsc.edu/admin/git.html
>
>
> I made the following changes, similar to those described previously:
>
> git diff
> diff --git a/src/inc/common.mk b/src/inc/common.mk
> index c7fc557..5187901 100644
> --- a/src/inc/common.mk
> +++ b/src/inc/common.mk
> @@ -3,7 +3,7 @@ CC=gcc
> ?ifeq (${COPT},)
> ? ? COPT=-O -g
> ?endif
> -CFLAGS=
> +CFLAGS=-fPIC
> ?HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> -DMACHTYPE_${MACHTYPE}
> ?HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> -I../../../../../inc
>
> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> index fa2292b..acb97d2 100644
> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
> ? ? /* Parse current line. */
> ? ? wordCount = chopLine(line, row);
> ? ? if (wordCount == ArraySize(row))
> - ? ? ? ? errAbort("Too many fields (%d max is %lu) line %d of %s",
> wordCount, ArraySize(row),
> + ? ? ? ? errAbort("Too many fields (%d max is %u) line %d of %s",
> wordCount, ArraySize(row),
> ? ? ? ? ? ? lf->lineIx, lf->fileName);
> ? ? char *chrom = row[0];
> ? ? unsigned int start = lineFileNeedNum(lf, row, 1);
>
>
> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> correctly after typing 'make' in kent/src (should I be building it
> differently?)
>
>
>
> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>
> cpan
>
> cpan shell -- CPAN exploration and modules installation (v1.9600)
> Enter 'h' for help.
>
> cpan[1]> install Bio::DB::BigWig
> CPAN: Storable loaded ok (v2.25)
> Going to read '/homes/dbolser/.cpan/Metadata'
> ?Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> Running install for module 'Bio::DB::BigWig'
> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> CPAN: Digest::SHA loaded ok (v5.61)
> CPAN: Compress::Zlib loaded ok (v2.03)
> Checksum for /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> ok
> CPAN: Archive::Tar loaded ok (v1.76)
> Bio-BigFile-1.05
> Bio-BigFile-1.05/Changes
> Bio-BigFile-1.05/LICENSE
> Bio-BigFile-1.05/DISCLAIMER
> Bio-BigFile-1.05/Build.PL
> Bio-BigFile-1.05/typemap
> Bio-BigFile-1.05/META.yml
> Bio-BigFile-1.05/README
> Bio-BigFile-1.05/MANIFEST
> Bio-BigFile-1.05/ExampleData
> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> Bio-BigFile-1.05/bin
> Bio-BigFile-1.05/bin/bigWigToWig.pl
> Bio-BigFile-1.05/bin/wigToBigWig.pl
> Bio-BigFile-1.05/bin/index_bigwigset.pl
> Bio-BigFile-1.05/lib
> Bio-BigFile-1.05/lib/Bio
> Bio-BigFile-1.05/lib/Bio/DB
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> Bio-BigFile-1.05/t
> Bio-BigFile-1.05/t/02.bigbed.t
> Bio-BigFile-1.05/t/03.bigwig_high.t
> Bio-BigFile-1.05/t/04.bigbed_high.t
> Bio-BigFile-1.05/t/05.bigwig_set.t
> /bin/tar: Read 9216 bytes from -
> Bio-BigFile-1.05/t/01.bigwig.t
> Bio-BigFile-1.05/patches
> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> CPAN: File::Temp loaded ok (v0.22)
> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> CPAN: CPAN::Meta loaded ok (v2.110580)
> CPAN: Module::CoreList loaded ok (v2.46)
> CPAN: Time::HiRes loaded ok (v1.9717)
>
> ?CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>
>
> This module requires the compiled jkweb.a library from Jim Kent's source tree.
> If you haven't already done so, please download the source from
> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
> contents of the "kent/src/lib" subdirectory as directed in the README. Then
> enter the location of the "kent/src" subdirectory at the prompt below.
> To prevent
> this message from appearing in the future, set the environment
> variable KENT_SRC
> to point to the "kent/src" subdirectory.
>
> Please enter the location of Kent source tree: /homes/dbolser/build/src/kent/src
>
> Created MYMETA.yml and MYMETA.json
> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> Building Bio-BigFile
> gcc -I/homes/dbolser/build/src/kent/src/inc
> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> lib/Bio/DB/BigFile.c
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be undefined
> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be undefined
> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
> ?LDS/Bio-BigFile-1.05.tar.gz
> ?./Build -- OK
> CPAN: YAML loaded ok (v0.72)
> Running Build test
> t/01.bigwig.t ....... Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at t/01.bigwig.t line 28
> Compilation failed in require at t/01.bigwig.t line 28.
> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 29/29 subtests
> t/02.bigbed.t ....... Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at t/02.bigbed.t line 28
> Compilation failed in require at t/02.bigbed.t line 28.
> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 15/15 subtests
> t/03.bigwig_high.t .. Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at t/03.bigwig_high.t line 28.
> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 32/32 subtests
> t/04.bigbed_high.t .. Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> Compilation failed in require at t/04.bigbed_high.t line 28.
> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 35/35 subtests
> t/05.bigwig_set.t ... Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> Compilation failed in require at t/05.bigwig_set.t line 19.
> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> No subtests run
>
> Test Summary Report
> -------------------
> t/01.bigwig.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: Bad plan. ?You planned 29 tests but ran 0.
> t/02.bigbed.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: Bad plan. ?You planned 15 tests but ran 0.
> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: Bad plan. ?You planned 32 tests but ran 0.
> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: Bad plan. ?You planned 35 tests but ran 0.
> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: No plan found in TAP output
> Files=5, Tests=0, ?1 wallclock secs ( 0.04 usr ?0.01 sys + ?0.93 cusr
> 0.11 csys = ?1.09 CPU)
> Result: FAIL
> Failed 5/5 test programs. 0/0 subtests failed.
> ?LDS/Bio-BigFile-1.05.tar.gz
> ?./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module, try:
> ?reports LDS/Bio-BigFile-1.05.tar.gz
> Running Build install
> ?make test had returned bad status, won't install without force
> Failed during this command:
> ?LDS/Bio-BigFile-1.05.tar.gz ? ? ? ? ? ? ? ? ?: make_test NO
>
> cpan[2]>
>
>
>
>
>
>
> Any hints?
>
> Cheers,
> Dan.
>


From dan.bolser at gmail.com  Mon Mar 28 16:08:52 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 28 Mar 2011 21:08:52 +0100
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <4960971A-8C61-49F2-B43A-E32BAFC4C59E@illinois.edu>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
	<4D8F73A4.8050408@bioperl.org>
	<AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
	<4960971A-8C61-49F2-B43A-E32BAFC4C59E@illinois.edu>
Message-ID: <AANLkTi=H4opbLx+qv8XM5+VpQNy2Fhxtbyx54iumRcE5@mail.gmail.com>

On 27 March 2011 21:13, Chris Fields <cjfields at illinois.edu> wrote:
> On Mar 27, 2011, at 12:55 PM, Dan Bolser wrote:
>
>> On 27 March 2011 18:28, Jason Stajich <jason at bioperl.org> wrote:
>>> Dan - not sure why you would need to do this as length on an undef should
>>> still return false (an undef).
>>>
>>> $ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} print
>>> "\n"'
>>> no
>>> $ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"}
>>> print "\n"'
>>> no
>>
>> Doesn't the latter spew a warning? (The output before / after my 'bug
>> fix' is the same, I just don't see 100s of warnings about undefined
>> values).
>
> Only with later versions of perl (I think perl 5.12).
>
>>> Also, having no 'source' is probably not proper GFF3.
>>
>> I'm quite sure it is, but by GFF does have a source. I'm just calling
>> 'features' with only a feature type and not a feature type and a
>> source (because I only care about source). My call is pretty similar
>> to the example here:
>>
>> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/DB/SeqFeature/Store.pm#features
>>
>> @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');
>
> I think Jason is inferring that the GFF3 is invalid from your statement below re: $source_tag not being defined, which to me means the source attribute for the feature is not defined.
>
> Note: b/c something works with SF::Store does NOT mean the source is proper GFF3; it is quite possible to have invalid GFF3 loaded into the database w/o a hiccup. ?I think the loader assumes the data loaded has already been validated; IIRC there is very little validation done on GFF3 loaded into SF::Store, particularly the 'type'.

As I said, my GFF3 does have a source. I'll try to put together a test
script, as it seems like the value should not be undef (but thanks for
the tip Roy).

I had a feeling that this relatively trivial fix was a sticking
plaster on a larger problem.


> chris
Dan


From dan.bolser at gmail.com  Mon Mar 28 16:12:19 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 28 Mar 2011 21:12:19 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTikQgn2-YU4-4JBdLkSopFFihhJ-=2KG25P0Ugv6@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTikQgn2-YU4-4JBdLkSopFFihhJ-=2KG25P0Ugv6@mail.gmail.com>
Message-ID: <AANLkTikjJpMcFWvvAt+bJoXJHHaORfecYmz053RScFjn@mail.gmail.com>

Context, this patch in the distro's Build.PL fixes the errors with the
tests, but doesn't fix the warnings.

On 28 March 2011 18:15, Dan Bolser <dan.bolser at gmail.com> wrote:
> --- Build.PL~ ? 2011-03-14 20:27:57.000000000 +0000
> +++ Build.PL ? ?2011-03-28 18:06:45.503757000 +0100
> @@ -16,7 +16,7 @@
> ? ? dist_abstract ? ? ?=> "Manipulate Jim Kent's BigWig and BigBed
> index files for genomic features.",
> ? ? license ? ? ? ? ? ?=> 'perl',
> ? ? include_dirs ? ? ? => [$jk_include],
> - ? ?extra_linker_flags => ["$jk_lib/$LibFile",'-lz'],
> + ? ?extra_linker_flags => ["$jk_lib/$LibFile",'-lz','-lssl'],
>
> ? ? extra_compiler_flags=>[
> ? ? ? ?# turn off warnings originating in Perl's Newx* calls


From cjfields at illinois.edu  Mon Mar 28 16:23:38 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 28 Mar 2011 15:23:38 -0500
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTikjJpMcFWvvAt+bJoXJHHaORfecYmz053RScFjn@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTikQgn2-YU4-4JBdLkSopFFihhJ-=2KG25P0Ugv6@mail.gmail.com>
	<AANLkTikjJpMcFWvvAt+bJoXJHHaORfecYmz053RScFjn@mail.gmail.com>
Message-ID: <91759940-6457-460D-95F5-EF7098A7412C@illinois.edu>

Dan,

Was this using the latest kent src and Bio::DB::BigWig?

chris

PS : cc'ing gbrowse, which is where these seem to get answered a bit faster, context thread here: http://lists.open-bio.org/pipermail/bioperl-l/2011-March/034738.html

On Mar 28, 2011, at 3:12 PM, Dan Bolser wrote:

> Context, this patch in the distro's Build.PL fixes the errors with the
> tests, but doesn't fix the warnings.
> 
> On 28 March 2011 18:15, Dan Bolser <dan.bolser at gmail.com> wrote:
>> --- Build.PL~   2011-03-14 20:27:57.000000000 +0000
>> +++ Build.PL    2011-03-28 18:06:45.503757000 +0100
>> @@ -16,7 +16,7 @@
>>     dist_abstract      => "Manipulate Jim Kent's BigWig and BigBed
>> index files for genomic features.",
>>     license            => 'perl',
>>     include_dirs       => [$jk_include],
>> -    extra_linker_flags => ["$jk_lib/$LibFile",'-lz'],
>> +    extra_linker_flags => ["$jk_lib/$LibFile",'-lz','-lssl'],
>> 
>>     extra_compiler_flags=>[
>>        # turn off warnings originating in Perl's Newx* calls
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From lincoln.stein at gmail.com  Mon Mar 28 17:26:20 2011
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Mon, 28 Mar 2011 17:26:20 -0400
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
Message-ID: <AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>

Hi Dan,

There are two problems that I can see. One is a series of compiler warnings
when compiling the Perl .XS interface file. These are likely nothing to
worry about, but I should fix them. What versions of Perl and gcc do you
have installed? I don't see them when I compile on my system.

The second issue is that the SSL library is not being linked in. Previously
there was no dependency on SSL, but Jim may recently have added this to the
BigWig library in order to allow it to read bigwig files from https servers.
I see that you added a -lssl to Build.PL; does this make the tests work
again?

Lincoln


On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com> wrote:

> Hello,
>
> I'm trying to get Bio::DB::BigWig installed again, this time on a different
> box.
>
> I installed kent from git as described here:
> http://genome.ucsc.edu/admin/git.html
>
>
> I made the following changes, similar to those described previously:
>
> git diff
> diff --git a/src/inc/common.mk b/src/inc/common.mk
> index c7fc557..5187901 100644
> --- a/src/inc/common.mk
> +++ b/src/inc/common.mk
> @@ -3,7 +3,7 @@ CC=gcc
>  ifeq (${COPT},)
>     COPT=-O -g
>  endif
> -CFLAGS=
> +CFLAGS=-fPIC
>  HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> -DMACHTYPE_${MACHTYPE}
>  HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> -I../../../../../inc
>
> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> index fa2292b..acb97d2 100644
> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
>     /* Parse current line. */
>     wordCount = chopLine(line, row);
>     if (wordCount == ArraySize(row))
> -         errAbort("Too many fields (%d max is %lu) line %d of %s",
> wordCount, ArraySize(row),
> +         errAbort("Too many fields (%d max is %u) line %d of %s",
> wordCount, ArraySize(row),
>             lf->lineIx, lf->fileName);
>     char *chrom = row[0];
>     unsigned int start = lineFileNeedNum(lf, row, 1);
>
>
> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> correctly after typing 'make' in kent/src (should I be building it
> differently?)
>
>
>
> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>
> cpan
>
> cpan shell -- CPAN exploration and modules installation (v1.9600)
> Enter 'h' for help.
>
> cpan[1]> install Bio::DB::BigWig
> CPAN: Storable loaded ok (v2.25)
> Going to read '/homes/dbolser/.cpan/Metadata'
>  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> Running install for module 'Bio::DB::BigWig'
> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> CPAN: Digest::SHA loaded ok (v5.61)
> CPAN: Compress::Zlib loaded ok (v2.03)
> Checksum for
> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> ok
> CPAN: Archive::Tar loaded ok (v1.76)
> Bio-BigFile-1.05
> Bio-BigFile-1.05/Changes
> Bio-BigFile-1.05/LICENSE
> Bio-BigFile-1.05/DISCLAIMER
> Bio-BigFile-1.05/Build.PL
> Bio-BigFile-1.05/typemap
> Bio-BigFile-1.05/META.yml
> Bio-BigFile-1.05/README
> Bio-BigFile-1.05/MANIFEST
> Bio-BigFile-1.05/ExampleData
> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> Bio-BigFile-1.05/bin
> Bio-BigFile-1.05/bin/bigWigToWig.pl
> Bio-BigFile-1.05/bin/wigToBigWig.pl
> Bio-BigFile-1.05/bin/index_bigwigset.pl
> Bio-BigFile-1.05/lib
> Bio-BigFile-1.05/lib/Bio
> Bio-BigFile-1.05/lib/Bio/DB
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> Bio-BigFile-1.05/t
> Bio-BigFile-1.05/t/02.bigbed.t
> Bio-BigFile-1.05/t/03.bigwig_high.t
> Bio-BigFile-1.05/t/04.bigbed_high.t
> Bio-BigFile-1.05/t/05.bigwig_set.t
> /bin/tar: Read 9216 bytes from -
> Bio-BigFile-1.05/t/01.bigwig.t
> Bio-BigFile-1.05/patches
> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> CPAN: File::Temp loaded ok (v0.22)
> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> CPAN: CPAN::Meta loaded ok (v2.110580)
> CPAN: Module::CoreList loaded ok (v2.46)
> CPAN: Time::HiRes loaded ok (v1.9717)
>
>  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>
>
> This module requires the compiled jkweb.a library from Jim Kent's source
> tree.
> If you haven't already done so, please download the source from
> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
> contents of the "kent/src/lib" subdirectory as directed in the README. Then
> enter the location of the "kent/src" subdirectory at the prompt below.
> To prevent
> this message from appearing in the future, set the environment
> variable KENT_SRC
> to point to the "kent/src" subdirectory.
>
> Please enter the location of Kent source tree:
> /homes/dbolser/build/src/kent/src
>
> Created MYMETA.yml and MYMETA.json
> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> Building Bio-BigFile
> gcc -I/homes/dbolser/build/src/kent/src/inc
> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> lib/Bio/DB/BigFile.c
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
> undefined
> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
> undefined
> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
>
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build -- OK
> CPAN: YAML loaded ok (v0.72)
> Running Build test
> t/01.bigwig.t ....... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/01.bigwig.t line 28
> Compilation failed in require at t/01.bigwig.t line 28.
> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 29/29 subtests
> t/02.bigbed.t ....... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/02.bigbed.t line 28
> Compilation failed in require at t/02.bigbed.t line 28.
> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 15/15 subtests
> t/03.bigwig_high.t .. Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at t/03.bigwig_high.t line 28.
> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 32/32 subtests
> t/04.bigbed_high.t .. Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> Compilation failed in require at t/04.bigbed_high.t line 28.
> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 35/35 subtests
> t/05.bigwig_set.t ... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> Compilation failed in require at t/05.bigwig_set.t line 19.
> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> No subtests run
>
> Test Summary Report
> -------------------
> t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 29 tests but ran 0.
> t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 32 tests but ran 0.
> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 35 tests but ran 0.
> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: No plan found in TAP output
> Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
> 0.11 csys =  1.09 CPU)
> Result: FAIL
> Failed 5/5 test programs. 0/0 subtests failed.
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module, try:
>  reports LDS/Bio-BigFile-1.05.tar.gz
> Running Build install
>  make test had returned bad status, won't install without force
> Failed during this command:
>  LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO
>
> cpan[2]>
>
>
>
>
>
>
> Any hints?
>
> Cheers,
> Dan.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>


From lincoln.stein at gmail.com  Mon Mar 28 17:26:20 2011
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Mon, 28 Mar 2011 17:26:20 -0400
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
Message-ID: <AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>

Hi Dan,

There are two problems that I can see. One is a series of compiler warnings
when compiling the Perl .XS interface file. These are likely nothing to
worry about, but I should fix them. What versions of Perl and gcc do you
have installed? I don't see them when I compile on my system.

The second issue is that the SSL library is not being linked in. Previously
there was no dependency on SSL, but Jim may recently have added this to the
BigWig library in order to allow it to read bigwig files from https servers.
I see that you added a -lssl to Build.PL; does this make the tests work
again?

Lincoln


On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com> wrote:

> Hello,
>
> I'm trying to get Bio::DB::BigWig installed again, this time on a different
> box.
>
> I installed kent from git as described here:
> http://genome.ucsc.edu/admin/git.html
>
>
> I made the following changes, similar to those described previously:
>
> git diff
> diff --git a/src/inc/common.mk b/src/inc/common.mk
> index c7fc557..5187901 100644
> --- a/src/inc/common.mk
> +++ b/src/inc/common.mk
> @@ -3,7 +3,7 @@ CC=gcc
>  ifeq (${COPT},)
>     COPT=-O -g
>  endif
> -CFLAGS=
> +CFLAGS=-fPIC
>  HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> -DMACHTYPE_${MACHTYPE}
>  HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> -I../../../../../inc
>
> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> index fa2292b..acb97d2 100644
> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
>     /* Parse current line. */
>     wordCount = chopLine(line, row);
>     if (wordCount == ArraySize(row))
> -         errAbort("Too many fields (%d max is %lu) line %d of %s",
> wordCount, ArraySize(row),
> +         errAbort("Too many fields (%d max is %u) line %d of %s",
> wordCount, ArraySize(row),
>             lf->lineIx, lf->fileName);
>     char *chrom = row[0];
>     unsigned int start = lineFileNeedNum(lf, row, 1);
>
>
> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> correctly after typing 'make' in kent/src (should I be building it
> differently?)
>
>
>
> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>
> cpan
>
> cpan shell -- CPAN exploration and modules installation (v1.9600)
> Enter 'h' for help.
>
> cpan[1]> install Bio::DB::BigWig
> CPAN: Storable loaded ok (v2.25)
> Going to read '/homes/dbolser/.cpan/Metadata'
>  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> Running install for module 'Bio::DB::BigWig'
> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> CPAN: Digest::SHA loaded ok (v5.61)
> CPAN: Compress::Zlib loaded ok (v2.03)
> Checksum for
> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> ok
> CPAN: Archive::Tar loaded ok (v1.76)
> Bio-BigFile-1.05
> Bio-BigFile-1.05/Changes
> Bio-BigFile-1.05/LICENSE
> Bio-BigFile-1.05/DISCLAIMER
> Bio-BigFile-1.05/Build.PL
> Bio-BigFile-1.05/typemap
> Bio-BigFile-1.05/META.yml
> Bio-BigFile-1.05/README
> Bio-BigFile-1.05/MANIFEST
> Bio-BigFile-1.05/ExampleData
> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> Bio-BigFile-1.05/bin
> Bio-BigFile-1.05/bin/bigWigToWig.pl
> Bio-BigFile-1.05/bin/wigToBigWig.pl
> Bio-BigFile-1.05/bin/index_bigwigset.pl
> Bio-BigFile-1.05/lib
> Bio-BigFile-1.05/lib/Bio
> Bio-BigFile-1.05/lib/Bio/DB
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> Bio-BigFile-1.05/t
> Bio-BigFile-1.05/t/02.bigbed.t
> Bio-BigFile-1.05/t/03.bigwig_high.t
> Bio-BigFile-1.05/t/04.bigbed_high.t
> Bio-BigFile-1.05/t/05.bigwig_set.t
> /bin/tar: Read 9216 bytes from -
> Bio-BigFile-1.05/t/01.bigwig.t
> Bio-BigFile-1.05/patches
> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> CPAN: File::Temp loaded ok (v0.22)
> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> CPAN: CPAN::Meta loaded ok (v2.110580)
> CPAN: Module::CoreList loaded ok (v2.46)
> CPAN: Time::HiRes loaded ok (v1.9717)
>
>  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>
>
> This module requires the compiled jkweb.a library from Jim Kent's source
> tree.
> If you haven't already done so, please download the source from
> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
> contents of the "kent/src/lib" subdirectory as directed in the README. Then
> enter the location of the "kent/src" subdirectory at the prompt below.
> To prevent
> this message from appearing in the future, set the environment
> variable KENT_SRC
> to point to the "kent/src" subdirectory.
>
> Please enter the location of Kent source tree:
> /homes/dbolser/build/src/kent/src
>
> Created MYMETA.yml and MYMETA.json
> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> Building Bio-BigFile
> gcc -I/homes/dbolser/build/src/kent/src/inc
> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> lib/Bio/DB/BigFile.c
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
> undefined
> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
> undefined
> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
>
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build -- OK
> CPAN: YAML loaded ok (v0.72)
> Running Build test
> t/01.bigwig.t ....... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/01.bigwig.t line 28
> Compilation failed in require at t/01.bigwig.t line 28.
> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 29/29 subtests
> t/02.bigbed.t ....... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/02.bigbed.t line 28
> Compilation failed in require at t/02.bigbed.t line 28.
> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 15/15 subtests
> t/03.bigwig_high.t .. Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at t/03.bigwig_high.t line 28.
> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 32/32 subtests
> t/04.bigbed_high.t .. Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> Compilation failed in require at t/04.bigbed_high.t line 28.
> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 35/35 subtests
> t/05.bigwig_set.t ... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> Compilation failed in require at t/05.bigwig_set.t line 19.
> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> No subtests run
>
> Test Summary Report
> -------------------
> t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 29 tests but ran 0.
> t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 32 tests but ran 0.
> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 35 tests but ran 0.
> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: No plan found in TAP output
> Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
> 0.11 csys =  1.09 CPU)
> Result: FAIL
> Failed 5/5 test programs. 0/0 subtests failed.
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module, try:
>  reports LDS/Bio-BigFile-1.05.tar.gz
> Running Build install
>  make test had returned bad status, won't install without force
> Failed during this command:
>  LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO
>
> cpan[2]>
>
>
>
>
>
>
> Any hints?
>
> Cheers,
> Dan.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>


From bosborne11 at verizon.net  Mon Mar 28 16:43:51 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Mon, 28 Mar 2011 16:43:51 -0400
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <6CE8AACF-0D78-4BBA-8094-CC189B0FF872@illinois.edu>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
	<AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
	<6CE8AACF-0D78-4BBA-8094-CC189B0FF872@illinois.edu>
Message-ID: <63E35F39-D70C-4D6F-A792-D2738B850567@verizon.net>

Chris,

I'll get started on dissembling bptutorial. There's certainly useful text in there but there's also duplicated or outdated material. Looks like there are 3 options for any given section:

- put it into an existing HOWTO
- make it into a new HOWTO
- delete it

BIO

On Mar 28, 2011, at 9:27 AM, Chris Fields wrote:

> Dave,
> 
> +1 on removing old docs to prevent confusion.  Or, alternatively, +1 to syncing those to current docs (though I think decreasing the replication effort in keeping docs up-to-date is probably the best tact).
> 
> chris
> 
> On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:
> 
>>> 
>>> Thank you very much. It is working. I got the program code from the
>>> following link.
>>> 
>>> http://www.bioperl.org/Core/Latest/bptutorial.html
>> 
>> 
>> Aha, okay. You got there from Google, I guess? That is *way* out of date.
>> 
>> To the other core devs, in order to prevent this confusion in the future,
>> I'd like to delete the Core/ directory from our website since it's been
>> superseded at this point by other docs and is not current. I intend to put
>> up a ticket at Redmine, but I will wait a bit before doing so to allow time
>> for people to see this and comment ? please do speak up if there's good
>> reason to keep it.
>> 
>> 
>> Could you please give me the link to join this forum to see other
>>> discussions, which would be more helpful to me?
>>> 
>> 
>> Sure, you can sign up for the mailing list here:
>> 
>> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> And the archives are also searchable:
>> 
>>   http://news.gmane.org/gmane.comp.lang.perl.bio.general
>> 
>> 
>> Please let me know if you have any suggestion for me to keep learning the
>>> bioperl.
>> 
>> 
>> I would also suggest reading the (current) tutorial and HOWTOs at
>> www.bioperl.org . Lots of good links on the main page there, particularly
>> under the Documentation heading.
>> 
>> 
>> Dave
>> 
>> 
>> 
>> 
>> 
>>> With regards,
>>> Ravi.
>>> 
>>> 
>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>>> 
>>>> Hi Ravi,
>>>> 
>>>> Please make sure to "Reply All" so that everyone on the mailing list can
>>>> follow (and add to) the discussion.
>>>> 
>>>> If you read the first line of the exception, you'll see it states what the
>>>> error is:
>>>> "WebDBSeqI Error ? check query sequences!"
>>>> 
>>>> You'd have no way of knowing this, but that ID and database combination is
>>>> not functioning anymore, so that's why in this case you're getting an error.
>>>> Please try using the example in the tutorial here:
>>>> 
>>>> 
>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>>> 
>>>> which has been updated to a different ID which should work.
>>>> 
>>>> Sorry for the confusion! So that we can prevent other people from having
>>>> the same issue, could you tell me where you got that example code?
>>>> 
>>>> Dave
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>>> 
>>>>> Hi Dave,
>>>>> 
>>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>>> screenshot after making the change you pointed out. But I am getting
>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>>> environment variables but I am not sure how to do that. Could you please
>>>>> guide me on this too.
>>>>> 
>>>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>>>> what to enter once I click "New" on that window.
>>>>> 
>>>>> Thanks in advance.
>>>>> 
>>>>> With regards,
>>>>> Ravi.
>>>>> 
>>>>> 
>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>>> 
>>>>>> Hi Ravi,
>>>>>> 
>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>>>> not Bio::Seq. So your first line
>>>>>> 
>>>>>> use Bio::Seq;
>>>>>> 
>>>>>> should be replaced with
>>>>>> 
>>>>>> use Bio::Perl;
>>>>>> 
>>>>>> 
>>>>>> More examples in the BioPerl Tutorial here:
>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>>> 
>>>>>> 
>>>>>> Dve
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>>> 
>>>>>>> Hi,
>>>>>>> 
>>>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>>>> packages
>>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>>> message I
>>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>>> 
>>>>>>> Thanks,
>>>>>>> 
>>>>>>> With regards,
>>>>>>> Ravi.
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Mon Mar 28 18:40:39 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 28 Mar 2011 17:40:39 -0500
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <63E35F39-D70C-4D6F-A792-D2738B850567@verizon.net>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
	<AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
	<6CE8AACF-0D78-4BBA-8094-CC189B0FF872@illinois.edu>
	<63E35F39-D70C-4D6F-A792-D2738B850567@verizon.net>
Message-ID: <1569920B-D132-487F-BBC6-9A81A430E6E0@illinois.edu>

Brian,

I think this was started:

http://www.bioperl.org/wiki/Bptutorial.pl

It certainly could be cleaned up, organized, and updated (that and the FAQ).  Makes sense to have it as a HOWTO or maybe split it into several HOWTOs.  Maybe even combine it with the beginner's HOWTO into various sections?

chris

On Mar 28, 2011, at 3:43 PM, Brian Osborne wrote:

> Chris,
> 
> I'll get started on dissembling bptutorial. There's certainly useful text in there but there's also duplicated or outdated material. Looks like there are 3 options for any given section:
> 
> - put it into an existing HOWTO
> - make it into a new HOWTO
> - delete it
> 
> BIO
> 
> On Mar 28, 2011, at 9:27 AM, Chris Fields wrote:
> 
>> Dave,
>> 
>> +1 on removing old docs to prevent confusion.  Or, alternatively, +1 to syncing those to current docs (though I think decreasing the replication effort in keeping docs up-to-date is probably the best tact).
>> 
>> chris
>> 
>> On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:
>> 
>>>> 
>>>> Thank you very much. It is working. I got the program code from the
>>>> following link.
>>>> 
>>>> http://www.bioperl.org/Core/Latest/bptutorial.html
>>> 
>>> 
>>> Aha, okay. You got there from Google, I guess? That is *way* out of date.
>>> 
>>> To the other core devs, in order to prevent this confusion in the future,
>>> I'd like to delete the Core/ directory from our website since it's been
>>> superseded at this point by other docs and is not current. I intend to put
>>> up a ticket at Redmine, but I will wait a bit before doing so to allow time
>>> for people to see this and comment ? please do speak up if there's good
>>> reason to keep it.
>>> 
>>> 
>>> Could you please give me the link to join this forum to see other
>>>> discussions, which would be more helpful to me?
>>>> 
>>> 
>>> Sure, you can sign up for the mailing list here:
>>> 
>>> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>>> And the archives are also searchable:
>>> 
>>>  http://news.gmane.org/gmane.comp.lang.perl.bio.general
>>> 
>>> 
>>> Please let me know if you have any suggestion for me to keep learning the
>>>> bioperl.
>>> 
>>> 
>>> I would also suggest reading the (current) tutorial and HOWTOs at
>>> www.bioperl.org . Lots of good links on the main page there, particularly
>>> under the Documentation heading.
>>> 
>>> 
>>> Dave
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> With regards,
>>>> Ravi.
>>>> 
>>>> 
>>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>>>> 
>>>>> Hi Ravi,
>>>>> 
>>>>> Please make sure to "Reply All" so that everyone on the mailing list can
>>>>> follow (and add to) the discussion.
>>>>> 
>>>>> If you read the first line of the exception, you'll see it states what the
>>>>> error is:
>>>>> "WebDBSeqI Error ? check query sequences!"
>>>>> 
>>>>> You'd have no way of knowing this, but that ID and database combination is
>>>>> not functioning anymore, so that's why in this case you're getting an error.
>>>>> Please try using the example in the tutorial here:
>>>>> 
>>>>> 
>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>>>> 
>>>>> which has been updated to a different ID which should work.
>>>>> 
>>>>> Sorry for the confusion! So that we can prevent other people from having
>>>>> the same issue, could you tell me where you got that example code?
>>>>> 
>>>>> Dave
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>>>> 
>>>>>> Hi Dave,
>>>>>> 
>>>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>>>> screenshot after making the change you pointed out. But I am getting
>>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>>>> environment variables but I am not sure how to do that. Could you please
>>>>>> guide me on this too.
>>>>>> 
>>>>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>>>>> what to enter once I click "New" on that window.
>>>>>> 
>>>>>> Thanks in advance.
>>>>>> 
>>>>>> With regards,
>>>>>> Ravi.
>>>>>> 
>>>>>> 
>>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>>>> 
>>>>>>> Hi Ravi,
>>>>>>> 
>>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>>>>> not Bio::Seq. So your first line
>>>>>>> 
>>>>>>> use Bio::Seq;
>>>>>>> 
>>>>>>> should be replaced with
>>>>>>> 
>>>>>>> use Bio::Perl;
>>>>>>> 
>>>>>>> 
>>>>>>> More examples in the BioPerl Tutorial here:
>>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>>>> 
>>>>>>> 
>>>>>>> Dve
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>>>> 
>>>>>>>> Hi,
>>>>>>>> 
>>>>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>>>>> packages
>>>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>>>> message I
>>>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>>>> 
>>>>>>>> Thanks,
>>>>>>>> 
>>>>>>>> With regards,
>>>>>>>> Ravi.
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From dan.kortschak at adelaide.edu.au  Mon Mar 28 21:12:55 2011
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Tue, 29 Mar 2011 11:42:55 +1030
Subject: [Bioperl-l] GuessSeqFormat GFF vs VCF
Message-ID: <1301361175.4727.17.camel@sueno>

Hi All,

I'm going through the BEDTools wrapper to bring it up to date. A number
BEDTools executables now accept GFF and VCF as well as BED format input
files.

Part of the WrapperBase::CommandExts give acceptable input formats, so
I'm adding to GuessSeqFormat guessers for GFF and VCF, which from the
point of view of a stateless guesser, are indistinguishable unless (and
I don't like this idea), GFF is additionally defined as not VCF and VCF
is additionally defined as not VCF (these can be identified from the
##gff-version and ##fileformat=VCF lines).

Can people provide their thoughts on this?

cheers
Dan


From dan.bolser at gmail.com  Tue Mar 29 04:57:29 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 29 Mar 2011 09:57:29 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
Message-ID: <AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>

On 28 March 2011 22:26, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Hi Dan,
> There are two problems that I can see. One is a series of compiler warnings
> when compiling the Perl .XS interface file. These are likely nothing to
> worry about, but I should fix them. What versions of Perl and gcc do you
> have installed? I don't see them when I compile on my system.

gcc --version # gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
perl --version # v5.8.8 built for i386-linux-thread-multi

uname -a # Linux cricket 2.6.18-194.32.1.el5PAE #1 SMP Wed Jan 5
18:43:13 EST 2011 i686 i686 i386 GNU/Linux



I got kent from git and built it with the following commands:

cd kent/src/lib/
echo $MACHTYPE # i686-redhat-linux-gnu
export MACHTYPE=i686
make
cd ../
export KENT_SRC=`pwd`

# NOTE, both $MACHTYPE and $KENT_SRC should be defined here
cpan -i Bio::DB::BigWig # FAILS AS DESCRIBED

cd /tmp
wget http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
tar zxfv Bio-BigFile-1.05.tar.gz
cd Bio-BigFile-1.05
# PATCH  Build.PL AS DESCRIBED (add -lssl after -lz)
perl Build.PL
./Build # SEE WARNINGS AS BEFORE
./Build test # Files=5, Tests=135, Result: PASS
./Build install


Note, above I didn't patch kent to include -fPIC as suggested
previously. I don't see any noticeable difference if I do on this
arch.

It would be good if the instructions above could make it into the
Bio::DB::BigWig README, as a few people have expressed confusion about
the exact steps (the README in kent is a bit confusing, and mostly
unnecessary for the purposes of building Bio::DB::BigWig).


> The second issue is that the SSL library is not being linked in. Previously
> there was no dependency on SSL, but Jim may recently have added this to the
> BigWig library in order to allow it to read bigwig files from https servers.
> I see that you added a -lssl to Build.PL; does this make the tests work
> again?

Yup, when I add -lssl to Build.PL (as per the previous diff), the
tests pass, but I still see the warnings.

I'm sure I saw the warnings disappear when I was playing with
different versions of Bio::DB::BigWig, but now they occur without
fail... if you pardon the pun.

I have a seeking suspicion that it's related to my perl 'build kit'...
However, since I'm not sure what module versions to report, and since
you promised to fix these issues anyway, I won't dig into it.


Thanks for help, and thanks for the support on
irc://irc.freenode.net/#bioperl, without which I would have probably
give up!

Cheers,
Dan.

> Lincoln
>
> On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com> wrote:
>>
>> Hello,
>>
>> I'm trying to get Bio::DB::BigWig installed again, this time on a
>> different box.
>>
>> I installed kent from git as described here:
>> http://genome.ucsc.edu/admin/git.html
>>
>>
>> I made the following changes, similar to those described previously:
>>
>> git diff
>> diff --git a/src/inc/common.mk b/src/inc/common.mk
>> index c7fc557..5187901 100644
>> --- a/src/inc/common.mk
>> +++ b/src/inc/common.mk
>> @@ -3,7 +3,7 @@ CC=gcc
>> ?ifeq (${COPT},)
>> ? ? COPT=-O -g
>> ?endif
>> -CFLAGS=
>> +CFLAGS=-fPIC
>> ?HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
>> -DMACHTYPE_${MACHTYPE}
>> ?HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
>> -I../../../../../inc
>>
>> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> index fa2292b..acb97d2 100644
>> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
>> ? ? /* Parse current line. */
>> ? ? wordCount = chopLine(line, row);
>> ? ? if (wordCount == ArraySize(row))
>> - ? ? ? ? errAbort("Too many fields (%d max is %lu) line %d of %s",
>> wordCount, ArraySize(row),
>> + ? ? ? ? errAbort("Too many fields (%d max is %u) line %d of %s",
>> wordCount, ArraySize(row),
>> ? ? ? ? ? ? lf->lineIx, lf->fileName);
>> ? ? char *chrom = row[0];
>> ? ? unsigned int start = lineFileNeedNum(lf, row, 1);
>>
>>
>> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
>> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
>> correctly after typing 'make' in kent/src (should I be building it
>> differently?)
>>
>>
>>
>> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>>
>> cpan
>>
>> cpan shell -- CPAN exploration and modules installation (v1.9600)
>> Enter 'h' for help.
>>
>> cpan[1]> install Bio::DB::BigWig
>> CPAN: Storable loaded ok (v2.25)
>> Going to read '/homes/dbolser/.cpan/Metadata'
>> ?Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
>> Running install for module 'Bio::DB::BigWig'
>> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
>> CPAN: Digest::SHA loaded ok (v5.61)
>> CPAN: Compress::Zlib loaded ok (v2.03)
>> Checksum for
>> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
>> ok
>> CPAN: Archive::Tar loaded ok (v1.76)
>> Bio-BigFile-1.05
>> Bio-BigFile-1.05/Changes
>> Bio-BigFile-1.05/LICENSE
>> Bio-BigFile-1.05/DISCLAIMER
>> Bio-BigFile-1.05/Build.PL
>> Bio-BigFile-1.05/typemap
>> Bio-BigFile-1.05/META.yml
>> Bio-BigFile-1.05/README
>> Bio-BigFile-1.05/MANIFEST
>> Bio-BigFile-1.05/ExampleData
>> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
>> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
>> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
>> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
>> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
>> Bio-BigFile-1.05/ExampleData/refSeqTest.as
>> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
>> Bio-BigFile-1.05/bin
>> Bio-BigFile-1.05/bin/bigWigToWig.pl
>> Bio-BigFile-1.05/bin/wigToBigWig.pl
>> Bio-BigFile-1.05/bin/index_bigwigset.pl
>> Bio-BigFile-1.05/lib
>> Bio-BigFile-1.05/lib/Bio
>> Bio-BigFile-1.05/lib/Bio/DB
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
>> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
>> Bio-BigFile-1.05/t
>> Bio-BigFile-1.05/t/02.bigbed.t
>> Bio-BigFile-1.05/t/03.bigwig_high.t
>> Bio-BigFile-1.05/t/04.bigbed_high.t
>> Bio-BigFile-1.05/t/05.bigwig_set.t
>> /bin/tar: Read 9216 bytes from -
>> Bio-BigFile-1.05/t/01.bigwig.t
>> Bio-BigFile-1.05/patches
>> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
>> CPAN: File::Temp loaded ok (v0.22)
>> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
>> CPAN: CPAN::Meta loaded ok (v2.110580)
>> CPAN: Module::CoreList loaded ok (v2.46)
>> CPAN: Time::HiRes loaded ok (v1.9717)
>>
>> ?CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>>
>>
>> This module requires the compiled jkweb.a library from Jim Kent's source
>> tree.
>> If you haven't already done so, please download the source from
>> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
>> contents of the "kent/src/lib" subdirectory as directed in the README.
>> Then
>> enter the location of the "kent/src" subdirectory at the prompt below.
>> To prevent
>> this message from appearing in the future, set the environment
>> variable KENT_SRC
>> to point to the "kent/src" subdirectory.
>>
>> Please enter the location of Kent source tree:
>> /homes/dbolser/build/src/kent/src
>>
>> Created MYMETA.yml and MYMETA.json
>> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
>> Building Bio-BigFile
>> gcc -I/homes/dbolser/build/src/kent/src/inc
>> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
>> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
>> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
>> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
>> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
>> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
>> lib/Bio/DB/BigFile.c
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
>> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
>> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
>> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
>> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
>> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
>> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
>> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
>> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
>> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
>>
>> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
>> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
>> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
>> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
>> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
>> ?LDS/Bio-BigFile-1.05.tar.gz
>> ?./Build -- OK
>> CPAN: YAML loaded ok (v0.72)
>> Running Build test
>> t/01.bigwig.t ....... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at t/01.bigwig.t line 28
>> Compilation failed in require at t/01.bigwig.t line 28.
>> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
>> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 29/29 subtests
>> t/02.bigbed.t ....... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at t/02.bigbed.t line 28
>> Compilation failed in require at t/02.bigbed.t line 28.
>> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
>> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 15/15 subtests
>> t/03.bigwig_high.t .. Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at t/03.bigwig_high.t line 28.
>> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
>> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 32/32 subtests
>> t/04.bigbed_high.t .. Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
>> line 7.
>> Compilation failed in require at t/04.bigbed_high.t line 28.
>> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
>> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 35/35 subtests
>> t/05.bigwig_set.t ... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
>> line 177.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
>> line 177.
>> Compilation failed in require at t/05.bigwig_set.t line 19.
>> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
>> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
>> No subtests run
>>
>> Test Summary Report
>> -------------------
>> t/01.bigwig.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 29 tests but ran 0.
>> t/02.bigbed.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 15 tests but ran 0.
>> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 32 tests but ran 0.
>> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 35 tests but ran 0.
>> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: No plan found in TAP output
>> Files=5, Tests=0, ?1 wallclock secs ( 0.04 usr ?0.01 sys + ?0.93 cusr
>> 0.11 csys = ?1.09 CPU)
>> Result: FAIL
>> Failed 5/5 test programs. 0/0 subtests failed.
>> ?LDS/Bio-BigFile-1.05.tar.gz
>> ?./Build test -- NOT OK
>> //hint// to see the cpan-testers results for installing this module, try:
>> ?reports LDS/Bio-BigFile-1.05.tar.gz
>> Running Build install
>> ?make test had returned bad status, won't install without force
>> Failed during this command:
>> ?LDS/Bio-BigFile-1.05.tar.gz ? ? ? ? ? ? ? ? ?: make_test NO
>>
>> cpan[2]>
>>
>>
>>
>>
>>
>>
>> Any hints?
>>
>> Cheers,
>> Dan.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
>


From dan.bolser at gmail.com  Tue Mar 29 04:57:29 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 29 Mar 2011 09:57:29 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
Message-ID: <AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>

On 28 March 2011 22:26, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Hi Dan,
> There are two problems that I can see. One is a series of compiler warnings
> when compiling the Perl .XS interface file. These are likely nothing to
> worry about, but I should fix them. What versions of Perl and gcc do you
> have installed? I don't see them when I compile on my system.

gcc --version # gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
perl --version # v5.8.8 built for i386-linux-thread-multi

uname -a # Linux cricket 2.6.18-194.32.1.el5PAE #1 SMP Wed Jan 5
18:43:13 EST 2011 i686 i686 i386 GNU/Linux



I got kent from git and built it with the following commands:

cd kent/src/lib/
echo $MACHTYPE # i686-redhat-linux-gnu
export MACHTYPE=i686
make
cd ../
export KENT_SRC=`pwd`

# NOTE, both $MACHTYPE and $KENT_SRC should be defined here
cpan -i Bio::DB::BigWig # FAILS AS DESCRIBED

cd /tmp
wget http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
tar zxfv Bio-BigFile-1.05.tar.gz
cd Bio-BigFile-1.05
# PATCH  Build.PL AS DESCRIBED (add -lssl after -lz)
perl Build.PL
./Build # SEE WARNINGS AS BEFORE
./Build test # Files=5, Tests=135, Result: PASS
./Build install


Note, above I didn't patch kent to include -fPIC as suggested
previously. I don't see any noticeable difference if I do on this
arch.

It would be good if the instructions above could make it into the
Bio::DB::BigWig README, as a few people have expressed confusion about
the exact steps (the README in kent is a bit confusing, and mostly
unnecessary for the purposes of building Bio::DB::BigWig).


> The second issue is that the SSL library is not being linked in. Previously
> there was no dependency on SSL, but Jim may recently have added this to the
> BigWig library in order to allow it to read bigwig files from https servers.
> I see that you added a -lssl to Build.PL; does this make the tests work
> again?

Yup, when I add -lssl to Build.PL (as per the previous diff), the
tests pass, but I still see the warnings.

I'm sure I saw the warnings disappear when I was playing with
different versions of Bio::DB::BigWig, but now they occur without
fail... if you pardon the pun.

I have a seeking suspicion that it's related to my perl 'build kit'...
However, since I'm not sure what module versions to report, and since
you promised to fix these issues anyway, I won't dig into it.


Thanks for help, and thanks for the support on
irc://irc.freenode.net/#bioperl, without which I would have probably
give up!

Cheers,
Dan.

> Lincoln
>
> On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com> wrote:
>>
>> Hello,
>>
>> I'm trying to get Bio::DB::BigWig installed again, this time on a
>> different box.
>>
>> I installed kent from git as described here:
>> http://genome.ucsc.edu/admin/git.html
>>
>>
>> I made the following changes, similar to those described previously:
>>
>> git diff
>> diff --git a/src/inc/common.mk b/src/inc/common.mk
>> index c7fc557..5187901 100644
>> --- a/src/inc/common.mk
>> +++ b/src/inc/common.mk
>> @@ -3,7 +3,7 @@ CC=gcc
>> ?ifeq (${COPT},)
>> ? ? COPT=-O -g
>> ?endif
>> -CFLAGS=
>> +CFLAGS=-fPIC
>> ?HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
>> -DMACHTYPE_${MACHTYPE}
>> ?HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
>> -I../../../../../inc
>>
>> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> index fa2292b..acb97d2 100644
>> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
>> ? ? /* Parse current line. */
>> ? ? wordCount = chopLine(line, row);
>> ? ? if (wordCount == ArraySize(row))
>> - ? ? ? ? errAbort("Too many fields (%d max is %lu) line %d of %s",
>> wordCount, ArraySize(row),
>> + ? ? ? ? errAbort("Too many fields (%d max is %u) line %d of %s",
>> wordCount, ArraySize(row),
>> ? ? ? ? ? ? lf->lineIx, lf->fileName);
>> ? ? char *chrom = row[0];
>> ? ? unsigned int start = lineFileNeedNum(lf, row, 1);
>>
>>
>> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
>> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
>> correctly after typing 'make' in kent/src (should I be building it
>> differently?)
>>
>>
>>
>> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>>
>> cpan
>>
>> cpan shell -- CPAN exploration and modules installation (v1.9600)
>> Enter 'h' for help.
>>
>> cpan[1]> install Bio::DB::BigWig
>> CPAN: Storable loaded ok (v2.25)
>> Going to read '/homes/dbolser/.cpan/Metadata'
>> ?Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
>> Running install for module 'Bio::DB::BigWig'
>> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
>> CPAN: Digest::SHA loaded ok (v5.61)
>> CPAN: Compress::Zlib loaded ok (v2.03)
>> Checksum for
>> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
>> ok
>> CPAN: Archive::Tar loaded ok (v1.76)
>> Bio-BigFile-1.05
>> Bio-BigFile-1.05/Changes
>> Bio-BigFile-1.05/LICENSE
>> Bio-BigFile-1.05/DISCLAIMER
>> Bio-BigFile-1.05/Build.PL
>> Bio-BigFile-1.05/typemap
>> Bio-BigFile-1.05/META.yml
>> Bio-BigFile-1.05/README
>> Bio-BigFile-1.05/MANIFEST
>> Bio-BigFile-1.05/ExampleData
>> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
>> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
>> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
>> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
>> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
>> Bio-BigFile-1.05/ExampleData/refSeqTest.as
>> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
>> Bio-BigFile-1.05/bin
>> Bio-BigFile-1.05/bin/bigWigToWig.pl
>> Bio-BigFile-1.05/bin/wigToBigWig.pl
>> Bio-BigFile-1.05/bin/index_bigwigset.pl
>> Bio-BigFile-1.05/lib
>> Bio-BigFile-1.05/lib/Bio
>> Bio-BigFile-1.05/lib/Bio/DB
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
>> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
>> Bio-BigFile-1.05/t
>> Bio-BigFile-1.05/t/02.bigbed.t
>> Bio-BigFile-1.05/t/03.bigwig_high.t
>> Bio-BigFile-1.05/t/04.bigbed_high.t
>> Bio-BigFile-1.05/t/05.bigwig_set.t
>> /bin/tar: Read 9216 bytes from -
>> Bio-BigFile-1.05/t/01.bigwig.t
>> Bio-BigFile-1.05/patches
>> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
>> CPAN: File::Temp loaded ok (v0.22)
>> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
>> CPAN: CPAN::Meta loaded ok (v2.110580)
>> CPAN: Module::CoreList loaded ok (v2.46)
>> CPAN: Time::HiRes loaded ok (v1.9717)
>>
>> ?CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>>
>>
>> This module requires the compiled jkweb.a library from Jim Kent's source
>> tree.
>> If you haven't already done so, please download the source from
>> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
>> contents of the "kent/src/lib" subdirectory as directed in the README.
>> Then
>> enter the location of the "kent/src" subdirectory at the prompt below.
>> To prevent
>> this message from appearing in the future, set the environment
>> variable KENT_SRC
>> to point to the "kent/src" subdirectory.
>>
>> Please enter the location of Kent source tree:
>> /homes/dbolser/build/src/kent/src
>>
>> Created MYMETA.yml and MYMETA.json
>> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
>> Building Bio-BigFile
>> gcc -I/homes/dbolser/build/src/kent/src/inc
>> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
>> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
>> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
>> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
>> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
>> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
>> lib/Bio/DB/BigFile.c
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
>> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
>> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
>> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
>> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
>> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
>> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
>> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
>> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
>> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
>>
>> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
>> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
>> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
>> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
>> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
>> ?LDS/Bio-BigFile-1.05.tar.gz
>> ?./Build -- OK
>> CPAN: YAML loaded ok (v0.72)
>> Running Build test
>> t/01.bigwig.t ....... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at t/01.bigwig.t line 28
>> Compilation failed in require at t/01.bigwig.t line 28.
>> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
>> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 29/29 subtests
>> t/02.bigbed.t ....... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at t/02.bigbed.t line 28
>> Compilation failed in require at t/02.bigbed.t line 28.
>> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
>> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 15/15 subtests
>> t/03.bigwig_high.t .. Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at t/03.bigwig_high.t line 28.
>> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
>> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 32/32 subtests
>> t/04.bigbed_high.t .. Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
>> line 7.
>> Compilation failed in require at t/04.bigbed_high.t line 28.
>> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
>> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 35/35 subtests
>> t/05.bigwig_set.t ... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
>> line 177.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
>> line 177.
>> Compilation failed in require at t/05.bigwig_set.t line 19.
>> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
>> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
>> No subtests run
>>
>> Test Summary Report
>> -------------------
>> t/01.bigwig.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 29 tests but ran 0.
>> t/02.bigbed.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 15 tests but ran 0.
>> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 32 tests but ran 0.
>> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 35 tests but ran 0.
>> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: No plan found in TAP output
>> Files=5, Tests=0, ?1 wallclock secs ( 0.04 usr ?0.01 sys + ?0.93 cusr
>> 0.11 csys = ?1.09 CPU)
>> Result: FAIL
>> Failed 5/5 test programs. 0/0 subtests failed.
>> ?LDS/Bio-BigFile-1.05.tar.gz
>> ?./Build test -- NOT OK
>> //hint// to see the cpan-testers results for installing this module, try:
>> ?reports LDS/Bio-BigFile-1.05.tar.gz
>> Running Build install
>> ?make test had returned bad status, won't install without force
>> Failed during this command:
>> ?LDS/Bio-BigFile-1.05.tar.gz ? ? ? ? ? ? ? ? ?: make_test NO
>>
>> cpan[2]>
>>
>>
>>
>>
>>
>>
>> Any hints?
>>
>> Cheers,
>> Dan.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
>


From David.Messina at sbc.su.se  Tue Mar 29 05:11:26 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 29 Mar 2011 11:11:26 +0200
Subject: [Bioperl-l] GSoC 2011
In-Reply-To: <AANLkTim6o3bJ6NkBRmoUC5e76GaGzpjP5+xE+ZrWcEdc@mail.gmail.com>
References: <AANLkTim6o3bJ6NkBRmoUC5e76GaGzpjP5+xE+ZrWcEdc@mail.gmail.com>
Message-ID: <AANLkTi=OW4OYGwB1AWRe4TXZTXyLuENxZakArcVoAjHF@mail.gmail.com>

Hi Fei,

Glad to hear you're interested in working on BioPerl!

Just to throw in my two cents, I think it would be great to have a RAxML
wrapper in BioPerl. Although actually any of the projects you mentioned
sound like they're about the right size for a summer project.

I'm not directly involved with GSoC, so I think if you haven't already you
should take a look at our GsOC page here

    http://news.open-bio.org/news/2011/03/obf-gsoc-2011/

and get in touch with Rob Buels, our coordinator (rmb32 at cornell.edu)



Best,
Dave





On Tue, Mar 22, 2011 at 20:14, Fei Hu <hufeiyc at gmail.com> wrote:

> Hi, All.
>
> My name is Fei Hu from U. of South Carolina. I am currently a second-year
> Ph.D student in computer science focusing on gene order and sequence(DNA &
> AA) phylogeny as well as whole genome alignment. I am instreseted in
> joining
> bioperl project of GSoC 2011. I have two ideas that would like to share.
>
> My first idea is to extend the bioperl so that it can process and analysis
> gene order data using published package such as MGR, GRAPPA and distance
> estimator. This is a relatively new type of data and many great researchers
> have contributed to this type of phylogeny reconstruction (Dr. Pavel
> Penzer,
> Dr. Bernard Moret and Dr. David Sankoff).
>
> Secondly as maximum likelihood becomes more and more popular, especially
> RAxML has been widely recognized and used(over 1000 citations). I think
> it's
> time to integrate that as well as GARLI into the Bio::Tools. I extensively
> used and explored RAxML in my last publication on gene order phylogeny.
>
> Those are just my preliminary thoughts, not even a plan and any suggestion
> is greatly appreciated!!! I use perl on daily bases for data processing and
> composing testing scripts, but not much OOP involved.
>
> PS: Rest api for CIPRES is no longer available. So this following task
> can't
> be finished right now:
> Development of a
> Bio::Tools::Run::RemoteBlast<
> http://bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast>-like
> interface to CIPRES remote analyses; for more see this
> thread<http://thread.gmane.org/gmane.comp.lang.perl.bio.general/16524>
> .
>
> And Thank you all.
> Best
>
> Fei
>
> --
> *Fei Hu
> Bioinformatics Lab
> 3D-11 Swearingen Building
> U of South Carolina
> Tel: 803-397-5240*
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From tzhu at mail.bnu.edu.cn  Tue Mar 29 06:33:59 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Tue, 29 Mar 2011 18:33:59 +0800
Subject: [Bioperl-l] How to use module Bio::SeqFeature::Gene::GeneStructure?
Message-ID: <1301394839.6397.1.camel@ubuntu>

I've referred the ducument
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
It says, @transcripts = $gene->transcripts(); @exons = $gene->exons();
The object $gene should mean a Bio::SeqFeature::Gene::GeneStructure
object. But how could I get such object? I hope to see a good example.
Thank you! 


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)



From lincoln.stein at gmail.com  Tue Mar 29 09:59:22 2011
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Tue, 29 Mar 2011 09:59:22 -0400
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
	<AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>
Message-ID: <AANLkTi=Jrw3adAgigbAeG_-KT4VqLBsPBE08x_NQyOHD@mail.gmail.com>

I'll release a new version with a fixed Build.PL and README today.

Lincoln

On Tue, Mar 29, 2011 at 4:57 AM, Dan Bolser <dan.bolser at gmail.com> wrote:

> On 28 March 2011 22:26, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> > Hi Dan,
> > There are two problems that I can see. One is a series of compiler
> warnings
> > when compiling the Perl .XS interface file. These are likely nothing to
> > worry about, but I should fix them. What versions of Perl and gcc do you
> > have installed? I don't see them when I compile on my system.
>
> gcc --version # gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
> perl --version # v5.8.8 built for i386-linux-thread-multi
>
> uname -a # Linux cricket 2.6.18-194.32.1.el5PAE #1 SMP Wed Jan 5
> 18:43:13 EST 2011 i686 i686 i386 GNU/Linux
>
>
>
> I got kent from git and built it with the following commands:
>
> cd kent/src/lib/
> echo $MACHTYPE # i686-redhat-linux-gnu
> export MACHTYPE=i686
> make
> cd ../
> export KENT_SRC=`pwd`
>
> # NOTE, both $MACHTYPE and $KENT_SRC should be defined here
> cpan -i Bio::DB::BigWig # FAILS AS DESCRIBED
>
> cd /tmp
> wget
> http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> tar zxfv Bio-BigFile-1.05.tar.gz
> cd Bio-BigFile-1.05
> # PATCH  Build.PL AS DESCRIBED (add -lssl after -lz)
> perl Build.PL
> ./Build # SEE WARNINGS AS BEFORE
> ./Build test # Files=5, Tests=135, Result: PASS
> ./Build install
>
>
> Note, above I didn't patch kent to include -fPIC as suggested
> previously. I don't see any noticeable difference if I do on this
> arch.
>
> It would be good if the instructions above could make it into the
> Bio::DB::BigWig README, as a few people have expressed confusion about
> the exact steps (the README in kent is a bit confusing, and mostly
> unnecessary for the purposes of building Bio::DB::BigWig).
>
>
> > The second issue is that the SSL library is not being linked in.
> Previously
> > there was no dependency on SSL, but Jim may recently have added this to
> the
> > BigWig library in order to allow it to read bigwig files from https
> servers.
> > I see that you added a -lssl to Build.PL; does this make the tests work
> > again?
>
> Yup, when I add -lssl to Build.PL (as per the previous diff), the
> tests pass, but I still see the warnings.
>
> I'm sure I saw the warnings disappear when I was playing with
> different versions of Bio::DB::BigWig, but now they occur without
> fail... if you pardon the pun.
>
> I have a seeking suspicion that it's related to my perl 'build kit'...
> However, since I'm not sure what module versions to report, and since
> you promised to fix these issues anyway, I won't dig into it.
>
>
> Thanks for help, and thanks for the support on
> irc://irc.freenode.net/#bioperl, without which I would have probably
> give up!
>
> Cheers,
> Dan.
>
> > Lincoln
> >
> > On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com>
> wrote:
> >>
> >> Hello,
> >>
> >> I'm trying to get Bio::DB::BigWig installed again, this time on a
> >> different box.
> >>
> >> I installed kent from git as described here:
> >> http://genome.ucsc.edu/admin/git.html
> >>
> >>
> >> I made the following changes, similar to those described previously:
> >>
> >> git diff
> >> diff --git a/src/inc/common.mk b/src/inc/common.mk
> >> index c7fc557..5187901 100644
> >> --- a/src/inc/common.mk
> >> +++ b/src/inc/common.mk
> >> @@ -3,7 +3,7 @@ CC=gcc
> >>  ifeq (${COPT},)
> >>     COPT=-O -g
> >>  endif
> >> -CFLAGS=
> >> +CFLAGS=-fPIC
> >>  HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> >> -DMACHTYPE_${MACHTYPE}
> >>  HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> >> -I../../../../../inc
> >>
> >> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> index fa2292b..acb97d2 100644
> >> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
> >>     /* Parse current line. */
> >>     wordCount = chopLine(line, row);
> >>     if (wordCount == ArraySize(row))
> >> -         errAbort("Too many fields (%d max is %lu) line %d of %s",
> >> wordCount, ArraySize(row),
> >> +         errAbort("Too many fields (%d max is %u) line %d of %s",
> >> wordCount, ArraySize(row),
> >>             lf->lineIx, lf->fileName);
> >>     char *chrom = row[0];
> >>     unsigned int start = lineFileNeedNum(lf, row, 1);
> >>
> >>
> >> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> >> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> >> correctly after typing 'make' in kent/src (should I be building it
> >> differently?)
> >>
> >>
> >>
> >> Now when I try to install Bio::DB::BigWig via cpan, things look like
> this:
> >>
> >> cpan
> >>
> >> cpan shell -- CPAN exploration and modules installation (v1.9600)
> >> Enter 'h' for help.
> >>
> >> cpan[1]> install Bio::DB::BigWig
> >> CPAN: Storable loaded ok (v2.25)
> >> Going to read '/homes/dbolser/.cpan/Metadata'
> >>  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> >> Running install for module 'Bio::DB::BigWig'
> >> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >> CPAN: Digest::SHA loaded ok (v5.61)
> >> CPAN: Compress::Zlib loaded ok (v2.03)
> >> Checksum for
> >> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >> ok
> >> CPAN: Archive::Tar loaded ok (v1.76)
> >> Bio-BigFile-1.05
> >> Bio-BigFile-1.05/Changes
> >> Bio-BigFile-1.05/LICENSE
> >> Bio-BigFile-1.05/DISCLAIMER
> >> Bio-BigFile-1.05/Build.PL
> >> Bio-BigFile-1.05/typemap
> >> Bio-BigFile-1.05/META.yml
> >> Bio-BigFile-1.05/README
> >> Bio-BigFile-1.05/MANIFEST
> >> Bio-BigFile-1.05/ExampleData
> >> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> >> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> >> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> >> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> >> Bio-BigFile-1.05/bin
> >> Bio-BigFile-1.05/bin/bigWigToWig.pl
> >> Bio-BigFile-1.05/bin/wigToBigWig.pl
> >> Bio-BigFile-1.05/bin/index_bigwigset.pl
> >> Bio-BigFile-1.05/lib
> >> Bio-BigFile-1.05/lib/Bio
> >> Bio-BigFile-1.05/lib/Bio/DB
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> >> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> >> Bio-BigFile-1.05/t
> >> Bio-BigFile-1.05/t/02.bigbed.t
> >> Bio-BigFile-1.05/t/03.bigwig_high.t
> >> Bio-BigFile-1.05/t/04.bigbed_high.t
> >> Bio-BigFile-1.05/t/05.bigwig_set.t
> >> /bin/tar: Read 9216 bytes from -
> >> Bio-BigFile-1.05/t/01.bigwig.t
> >> Bio-BigFile-1.05/patches
> >> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> >> CPAN: File::Temp loaded ok (v0.22)
> >> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> >> CPAN: CPAN::Meta loaded ok (v2.110580)
> >> CPAN: Module::CoreList loaded ok (v2.46)
> >> CPAN: Time::HiRes loaded ok (v1.9717)
> >>
> >>  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >>
> >>
> >> This module requires the compiled jkweb.a library from Jim Kent's source
> >> tree.
> >> If you haven't already done so, please download the source from
> >> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build
> the
> >> contents of the "kent/src/lib" subdirectory as directed in the README.
> >> Then
> >> enter the location of the "kent/src" subdirectory at the prompt below.
> >> To prevent
> >> this message from appearing in the future, set the environment
> >> variable KENT_SRC
> >> to point to the "kent/src" subdirectory.
> >>
> >> Please enter the location of Kent source tree:
> >> /homes/dbolser/build/src/kent/src
> >>
> >> Created MYMETA.yml and MYMETA.json
> >> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> >> Building Bio-BigFile
> >> gcc -I/homes/dbolser/build/src/kent/src/inc
> >> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> >> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> >> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> >> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> >> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> >> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> >> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> >> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> >> lib/Bio/DB/BigFile.c
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> >> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> >> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> >> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> >> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> >> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> >> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> >> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> >> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> >> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
> >>
> >>
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> >> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> >> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> >> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> >> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> >> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
> >>  LDS/Bio-BigFile-1.05.tar.gz
> >>  ./Build -- OK
> >> CPAN: YAML loaded ok (v0.72)
> >> Running Build test
> >> t/01.bigwig.t ....... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at t/01.bigwig.t line 28
> >> Compilation failed in require at t/01.bigwig.t line 28.
> >> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> >> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 29/29 subtests
> >> t/02.bigbed.t ....... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at t/02.bigbed.t line 28
> >> Compilation failed in require at t/02.bigbed.t line 28.
> >> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> >> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 15/15 subtests
> >> t/03.bigwig_high.t .. Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at t/03.bigwig_high.t line 28.
> >> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> >> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 32/32 subtests
> >> t/04.bigbed_high.t .. Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> >> line 7.
> >> Compilation failed in require at t/04.bigbed_high.t line 28.
> >> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> >> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 35/35 subtests
> >> t/05.bigwig_set.t ... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> >> line 177.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> >> line 177.
> >> Compilation failed in require at t/05.bigwig_set.t line 19.
> >> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> >> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> >> No subtests run
> >>
> >> Test Summary Report
> >> -------------------
> >> t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 29 tests but ran 0.
> >> t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> >> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 32 tests but ran 0.
> >> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 35 tests but ran 0.
> >> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: No plan found in TAP output
> >> Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
> >> 0.11 csys =  1.09 CPU)
> >> Result: FAIL
> >> Failed 5/5 test programs. 0/0 subtests failed.
> >>  LDS/Bio-BigFile-1.05.tar.gz
> >>  ./Build test -- NOT OK
> >> //hint// to see the cpan-testers results for installing this module,
> try:
> >>  reports LDS/Bio-BigFile-1.05.tar.gz
> >> Running Build install
> >>  make test had returned bad status, won't install without force
> >> Failed during this command:
> >>  LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO
> >>
> >> cpan[2]>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Any hints?
> >>
> >> Cheers,
> >> Dan.
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
> > --
> > Lincoln D. Stein
> > Director, Informatics and Biocomputing Platform
> > Ontario Institute for Cancer Research
> > 101 College St., Suite 800
> > Toronto, ON, Canada M5G0A3
> > 416 673-8514
> > Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> >
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>


From lincoln.stein at gmail.com  Tue Mar 29 09:59:22 2011
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Tue, 29 Mar 2011 09:59:22 -0400
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
	<AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>
Message-ID: <AANLkTi=Jrw3adAgigbAeG_-KT4VqLBsPBE08x_NQyOHD@mail.gmail.com>

I'll release a new version with a fixed Build.PL and README today.

Lincoln

On Tue, Mar 29, 2011 at 4:57 AM, Dan Bolser <dan.bolser at gmail.com> wrote:

> On 28 March 2011 22:26, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> > Hi Dan,
> > There are two problems that I can see. One is a series of compiler
> warnings
> > when compiling the Perl .XS interface file. These are likely nothing to
> > worry about, but I should fix them. What versions of Perl and gcc do you
> > have installed? I don't see them when I compile on my system.
>
> gcc --version # gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
> perl --version # v5.8.8 built for i386-linux-thread-multi
>
> uname -a # Linux cricket 2.6.18-194.32.1.el5PAE #1 SMP Wed Jan 5
> 18:43:13 EST 2011 i686 i686 i386 GNU/Linux
>
>
>
> I got kent from git and built it with the following commands:
>
> cd kent/src/lib/
> echo $MACHTYPE # i686-redhat-linux-gnu
> export MACHTYPE=i686
> make
> cd ../
> export KENT_SRC=`pwd`
>
> # NOTE, both $MACHTYPE and $KENT_SRC should be defined here
> cpan -i Bio::DB::BigWig # FAILS AS DESCRIBED
>
> cd /tmp
> wget
> http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> tar zxfv Bio-BigFile-1.05.tar.gz
> cd Bio-BigFile-1.05
> # PATCH  Build.PL AS DESCRIBED (add -lssl after -lz)
> perl Build.PL
> ./Build # SEE WARNINGS AS BEFORE
> ./Build test # Files=5, Tests=135, Result: PASS
> ./Build install
>
>
> Note, above I didn't patch kent to include -fPIC as suggested
> previously. I don't see any noticeable difference if I do on this
> arch.
>
> It would be good if the instructions above could make it into the
> Bio::DB::BigWig README, as a few people have expressed confusion about
> the exact steps (the README in kent is a bit confusing, and mostly
> unnecessary for the purposes of building Bio::DB::BigWig).
>
>
> > The second issue is that the SSL library is not being linked in.
> Previously
> > there was no dependency on SSL, but Jim may recently have added this to
> the
> > BigWig library in order to allow it to read bigwig files from https
> servers.
> > I see that you added a -lssl to Build.PL; does this make the tests work
> > again?
>
> Yup, when I add -lssl to Build.PL (as per the previous diff), the
> tests pass, but I still see the warnings.
>
> I'm sure I saw the warnings disappear when I was playing with
> different versions of Bio::DB::BigWig, but now they occur without
> fail... if you pardon the pun.
>
> I have a seeking suspicion that it's related to my perl 'build kit'...
> However, since I'm not sure what module versions to report, and since
> you promised to fix these issues anyway, I won't dig into it.
>
>
> Thanks for help, and thanks for the support on
> irc://irc.freenode.net/#bioperl, without which I would have probably
> give up!
>
> Cheers,
> Dan.
>
> > Lincoln
> >
> > On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com>
> wrote:
> >>
> >> Hello,
> >>
> >> I'm trying to get Bio::DB::BigWig installed again, this time on a
> >> different box.
> >>
> >> I installed kent from git as described here:
> >> http://genome.ucsc.edu/admin/git.html
> >>
> >>
> >> I made the following changes, similar to those described previously:
> >>
> >> git diff
> >> diff --git a/src/inc/common.mk b/src/inc/common.mk
> >> index c7fc557..5187901 100644
> >> --- a/src/inc/common.mk
> >> +++ b/src/inc/common.mk
> >> @@ -3,7 +3,7 @@ CC=gcc
> >>  ifeq (${COPT},)
> >>     COPT=-O -g
> >>  endif
> >> -CFLAGS=
> >> +CFLAGS=-fPIC
> >>  HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> >> -DMACHTYPE_${MACHTYPE}
> >>  HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> >> -I../../../../../inc
> >>
> >> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> index fa2292b..acb97d2 100644
> >> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
> >>     /* Parse current line. */
> >>     wordCount = chopLine(line, row);
> >>     if (wordCount == ArraySize(row))
> >> -         errAbort("Too many fields (%d max is %lu) line %d of %s",
> >> wordCount, ArraySize(row),
> >> +         errAbort("Too many fields (%d max is %u) line %d of %s",
> >> wordCount, ArraySize(row),
> >>             lf->lineIx, lf->fileName);
> >>     char *chrom = row[0];
> >>     unsigned int start = lineFileNeedNum(lf, row, 1);
> >>
> >>
> >> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> >> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> >> correctly after typing 'make' in kent/src (should I be building it
> >> differently?)
> >>
> >>
> >>
> >> Now when I try to install Bio::DB::BigWig via cpan, things look like
> this:
> >>
> >> cpan
> >>
> >> cpan shell -- CPAN exploration and modules installation (v1.9600)
> >> Enter 'h' for help.
> >>
> >> cpan[1]> install Bio::DB::BigWig
> >> CPAN: Storable loaded ok (v2.25)
> >> Going to read '/homes/dbolser/.cpan/Metadata'
> >>  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> >> Running install for module 'Bio::DB::BigWig'
> >> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >> CPAN: Digest::SHA loaded ok (v5.61)
> >> CPAN: Compress::Zlib loaded ok (v2.03)
> >> Checksum for
> >> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >> ok
> >> CPAN: Archive::Tar loaded ok (v1.76)
> >> Bio-BigFile-1.05
> >> Bio-BigFile-1.05/Changes
> >> Bio-BigFile-1.05/LICENSE
> >> Bio-BigFile-1.05/DISCLAIMER
> >> Bio-BigFile-1.05/Build.PL
> >> Bio-BigFile-1.05/typemap
> >> Bio-BigFile-1.05/META.yml
> >> Bio-BigFile-1.05/README
> >> Bio-BigFile-1.05/MANIFEST
> >> Bio-BigFile-1.05/ExampleData
> >> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> >> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> >> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> >> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> >> Bio-BigFile-1.05/bin
> >> Bio-BigFile-1.05/bin/bigWigToWig.pl
> >> Bio-BigFile-1.05/bin/wigToBigWig.pl
> >> Bio-BigFile-1.05/bin/index_bigwigset.pl
> >> Bio-BigFile-1.05/lib
> >> Bio-BigFile-1.05/lib/Bio
> >> Bio-BigFile-1.05/lib/Bio/DB
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> >> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> >> Bio-BigFile-1.05/t
> >> Bio-BigFile-1.05/t/02.bigbed.t
> >> Bio-BigFile-1.05/t/03.bigwig_high.t
> >> Bio-BigFile-1.05/t/04.bigbed_high.t
> >> Bio-BigFile-1.05/t/05.bigwig_set.t
> >> /bin/tar: Read 9216 bytes from -
> >> Bio-BigFile-1.05/t/01.bigwig.t
> >> Bio-BigFile-1.05/patches
> >> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> >> CPAN: File::Temp loaded ok (v0.22)
> >> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> >> CPAN: CPAN::Meta loaded ok (v2.110580)
> >> CPAN: Module::CoreList loaded ok (v2.46)
> >> CPAN: Time::HiRes loaded ok (v1.9717)
> >>
> >>  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >>
> >>
> >> This module requires the compiled jkweb.a library from Jim Kent's source
> >> tree.
> >> If you haven't already done so, please download the source from
> >> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build
> the
> >> contents of the "kent/src/lib" subdirectory as directed in the README.
> >> Then
> >> enter the location of the "kent/src" subdirectory at the prompt below.
> >> To prevent
> >> this message from appearing in the future, set the environment
> >> variable KENT_SRC
> >> to point to the "kent/src" subdirectory.
> >>
> >> Please enter the location of Kent source tree:
> >> /homes/dbolser/build/src/kent/src
> >>
> >> Created MYMETA.yml and MYMETA.json
> >> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> >> Building Bio-BigFile
> >> gcc -I/homes/dbolser/build/src/kent/src/inc
> >> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> >> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> >> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> >> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> >> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> >> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> >> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> >> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> >> lib/Bio/DB/BigFile.c
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> >> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> >> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> >> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> >> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> >> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> >> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> >> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> >> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> >> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
> >>
> >>
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> >> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> >> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> >> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> >> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> >> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
> >>  LDS/Bio-BigFile-1.05.tar.gz
> >>  ./Build -- OK
> >> CPAN: YAML loaded ok (v0.72)
> >> Running Build test
> >> t/01.bigwig.t ....... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at t/01.bigwig.t line 28
> >> Compilation failed in require at t/01.bigwig.t line 28.
> >> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> >> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 29/29 subtests
> >> t/02.bigbed.t ....... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at t/02.bigbed.t line 28
> >> Compilation failed in require at t/02.bigbed.t line 28.
> >> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> >> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 15/15 subtests
> >> t/03.bigwig_high.t .. Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at t/03.bigwig_high.t line 28.
> >> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> >> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 32/32 subtests
> >> t/04.bigbed_high.t .. Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> >> line 7.
> >> Compilation failed in require at t/04.bigbed_high.t line 28.
> >> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> >> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 35/35 subtests
> >> t/05.bigwig_set.t ... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> >> line 177.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> >> line 177.
> >> Compilation failed in require at t/05.bigwig_set.t line 19.
> >> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> >> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> >> No subtests run
> >>
> >> Test Summary Report
> >> -------------------
> >> t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 29 tests but ran 0.
> >> t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> >> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 32 tests but ran 0.
> >> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 35 tests but ran 0.
> >> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: No plan found in TAP output
> >> Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
> >> 0.11 csys =  1.09 CPU)
> >> Result: FAIL
> >> Failed 5/5 test programs. 0/0 subtests failed.
> >>  LDS/Bio-BigFile-1.05.tar.gz
> >>  ./Build test -- NOT OK
> >> //hint// to see the cpan-testers results for installing this module,
> try:
> >>  reports LDS/Bio-BigFile-1.05.tar.gz
> >> Running Build install
> >>  make test had returned bad status, won't install without force
> >> Failed during this command:
> >>  LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO
> >>
> >> cpan[2]>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Any hints?
> >>
> >> Cheers,
> >> Dan.
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
> > --
> > Lincoln D. Stein
> > Director, Informatics and Biocomputing Platform
> > Ontario Institute for Cancer Research
> > 101 College St., Suite 800
> > Toronto, ON, Canada M5G0A3
> > 416 673-8514
> > Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> >
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>


From ravimbt at gmail.com  Mon Mar 28 05:56:58 2011
From: ravimbt at gmail.com (=?UTF-8?B?wrbigKLil4/guYvigKLgrofgrrDgrrXgrr/Rj86xzr3OueKXj+C5i+KAouKAosK2?=)
Date: Mon, 28 Mar 2011 15:26:58 +0530
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
Message-ID: <AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>

Hi Dave,

Thank you very much. It is working. I got the program code from the
following link.

http://www.bioperl.org/Core/Latest/bptutorial.html

I spent so much time on browsing, downloading and installing programs and
packages. But, it seems like the code error is the reason it dint work.
Thanks Dave.

Could you please give me the link to join this forum to see other
discussions, which would be more helpful to me? Please let me know if you
have any suggestion for me to keep learning the bioperl.

With regards,
Ravi.

2011/3/28 Dave Messina <David.Messina at sbc.su.se>

> Hi Ravi,
>
> Please make sure to "Reply All" so that everyone on the mailing list can
> follow (and add to) the discussion.
>
> If you read the first line of the exception, you'll see it states what the
> error is:
> "WebDBSeqI Error ? check query sequences!"
>
> You'd have no way of knowing this, but that ID and database combination is
> not functioning anymore, so that's why in this case you're getting an error.
> Please try using the example in the tutorial here:
>
>
> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>
> which has been updated to a different ID which should work.
>
> Sorry for the confusion! So that we can prevent other people from having
> the same issue, could you tell me where you got that example code?
>
> Dave
>
>
>
>
>
>
> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>
>> Hi Dave,
>>
>> Thanks a lot for your reply. It is really helpful. Please find the
>> screenshot after making the change you pointed out. But I am getting
>> "Exception: Bio::Root::Exception" error. I think I have to set the
>> environment variables but I am not sure how to do that. Could you please
>> guide me on this too.
>>
>> I can go to the "Environment Variable" Window in my pc. But I dont know
>> what to enter once I click "New" on that window.
>>
>> Thanks in advance.
>>
>> With regards,
>> Ravi.
>>
>>
>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>
>>> Hi Ravi,
>>>
>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>> not Bio::Seq. So your first line
>>>
>>> use Bio::Seq;
>>>
>>> should be replaced with
>>>
>>> use Bio::Perl;
>>>
>>>
>>> More examples in the BioPerl Tutorial here:
>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>
>>>
>>> Dve
>>>
>>>
>>>
>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>
>>>> Hi,
>>>>
>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>> packages
>>>> using ppm on windows 7? Please find the attachment for the error message
>>>> I
>>>> get. I would really appreciate if you help me fix this issue.
>>>>
>>>> Thanks,
>>>>
>>>> With regards,
>>>> Ravi.
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>>
>>
>


From rmb32 at cornell.edu  Tue Mar 29 17:20:41 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Tue, 29 Mar 2011 14:20:41 -0700
Subject: [Bioperl-l] Announcing OBF Summer of Code - please forward!
Message-ID: <4D924D29.3020707@cornell.edu>

Hi all,

Here's an advertising-ready announcement for OBF's Summer of Code, 
thanks to Christian Zmasek and Hilmar Lapp for their excellent writing.

Student applications are due April 8!  Please spread it widely, we need 
to reach lots of students with it!

Rob Buels
OBF GSoC 2011 Admin


============================================================

*** Please disseminate widely at your local institutions ***
*** including posting to message and job boards, so that ***
*** we reach as many students as possible.               ***

============================================================


OPEN BIOINFORMATICS FOUNDATION SUMMER OF CODE 2011

Applications due 19:00 UTC, April 8, 2010.
http://www.open-bio.org/wiki/Google_Summer_of_Code

The Open Bioinformatics Foundation Summer of Code program provides a 
unique opportunity for undergraduate, masters, and PhD students to 
obtain hands-on experience writing and extending open-source software 
for bioinformatics under the mentorship of experienced developers from 
around the world. The program is the participation of the Open 
Bioinformatics Foundation (OBF) as a mentoring organization in the 
Google Summer of Code(tm) (http://code.google.com/soc/).

Students successfully completing the 3 month program receive a $5,000 
USD stipend, and may work entirely from their home or home institution. 
  Participation is open to students from any country in the world except 
countries subject to US trade restrictions.  Each student will have at 
least one dedicated mentor to show them the ropes and help them complete 
their project.

The Open Bioinformatics Foundation is particularly seeking students 
interested in both bioinformatics (computational biology) and software 
development. Some initial project ideas are listed on the website. These 
range from Galaxy phylogenetics pipeline development in Biopython to 
lightweight sequence objects and lazy parsing in BioPerl, a DAS Server 
for large files on local filesystems, and mapping Java libraries to 
Perl/Ruby/Python using Biolib+SWIG+JNI.  All project ideas are flexible 
and many can be adjusted in scope to match the skills of the student. We 
also welcome and encourage students proposing their own project ideas; 
historically some of the most successful Summer of Code projects are 
ones proposed by the students themselves.

TO APPLY: Apply online at the Google Summer of Code website 
(http://socghop.appspot.com/), where you will also find GSoC program 
rules and eligibility requirements. The 12-day application period for 
students runs from Monday, March 28 through Friday, April 8th, 2011.

INQUIRIES:

We strongly encourage all interested students to get in touch with us 
with their ideas as early on as possible.  See the OBF GSoC page for 
contact details.

2011 OBF Summer of Code:
http://www.open-bio.org/wiki/Google_Summer_of_Code

Google Summer of Code FAQ:
http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs




From cjfields at illinois.edu  Wed Mar 30 09:58:00 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 30 Mar 2011 08:58:00 -0500
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
Message-ID: <9EDCB97E-3256-476C-AA40-EDE27BF96033@illinois.edu>

Ravi,

You can sign up for the email list here:

http://lists.open-bio.org/mailman/listinfo/bioperl-l

Once you are signed up, you should be able to post questions.

chris

On Mar 28, 2011, at 4:56 AM, ?????????????????? wrote:

> Hi Dave,
> 
> Thank you very much. It is working. I got the program code from the
> following link.
> 
> http://www.bioperl.org/Core/Latest/bptutorial.html
> 
> I spent so much time on browsing, downloading and installing programs and
> packages. But, it seems like the code error is the reason it dint work.
> Thanks Dave.
> 
> Could you please give me the link to join this forum to see other
> discussions, which would be more helpful to me? Please let me know if you
> have any suggestion for me to keep learning the bioperl.
> 
> With regards,
> Ravi.
> 
> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
> 
>> Hi Ravi,
>> 
>> Please make sure to "Reply All" so that everyone on the mailing list can
>> follow (and add to) the discussion.
>> 
>> If you read the first line of the exception, you'll see it states what the
>> error is:
>> "WebDBSeqI Error ? check query sequences!"
>> 
>> You'd have no way of knowing this, but that ID and database combination is
>> not functioning anymore, so that's why in this case you're getting an error.
>> Please try using the example in the tutorial here:
>> 
>> 
>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>> 
>> which has been updated to a different ID which should work.
>> 
>> Sorry for the confusion! So that we can prevent other people from having
>> the same issue, could you tell me where you got that example code?
>> 
>> Dave
>> 
>> 
>> 
>> 
>> 
>> 
>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>> 
>>> Hi Dave,
>>> 
>>> Thanks a lot for your reply. It is really helpful. Please find the
>>> screenshot after making the change you pointed out. But I am getting
>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>> environment variables but I am not sure how to do that. Could you please
>>> guide me on this too.
>>> 
>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>> what to enter once I click "New" on that window.
>>> 
>>> Thanks in advance.
>>> 
>>> With regards,
>>> Ravi.
>>> 
>>> 
>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>> 
>>>> Hi Ravi,
>>>> 
>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>> not Bio::Seq. So your first line
>>>> 
>>>> use Bio::Seq;
>>>> 
>>>> should be replaced with
>>>> 
>>>> use Bio::Perl;
>>>> 
>>>> 
>>>> More examples in the BioPerl Tutorial here:
>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>> 
>>>> 
>>>> Dve
>>>> 
>>>> 
>>>> 
>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>> 
>>>>> Hi,
>>>>> 
>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>> packages
>>>>> using ppm on windows 7? Please find the attachment for the error message
>>>>> I
>>>>> get. I would really appreciate if you help me fix this issue.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> With regards,
>>>>> Ravi.
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> 
>>>> 
>>>> 
>>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From dvadell at clustering.com.ar  Wed Mar 30 10:51:38 2011
From: dvadell at clustering.com.ar (Diego M. Vadell)
Date: Wed, 30 Mar 2011 11:51:38 -0300
Subject: [Bioperl-l] Newbie alert: Aligning and printing first position
Message-ID: <201103301151.38752.dvadell@clustering.com.ar>

Hi list,

    I have an alignment ( done with Bio::Tools::Run::Alignment::Clustalw ) 
that I can see ( printing $aln->match_line() along with the sequences ):

        ********* .:                                   (match_line)
.......TDDSFDTDVSSS.........[...].............   ($seq1)
SDKIIHLTDDSFDTDVLKADGA[...]EFLDANLA   ($seq2)

    It looks right ( that "[...]" is mine, it's larger ). Now I want to get 
the position of the match ( the first "T" ), which should be "7". I thought I 
needed to use something like:

my $seq = $aln->get_seq_by_pos(1);
my $loc = $seq->location_from_column(1);
say $loc;

And $loc would be 7, but it's undef. If I try to iterate from 1 to 10, I start 
getting Bio::Location::Simple objects at the 8th place. So, should I loop 
untill I location_from_column() gives me an object? Is it another way of 
finding the position of the match?

As you can see, I'm just starting with bioinformatics. Any pointer will be 
appreciated.

Thanks in advance,
 -- Diego 

From joshearl1 at hotmail.com  Wed Mar 30 11:23:21 2011
From: joshearl1 at hotmail.com (Josh Earl)
Date: Wed, 30 Mar 2011 11:23:21 -0400
Subject: [Bioperl-l] Difficulty downloading biosql schema
Message-ID: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>


Hello all,

I'm trying to download the schema for biosql, however, when I run the command:
svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql-schema

(as per the instructions @ https://github.com/biosql/biosql/blob/master/INSTALL)
I either get no response, or it times out.  I've tried this a couple of times, the last time was a few weeks ago.  Anyone know what's going on?

Here's an example error:
svn: Can't connect to host 'code.open-bio.org': Connection timed out

thanks,
~josh

Center for Genomic Sciences
(412)-359-8341

 		 	   		  

From hlapp at drycafe.net  Wed Mar 30 11:52:22 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 30 Mar 2011 11:52:22 -0400
Subject: [Bioperl-l] Difficulty downloading biosql schema
In-Reply-To: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
References: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
Message-ID: <4C1B95A9-0480-4B9B-91E2-1D35BCB568B4@drycafe.net>

(moving this to BioSQL list)
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================





From cjfields at illinois.edu  Wed Mar 30 11:54:00 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 30 Mar 2011 10:54:00 -0500
Subject: [Bioperl-l] Difficulty downloading biosql schema
In-Reply-To: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
References: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
Message-ID: <87CBA000-B964-40DA-BF35-BC229CF24BB6@illinois.edu>

BioSQL moved to github a while back:

https://github.com/biosql/biosql

(this might be better asked on the biosql-l list, which I've cc'd)

chris

On Mar 30, 2011, at 10:23 AM, Josh Earl wrote:

> 
> Hello all,
> 
> I'm trying to download the schema for biosql, however, when I run the command:
> svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql-schema
> 
> (as per the instructions @ https://github.com/biosql/biosql/blob/master/INSTALL)
> I either get no response, or it times out.  I've tried this a couple of times, the last time was a few weeks ago.  Anyone know what's going on?
> 
> Here's an example error:
> svn: Can't connect to host 'code.open-bio.org': Connection timed out
> 
> thanks,
> ~josh
> 
> Center for Genomic Sciences
> (412)-359-8341
> 
> 		 	   		  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From p.j.a.cock at googlemail.com  Wed Mar 30 11:55:49 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 30 Mar 2011 16:55:49 +0100
Subject: [Bioperl-l] Difficulty downloading biosql schema
In-Reply-To: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
References: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
Message-ID: <AANLkTi=v80WkLtJxiDu1MBLoyKD0RTR5eBhmb4NF5zO7@mail.gmail.com>

On Wed, Mar 30, 2011 at 4:23 PM, Josh Earl <joshearl1 at hotmail.com> wrote:
>
> Hello all,
>
> I'm trying to download the schema for biosql, however, when I run the command:
> svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql-schema
>
> (as per the instructions @ https://github.com/biosql/biosql/blob/master/INSTALL)
> I either get no response, or it times out. ?I've tried this a couple of times, the last
> time was a few weeks ago. ?Anyone know what's going on?
>
> Here's an example error:
> svn: Can't connect to host 'code.open-bio.org': Connection timed out
>
> thanks,
> ~josh

Hi Josh

First the code.open-bio.org has been having trouble and is being rebuilt.
Even if it did work, it would give you an out of date copy prior to the move
from SVN to git.

Secondly, the instructions you pointed to are out of date, we'll have to
fix that. Just use git:

git clone git://github.com/biosql/biosql.git

Thanks for the heads up!

Peter

P.S. There is a dedicated BioSQL mailing list.


From roy.chaudhuri at gmail.com  Wed Mar 30 11:43:35 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Wed, 30 Mar 2011 16:43:35 +0100
Subject: [Bioperl-l] Newbie alert: Aligning and printing first position
In-Reply-To: <201103301151.38752.dvadell@clustering.com.ar>
References: <201103301151.38752.dvadell@clustering.com.ar>
Message-ID: <4D934FA7.2080206@gmail.com>

Hi Diego,

Column refers to the position in the alignment, not the individual 
sequence. location_from_column therefore gives the position in the 
individual sequence that corresponds to the requested column (you get 
undef since there is a gap in the first column of the alignment for 
seq1). If I understand correctly, you want the reverse, the position in 
the alignment that corresponds to the first position in your sequence. 
For that you need the opposite function, column_from_residue_number:

my $loc=$seq->column_from_residue_number(1);

$loc will now contain 8 (not 7), since position 1 of your sequence is in 
column 8 of the alignment.

Hope this helps,
Roy.

On 30/03/2011 15:51, Diego M. Vadell wrote:
> Hi list,
>
>      I have an alignment ( done with Bio::Tools::Run::Alignment::Clustalw )
> that I can see ( printing $aln->match_line() along with the sequences ):
>
>          ********* .:                                   (match_line)
> .......TDDSFDTDVSSS.........[...].............   ($seq1)
> SDKIIHLTDDSFDTDVLKADGA[...]EFLDANLA   ($seq2)
>
>      It looks right ( that "[...]" is mine, it's larger ). Now I want to get
> the position of the match ( the first "T" ), which should be "7". I thought I
> needed to use something like:
>
> my $seq = $aln->get_seq_by_pos(1);
> my $loc = $seq->location_from_column(1);
> say $loc;
>
> And $loc would be 7, but it's undef. If I try to iterate from 1 to 10, I start
> getting Bio::Location::Simple objects at the 8th place. So, should I loop
> untill I location_from_column() gives me an object? Is it another way of
> finding the position of the match?
>
> As you can see, I'm just starting with bioinformatics. Any pointer will be
> appreciated.
>
> Thanks in advance,
>   -- Diego
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From zheboyang at gmail.com  Thu Mar 31 08:28:53 2011
From: zheboyang at gmail.com (boyang zhe)
Date: Thu, 31 Mar 2011 14:28:53 +0200
Subject: [Bioperl-l] blast best hit
Message-ID: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>

Hi,

I just want to parse the blast results ,and get the best hit.

One way is to parse the results as usual, then get the first hit and exit
the loop.

I checked the bioperl document, and find that there is a method
best_hit_only in Bio::SearchIO::blast.pm.
But it only return 1/0. So my question is how to use this method to get the
best hit.

Thank you very much!

Boyang

From dvadell at clustering.com.ar  Thu Mar 31 08:59:46 2011
From: dvadell at clustering.com.ar (Diego M. Vadell)
Date: Thu, 31 Mar 2011 09:59:46 -0300
Subject: [Bioperl-l] Newbie alert: Aligning and printing first position
In-Reply-To: <4D934FA7.2080206@gmail.com>
References: <201103301151.38752.dvadell@clustering.com.ar>
	<4D934FA7.2080206@gmail.com>
Message-ID: <201103311000.36567.dvadell@clustering.com.ar>

Hi Roy,

  Thanks!! I can't beleive I didn't see that method in the documentation. 
Thank you very much. It worked perfectly.

Cheers,
 -- Diego

On Wednesday, March 30, 2011 12:43:35 pm Roy Chaudhuri wrote:
> Hi Diego,
> 
> Column refers to the position in the alignment, not the individual
> sequence. location_from_column therefore gives the position in the
> individual sequence that corresponds to the requested column (you get
> undef since there is a gap in the first column of the alignment for
> seq1). If I understand correctly, you want the reverse, the position in
> the alignment that corresponds to the first position in your sequence.
> For that you need the opposite function, column_from_residue_number:
> 
> my $loc=$seq->column_from_residue_number(1);
> 
> $loc will now contain 8 (not 7), since position 1 of your sequence is in
> column 8 of the alignment.
> 
> Hope this helps,
> Roy.
> 
> On 30/03/2011 15:51, Diego M. Vadell wrote:
> > Hi list,
> > 
> >      I have an alignment ( done with Bio::Tools::Run::Alignment::Clustalw
> >      )
> > 
> > that I can see ( printing $aln->match_line() along with the sequences ):
> >          ********* .:                                   (match_line)
> > 
> > .......TDDSFDTDVSSS.........[...].............   ($seq1)
> > SDKIIHLTDDSFDTDVLKADGA[...]EFLDANLA   ($seq2)
> > 
> >      It looks right ( that "[...]" is mine, it's larger ). Now I want to
> >      get
> > 
> > the position of the match ( the first "T" ), which should be "7". I
> > thought I needed to use something like:
> > 
> > my $seq = $aln->get_seq_by_pos(1);
> > my $loc = $seq->location_from_column(1);
> > say $loc;
> > 
> > And $loc would be 7, but it's undef. If I try to iterate from 1 to 10, I
> > start getting Bio::Location::Simple objects at the 8th place. So, should
> > I loop untill I location_from_column() gives me an object? Is it another
> > way of finding the position of the match?
> > 
> > As you can see, I'm just starting with bioinformatics. Any pointer will
> > be appreciated.
> > 
> > Thanks in advance,
> > 
> >   -- Diego
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l

From bosborne11 at verizon.net  Thu Mar 31 09:04:22 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Thu, 31 Mar 2011 09:04:22 -0400
Subject: [Bioperl-l] blast best hit
In-Reply-To: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
References: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
Message-ID: <A29F9EB5-BEC6-4DF3-924F-F8F98F96C6F1@verizon.net>

Boyang,

You can sort the hits, by any criterion you want:

my @hits = $result->hits;
@hits = sort { $a-> bits <=> $b->bits } @hits;

BIO

On Mar 31, 2011, at 8:28 AM, boyang zhe wrote:

> Hi,
> 
> I just want to parse the blast results ,and get the best hit.
> 
> One way is to parse the results as usual, then get the first hit and exit
> the loop.
> 
> I checked the bioperl document, and find that there is a method
> best_hit_only in Bio::SearchIO::blast.pm.
> But it only return 1/0. So my question is how to use this method to get the
> best hit.
> 
> Thank you very much!
> 
> Boyang
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From jordi.durban at gmail.com  Thu Mar 31 10:23:54 2011
From: jordi.durban at gmail.com (Jordi Durban)
Date: Thu, 31 Mar 2011 16:23:54 +0200
Subject: [Bioperl-l] blast best hit
In-Reply-To: <A29F9EB5-BEC6-4DF3-924F-F8F98F96C6F1@verizon.net>
References: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
	<A29F9EB5-BEC6-4DF3-924F-F8F98F96C6F1@verizon.net>
Message-ID: <AANLkTimiAanHL89eJ3uKgnGXKbcbJh+jBmw6MRs1VC1t@mail.gmail.com>

Hi,
I did a pair of scripts to parse a blastxml report. I'd like know your
opinion.
First I obtained a file with tab separated results (whatever you want) from
the blast results according to some Bioperl modules as SearchIO. That is:
hit_name    query_name    e-value    score
hit_name    query-name   e-value     score
.
.

Then, I parse that file as an array where:
foreach my $line ($array[0]){ ###### best hit
        next if $seen {$line}++; ##### non-repeated lines
        push @unique , $line[1]; ### best hit outcome in a new array
       }

I hope this helps and I look forward some opinions.






2011/3/31 Brian Osborne <bosborne11 at verizon.net>

> Boyang,
>
> You can sort the hits, by any criterion you want:
>
> my @hits = $result->hits;
> @hits = sort { $a-> bits <=> $b->bits } @hits;
>
> BIO
>
> On Mar 31, 2011, at 8:28 AM, boyang zhe wrote:
>
> > Hi,
> >
> > I just want to parse the blast results ,and get the best hit.
> >
> > One way is to parse the results as usual, then get the first hit and exit
> > the loop.
> >
> > I checked the bioperl document, and find that there is a method
> > best_hit_only in Bio::SearchIO::blast.pm.
> > But it only return 1/0. So my question is how to use this method to get
> the
> > best hit.
> >
> > Thank you very much!
> >
> > Boyang
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Jordi

From fs5 at sanger.ac.uk  Thu Mar 31 10:23:33 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 31 Mar 2011 15:23:33 +0100
Subject: [Bioperl-l] blast best hit
In-Reply-To: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
References: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
Message-ID: <1301581413.12411.188.camel@deskpro15336.internal.sanger.ac.uk>

Yes, best_hit_only is a boolean that can be set to true if you only want
one hit to be returned from the stream of hits (the best hit). I have
never actualyl used this one but you shoud be able to set it in the
constructor as in:
my $blast = Bio::SearchIO->new( ...., -best_hit_only => 1 )



Frank

On Thu, 2011-03-31 at 14:28 +0200, boyang zhe wrote:
> Hi,
> 
> I just want to parse the blast results ,and get the best hit.
> 
> One way is to parse the results as usual, then get the first hit and exit
> the loop.
> 
> I checked the bioperl document, and find that there is a method
> best_hit_only in Bio::SearchIO::blast.pm.
> But it only return 1/0. So my question is how to use this method to get the
> best hit.
> 
> Thank you very much!
> 
> Boyang
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From fs5 at sanger.ac.uk  Thu Mar 31 11:06:41 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 31 Mar 2011 16:06:41 +0100
Subject: [Bioperl-l] blast best hit
In-Reply-To: <AANLkTimXj+D8VQO_Mb4vpgfadXqFfgD1dHQL+fwCMsX5@mail.gmail.com>
References: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
	<1301581413.12411.188.camel@deskpro15336.internal.sanger.ac.uk>
	<AANLkTimXj+D8VQO_Mb4vpgfadXqFfgD1dHQL+fwCMsX5@mail.gmail.com>
Message-ID: <1301584001.12411.202.camel@deskpro15336.internal.sanger.ac.uk>

Hi Boyang,

With best_hit_only set to "true" (as you have done now) you should be
able to use the usual way of parsing the BLAST report with 

while (my $result = $blast_io->next_result) {
  my $hit = $result->next_hit;
  ... (do something with the hit)
}

Because there should be only one hit now. 'best_hit_only' is a flag, an
indicator that tells the parser to limit the output to the best hit. It
does not itself return any hits.

Even if you used the 

while (my $hit=$result->next_hit){..

inner loop (as in the BioPerl HOWTOs) you should now only ever get one
hit retunred from that loop, which is the best hit for the result. I
haven't tried this but it should work.

Personally, I'd not use this option and rather sort or filter the hits
because tomorrow you might want to find out what the next best hit
actually was and how close the e-values and bits were or something like
that. 

Hope this helps,

Frank


On Thu, 2011-03-31 at 16:43 +0200, boyang zhe wrote:
> I try this at the constructor
> 
> my $blast_io = Bio::SearchIO->new(-file => 'test', -format => 'blast',
> -best_hit_only => 1);
> 
> What I need to do in the following steps? It seems that setting
> best_hit_only or not does not change the way of blast parser working.
> 
> In my opinion, if we can use it as a similar way following, it will be
> much better.
> 
> my $blast_io = Bio::SearchIO->new(-file => 'test', -format => 'blast',
> -best_hit_only => 1);
> 
> while (my $blast_result = $blast_io->next_result()) {
>       my $best_hit = $blast_result->best_hit_only();  # just assume it
> working here; in fact, it does not work
>       my $best_hit_name = $best_hit->name();
>       ...................................
> }
> 
> thank you !
> 
> On Thu, Mar 31, 2011 at 4:23 PM, Frank Schwach <fs5 at sanger.ac.uk>
> wrote:
>         Yes, best_hit_only is a boolean that can be set to true if you
>         only want
>         one hit to be returned from the stream of hits (the best hit).
>         I have
>         never actualyl used this one but you shoud be able to set it
>         in the
>         constructor as in:
>         my $blast = Bio::SearchIO->new( ...., -best_hit_only => 1 )
>         
>         
>         
>         Frank
>         
>         
>         On Thu, 2011-03-31 at 14:28 +0200, boyang zhe wrote:
>         > Hi,
>         >
>         > I just want to parse the blast results ,and get the best
>         hit.
>         >
>         > One way is to parse the results as usual, then get the first
>         hit and exit
>         > the loop.
>         >
>         > I checked the bioperl document, and find that there is a
>         method
>         > best_hit_only in Bio::SearchIO::blast.pm.
>         > But it only return 1/0. So my question is how to use this
>         method to get the
>         > best hit.
>         >
>         > Thank you very much!
>         >
>         > Boyang
>         
>         
>         > _______________________________________________
>         > Bioperl-l mailing list
>         > Bioperl-l at lists.open-bio.org
>         > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>         
>         
>         
>         
>         --
>          The Wellcome Trust Sanger Institute is operated by Genome
>         Research
>          Limited, a charity registered in England with number 1021457
>         and a
>          company registered in England with number 2742969, whose
>         registered
>          office is 215 Euston Road, London, NW1 2BE.
> 



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From suy at big.ac.cn  Thu Mar 31 03:24:55 2011
From: suy at big.ac.cn (suy)
Date: Thu, 31 Mar 2011 15:24:55 +0800
Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
Message-ID: <201103311524549534382@big.ac.cn>

I want to use Bio::Tools::HMM, but I can not find it in bioperl 1.6.1. Could anyone tell me how to do it ? 

2011-03-31 



suy 

From cjfields at illinois.edu  Thu Mar 31 13:01:13 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 31 Mar 2011 12:01:13 -0500
Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
In-Reply-To: <201103311524549534382@big.ac.cn>
References: <201103311524549534382@big.ac.cn>
Message-ID: <93E13DE0-5888-4B5C-AC9D-F68623D0D891@illinois.edu>

It's now in it's own distribution, along with the related C code.  See:

https://github.com/bioperl/Bio-Tools-HMM

It hasn't been released to CPAN yet, and (IIRC) it may be failing some tests.

chris

On Mar 31, 2011, at 2:24 AM, suy wrote:

> I want to use Bio::Tools::HMM, but I can not find it in bioperl 1.6.1. Could anyone tell me how to do it ? 
> 
> 2011-03-31 
> 
> 
> 
> suy 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From David.Messina at sbc.su.se  Thu Mar 31 13:07:54 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 31 Mar 2011 19:07:54 +0200
Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
In-Reply-To: <201103311524549534382@big.ac.cn>
References: <201103311524549534382@big.ac.cn>
Message-ID: <AANLkTin2qe1V=2swW1qd8O=s8eQTi5p1LDHc-=sViKPT@mail.gmail.com>

It's distributed separately from BioPerl now. You can get it here:

https://github.com/bioperl/Bio-Tools-HMM


Dave



On Thu, Mar 31, 2011 at 09:24, suy <suy at big.ac.cn> wrote:

> I want to use Bio::Tools::HMM, but I can not find it in bioperl 1.6.1.
> Could anyone tell me how to do it ?
>
> 2011-03-31
>
>
>
> suy
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From Kevin.M.Brown at asu.edu  Thu Mar 31 14:22:06 2011
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Thu, 31 Mar 2011 11:22:06 -0700
Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
In-Reply-To: <201103311524549534382@big.ac.cn>
References: <201103311524549534382@big.ac.cn>
Message-ID: <1A4207F8295607498283FE9E93B775B40781779B@EX02.asurite.ad.asu.edu>

https://github.com/bioperl/Bio-Tools-HMM

"moved Bio::Tools::HMM and Bio::Ext::HMM into their own distro, got them
compiling cleanly. tests not passing yet
svn path=/Bio-Tools-HMM/trunk/; revision=15966"

Kevin Brown
Center for Innovations in Medicine
Biodesign Institute
Arizona State University 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of suy
> Sent: Thursday, March 31, 2011 12:25 AM
> To: bioperl-l
> Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
> 
> I want to use Bio::Tools::HMM, but I can not find it in bioperl 1.6.1.
> Could anyone tell me how to do it ?
> 
> 2011-03-31
> 
> 
> 
> suy
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From David.Messina at sbc.su.se  Thu Mar 31 15:43:14 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 31 Mar 2011 21:43:14 +0200
Subject: [Bioperl-l] Old docs cleanup (was Re: Bioperl installation doubt)
Message-ID: <AANLkTikzx+iP6ws0CpwEEA2USiLwYVHTHjZU8KO+3vMo@mail.gmail.com>

Hi,

Just to clarify:

Brian, is it okay with you if I go ahead and remove the Core/ directory from
the website? (and okay with everyone else, too, for that matter? I haven't
heard any nays so far.)


Dave



On Tue, Mar 29, 2011 at 00:40, Chris Fields <cjfields at illinois.edu> wrote:

> Brian,
>
> I think this was started:
>
> http://www.bioperl.org/wiki/Bptutorial.pl
>
> It certainly could be cleaned up, organized, and updated (that and the
> FAQ).  Makes sense to have it as a HOWTO or maybe split it into several
> HOWTOs.  Maybe even combine it with the beginner's HOWTO into various
> sections?
>
> chris
>
> On Mar 28, 2011, at 3:43 PM, Brian Osborne wrote:
>
> > Chris,
> >
> > I'll get started on dissembling bptutorial. There's certainly useful text
> in there but there's also duplicated or outdated material. Looks like there
> are 3 options for any given section:
> >
> > - put it into an existing HOWTO
> > - make it into a new HOWTO
> > - delete it
> >
> > BIO
> >
> > On Mar 28, 2011, at 9:27 AM, Chris Fields wrote:
> >
> >> Dave,
> >>
> >> +1 on removing old docs to prevent confusion.  Or, alternatively, +1 to
> syncing those to current docs (though I think decreasing the replication
> effort in keeping docs up-to-date is probably the best tact).
> >>
> >> chris
> >>
> >> On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:
> >>
> >>>>
> >>>> Thank you very much. It is working. I got the program code from the
> >>>> following link.
> >>>>
> >>>> http://www.bioperl.org/Core/Latest/bptutorial.html
> >>>
> >>>
> >>> Aha, okay. You got there from Google, I guess? That is *way* out of
> date.
> >>>
> >>> To the other core devs, in order to prevent this confusion in the
> future,
> >>> I'd like to delete the Core/ directory from our website since it's been
> >>> superseded at this point by other docs and is not current. I intend to
> put
> >>> up a ticket at Redmine, but I will wait a bit before doing so to allow
> time
> >>> for people to see this and comment ? please do speak up if there's good
> >>> reason to keep it.
> >>>
> >>>
> >>> Could you please give me the link to join this forum to see other
> >>>> discussions, which would be more helpful to me?
> >>>>
> >>>
> >>> Sure, you can sign up for the mailing list here:
> >>>
> >>> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
> >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>>
> >>> And the archives are also searchable:
> >>>
> >>>  http://news.gmane.org/gmane.comp.lang.perl.bio.general
> >>>
> >>>
> >>> Please let me know if you have any suggestion for me to keep learning
> the
> >>>> bioperl.
> >>>
> >>>
> >>> I would also suggest reading the (current) tutorial and HOWTOs at
> >>> www.bioperl.org . Lots of good links on the main page there,
> particularly
> >>> under the Documentation heading.
> >>>
> >>>
> >>> Dave
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>> With regards,
> >>>> Ravi.
> >>>>
> >>>>
> >>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
> >>>>
> >>>>> Hi Ravi,
> >>>>>
> >>>>> Please make sure to "Reply All" so that everyone on the mailing list
> can
> >>>>> follow (and add to) the discussion.
> >>>>>
> >>>>> If you read the first line of the exception, you'll see it states
> what the
> >>>>> error is:
> >>>>> "WebDBSeqI Error ? check query sequences!"
> >>>>>
> >>>>> You'd have no way of knowing this, but that ID and database
> combination is
> >>>>> not functioning anymore, so that's why in this case you're getting an
> error.
> >>>>> Please try using the example in the tutorial here:
> >>>>>
> >>>>>
> >>>>>
> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
> >>>>>
> >>>>> which has been updated to a different ID which should work.
> >>>>>
> >>>>> Sorry for the confusion! So that we can prevent other people from
> having
> >>>>> the same issue, could you tell me where you got that example code?
> >>>>>
> >>>>> Dave
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
> >>>>>
> >>>>>> Hi Dave,
> >>>>>>
> >>>>>> Thanks a lot for your reply. It is really helpful. Please find the
> >>>>>> screenshot after making the change you pointed out. But I am getting
> >>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
> >>>>>> environment variables but I am not sure how to do that. Could you
> please
> >>>>>> guide me on this too.
> >>>>>>
> >>>>>> I can go to the "Environment Variable" Window in my pc. But I dont
> know
> >>>>>> what to enter once I click "New" on that window.
> >>>>>>
> >>>>>> Thanks in advance.
> >>>>>>
> >>>>>> With regards,
> >>>>>> Ravi.
> >>>>>>
> >>>>>>
> >>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
> >>>>>>
> >>>>>>> Hi Ravi,
> >>>>>>>
> >>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl
> module,
> >>>>>>> not Bio::Seq. So your first line
> >>>>>>>
> >>>>>>> use Bio::Seq;
> >>>>>>>
> >>>>>>> should be replaced with
> >>>>>>>
> >>>>>>> use Bio::Perl;
> >>>>>>>
> >>>>>>>
> >>>>>>> More examples in the BioPerl Tutorial here:
> >>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
> >>>>>>>
> >>>>>>>
> >>>>>>> Dve
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
> >>>>>>>
> >>>>>>>> Hi,
> >>>>>>>>
> >>>>>>>> Could you please help me installing bioperl-db, bioperl-run &
> other
> >>>>>>>> packages
> >>>>>>>> using ppm on windows 7? Please find the attachment for the error
> >>>>>>>> message I
> >>>>>>>> get. I would really appreciate if you help me fix this issue.
> >>>>>>>>
> >>>>>>>> Thanks,
> >>>>>>>>
> >>>>>>>> With regards,
> >>>>>>>> Ravi.
> >>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> Bioperl-l mailing list
> >>>>>>>> Bioperl-l at lists.open-bio.org
> >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>


From cjfields at illinois.edu  Thu Mar 31 15:49:08 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 31 Mar 2011 14:49:08 -0500
Subject: [Bioperl-l] Old docs cleanup (was Re: Bioperl installation
	doubt)
In-Reply-To: <AANLkTikzx+iP6ws0CpwEEA2USiLwYVHTHjZU8KO+3vMo@mail.gmail.com>
References: <AANLkTikzx+iP6ws0CpwEEA2USiLwYVHTHjZU8KO+3vMo@mail.gmail.com>
Message-ID: <1D3D2910-F1F9-40A1-9A39-656D3DF17847@illinois.edu>

+1 from me.  Go ahead.  Old misleading documentation is bad to have around.

chris

On Mar 31, 2011, at 2:43 PM, Dave Messina wrote:

> Hi,
> 
> Just to clarify:
> 
> Brian, is it okay with you if I go ahead and remove the Core/ directory from
> the website? (and okay with everyone else, too, for that matter? I haven't
> heard any nays so far.)
> 
> 
> Dave
> 
> 
> 
> On Tue, Mar 29, 2011 at 00:40, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Brian,
>> 
>> I think this was started:
>> 
>> http://www.bioperl.org/wiki/Bptutorial.pl
>> 
>> It certainly could be cleaned up, organized, and updated (that and the
>> FAQ).  Makes sense to have it as a HOWTO or maybe split it into several
>> HOWTOs.  Maybe even combine it with the beginner's HOWTO into various
>> sections?
>> 
>> chris
>> 
>> On Mar 28, 2011, at 3:43 PM, Brian Osborne wrote:
>> 
>>> Chris,
>>> 
>>> I'll get started on dissembling bptutorial. There's certainly useful text
>> in there but there's also duplicated or outdated material. Looks like there
>> are 3 options for any given section:
>>> 
>>> - put it into an existing HOWTO
>>> - make it into a new HOWTO
>>> - delete it
>>> 
>>> BIO
>>> 
>>> On Mar 28, 2011, at 9:27 AM, Chris Fields wrote:
>>> 
>>>> Dave,
>>>> 
>>>> +1 on removing old docs to prevent confusion.  Or, alternatively, +1 to
>> syncing those to current docs (though I think decreasing the replication
>> effort in keeping docs up-to-date is probably the best tact).
>>>> 
>>>> chris
>>>> 
>>>> On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:
>>>> 
>>>>>> 
>>>>>> Thank you very much. It is working. I got the program code from the
>>>>>> following link.
>>>>>> 
>>>>>> http://www.bioperl.org/Core/Latest/bptutorial.html
>>>>> 
>>>>> 
>>>>> Aha, okay. You got there from Google, I guess? That is *way* out of
>> date.
>>>>> 
>>>>> To the other core devs, in order to prevent this confusion in the
>> future,
>>>>> I'd like to delete the Core/ directory from our website since it's been
>>>>> superseded at this point by other docs and is not current. I intend to
>> put
>>>>> up a ticket at Redmine, but I will wait a bit before doing so to allow
>> time
>>>>> for people to see this and comment ? please do speak up if there's good
>>>>> reason to keep it.
>>>>> 
>>>>> 
>>>>> Could you please give me the link to join this forum to see other
>>>>>> discussions, which would be more helpful to me?
>>>>>> 
>>>>> 
>>>>> Sure, you can sign up for the mailing list here:
>>>>> 
>>>>> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> 
>>>>> 
>>>>> And the archives are also searchable:
>>>>> 
>>>>> http://news.gmane.org/gmane.comp.lang.perl.bio.general
>>>>> 
>>>>> 
>>>>> Please let me know if you have any suggestion for me to keep learning
>> the
>>>>>> bioperl.
>>>>> 
>>>>> 
>>>>> I would also suggest reading the (current) tutorial and HOWTOs at
>>>>> www.bioperl.org . Lots of good links on the main page there,
>> particularly
>>>>> under the Documentation heading.
>>>>> 
>>>>> 
>>>>> Dave
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> With regards,
>>>>>> Ravi.
>>>>>> 
>>>>>> 
>>>>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>>>>>> 
>>>>>>> Hi Ravi,
>>>>>>> 
>>>>>>> Please make sure to "Reply All" so that everyone on the mailing list
>> can
>>>>>>> follow (and add to) the discussion.
>>>>>>> 
>>>>>>> If you read the first line of the exception, you'll see it states
>> what the
>>>>>>> error is:
>>>>>>> "WebDBSeqI Error ? check query sequences!"
>>>>>>> 
>>>>>>> You'd have no way of knowing this, but that ID and database
>> combination is
>>>>>>> not functioning anymore, so that's why in this case you're getting an
>> error.
>>>>>>> Please try using the example in the tutorial here:
>>>>>>> 
>>>>>>> 
>>>>>>> 
>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>>>>>> 
>>>>>>> which has been updated to a different ID which should work.
>>>>>>> 
>>>>>>> Sorry for the confusion! So that we can prevent other people from
>> having
>>>>>>> the same issue, could you tell me where you got that example code?
>>>>>>> 
>>>>>>> Dave
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>>>>>> 
>>>>>>>> Hi Dave,
>>>>>>>> 
>>>>>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>>>>>> screenshot after making the change you pointed out. But I am getting
>>>>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>>>>>> environment variables but I am not sure how to do that. Could you
>> please
>>>>>>>> guide me on this too.
>>>>>>>> 
>>>>>>>> I can go to the "Environment Variable" Window in my pc. But I dont
>> know
>>>>>>>> what to enter once I click "New" on that window.
>>>>>>>> 
>>>>>>>> Thanks in advance.
>>>>>>>> 
>>>>>>>> With regards,
>>>>>>>> Ravi.
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>>>>>> 
>>>>>>>>> Hi Ravi,
>>>>>>>>> 
>>>>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl
>> module,
>>>>>>>>> not Bio::Seq. So your first line
>>>>>>>>> 
>>>>>>>>> use Bio::Seq;
>>>>>>>>> 
>>>>>>>>> should be replaced with
>>>>>>>>> 
>>>>>>>>> use Bio::Perl;
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> More examples in the BioPerl Tutorial here:
>>>>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> Dve
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>>>>>> 
>>>>>>>>>> Hi,
>>>>>>>>>> 
>>>>>>>>>> Could you please help me installing bioperl-db, bioperl-run &
>> other
>>>>>>>>>> packages
>>>>>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>>>>>> message I
>>>>>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>>>>>> 
>>>>>>>>>> Thanks,
>>>>>>>>>> 
>>>>>>>>>> With regards,
>>>>>>>>>> Ravi.
>>>>>>>>>> 
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Bioperl-l mailing list
>>>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From rmb32 at cornell.edu  Thu Mar 31 17:58:52 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 31 Mar 2011 14:58:52 -0700
Subject: [Bioperl-l] Reminder: GSoC proposals due in 1 week
Message-ID: <4D94F91C.1080005@cornell.edu>

Hi all,

Just a reminder, Google Summer of Code student applications are due April 8!

If you're a student planning to apply to GSoC with OBF, it's very much 
in your best interest to write your proposal *early*, like now, and get 
it into the hands of the developers and mentors on your subproject 
(BioPerl/Ruby/Python/etc) so that they can give you some feedback on it.

The final proposals must, of course, still be submitted to Google 
through the GSoC web application, as described on the main GSoC site 
(http://www.google-melange.com/gsoc/homepage/google/gsoc2011).

Rob Buels
OBF GSoC 2011 Administrator



From rmb32 at cornell.edu  Thu Mar 31 18:04:49 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 31 Mar 2011 15:04:49 -0700
Subject: [Bioperl-l] GSoC call for mentors
Message-ID: <4D94FA81.5090701@cornell.edu>

Hi all,

For current developers on OBF projects:

If you would not mind being a mentor to a Summer of Code student this 
summer, please make sure you sign up as an OBF mentor in the GSoC web 
app.  There's a link under "mentors: apply now!" midway down the page at 
http://www.google-melange.com/.  If you didn't do last year's summer of 
code, it would be a good idea to drop me an email introducing yourself, 
as well, or I won't know whether to approve your request. :-)

Being signed up as an OBF GSoC mentor will give you access to the 
student proposals, as they come in, and the ability to comment on them 
and assign scores to the ones you think show the most promise.

If you sign up as a mentor, please also add yourself to the two OBF GSoC 
mailing lists: OBF-GSoC and OBF-GSoC-mentors

OBF-GSoC list: http://lists.open-bio.org/mailman/listinfo/gsoc
OBF mentors:   http://lists.open-bio.org/mailman/listinfo/gsoc-mentors


Thanks in advance!

Rob

---
Robert Buels
OBF GSoC 2011 Administrator


From zuz17 at psu.edu  Thu Mar 31 18:18:59 2011
From: zuz17 at psu.edu (Zhenguo Zhang)
Date: Thu, 31 Mar 2011 18:18:59 -0400
Subject: [Bioperl-l] FW: How to specify color for each feature in a track?
In-Reply-To: 1301604855l.1593384l.0l@psu.edu
References: <1301604855l.1593384l.0l@psu.edu>
Message-ID: <1301609939l.901330l.0l@psu.edu>

Dear Dr. Stein,

Sorry for interruption. I found the problems, I used
$f->get_tag_values('color'); to return the tag value, it is not correct. The
list context should be provided. It is my mistake. Thanks.

Best wishes!

Zhenguo

---------------- Forwarded Message ----------------
From: "Zhenguo Zhang" <zuz17 at psu.edu>
Date: Thu, Mar 31, 2011 04:54 PM
Subject: How to specify color for each feature in a track?
To: lstein at cshl.edu, bioperl-l at lists.open-bio.org

Dear Dr. Stein,

I am using your excellent module Bio::Graphics for
programming to show protein domains. I want to put all the domains for a
sequence into one track, and give each domain (one feature here) one designated
color. The following is the cold to add_track:


 75        
$panel->add_track($seq,
 78                 -glyph    =>  'segments',
 81                 -bgcolor  => sub {
 82                     my $f = shift;
 87                     return $f->get_tag_values('color');
 88                 },
 89                 -fgcolor  => 'black',
 90                 -font2color => 'red',
 91                 -key      => "$seq",
 92                 -label    => 1,
 93                 -bump     => +1,
 94                 -height   => 8,
 95                 -description => 1,
 96 #               -part_label_merge => 1
 97                 );

Here $seq is an array reference, each element being one domain feature. I
specify the -bgcolor based on the tag 'color'  defined when domain feature was
constructed. However, it does not work. All the domains in all sequences show
the same color. Based on the document, the -glyph can be changed by calling
back the anonymous functions (I have not tried this). The color might be
changed in a similar way. Thank you in advance!

Best regards!

Zhenguo

**************************************************************
Zhenguo Zhang
Postdoctoral Scholar
Institute of Molecular Evolutionary Genetics
Penn State University
312 Mueller Lab
University Park, PA 16802
Tel: 814-865-2796
Homepage: <http://www.personal.psu.edu/zuz17/>
Lab page:  <http://homes.bio.psu.edu/people/Faculty/Nei/>




**************************************************************
Zhenguo Zhang
Postdoctoral Scholar
Institute of Molecular Evolutionary Genetics
Penn State University
312 Mueller Lab
University Park, PA 16802
Tel: 814-865-2796
Homepage: <http://www.personal.psu.edu/zuz17/>
Lab page:  <http://homes.bio.psu.edu/people/Faculty/Nei/>




From scott at scottcain.net  Thu Mar 31 19:13:06 2011
From: scott at scottcain.net (Scott Cain)
Date: Thu, 31 Mar 2011 19:13:06 -0400
Subject: [Bioperl-l] git help
Message-ID: <AANLkTin9BRdaSY_p-5rKSCFvpUr+rfCSZ8hjVTgyhxC5@mail.gmail.com>

Hi all,

I just want to know if it is safe for me to commit.  Here is what git
said to me:

scott-cains-macbook-pro:bioperl-live cain$ git commit
# On branch master
# Your branch is behind 'origin/master' by 47 commits, and can be
fast-forwarded.
#
# Changed but not updated:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#	modified:   Bio/DB/GFF.pm
#	modified:   Bio/FeatureIO/gff.pm
#	modified:   scripts/Bio-DB-GFF/bulk_load_gff.PLS
#	modified:   scripts/Bio-DB-GFF/fast_load_gff.PLS
#	modified:   t/SeqFeature/FeatureIO.t
#	modified:   t/data/knownGene.gff3
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#	scripts/Bio-DB-GFF/genbank2gff3.diff
no changes added to commit (use "git add" and/or "git commit -a")
----------------------

so should I do a git commit -a?

Also, when I try a git pull, this is what it tells me:

scott-cains-macbook-pro:bioperl-live cain$ git pull
Updating 1c2cf24..d5de022
error: Your local changes to 'Bio/FeatureIO/gff.pm' would be
overwritten by merge.  Aborting.
Please, commit your changes or stash them before you can merge.

Thanks,
Scott



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research


From dan.kortschak at adelaide.edu.au  Thu Mar 31 19:24:25 2011
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Fri, 01 Apr 2011 09:54:25 +1030
Subject: [Bioperl-l] BEDTools.pm update
Message-ID: <1301613865.3334.35.camel@sueno>

Hi All,

I have completed a revision of the BEDTools module that makes use of the
v2.10.1 BEDTools additions, including the ability to read GFF and VCF
file formats.

Because of the interactions between CommandExts/Config and the way
BEDTools executables can receive input files, I have had to change the
parameter names for a number of the filespecs from -bed* to -bvg* (for
BED/GFF/VCF). The alternative, though possible was much more involved
for little gain in my view.

This change will break BEDTools.pm-using scripts that use the -bed[12]?
filespecs (except for those wrapping genomeCoverageBed which cannot read
bgv and so which see no change).

I just wanted to get an idea if this is going to be a significant
problem for people before I push the changes to bioperl-run.

cheers
Dan


From scott at scottcain.net  Thu Mar 31 20:19:33 2011
From: scott at scottcain.net (Scott Cain)
Date: Thu, 31 Mar 2011 20:19:33 -0400
Subject: [Bioperl-l] git help
In-Reply-To: <AANLkTin9BRdaSY_p-5rKSCFvpUr+rfCSZ8hjVTgyhxC5@mail.gmail.com>
References: <AANLkTin9BRdaSY_p-5rKSCFvpUr+rfCSZ8hjVTgyhxC5@mail.gmail.com>
Message-ID: <AANLkTimaOpkH1+S3Yn-14uLj+OVy5T=PBH3KGPi6gjnN@mail.gmail.com>

I just went a head and:

  git commit -a
  git pull --rebase
  git push

as suggested by rbuels.  That appeared to work.

Scott


On Thu, Mar 31, 2011 at 7:13 PM, Scott Cain <scott at scottcain.net> wrote:
> Hi all,
>
> I just want to know if it is safe for me to commit. ?Here is what git
> said to me:
>
> scott-cains-macbook-pro:bioperl-live cain$ git commit
> # On branch master
> # Your branch is behind 'origin/master' by 47 commits, and can be
> fast-forwarded.
> #
> # Changed but not updated:
> # ? (use "git add <file>..." to update what will be committed)
> # ? (use "git checkout -- <file>..." to discard changes in working directory)
> #
> # ? ? ? modified: ? Bio/DB/GFF.pm
> # ? ? ? modified: ? Bio/FeatureIO/gff.pm
> # ? ? ? modified: ? scripts/Bio-DB-GFF/bulk_load_gff.PLS
> # ? ? ? modified: ? scripts/Bio-DB-GFF/fast_load_gff.PLS
> # ? ? ? modified: ? t/SeqFeature/FeatureIO.t
> # ? ? ? modified: ? t/data/knownGene.gff3
> #
> # Untracked files:
> # ? (use "git add <file>..." to include in what will be committed)
> #
> # ? ? ? scripts/Bio-DB-GFF/genbank2gff3.diff
> no changes added to commit (use "git add" and/or "git commit -a")
> ----------------------
>
> so should I do a git commit -a?
>
> Also, when I try a git pull, this is what it tells me:
>
> scott-cains-macbook-pro:bioperl-live cain$ git pull
> Updating 1c2cf24..d5de022
> error: Your local changes to 'Bio/FeatureIO/gff.pm' would be
> overwritten by merge. ?Aborting.
> Please, commit your changes or stash them before you can merge.
>
> Thanks,
> Scott
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
> Ontario Institute for Cancer Research
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research


From cjfields at illinois.edu  Thu Mar 31 20:43:33 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 31 Mar 2011 19:43:33 -0500
Subject: [Bioperl-l] BEDTools.pm update
In-Reply-To: <1301613865.3334.35.camel@sueno>
References: <1301613865.3334.35.camel@sueno>
Message-ID: <557CDC9D-E16D-4DF2-A27A-1DFD7092A926@illinois.edu>

I would say push away, I don't think this will be a problem. 

chris

On Mar 31, 2011, at 6:24 PM, Dan Kortschak wrote:

> Hi All,
> 
> I have completed a revision of the BEDTools module that makes use of the
> v2.10.1 BEDTools additions, including the ability to read GFF and VCF
> file formats.
> 
> Because of the interactions between CommandExts/Config and the way
> BEDTools executables can receive input files, I have had to change the
> parameter names for a number of the filespecs from -bed* to -bvg* (for
> BED/GFF/VCF). The alternative, though possible was much more involved
> for little gain in my view.
> 
> This change will break BEDTools.pm-using scripts that use the -bed[12]?
> filespecs (except for those wrapping genomeCoverageBed which cannot read
> bgv and so which see no change).
> 
> I just wanted to get an idea if this is going to be a significant
> problem for people before I push the changes to bioperl-run.
> 
> cheers
> Dan
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From cjfields at illinois.edu  Thu Mar 31 20:44:38 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 31 Mar 2011 19:44:38 -0500
Subject: [Bioperl-l] git help
In-Reply-To: <AANLkTimaOpkH1+S3Yn-14uLj+OVy5T=PBH3KGPi6gjnN@mail.gmail.com>
References: <AANLkTin9BRdaSY_p-5rKSCFvpUr+rfCSZ8hjVTgyhxC5@mail.gmail.com>
	<AANLkTimaOpkH1+S3Yn-14uLj+OVy5T=PBH3KGPi6gjnN@mail.gmail.com>
Message-ID: <27E55B19-4795-4F41-88DC-824CC9A9C3C4@illinois.edu>

Yep, that's generally the way to do it, though you sometimes have to be careful with the '--rebase' if there are changes in the same code (I think git will catch this if it occurs).

chris

On Mar 31, 2011, at 7:19 PM, Scott Cain wrote:

> I just went a head and:
> 
>  git commit -a
>  git pull --rebase
>  git push
> 
> as suggested by rbuels.  That appeared to work.
> 
> Scott
> 
> 
> On Thu, Mar 31, 2011 at 7:13 PM, Scott Cain <scott at scottcain.net> wrote:
>> Hi all,
>> 
>> I just want to know if it is safe for me to commit.  Here is what git
>> said to me:
>> 
>> scott-cains-macbook-pro:bioperl-live cain$ git commit
>> # On branch master
>> # Your branch is behind 'origin/master' by 47 commits, and can be
>> fast-forwarded.
>> #
>> # Changed but not updated:
>> #   (use "git add <file>..." to update what will be committed)
>> #   (use "git checkout -- <file>..." to discard changes in working directory)
>> #
>> #       modified:   Bio/DB/GFF.pm
>> #       modified:   Bio/FeatureIO/gff.pm
>> #       modified:   scripts/Bio-DB-GFF/bulk_load_gff.PLS
>> #       modified:   scripts/Bio-DB-GFF/fast_load_gff.PLS
>> #       modified:   t/SeqFeature/FeatureIO.t
>> #       modified:   t/data/knownGene.gff3
>> #
>> # Untracked files:
>> #   (use "git add <file>..." to include in what will be committed)
>> #
>> #       scripts/Bio-DB-GFF/genbank2gff3.diff
>> no changes added to commit (use "git add" and/or "git commit -a")
>> ----------------------
>> 
>> so should I do a git commit -a?
>> 
>> Also, when I try a git pull, this is what it tells me:
>> 
>> scott-cains-macbook-pro:bioperl-live cain$ git pull
>> Updating 1c2cf24..d5de022
>> error: Your local changes to 'Bio/FeatureIO/gff.pm' would be
>> overwritten by merge.  Aborting.
>> Please, commit your changes or stash them before you can merge.
>> 
>> Thanks,
>> Scott
>> 
>> 
>> 
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Thu Mar 31 20:47:49 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 31 Mar 2011 19:47:49 -0500
Subject: [Bioperl-l] git help
In-Reply-To: <AANLkTimaOpkH1+S3Yn-14uLj+OVy5T=PBH3KGPi6gjnN@mail.gmail.com>
References: <AANLkTin9BRdaSY_p-5rKSCFvpUr+rfCSZ8hjVTgyhxC5@mail.gmail.com>
	<AANLkTimaOpkH1+S3Yn-14uLj+OVy5T=PBH3KGPi6gjnN@mail.gmail.com>
Message-ID: <9E536349-3EA4-43FC-B4C9-665BC81D68F8@illinois.edu>

Also, forgot to mention but we've moved FeatureIO out to it's own repo to reorganize it somewhat, so I'll likely migrate your changes over there.  We're eschewing Bio::SeqFeature::Annotated for simpler features and a few other bits that should allow for more flexibility in the future.  

chris

On Mar 31, 2011, at 7:19 PM, Scott Cain wrote:

> I just went a head and:
> 
>  git commit -a
>  git pull --rebase
>  git push
> 
> as suggested by rbuels.  That appeared to work.
> 
> Scott
> 
> 
> On Thu, Mar 31, 2011 at 7:13 PM, Scott Cain <scott at scottcain.net> wrote:
>> Hi all,
>> 
>> I just want to know if it is safe for me to commit.  Here is what git
>> said to me:
>> 
>> scott-cains-macbook-pro:bioperl-live cain$ git commit
>> # On branch master
>> # Your branch is behind 'origin/master' by 47 commits, and can be
>> fast-forwarded.
>> #
>> # Changed but not updated:
>> #   (use "git add <file>..." to update what will be committed)
>> #   (use "git checkout -- <file>..." to discard changes in working directory)
>> #
>> #       modified:   Bio/DB/GFF.pm
>> #       modified:   Bio/FeatureIO/gff.pm
>> #       modified:   scripts/Bio-DB-GFF/bulk_load_gff.PLS
>> #       modified:   scripts/Bio-DB-GFF/fast_load_gff.PLS
>> #       modified:   t/SeqFeature/FeatureIO.t
>> #       modified:   t/data/knownGene.gff3
>> #
>> # Untracked files:
>> #   (use "git add <file>..." to include in what will be committed)
>> #
>> #       scripts/Bio-DB-GFF/genbank2gff3.diff
>> no changes added to commit (use "git add" and/or "git commit -a")
>> ----------------------
>> 
>> so should I do a git commit -a?
>> 
>> Also, when I try a git pull, this is what it tells me:
>> 
>> scott-cains-macbook-pro:bioperl-live cain$ git pull
>> Updating 1c2cf24..d5de022
>> error: Your local changes to 'Bio/FeatureIO/gff.pm' would be
>> overwritten by merge.  Aborting.
>> Please, commit your changes or stash them before you can merge.
>> 
>> Thanks,
>> Scott
>> 
>> 
>> 
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From armendarez77 at hotmail.com  Thu Mar 31 20:45:11 2011
From: armendarez77 at hotmail.com (Veronica A.)
Date: Thu, 31 Mar 2011 17:45:11 -0700
Subject: [Bioperl-l] StandAloneBlastPlus Question
Message-ID: <BLU156-w251B5A50D1CFF47EE8CA4ED2BE0@phx.gbl>





Hello,

I'm trying to create a Perl script using StandAloneBlastPlus that can either create a new database or update it with new FASTA sequences.  However, I can only find information on the creation of a new database.  I've checked the information on doc.bioperl.org but a lot of the Methods don't have descriptions yet.


Is it possible to use StandAloneBlastPlus or is there another/a better way?

Thank you,

Veronica




 		 	   		  

From zuz17 at psu.edu  Thu Mar 31 16:54:15 2011
From: zuz17 at psu.edu (Zhenguo Zhang)
Date: Thu, 31 Mar 2011 16:54:15 -0400
Subject: [Bioperl-l] How to specify color for each feature in a track?
Message-ID: <1301604855l.1593384l.0l@psu.edu>

Dear Dr. Stein,

I am using your excellent module Bio::Graphics for programming to show protein
domains. I want to put all the domains for a sequence into one track, and give
each domain (one feature here) one designated color. The following is the cold
to add_track: 

 75         $panel->add_track($seq,
 78                 -glyph    =>  'segments',
 81                 -bgcolor  => sub {
 82                     my $f = shift;
 87                     return $f->get_tag_values('color');
 88                 },
 89                 -fgcolor  => 'black',
 90                 -font2color => 'red',
 91                 -key      => "$seq",
 92                 -label    => 1,
 93                 -bump     => +1,
 94                 -height   => 8,
 95                 -description => 1,
 96 #               -part_label_merge => 1
 97                 );

Here $seq is an array reference, each element being one domain feature. I
specify the -bgcolor based on the tag 'color'  defined when domain feature was
constructed. However, it does not work. All the domains in all sequences show
the same color. Based on the document, the -glyph can be changed by calling
back the anonymous functions (I have not tried this). The color might be
changed in a similar way. Thank you in advance!

Best regards!

Zhenguo

**************************************************************
Zhenguo Zhang
Postdoctoral Scholar
Institute of Molecular Evolutionary Genetics
Penn State University
312 Mueller Lab
University Park, PA 16802
Tel: 814-865-2796
Homepage: <http://www.personal.psu.edu/zuz17/>
Lab page:  <http://homes.bio.psu.edu/people/Faculty/Nei/>




From David.Messina at sbc.su.se  Tue Mar  1 09:02:59 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 1 Mar 2011 15:02:59 +0100
Subject: [Bioperl-l] Plans for the next release (and beyond)
In-Reply-To: <11F5BA8C-D4F4-419B-870B-D4B5180F4D7D@illinois.edu>
References: <11F5BA8C-D4F4-419B-870B-D4B5180F4D7D@illinois.edu>
Message-ID: <AANLkTinSR+RwUrvTeyund+CoxDzgEEqrGP0F2RW0_666@mail.gmail.com>

Hi Chris and everyone,

The plans sound great.

My only concern would be on point 3, moving some of the wiki docs into the
distros.

- In what format would the docs be in the distros?

Would it be POD? There is rich markup (URLs, code blocks, syntax coloring,
font sizes, etc) available on the wiki that I'd hate to lose.


- Are there discordant versions now?

I agree that we shouldn't maintain separate versions of these, but I thought
the tutorial had been moved completely to the wiki a while ago, and AFAIK,
the HOWTOs are only present on the wiki. I admit, though, I haven't looked
into this extensively.


- Tying the docs to the version of the code they came with

This could be beneficial if we expect people to have a (good) reason to be
using different (read: OLD) versions of the code. But in practice we're
pretty much always going to recommend people use the latest version, right?
In which case having the docs on the wiki (in sync with the latest, greatest
version) would be fairly practical.

Even if there is a good case for supporting older versions of the code and
docs, I don't know that that's enough of an asset to outweigh the downsides
such as loss of rich formatting and having to have some POD->wiki bridge and
keep it in sync.


I raise all the above mostly to ask for more information on that part of the
plan ? I suspect you've considered most of my concerns already, so I'm quite
open to seeing a different point of view on this.


Dave








3) I would like to work on moving the HOWTO's and other relevant
> documentation (Tutorial) back into the distributions, maybe in a particular
> namespace (Bio::Manual or similar).  The reason is simple: maintaining
> possibly discordant versions of documentation is unsustainable.  We could
> possibly set up a way of converting POD->wiki for on-line documentation, but
> I would like the documentation be tied to the version of the code it comes
> with, and the only easy way to do so is to package them all together.
>



From awitney at sgul.ac.uk  Tue Mar  1 12:08:12 2011
From: awitney at sgul.ac.uk (Adam Witney)
Date: Tue, 1 Mar 2011 17:08:12 +0000
Subject: [Bioperl-l] building NGS pipeline
In-Reply-To: <0FF71A5D-F5F6-4AAD-9501-4F4911DB40D8@illinois.edu>
References: <86D567CE-1735-4D85-B40F-B67823749FB7@sgul.ac.uk>
	<AANLkTi=eU0f=GuHE=zLfLoc5LhaiHBG_A2mjmMybQeNH@mail.gmail.com>
	<0FF71A5D-F5F6-4AAD-9501-4F4911DB40D8@illinois.edu>
Message-ID: <066A6A2B-05F7-4523-8A22-A91209953BB7@sgul.ac.uk>


On 28 Feb 2011, at 15:03, Chris Fields wrote:

> On Feb 28, 2011, at 6:04 AM, Sean Davis wrote:
> 
>> On Mon, Feb 28, 2011 at 6:06 AM, Adam Witney <awitney at sgul.ac.uk> wrote:
>> 
>>> Hi,
>>> 
>>> I'm trying to put together a set of steps to runs some analysis on NGS data
>>> we have. I have found modules that wrap alignment software such as
>>> bowtie/bwa/maq, but are there any packages to calculate RPKM's etc? what are
>>> people using for this?
>>> 
>>> 
>> scripture, cufflinks/cuffdiff, bioconductor (GenomicFeatures package, for
>> example), ERANGE (wold lab), and several others.  I don't know of perl
>> wrappers for these, but they are all command-line applications, generally
>> speaking.
>> 
>> This is an interesting site to follow for RNA-seq analysis and applications:
>> 
>> http://rna-seqblog.com/
>> 
>> Sean
> 
> BioPerl does have wrappers and interfaces for some packages, particularly Lincoln's Bio::DB::Sam (samtools package) and wrappers for bowtie, tophat, and bwa.  Locally, for comparative gene expression analyses we use bioconductor (many packages to choose from) as well as the command-line tools Sean mentions.
> 
> chris 

Thanks Sean, Chris,

the bowtie/tophat/cufflinks set of tools seem to work well. I have also come across myrna also but I am still getting that setup.

Thanks again

adam




From cjfields at illinois.edu  Tue Mar  1 12:37:29 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 1 Mar 2011 11:37:29 -0600
Subject: [Bioperl-l] Plans for the next release (and beyond)
In-Reply-To: <AANLkTinSR+RwUrvTeyund+CoxDzgEEqrGP0F2RW0_666@mail.gmail.com>
References: <11F5BA8C-D4F4-419B-870B-D4B5180F4D7D@illinois.edu>
	<AANLkTinSR+RwUrvTeyund+CoxDzgEEqrGP0F2RW0_666@mail.gmail.com>
Message-ID: <90D9611F-0DFA-43A6-A3C4-65948DF3F071@illinois.edu>

On Mar 1, 2011, at 8:02 AM, Dave Messina wrote:

> Hi Chris and everyone,
> 
> The plans sound great.
> 
> My only concern would be on point 3, moving some of the wiki docs into the distros.
> 
> - In what format would the docs be in the distros?
> 
> Would it be POD? There is rich markup (URLs, code blocks, syntax coloring, font sizes, etc) available on the wiki that I'd hate to lose.

It would very likely be POD, though I believe there are POD extensions for adding additional markup in CPAN.  We wouldn't necessarily lose the wiki HOWTOs, but they would be only editable via changes to the official docs in github.  My thought is to have wiki pages tied to the latest version in github via POD->wiki, with additional markup added in for syntax highlighting, etc.  Lots of CPAN modules that could help with this, but it needs further investigation.  Might need a HOWTO unto itself :)

One other point: inclusion of docs may also allow easier implementation of inline testing, where synopsis or HOWTO code can be directly tested from POD when specific directives allow for it.  I believe Dist::Zilla has plugins for this, and of course there is Test::Inline:

http://search.cpan.org/dist/Test-Inline/lib/Test/Inline.pm

This pushes the developers a bit to make sure code examples actually pass tests.  In particular I have thought about using this with the eutils cookbook, just to catch any changes on NCBI's end, but then realized it's broadly applicable to other areas as well.  

> - Are there discordant versions now?
> 
> I agree that we shouldn't maintain separate versions of these, but I thought the tutorial had been moved completely to the wiki a while ago, and AFAIK, the HOWTOs are only present on the wiki. I admit, though, I haven't looked into this extensively.

The original intent on moving docs to the wiki was somewhat correct: we wanted dynamic documentation that could be marked up for easier reading, better annotation, etc.  Wiki markup and templates has proved more useful than simple POD (HOWTO for Bio::Graphics, for example).  

However, at least to me there seems to be a fundamental disconnect between the code being developed in one repository (github) and the documentation being maintained elsewhere (wiki).  In many cases, once docs are placed on the wiki they seem to be largely forgotten by the devs once they have reached 'completeness'.  Our focus tends to be the code itself, not the documentation.  I'm basically looking for ways to resolve that and have documentation evolve along with the code, if possible making it testable.

Lastly, access to critical documentation is now reliant on access to the wiki, which may not always be possible.  We've had several wiki outages over the years and have recently talked about (off-list) migrating some resource away from open bio servers, wikis being one due to maintenance overhead and spam.  We'll always have a centralized website of some sort, I just want to make sure that one has means to access good documentation all the time.  Installing it with the code seems the best way currently, but I'm open to suggestions.

> - Tying the docs to the version of the code they came with
> 
> This could be beneficial if we expect people to have a (good) reason to be using different (read: OLD) versions of the code. But in practice we're pretty much always going to recommend people use the latest version, right? In which case having the docs on the wiki (in sync with the latest, greatest version) would be fairly practical.

Right, I agree, and I believe the wikis should only contain a very specific version of the docs, probably either the latest CPAN release or master.  However, I'm thinking of cases where users might not be able to get the latest/greatest, perhaps b/c they are constrained in using a specific version: with Ensembl (v. 1.2.3) or via sysadmin restrictions. 

If we consistently point to the official documentation as being on the wiki, we're not tying it to any specific version (unless it's explicitly stated), only what should work with the current version.    The only history is via the edits on the wiki page, which is not associated with anything, just the edits made.  

We should be able to demonstrate via tests that code and examples released with a specific version of BioPerl, including those in the HOWTOs and the tutorial, should work with that version of the software; anything else is a documentation error or a bug.  We can't do that currently.

> Even if there is a good case for supporting older versions of the code and docs, I don't know that that's enough of an asset to outweigh the downsides such as loss of rich formatting and having to have some POD->wiki bridge and keep it in sync.

The actual process of including documentation with the code works as the archival process itself (v 1.7 docs go with v 1.7 code, v 2 with v2 code, etc).  And I think there are ways around the lack of rich formatting with POD, just need to look into it more.

> I raise all the above mostly to ask for more information on that part of the plan ? I suspect you've considered most of my concerns already, so I'm quite open to seeing a different point of view on this.
> 
> 
> Dave

I've thought about it (as you can probably tell) but I think thought is needed about how to approach it.  It might require testing things out a bit first.

chris




From moitrayee at mbu.iisc.ernet.in  Tue Mar  1 06:22:54 2011
From: moitrayee at mbu.iisc.ernet.in (moitrayee at mbu.iisc.ernet.in)
Date: Tue, 1 Mar 2011 16:52:54 +0530 (IST)
Subject: [Bioperl-l] clustering trees obtained from phylip neighbor
Message-ID: <57675.10.128.10.17.1298978574.squirrel@mbu.iisc.ernet.in>

Dear BioPerl Users/Developers,

I have obtained a tree using a very large number of nodes
(1000 nodes) using the neighbor joining in PHYLIP. A small
test output looks like the following:

  +------------------------------------------------Bovine
--6
  !    +-------------------------------------------Mouse
  +----5
       !                        +------------------Gibbon
       +------------------------4
                                !    +-------------Orang
                                +----3
                                     !   +---------Gorilla
                                     +---2
                                         ! +-------Chimp
                                         +-1
                                           +-------Human

The outtree in Newick format is:

(Bovine:0.81551,(Mouse:0.73556,(Gibbon:0.31044,(Orang:0.24003,
(Gorilla:0.16418,(Chimp:0.13460,Human:0.13460):0.02958):0.07586):0.07040):0.42512):0.07995);


I am trying to obtain the cluster at different fork level of this tree.

The fork level goes as an user input. I looked into the link

http://www.bioperl.org/wiki/HOWTO:Trees#Related_Modules

But the Node connectivity methods described there does not apply
to the tree I have pasted above.

Any help / suggestions would be thankfully appreciated.

Thanks a lot in advance and looking forward to hear from you.

Sincere Regards,
Moitrayee Bhattacharyya
Molecular Biophysics Unit,
Indian Institute of Science
Bangalore-560012
India



-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.



From lskatz at gmail.com  Wed Mar  2 09:32:24 2011
From: lskatz at gmail.com (Lee Katz)
Date: Wed, 2 Mar 2011 09:32:24 -0500
Subject: [Bioperl-l] GuessSeqFormat
Message-ID: <AANLkTi=Aa=a-gs4shAM3yxk7w=h5MVqPy0VKKhLYoDah@mail.gmail.com>

Hi,
I noticed that even though there is a GuessSeqFormat module, SeqIO and
probably other modules first rely on the extension of a filename rather than
the content.  Could the behavior be altered so that it first checks the
content of the file, and if it turns up nothing then check the file
extension?


From daniel.standage at gmail.com  Wed Mar  2 11:01:12 2011
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 2 Mar 2011 10:01:12 -0600
Subject: [Bioperl-l] BioPerl POD
Message-ID: <AANLkTi=tfUzD78O-mA0tq84sFrtsCnaN4ZYD7Y0T+xnk@mail.gmail.com>

BioPerl,

I've been writing Perl (and BioPerl) for several years now, but I have
little to know experience using POD. I've added some POD to a module I wrote
and now I am trying to create an HTML page from it. I was able to do so with
*pod2html*, but the output is...underwhelming. The docs at
http://doc.bioperl.org aren't the essence of beauty themselves, but they do
have a bit of color and really nice features (like links to the code, etc).

Which tool(s) was/were used to generate the BioPerl HTML docs?

--
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University


From cjfields at illinois.edu  Wed Mar  2 11:26:58 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 2 Mar 2011 10:26:58 -0600
Subject: [Bioperl-l] GuessSeqFormat
In-Reply-To: <AANLkTi=Aa=a-gs4shAM3yxk7w=h5MVqPy0VKKhLYoDah@mail.gmail.com>
References: <AANLkTi=Aa=a-gs4shAM3yxk7w=h5MVqPy0VKKhLYoDah@mail.gmail.com>
Message-ID: <4F41B8DA-93D6-4442-95DC-D0EA24322351@illinois.edu>

On Mar 2, 2011, at 8:32 AM, Lee Katz wrote:

> Hi,
> I noticed that even though there is a GuessSeqFormat module, SeqIO and
> probably other modules first rely on the extension of a filename rather than
> the content.  Could the behavior be altered so that it first checks the
> content of the file, and if it turns up nothing then check the file
> extension?

The current behavior is the most common use case; stipulating the format with the file extension is pretty common and a surer way to get the correct format beyond explicitly setting it.  

If you want the opposite you can manually run the file through GuessSeqFormat and then (using the guess) use SeqIO with the guessed format, but I'm curious as to why you would want this behavior.  If it's for validation, I would highly recommend NOT using that module for validation purposes...

chris




From cjfields at illinois.edu  Wed Mar  2 11:40:22 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 2 Mar 2011 10:40:22 -0600
Subject: [Bioperl-l] BioPerl POD
In-Reply-To: <AANLkTi=tfUzD78O-mA0tq84sFrtsCnaN4ZYD7Y0T+xnk@mail.gmail.com>
References: <AANLkTi=tfUzD78O-mA0tq84sFrtsCnaN4ZYD7Y0T+xnk@mail.gmail.com>
Message-ID: <26289423-6B39-418C-B16B-1CECA73B5983@illinois.edu>

pdoc, I believe, is used for the doc.bioperl.org site:

http://pdoc.sourceforge.net/

Most POD->HTML converters are simple for a reason, sites generally use CSS to deal with formatting.  You could get around that with a few tools that embed the formatting with the HTML elements (see below link for examples), but I highly suggest using CSS if possible.  

Here's a stackoverflow article on the search.cpan.org HTML output:

http://stackoverflow.com/questions/4996684/modern-pod-to-html-converter-to-produce-results-like-search-cpan-org

Also, ActiveState has another one that generates their custom HTML (pretty nice), it comes with their perl dist I think.

chris

On Mar 2, 2011, at 10:01 AM, Daniel Standage wrote:

> BioPerl,
> 
> I've been writing Perl (and BioPerl) for several years now, but I have
> little to know experience using POD. I've added some POD to a module I wrote
> and now I am trying to create an HTML page from it. I was able to do so with
> *pod2html*, but the output is...underwhelming. The docs at
> http://doc.bioperl.org aren't the essence of beauty themselves, but they do
> have a bit of color and really nice features (like links to the code, etc).
> 
> Which tool(s) was/were used to generate the BioPerl HTML docs?
> 
> --
> Daniel S. Standage
> Graduate Research Assistant
> Bioinformatics and Computational Biology Program
> Iowa State University
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From lskatz at gmail.com  Wed Mar  2 11:53:52 2011
From: lskatz at gmail.com (Lee Katz)
Date: Wed, 2 Mar 2011 11:53:52 -0500
Subject: [Bioperl-l] GuessSeqFormat
In-Reply-To: <4F41B8DA-93D6-4442-95DC-D0EA24322351@illinois.edu>
References: <AANLkTi=Aa=a-gs4shAM3yxk7w=h5MVqPy0VKKhLYoDah@mail.gmail.com>
	<4F41B8DA-93D6-4442-95DC-D0EA24322351@illinois.edu>
Message-ID: <AANLkTimNeG4+n21mAVQfN3PS10snVStD6WTwAqT1EMhm@mail.gmail.com>

>
> The current behavior is the most common use case; stipulating the format
> with the file extension is pretty common and a surer way to get the correct
> format beyond explicitly setting it.
>
> If you want the opposite you can manually run the file through
> GuessSeqFormat and then (using the guess) use SeqIO with the guessed format,
> but I'm curious as to why you would want this behavior.  If it's for
> validation, I would highly recommend NOT using that module for validation
> purposes...
>
> chris
>


I understand your reasoning that checking a file extension is almost like a
user setting for providing the correct format.  Also I understand that I can
use the guessing module to discover the format on my own if I should choose
to do so.

However for your curiosity I'll try to explain why I would want this.
 Occasionally I get an error that I gave the wrong format for an input file.
 This could be quickly remedied by BioPerl figuring out the format by the
contents of the file rather than the extension.

Although now that I think about it--perhaps it is not a very fast method for
discovering the format and that it only looks at the first numbers of lines
before making a decision.  This would make it error-prone and slow I
suppose.


From daniel.standage at gmail.com  Wed Mar  2 11:55:46 2011
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 2 Mar 2011 10:55:46 -0600
Subject: [Bioperl-l] BioPerl POD
In-Reply-To: <26289423-6B39-418C-B16B-1CECA73B5983@illinois.edu>
References: <AANLkTi=tfUzD78O-mA0tq84sFrtsCnaN4ZYD7Y0T+xnk@mail.gmail.com>
	<26289423-6B39-418C-B16B-1CECA73B5983@illinois.edu>
Message-ID: <AANLkTikyhzULFY9foc5rOQ4yxMEpwS-4=RxFSBjfSioD@mail.gmail.com>

Great! Thanks!

--
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University



On Wed, Mar 2, 2011 at 10:40 AM, Chris Fields <cjfields at illinois.edu> wrote:

> pdoc, I believe, is used for the doc.bioperl.org site:
>
> http://pdoc.sourceforge.net/
>
> Most POD->HTML converters are simple for a reason, sites generally use CSS
> to deal with formatting.  You could get around that with a few tools that
> embed the formatting with the HTML elements (see below link for examples),
> but I highly suggest using CSS if possible.
>
> Here's a stackoverflow article on the search.cpan.org HTML output:
>
>
> http://stackoverflow.com/questions/4996684/modern-pod-to-html-converter-to-produce-results-like-search-cpan-org
>
> Also, ActiveState has another one that generates their custom HTML (pretty
> nice), it comes with their perl dist I think.
>
> chris
>
> On Mar 2, 2011, at 10:01 AM, Daniel Standage wrote:
>
> > BioPerl,
> >
> > I've been writing Perl (and BioPerl) for several years now, but I have
> > little to know experience using POD. I've added some POD to a module I
> wrote
> > and now I am trying to create an HTML page from it. I was able to do so
> with
> > *pod2html*, but the output is...underwhelming. The docs at
> > http://doc.bioperl.org aren't the essence of beauty themselves, but they
> do
> > have a bit of color and really nice features (like links to the code,
> etc).
> >
> > Which tool(s) was/were used to generate the BioPerl HTML docs?
> >
> > --
> > Daniel S. Standage
> > Graduate Research Assistant
> > Bioinformatics and Computational Biology Program
> > Iowa State University
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From roy.chaudhuri at gmail.com  Wed Mar  2 13:06:48 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Wed, 02 Mar 2011 18:06:48 +0000
Subject: [Bioperl-l] clustering trees obtained from phylip neighbor
In-Reply-To: <57675.10.128.10.17.1298978574.squirrel@mbu.iisc.ernet.in>
References: <57675.10.128.10.17.1298978574.squirrel@mbu.iisc.ernet.in>
Message-ID: <4D6E8738.7010103@gmail.com>

Hi Moitrayee,

I know a fair amount about phylogenetics, but I have no idea what you 
mean by the "fork level" of a tree. Perhaps you could use your example 
tree to explain what input you want the user to specify, and what output 
you want to produce?

Roy.

On 01/03/2011 11:22, moitrayee at mbu.iisc.ernet.in wrote:
> Dear BioPerl Users/Developers,
>
> I have obtained a tree using a very large number of nodes
> (1000 nodes) using the neighbor joining in PHYLIP. A small
> test output looks like the following:
>
>    +------------------------------------------------Bovine
> --6
>    !    +-------------------------------------------Mouse
>    +----5
>         !                        +------------------Gibbon
>         +------------------------4
>                                  !    +-------------Orang
>                                  +----3
>                                       !   +---------Gorilla
>                                       +---2
>                                           ! +-------Chimp
>                                           +-1
>                                             +-------Human
>
> The outtree in Newick format is:
>
> (Bovine:0.81551,(Mouse:0.73556,(Gibbon:0.31044,(Orang:0.24003,
> (Gorilla:0.16418,(Chimp:0.13460,Human:0.13460):0.02958):0.07586):0.07040):0.42512):0.07995);
>
>
> I am trying to obtain the cluster at different fork level of this tree.
>
> The fork level goes as an user input. I looked into the link
>
> http://www.bioperl.org/wiki/HOWTO:Trees#Related_Modules
>
> But the Node connectivity methods described there does not apply
> to the tree I have pasted above.
>
> Any help / suggestions would be thankfully appreciated.
>
> Thanks a lot in advance and looking forward to hear from you.
>
> Sincere Regards,
> Moitrayee Bhattacharyya
> Molecular Biophysics Unit,
> Indian Institute of Science
> Bangalore-560012
> India
>
>
>



From David.Messina at sbc.su.se  Thu Mar  3 10:52:44 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 3 Mar 2011 16:52:44 +0100
Subject: [Bioperl-l] Plans for the next release (and beyond)
In-Reply-To: <90D9611F-0DFA-43A6-A3C4-65948DF3F071@illinois.edu>
References: <11F5BA8C-D4F4-419B-870B-D4B5180F4D7D@illinois.edu>
	<AANLkTinSR+RwUrvTeyund+CoxDzgEEqrGP0F2RW0_666@mail.gmail.com>
	<90D9611F-0DFA-43A6-A3C4-65948DF3F071@illinois.edu>
Message-ID: <AANLkTikiWXv9yhVDYiPcAZ9D_12=d5TrKWcCMvsir0P4@mail.gmail.com>

Thanks, Chris.


> [re inline testing]
>


> This pushes the developers a bit to make sure code examples actually pass
> tests.  In particular I have thought about using this with the eutils
> cookbook, just to catch any changes on NCBI's end, but then realized it's
> broadly applicable to other areas as well.


This is a great idea, and goes well with the docs being version controlled
(your point below) along with the code itself.



> However, at least to me there seems to be a fundamental disconnect between
> the code being developed in one repository (github) and the documentation
> being maintained elsewhere (wiki).  In many cases, once docs are placed on
> the wiki they seem to be largely forgotten by the devs once they have
> reached 'completeness'.  Our focus tends to be the code itself, not the
> documentation.  I'm basically looking for ways to resolve that and have
> documentation evolve along with the code, if possible making it testable.
>

Yes, I can't argue. This has been a problem.



>   We should be able to demonstrate via tests that code and examples
> released with a specific version of BioPerl, including those in the HOWTOs
> and the tutorial, should work with that version of the software; anything
> else is a documentation error or a bug.  We can't do that currently.


That would be great.

In the end I'd have to say correct, up-to-date, and testable documentation
is the most important thing. Hopefully, we can find a way to keep the
readability/usability high ? which I think pretty much requires richer
formatting ? at the same time. Certainly worth trying in any case!


Dave



From p.j.a.cock at googlemail.com  Thu Mar  3 15:35:29 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 3 Mar 2011 20:35:29 +0000
Subject: [Bioperl-l] Fwd: [Bosc] Bioinformatics Open Source Conference (BOSC
 2011)--Call for Abstracts
In-Reply-To: <3922D2BE-5A99-4CDE-91AB-B311C42E10CE@lbl.gov>
References: <3922D2BE-5A99-4CDE-91AB-B311C42E10CE@lbl.gov>
Message-ID: <AANLkTinwgazvb5WPV-tiS41tO8wVkQ65NT0m75TPUVVw@mail.gmail.com>

Dear all,

I hope some of you will consider coming to BOSC 2011 in Vienna, and
maybe even submitting a talk or poster abstract.

Thank you,

Peter
(Biopython)


---------- Forwarded message ----------
From: Nomi Harris <nlharris at lbl.gov>
Date: Thu, Mar 3, 2011 at 7:37 PM
Subject: [Bosc] Bioinformatics Open Source Conference (BOSC
2011)--Call for Abstracts
To: bosc-announce at lists.open-bio.org, members at open-bio.org, GMOD
Announcements List <gmod-announce at lists.sourceforge.net>, GMOD
Developers List <gmod-devel at lists.sourceforge.net>
Cc: Nomi Harris <nlharris at lbl.gov>


We invite you to submit an abstract to BOSC 2011! ?Please forward this
message as appropriate, and forgive multiple postings.

Call for Abstracts for the 12th Annual Bioinformatics Open Source
Conference (BOSC 2011)
An ISMB 2011 Special Interest Group (SIG)

Dates: July 15-16, 2011
Location: Vienna, Austria
Web site: http://www.open-bio.org/wiki/BOSC_2011
Email: bosc at open-bio.org
BOSC announcements mailing list:
http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:
April 18, 2011: Deadline for submitting abstracts to BOSC 2011
May 9, 2011: Notifications of accepted abstracts emailed to
corresponding authors
July 13-14, 2011: Codefest 2011 programming session (see
http://www.open-bio.org/wiki/Codefest_2011 for details)
July 15-16, 2011: BOSC 2011
July 17-19, 2011: ISMB 2011

The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.

We invite you to submit abstracts for talks and posters. ?Sessions include:
- Approaches to parallel processing
- Cloud-based approaches to improving software and data accessibility
- The Semantic Web in open source bioinformatics
- Data visualization
- Tools for next-generation sequencing
- Other Open Source software

In addition to the above sessions, there will be a panel discussion
about "Meeting the challenges of inter-institutional collaboration".
We are also working to arrange a joint session with one of the other
ISMB SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student
Travel Awards for BOSC 2011. Each winner will be awarded $250 to
defray the costs of travel to BOSC 2011.

For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee:
Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock,
Erwin Frise, Darin London, Ron Taylor


_______________________________________________
BOSC mailing list
BOSC at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bosc



From sac at bioperl.org  Thu Mar  3 16:45:27 2011
From: sac at bioperl.org (Steve Chervitz)
Date: Thu, 3 Mar 2011 13:45:27 -0800
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
Message-ID: <AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>

Good catch, Elia. Looks like an legitimate edge case. Your fix looks
reasonable to me, but I haven't tried running it through the regression
tests to see if it breaks anything else.

Would be good to get this fix into the upcoming release.

Cheers,
Steve


On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:

> Hi Steve and Rob,
>
> it's been sometime since I last plunged my head into the code, but today we
> nailed a bug in Bio::Restriction::Analysis.
>
> Basically if a sequence has a restriction site which is exactly at the
> start of the sequence, it fails to produce any sites. The  culprits is this
> line (536 of Analysis.pm)
>
> unless ($cut_positions[0]) {
>
> where if the position is zero, it will fail to execute the rest of the
> code, so I changed it to:
>
> unless (defined($cut_positions[0])) {
>
> Also, for similar reasons a bit further down this line:
>
> my $start=1; my $stop; my %seq; my %stop;
>
> needs to change to:
> my $start=0; my $stop; my %seq; my %stop;
>
> I didn't commit the changes because I wanted to check if it makes sense,
> etc.
>
> The bug seems reproducible also in older, stable versions of bioperl, such
> as 1.4 and 1.6...
>
> best
>
> Elia
>
>
>
> ---
> Scientific Director - Bioinformatics, UCL Genomics
> Senior Lecturer, Bioinformatics
>
> UCL Cancer Institute
> Paul O' Gorman Building
> University College London
> 72, Huntley Street
> WC1E 6BT
> London
> UK
>
> Institute of Cell and Molecular Science
> Barts and The London School of Medicine and Dentistry
> 4 Newark Street
> Whitechapel
> London
> E1 2AT
>
> Office (UCL): +44 207 679 6493
> Fax: +44 0207 6796817
> Office (ICMS): +44 0207 8822374
>
> Mobile: +44 787 6478912
>
>
>
>
-- 
Steve Chervitz, Ph.D.
Omicia Inc. |  Senior Computational Biologist
2200 Powell Street, Ste 525, Emeryville CA 94608
T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com

Omicia.com: Unlocking Individualized Medicine.


From cjfields at illinois.edu  Thu Mar  3 17:42:41 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 3 Mar 2011 16:42:41 -0600
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
Message-ID: <E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>

Elia, Steve,

Any tests we can add for this?  I ran tests with the changes below and had several failing ones, but when only implementing the first fix ('unless (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate issue (string-based positions are 0-based, bioperl coords are 1-based).

chris

On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:

> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
> reasonable to me, but I haven't tried running it through the regression
> tests to see if it breaks anything else.
> 
> Would be good to get this fix into the upcoming release.
> 
> Cheers,
> Steve
> 
> 
> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
> 
>> Hi Steve and Rob,
>> 
>> it's been sometime since I last plunged my head into the code, but today we
>> nailed a bug in Bio::Restriction::Analysis.
>> 
>> Basically if a sequence has a restriction site which is exactly at the
>> start of the sequence, it fails to produce any sites. The  culprits is this
>> line (536 of Analysis.pm)
>> 
>> unless ($cut_positions[0]) {
>> 
>> where if the position is zero, it will fail to execute the rest of the
>> code, so I changed it to:
>> 
>> unless (defined($cut_positions[0])) {
>> 
>> Also, for similar reasons a bit further down this line:
>> 
>> my $start=1; my $stop; my %seq; my %stop;
>> 
>> needs to change to:
>> my $start=0; my $stop; my %seq; my %stop;
>> 
>> I didn't commit the changes because I wanted to check if it makes sense,
>> etc.
>> 
>> The bug seems reproducible also in older, stable versions of bioperl, such
>> as 1.4 and 1.6...
>> 
>> best
>> 
>> Elia
>> 
>> 
>> 
>> ---
>> Scientific Director - Bioinformatics, UCL Genomics
>> Senior Lecturer, Bioinformatics
>> 
>> UCL Cancer Institute
>> Paul O' Gorman Building
>> University College London
>> 72, Huntley Street
>> WC1E 6BT
>> London
>> UK
>> 
>> Institute of Cell and Molecular Science
>> Barts and The London School of Medicine and Dentistry
>> 4 Newark Street
>> Whitechapel
>> London
>> E1 2AT
>> 
>> Office (UCL): +44 207 679 6493
>> Fax: +44 0207 6796817
>> Office (ICMS): +44 0207 8822374
>> 
>> Mobile: +44 787 6478912
>> 
>> 
>> 
>> 
> -- 
> Steve Chervitz, Ph.D.
> Omicia Inc. |  Senior Computational Biologist
> 2200 Powell Street, Ste 525, Emeryville CA 94608
> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
> 
> Omicia.com: Unlocking Individualized Medicine.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Thu Mar  3 17:57:57 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 3 Mar 2011 16:57:57 -0600
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
	<E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
Message-ID: <CADBF252-9F51-4C7C-8062-C98B0E8E3B13@illinois.edu>

Forgot to add the summary, just for completeness. lots of errors like this that are halting tests:

------------- EXCEPTION -------------
MSG: Bad start parameter (0). Start must be positive.
STACK Bio::PrimarySeq::subseq /Users/cjfields/bioperl/bioperl-live/blib/lib/Bio/PrimarySeq.pm:400
STACK Bio::Restriction::Analysis::fragment_maps Bio/Restriction/Analysis.pm:556
STACK toplevel t/Restriction/Analysis-refac.t:143
-------------------------------------

Test Summary Report
-------------------
t/Restriction/Analysis-refac.t (Wstat: 65280 Tests: 26 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 91 tests but ran 26.
t/Restriction/Analysis.t      (Wstat: 65280 Tests: 118 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 177 tests but ran 118.
t/Restriction/Gel.t           (Wstat: 65280 Tests: 3 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 9 tests but ran 3.
Files=4, Tests=165, 29 wallclock secs ( 0.05 usr  0.03 sys +  3.44 cusr  0.21 csys =  3.73 CPU)
Result: FAIL
Failed 3/4 test programs. 0/165 subtests failed.

-c

On Mar 3, 2011, at 4:42 PM, Chris Fields wrote:

> Elia, Steve,
> 
> Any tests we can add for this?  I ran tests with the changes below and had several failing ones, but when only implementing the first fix ('unless (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate issue (string-based positions are 0-based, bioperl coords are 1-based).
> 
> chris
> 
> On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:
> 
>> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
>> reasonable to me, but I haven't tried running it through the regression
>> tests to see if it breaks anything else.
>> 
>> Would be good to get this fix into the upcoming release.
>> 
>> Cheers,
>> Steve
>> 
>> 
>> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
>> 
>>> Hi Steve and Rob,
>>> 
>>> it's been sometime since I last plunged my head into the code, but today we
>>> nailed a bug in Bio::Restriction::Analysis.
>>> 
>>> Basically if a sequence has a restriction site which is exactly at the
>>> start of the sequence, it fails to produce any sites. The  culprits is this
>>> line (536 of Analysis.pm)
>>> 
>>> unless ($cut_positions[0]) {
>>> 
>>> where if the position is zero, it will fail to execute the rest of the
>>> code, so I changed it to:
>>> 
>>> unless (defined($cut_positions[0])) {
>>> 
>>> Also, for similar reasons a bit further down this line:
>>> 
>>> my $start=1; my $stop; my %seq; my %stop;
>>> 
>>> needs to change to:
>>> my $start=0; my $stop; my %seq; my %stop;
>>> 
>>> I didn't commit the changes because I wanted to check if it makes sense,
>>> etc.
>>> 
>>> The bug seems reproducible also in older, stable versions of bioperl, such
>>> as 1.4 and 1.6...
>>> 
>>> best
>>> 
>>> Elia
>>> 
>>> 
>>> 
>>> ---
>>> Scientific Director - Bioinformatics, UCL Genomics
>>> Senior Lecturer, Bioinformatics
>>> 
>>> UCL Cancer Institute
>>> Paul O' Gorman Building
>>> University College London
>>> 72, Huntley Street
>>> WC1E 6BT
>>> London
>>> UK
>>> 
>>> Institute of Cell and Molecular Science
>>> Barts and The London School of Medicine and Dentistry
>>> 4 Newark Street
>>> Whitechapel
>>> London
>>> E1 2AT
>>> 
>>> Office (UCL): +44 207 679 6493
>>> Fax: +44 0207 6796817
>>> Office (ICMS): +44 0207 8822374
>>> 
>>> Mobile: +44 787 6478912
>>> 
>>> 
>>> 
>>> 
>> -- 
>> Steve Chervitz, Ph.D.
>> Omicia Inc. |  Senior Computational Biologist
>> 2200 Powell Street, Ste 525, Emeryville CA 94608
>> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
>> 
>> Omicia.com: Unlocking Individualized Medicine.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From sac at bioperl.org  Thu Mar  3 18:07:52 2011
From: sac at bioperl.org (Steve Chervitz)
Date: Thu, 3 Mar 2011 15:07:52 -0800
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <CADBF252-9F51-4C7C-8062-C98B0E8E3B13@illinois.edu>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
	<E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
	<CADBF252-9F51-4C7C-8062-C98B0E8E3B13@illinois.edu>
Message-ID: <AANLkTik7CGWADGzJvenQt7kbmOoMGij4u6Q5U9NOP_rd@mail.gmail.com>

Chris: Thanks or checking. I'm not sure about this.

Elia: Can you send an example sequence + enzyme name that causes the issue
you found?

Steve

On Thu, Mar 3, 2011 at 2:57 PM, Chris Fields <cjfields at illinois.edu> wrote:

> Forgot to add the summary, just for completeness. lots of errors like this
> that are halting tests:
>
> ------------- EXCEPTION -------------
> MSG: Bad start parameter (0). Start must be positive.
> STACK Bio::PrimarySeq::subseq
> /Users/cjfields/bioperl/bioperl-live/blib/lib/Bio/PrimarySeq.pm:400
> STACK Bio::Restriction::Analysis::fragment_maps
> Bio/Restriction/Analysis.pm:556
> STACK toplevel t/Restriction/Analysis-refac.t:143
> -------------------------------------
>
> Test Summary Report
> -------------------
> t/Restriction/Analysis-refac.t (Wstat: 65280 Tests: 26 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 91 tests but ran 26.
> t/Restriction/Analysis.t      (Wstat: 65280 Tests: 118 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 177 tests but ran 118.
> t/Restriction/Gel.t           (Wstat: 65280 Tests: 3 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 9 tests but ran 3.
> Files=4, Tests=165, 29 wallclock secs ( 0.05 usr  0.03 sys +  3.44 cusr
>  0.21 csys =  3.73 CPU)
> Result: FAIL
> Failed 3/4 test programs. 0/165 subtests failed.
>
> -c
>
> On Mar 3, 2011, at 4:42 PM, Chris Fields wrote:
>
> > Elia, Steve,
> >
> > Any tests we can add for this?  I ran tests with the changes below and
> had several failing ones, but when only implementing the first fix ('unless
> (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate
> issue (string-based positions are 0-based, bioperl coords are 1-based).
> >
> > chris
> >
> > On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:
> >
> >> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
> >> reasonable to me, but I haven't tried running it through the regression
> >> tests to see if it breaks anything else.
> >>
> >> Would be good to get this fix into the upcoming release.
> >>
> >> Cheers,
> >> Steve
> >>
> >>
> >> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
> >>
> >>> Hi Steve and Rob,
> >>>
> >>> it's been sometime since I last plunged my head into the code, but
> today we
> >>> nailed a bug in Bio::Restriction::Analysis.
> >>>
> >>> Basically if a sequence has a restriction site which is exactly at the
> >>> start of the sequence, it fails to produce any sites. The  culprits is
> this
> >>> line (536 of Analysis.pm)
> >>>
> >>> unless ($cut_positions[0]) {
> >>>
> >>> where if the position is zero, it will fail to execute the rest of the
> >>> code, so I changed it to:
> >>>
> >>> unless (defined($cut_positions[0])) {
> >>>
> >>> Also, for similar reasons a bit further down this line:
> >>>
> >>> my $start=1; my $stop; my %seq; my %stop;
> >>>
> >>> needs to change to:
> >>> my $start=0; my $stop; my %seq; my %stop;
> >>>
> >>> I didn't commit the changes because I wanted to check if it makes
> sense,
> >>> etc.
> >>>
> >>> The bug seems reproducible also in older, stable versions of bioperl,
> such
> >>> as 1.4 and 1.6...
> >>>
> >>> best
> >>>
> >>> Elia
> >>>
> >>>
> >>>
> >>> ---
> >>> Scientific Director - Bioinformatics, UCL Genomics
> >>> Senior Lecturer, Bioinformatics
> >>>
> >>> UCL Cancer Institute
> >>> Paul O' Gorman Building
> >>> University College London
> >>> 72, Huntley Street
> >>> WC1E 6BT
> >>> London
> >>> UK
> >>>
> >>> Institute of Cell and Molecular Science
> >>> Barts and The London School of Medicine and Dentistry
> >>> 4 Newark Street
> >>> Whitechapel
> >>> London
> >>> E1 2AT
> >>>
> >>> Office (UCL): +44 207 679 6493
> >>> Fax: +44 0207 6796817
> >>> Office (ICMS): +44 0207 8822374
> >>>
> >>> Mobile: +44 787 6478912
> >>>
> >>>
> >>>
> >>>
> >> --
> >> Steve Chervitz, Ph.D.
> >> Omicia Inc. |  Senior Computational Biologist
> >> 2200 Powell Street, Ste 525, Emeryville CA 94608
> >> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
> >>
> >> Omicia.com: Unlocking Individualized Medicine.
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From hartzell at alerce.com  Thu Mar  3 18:04:34 2011
From: hartzell at alerce.com (George Hartzell)
Date: Thu, 3 Mar 2011 15:04:34 -0800
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
Message-ID: <19824.7810.437300.584113@gargle.gargle.HOWL>


Hi all,

I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
seems to have it.  The only tarballs that end up in Chris' directory
are these:

/Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
/Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
/Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz

It is listed in the 02packages.details.txt.gz file that is mirrored.

Thoughts, suggestions?

Thanks,

g.


From cjfields at illinois.edu  Thu Mar  3 21:24:05 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 3 Mar 2011 20:24:05 -0600
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <19824.7810.437300.584113@gargle.gargle.HOWL>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
Message-ID: <5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>

On Mar 3, 2011, at 5:04 PM, George Hartzell wrote:

> Hi all,
> 
> I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
> does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
> seems to have it.  The only tarballs that end up in Chris' directory
> are these:
> 
> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
> 
> It is listed in the 02packages.details.txt.gz file that is mirrored.
> 
> Thoughts, suggestions?
> 
> Thanks,
> 
> g.

That's odd; could it be the repo you created the mirror from?

This is my PAUSE account:

 BioPerl-1.6.0.meta                                   78518  Sun, 25 Jan 2009 05:19:20 GMT
 BioPerl-1.6.0.readme                                 12174  Sun, 25 Jan 2009 05:19:41 GMT
 BioPerl-1.6.0.tar.gz                               6813396  Sun, 25 Jan 2009 17:14:12 GMT
 BioPerl-1.6.1.meta                                   82231  Tue, 29 Sep 2009 16:33:52 GMT
 BioPerl-1.6.1.readme                                 12174  Tue, 29 Sep 2009 16:33:49 GMT
 BioPerl-1.6.1.tar.gz                               10462526  Tue, 29 Sep 2009 16:43:11 GMT
 BioPerl-DB-1.6.0_001.tar.gz                         494106  Wed, 30 Sep 2009 20:49:59 GMT
 BioPerl-Network-1.6.0_001.tar.gz                   2198338  Wed, 30 Sep 2009 20:50:18 GMT
 BioPerl-Run-1.6.1_001.tar.gz                       4289239  Wed, 30 Sep 2009 21:07:38 GMT
 BioPerl-db-1.6.0.meta                                 7728  Tue, 24 Feb 2009 02:58:05 GMT
 BioPerl-db-1.6.0.readme                               7066  Tue, 24 Feb 2009 02:58:05 GMT
 BioPerl-db-1.6.0.tar.gz                             392773  Tue, 24 Feb 2009 15:33:05 GMT
 BioPerl-network-1.6.0.meta                            1268  Tue, 24 Feb 2009 03:00:26 GMT
 BioPerl-network-1.6.0.readme                          3669  Tue, 24 Feb 2009 03:00:28 GMT
 BioPerl-network-1.6.0.tar.gz                       1410782  Tue, 24 Feb 2009 15:33:16 GMT
 BioPerl-run-1.6.0.meta                               10289  Tue, 24 Feb 2009 02:59:26 GMT
 BioPerl-run-1.6.0.readme                               576  Tue, 24 Feb 2009 02:59:26 GMT
 BioPerl-run-1.6.0.tar.gz                           4082430  Tue, 24 Feb 2009 15:34:43 GMT
 BioPerl-run-1.6.1.meta                               10289  Wed, 25 Feb 2009 16:07:06 GMT
 BioPerl-run-1.6.1.readme                               576  Wed, 25 Feb 2009 16:07:06 GMT
 BioPerl-run-1.6.1.tar.gz                           4082463  Wed, 25 Feb 2009 16:14:37 GMT
 CHECKSUMS                                             5035  Sun, 03 Oct 2010 19:21:56 GMT

chris


From hartzell at alerce.com  Fri Mar  4 00:50:49 2011
From: hartzell at alerce.com (George Hartzell)
Date: Thu, 3 Mar 2011 21:50:49 -0800
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
	<5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
Message-ID: <19824.32185.570232.624286@gargle.gargle.HOWL>

Chris Fields writes:
 > On Mar 3, 2011, at 5:04 PM, George Hartzell wrote:
 > 
 > > Hi all,
 > > 
 > > I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
 > > does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
 > > seems to have it.  The only tarballs that end up in Chris' directory
 > > are these:
 > > 
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
 > > 
 > > It is listed in the 02packages.details.txt.gz file that is mirrored.
 > > 
 > > Thoughts, suggestions?
 > > 
 > > Thanks,
 > > 
 > > g.
 > 
 > That's odd; could it be the repo you created the mirror from?
 > 
 > This is my PAUSE account:
 > 
 >  BioPerl-1.6.0.meta                                   78518  Sun, 25 Jan 2009 05:19:20 GMT
 >  BioPerl-1.6.0.readme                                 12174  Sun, 25 Jan 2009 05:19:41 GMT
 >  BioPerl-1.6.0.tar.gz                               6813396  Sun, 25 Jan 2009 17:14:12 GMT
 >  BioPerl-1.6.1.meta                                   82231  Tue, 29 Sep 2009 16:33:52 GMT
 >  BioPerl-1.6.1.readme                                 12174  Tue, 29 Sep 2009 16:33:49 GMT
 >  BioPerl-1.6.1.tar.gz                               10462526  Tue, 29 Sep 2009 16:43:11 GMT
 >  BioPerl-DB-1.6.0_001.tar.gz                         494106  Wed, 30 Sep 2009 20:49:59 GMT
 >  BioPerl-Network-1.6.0_001.tar.gz                   2198338  Wed, 30 Sep 2009 20:50:18 GMT
 >  BioPerl-Run-1.6.1_001.tar.gz                       4289239  Wed, 30 Sep 2009 21:07:38 GMT
 >  BioPerl-db-1.6.0.meta                                 7728  Tue, 24 Feb 2009 02:58:05 GMT
 >  BioPerl-db-1.6.0.readme                               7066  Tue, 24 Feb 2009 02:58:05 GMT
 >  BioPerl-db-1.6.0.tar.gz                             392773  Tue, 24 Feb 2009 15:33:05 GMT
 >  BioPerl-network-1.6.0.meta                            1268  Tue, 24 Feb 2009 03:00:26 GMT
 >  BioPerl-network-1.6.0.readme                          3669  Tue, 24 Feb 2009 03:00:28 GMT
 >  BioPerl-network-1.6.0.tar.gz                       1410782  Tue, 24 Feb 2009 15:33:16 GMT
 >  BioPerl-run-1.6.0.meta                               10289  Tue, 24 Feb 2009 02:59:26 GMT
 >  BioPerl-run-1.6.0.readme                               576  Tue, 24 Feb 2009 02:59:26 GMT
 >  BioPerl-run-1.6.0.tar.gz                           4082430  Tue, 24 Feb 2009 15:34:43 GMT
 >  BioPerl-run-1.6.1.meta                               10289  Wed, 25 Feb 2009 16:07:06 GMT
 >  BioPerl-run-1.6.1.readme                               576  Wed, 25 Feb 2009 16:07:06 GMT
 >  BioPerl-run-1.6.1.tar.gz                           4082463  Wed, 25 Feb 2009 16:14:37 GMT
 >  CHECKSUMS                                             5035  Sun, 03 Oct 2010 19:21:56 GMT
 > 
 > chris
 > 
 > 

I've tried a couple of them, a couple of times.  Wouldn't surprise me
if it's something on my end.  I'll peek under the minicpan kilt over
the weekend and see if I can see what's going on.

g.


From e.stupka at ucl.ac.uk  Fri Mar  4 04:30:17 2011
From: e.stupka at ucl.ac.uk (Elia Stupka)
Date: Fri, 4 Mar 2011 09:30:17 +0000
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
	<E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
Message-ID: <535DCA0E-A74D-483B-96FB-544387EF08C3@ucl.ac.uk>

Ignore the second fix, the first one is the useful and correct one. The 2nd one was an oversight.

Elia


---
Scientific Director - Bioinformatics, UCL Genomics
Senior Lecturer, Bioinformatics

UCL Cancer Institute
Paul O' Gorman Building
University College London
Gower Street
WC1E 6BT
London
UK

Institute of Cell and Molecular Science
Barts and The London School of Medicine and Dentistry
4 Newark Street
Whitechapel
London
E1 2AT

Office (UCL): +44 207 679 6493
Fax: +44 0207 6796817 
Office (ICMS): +44 0207 8822374

On 3 Mar 2011, at 22:42, Chris Fields <cjfields at illinois.edu> wrote:

> Elia, Steve,
> 
> Any tests we can add for this?  I ran tests with the changes below and had several failing ones, but when only implementing the first fix ('unless (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate issue (string-based positions are 0-based, bioperl coords are 1-based).
> 
> chris
> 
> On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:
> 
>> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
>> reasonable to me, but I haven't tried running it through the regression
>> tests to see if it breaks anything else.
>> 
>> Would be good to get this fix into the upcoming release.
>> 
>> Cheers,
>> Steve
>> 
>> 
>> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
>> 
>>> Hi Steve and Rob,
>>> 
>>> it's been sometime since I last plunged my head into the code, but today we
>>> nailed a bug in Bio::Restriction::Analysis.
>>> 
>>> Basically if a sequence has a restriction site which is exactly at the
>>> start of the sequence, it fails to produce any sites. The  culprits is this
>>> line (536 of Analysis.pm)
>>> 
>>> unless ($cut_positions[0]) {
>>> 
>>> where if the position is zero, it will fail to execute the rest of the
>>> code, so I changed it to:
>>> 
>>> unless (defined($cut_positions[0])) {
>>> 
>>> Also, for similar reasons a bit further down this line:
>>> 
>>> my $start=1; my $stop; my %seq; my %stop;
>>> 
>>> needs to change to:
>>> my $start=0; my $stop; my %seq; my %stop;
>>> 
>>> I didn't commit the changes because I wanted to check if it makes sense,
>>> etc.
>>> 
>>> The bug seems reproducible also in older, stable versions of bioperl, such
>>> as 1.4 and 1.6...
>>> 
>>> best
>>> 
>>> Elia
>>> 
>>> 
>>> 
>>> ---
>>> Scientific Director - Bioinformatics, UCL Genomics
>>> Senior Lecturer, Bioinformatics
>>> 
>>> UCL Cancer Institute
>>> Paul O' Gorman Building
>>> University College London
>>> 72, Huntley Street
>>> WC1E 6BT
>>> London
>>> UK
>>> 
>>> Institute of Cell and Molecular Science
>>> Barts and The London School of Medicine and Dentistry
>>> 4 Newark Street
>>> Whitechapel
>>> London
>>> E1 2AT
>>> 
>>> Office (UCL): +44 207 679 6493
>>> Fax: +44 0207 6796817
>>> Office (ICMS): +44 0207 8822374
>>> 
>>> Mobile: +44 787 6478912
>>> 
>>> 
>>> 
>>> 
>> -- 
>> Steve Chervitz, Ph.D.
>> Omicia Inc. |  Senior Computational Biologist
>> 2200 Powell Street, Ste 525, Emeryville CA 94608
>> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
>> 
>> Omicia.com: Unlocking Individualized Medicine.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From cjfields at illinois.edu  Fri Mar  4 11:09:42 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 4 Mar 2011 10:09:42 -0600
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <535DCA0E-A74D-483B-96FB-544387EF08C3@ucl.ac.uk>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
	<E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
	<535DCA0E-A74D-483B-96FB-544387EF08C3@ucl.ac.uk>
Message-ID: <243A2900-C5D3-4772-AC88-69A3ABF238E6@illinois.edu>

Committed to github, should be in the next release.  I'll see if I can add a simple test for this.

chris


On Mar 4, 2011, at 3:30 AM, Elia Stupka wrote:

> Ignore the second fix, the first one is the useful and correct one. The 2nd one was an oversight.
> 
> Elia
> 
> 
> ---
> Scientific Director - Bioinformatics, UCL Genomics
> Senior Lecturer, Bioinformatics
> 
> UCL Cancer Institute
> Paul O' Gorman Building
> University College London
> Gower Street
> WC1E 6BT
> London
> UK
> 
> Institute of Cell and Molecular Science
> Barts and The London School of Medicine and Dentistry
> 4 Newark Street
> Whitechapel
> London
> E1 2AT
> 
> Office (UCL): +44 207 679 6493
> Fax: +44 0207 6796817 
> Office (ICMS): +44 0207 8822374
> 
> On 3 Mar 2011, at 22:42, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Elia, Steve,
>> 
>> Any tests we can add for this?  I ran tests with the changes below and had several failing ones, but when only implementing the first fix ('unless (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate issue (string-based positions are 0-based, bioperl coords are 1-based).
>> 
>> chris
>> 
>> On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:
>> 
>>> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
>>> reasonable to me, but I haven't tried running it through the regression
>>> tests to see if it breaks anything else.
>>> 
>>> Would be good to get this fix into the upcoming release.
>>> 
>>> Cheers,
>>> Steve
>>> 
>>> 
>>> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
>>> 
>>>> Hi Steve and Rob,
>>>> 
>>>> it's been sometime since I last plunged my head into the code, but today we
>>>> nailed a bug in Bio::Restriction::Analysis.
>>>> 
>>>> Basically if a sequence has a restriction site which is exactly at the
>>>> start of the sequence, it fails to produce any sites. The  culprits is this
>>>> line (536 of Analysis.pm)
>>>> 
>>>> unless ($cut_positions[0]) {
>>>> 
>>>> where if the position is zero, it will fail to execute the rest of the
>>>> code, so I changed it to:
>>>> 
>>>> unless (defined($cut_positions[0])) {
>>>> 
>>>> Also, for similar reasons a bit further down this line:
>>>> 
>>>> my $start=1; my $stop; my %seq; my %stop;
>>>> 
>>>> needs to change to:
>>>> my $start=0; my $stop; my %seq; my %stop;
>>>> 
>>>> I didn't commit the changes because I wanted to check if it makes sense,
>>>> etc.
>>>> 
>>>> The bug seems reproducible also in older, stable versions of bioperl, such
>>>> as 1.4 and 1.6...
>>>> 
>>>> best
>>>> 
>>>> Elia
>>>> 
>>>> 
>>>> 
>>>> ---
>>>> Scientific Director - Bioinformatics, UCL Genomics
>>>> Senior Lecturer, Bioinformatics
>>>> 
>>>> UCL Cancer Institute
>>>> Paul O' Gorman Building
>>>> University College London
>>>> 72, Huntley Street
>>>> WC1E 6BT
>>>> London
>>>> UK
>>>> 
>>>> Institute of Cell and Molecular Science
>>>> Barts and The London School of Medicine and Dentistry
>>>> 4 Newark Street
>>>> Whitechapel
>>>> London
>>>> E1 2AT
>>>> 
>>>> Office (UCL): +44 207 679 6493
>>>> Fax: +44 0207 6796817
>>>> Office (ICMS): +44 0207 8822374
>>>> 
>>>> Mobile: +44 787 6478912
>>>> 
>>>> 
>>>> 
>>>> 
>>> -- 
>>> Steve Chervitz, Ph.D.
>>> Omicia Inc. |  Senior Computational Biologist
>>> 2200 Powell Street, Ste 525, Emeryville CA 94608
>>> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
>>> 
>>> Omicia.com: Unlocking Individualized Medicine.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 




From hartzell at alerce.com  Fri Mar  4 13:16:03 2011
From: hartzell at alerce.com (George Hartzell)
Date: Fri, 4 Mar 2011 10:16:03 -0800
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
	<5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
Message-ID: <19825.11363.446731.724414@gargle.gargle.HOWL>

Chris Fields writes:
 > On Mar 3, 2011, at 5:04 PM, George Hartzell wrote:
 > 
 > > Hi all,
 > > 
 > > I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
 > > does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
 > > seems to have it.  The only tarballs that end up in Chris' directory
 > > are these:
 > > 
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
 > > 
 > > It is listed in the 02packages.details.txt.gz file that is mirrored.
 > > 
 > > Thoughts, suggestions?
 > > 
 > > Thanks,
 > > 
 > > g.
 > 
 > That's odd; could it be the repo you created the mirror from?
 > 
 > This is my PAUSE account:
 > 
 >  BioPerl-1.6.0.meta                                   78518  Sun, 25 Jan 2009 05:19:20 GMT
 >  BioPerl-1.6.0.readme                                 12174  Sun, 25 Jan 2009 05:19:41 GMT
 >  BioPerl-1.6.0.tar.gz                               6813396  Sun, 25 Jan 2009 17:14:12 GMT
 >  BioPerl-1.6.1.meta                                   82231  Tue, 29 Sep 2009 16:33:52 GMT
 >  BioPerl-1.6.1.readme                                 12174  Tue, 29 Sep 2009 16:33:49 GMT
 >  BioPerl-1.6.1.tar.gz                               10462526  Tue, 29 Sep 2009 16:43:11 GMT
 >  BioPerl-DB-1.6.0_001.tar.gz                         494106  Wed, 30 Sep 2009 20:49:59 GMT
 >  BioPerl-Network-1.6.0_001.tar.gz                   2198338  Wed, 30 Sep 2009 20:50:18 GMT
 >  BioPerl-Run-1.6.1_001.tar.gz                       4289239  Wed, 30 Sep 2009 21:07:38 GMT
 >  BioPerl-db-1.6.0.meta                                 7728  Tue, 24 Feb 2009 02:58:05 GMT
 >  BioPerl-db-1.6.0.readme                               7066  Tue, 24 Feb 2009 02:58:05 GMT
 >  BioPerl-db-1.6.0.tar.gz                             392773  Tue, 24 Feb 2009 15:33:05 GMT
 >  BioPerl-network-1.6.0.meta                            1268  Tue, 24 Feb 2009 03:00:26 GMT
 >  BioPerl-network-1.6.0.readme                          3669  Tue, 24 Feb 2009 03:00:28 GMT
 >  BioPerl-network-1.6.0.tar.gz                       1410782  Tue, 24 Feb 2009 15:33:16 GMT
 >  BioPerl-run-1.6.0.meta                               10289  Tue, 24 Feb 2009 02:59:26 GMT
 >  BioPerl-run-1.6.0.readme                               576  Tue, 24 Feb 2009 02:59:26 GMT
 >  BioPerl-run-1.6.0.tar.gz                           4082430  Tue, 24 Feb 2009 15:34:43 GMT
 >  BioPerl-run-1.6.1.meta                               10289  Wed, 25 Feb 2009 16:07:06 GMT
 >  BioPerl-run-1.6.1.readme                               576  Wed, 25 Feb 2009 16:07:06 GMT
 >  BioPerl-run-1.6.1.tar.gz                           4082463  Wed, 25 Feb 2009 16:14:37 GMT
 >  CHECKSUMS                                             5035  Sun, 03 Oct 2010 19:21:56 GMT
 > 
 > chris
 > 
 > 

Ok, apparently we've earned a reputation, and it has preceeded us....
Here's the code that Ricardo uses to filter the list of things to mirror:

  sub _filter_module {
    my $self = shift;
    my $args = shift;
  
    if ($self->{skip_perl}) {
      return 1 if $args->{path} =~ m{/(?:emb|syb|bio)?perl-\d}i;
      return 1 if $args->{path} =~ m{/(?:parrot|ponie)-\d}i;
      return 1 if $args->{path} =~ m{/(?:kurila)-\d}i;
      return 1 if $args->{path} =~ m{/\bperl-?5\.004}i;
      return 1 if $args->{path} =~ m{/\bperl_mlb\.zip}i;
    }
  
    return 1 if $self->__do_filter($self->{path_filters},   $args->{path});
    return 1 if $self->__do_filter($self->{module_filters}, $args->{module});
    return 0;
  }

I'll ask him why he's filtering bioperl out and we can see if we can
fix it.  I'm hoping that it's just an over-eager cut-n-paste of stuff
that he thinks of as the "perl" source (which is why it's within the
skip_perl test) and not that we've done something egregious.

g.


From cjfields at illinois.edu  Fri Mar  4 13:24:05 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 4 Mar 2011 12:24:05 -0600
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <19825.11363.446731.724414@gargle.gargle.HOWL>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
	<5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
	<19825.11363.446731.724414@gargle.gargle.HOWL>
Message-ID: <F8DFAE16-FE59-4EDF-80D0-4FE60620FFF8@illinois.edu>

On Mar 4, 2011, at 12:16 PM, George Hartzell wrote:

> Chris Fields writes:
>> On Mar 3, 2011, at 5:04 PM, George Hartzell wrote:
>> 
>>> Hi all,
>>> 
>>> I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
>>> does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
>>> seems to have it.  The only tarballs that end up in Chris' directory
>>> are these:
>>> 
>>> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
>>> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
>>> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
>>> 
>>> It is listed in the 02packages.details.txt.gz file that is mirrored.
>>> 
>>> Thoughts, suggestions?
>>> 
>>> Thanks,
>>> 
>>> g.
>> 
>> That's odd; could it be the repo you created the mirror from?
>> 
>> This is my PAUSE account:
>> 
>> BioPerl-1.6.0.meta                                   78518  Sun, 25 Jan 2009 05:19:20 GMT
>> BioPerl-1.6.0.readme                                 12174  Sun, 25 Jan 2009 05:19:41 GMT
>> BioPerl-1.6.0.tar.gz                               6813396  Sun, 25 Jan 2009 17:14:12 GMT
>> BioPerl-1.6.1.meta                                   82231  Tue, 29 Sep 2009 16:33:52 GMT
>> BioPerl-1.6.1.readme                                 12174  Tue, 29 Sep 2009 16:33:49 GMT
>> BioPerl-1.6.1.tar.gz                               10462526  Tue, 29 Sep 2009 16:43:11 GMT
>> BioPerl-DB-1.6.0_001.tar.gz                         494106  Wed, 30 Sep 2009 20:49:59 GMT
>> BioPerl-Network-1.6.0_001.tar.gz                   2198338  Wed, 30 Sep 2009 20:50:18 GMT
>> BioPerl-Run-1.6.1_001.tar.gz                       4289239  Wed, 30 Sep 2009 21:07:38 GMT
>> BioPerl-db-1.6.0.meta                                 7728  Tue, 24 Feb 2009 02:58:05 GMT
>> BioPerl-db-1.6.0.readme                               7066  Tue, 24 Feb 2009 02:58:05 GMT
>> BioPerl-db-1.6.0.tar.gz                             392773  Tue, 24 Feb 2009 15:33:05 GMT
>> BioPerl-network-1.6.0.meta                            1268  Tue, 24 Feb 2009 03:00:26 GMT
>> BioPerl-network-1.6.0.readme                          3669  Tue, 24 Feb 2009 03:00:28 GMT
>> BioPerl-network-1.6.0.tar.gz                       1410782  Tue, 24 Feb 2009 15:33:16 GMT
>> BioPerl-run-1.6.0.meta                               10289  Tue, 24 Feb 2009 02:59:26 GMT
>> BioPerl-run-1.6.0.readme                               576  Tue, 24 Feb 2009 02:59:26 GMT
>> BioPerl-run-1.6.0.tar.gz                           4082430  Tue, 24 Feb 2009 15:34:43 GMT
>> BioPerl-run-1.6.1.meta                               10289  Wed, 25 Feb 2009 16:07:06 GMT
>> BioPerl-run-1.6.1.readme                               576  Wed, 25 Feb 2009 16:07:06 GMT
>> BioPerl-run-1.6.1.tar.gz                           4082463  Wed, 25 Feb 2009 16:14:37 GMT
>> CHECKSUMS                                             5035  Sun, 03 Oct 2010 19:21:56 GMT
>> 
>> chris
>> 
>> 
> 
> Ok, apparently we've earned a reputation, and it has preceeded us....
> Here's the code that Ricardo uses to filter the list of things to mirror:
> 
>  sub _filter_module {
>    my $self = shift;
>    my $args = shift;
> 
>    if ($self->{skip_perl}) {
>      return 1 if $args->{path} =~ m{/(?:emb|syb|bio)?perl-\d}i;
>      return 1 if $args->{path} =~ m{/(?:parrot|ponie)-\d}i;
>      return 1 if $args->{path} =~ m{/(?:kurila)-\d}i;
>      return 1 if $args->{path} =~ m{/\bperl-?5\.004}i;
>      return 1 if $args->{path} =~ m{/\bperl_mlb\.zip}i;
>    }
> 
>    return 1 if $self->__do_filter($self->{path_filters},   $args->{path});
>    return 1 if $self->__do_filter($self->{module_filters}, $args->{module});
>    return 0;
>  }
> 
> I'll ask him why he's filtering bioperl out and we can see if we can
> fix it.  I'm hoping that it's just an over-eager cut-n-paste of stuff
> that he thinks of as the "perl" source (which is why it's within the
> skip_perl test) and not that we've done something egregious.
> 
> g.

Could be the size of the distribution was considered egregious (we're at 10 MB compressed I think).  Most of the other dists that appear to be filtered are fairly large as well.  That's nothing really these days; would be interested to hear what Ricardo says.

chris




From hlapp at drycafe.net  Fri Mar  4 18:26:25 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Fri, 4 Mar 2011 18:26:25 -0500
Subject: [Bioperl-l] Informatics job opportunity at NESCent
Message-ID: <1878F27F-000D-4C80-B9EA-A83F7887828F@drycafe.net>

(Apologies if you receive multiple copies, and also if you are not  
interested in job opportunities.  In my defense, quite a few people on  
Bio* lists might qualify for (let alone enjoy) the position. And if  
you know someone who might be interested please forward.)

===================================================
User Interface Design and Web Application Developer
===================================================

The National Evolutionary Synthesis Center (NESCent) seeks a creative  
and enthusiastic individual to design user interfaces and web  
applications for scientific applications. The incumbent will work as  
part of a small informatics team in close collaboration with domain  
scientists.

NESCent is an NSF-funded center dedicated to cross-disciplinary  
research in evolutionary science. Our informatics team works closely  
with visiting and resident scientists to support their custom software  
and database development needs. All NESCent software products are open- 
source, and the Center has a number of initiatives to actively promote  
collaborative development of community software resources  
(informatics.nescent.org). Above all, we are enthusiastic about our  
work, about the mission of the Center, and about the contribution of  
informatics to that mission.

Job description: The incumbent will design and develop user interfaces  
and web applications for databases and other software tools for  
sponsored scientists and staff. The job responsibilities include all  
stages of the software development process, including requirements  
gathering, design, implementation, release packaging and  
documentation, as part of a small team (typically 2-3 individuals)  
following project management best practices. We expect the incumbent  
to present their work at conferences and contribute to publications  
with scientific collaborators; interact regularly with visiting and  
resident scientists, other members of the informatics team and Center  
staff; and generally serve as an expert resource for Center personnel.  
The position provides opportunities for professional development. Most  
informatics staff work at our Durham NC offices, located adjacent to  
Duke University, but we do support a wide range of technologies for  
virtual communication with off-site staff and collaborators.

Required Qualifications:
* Demonstrated success collaborating with clients on custom software  
solutions
* Experience with various stages of the software development cycle
* Expertise in development and testing of user interface designs
* Excellent communication skills, both virtual and face-to-face
* A four-year college degree in Computer Science, Bioinformatics or a  
related field

Preferred Qualifications:
* M.S. or Ph.D. in Computer Science, Bioinformatics or related field  
along with demonstrated interest in science, particularly biology
* Expertise in rapid application development and respective  
programming technologies and languages (e.g., modern scripting  
languages and web-application frameworks such as Python/Django, Ruby/ 
Ruby-on-Rails, and Perl/Catalyst), fluency in Java programming, and  
prior experience in relational database programming (PostgreSQL or  
MySQL)
* Expertise in dynamic and interactive web technologies (JavaScript,  
CGI), web service (SOAP, REST, XML, JSON) and semantic web technologies
* Experience with open-source, and collaborative, software  
development, software usability design and assessment
* Expertise in graphic design, data visualization and/or scientific  
data integration

How to apply: Please send cover letter, resume and contact information  
for three references to Dr. Karen Cranston, Training Coordinator and  
Bioinformatics Project Manager (karen.cranston at nescent.org). Review of  
applications will begin March 21, 2011. Informal inquires or requests  
for additional information may be directed to Dr. Cranston by email or  
phone (+1-919-613-2275).

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From hartzell at alerce.com  Sat Mar  5 16:18:50 2011
From: hartzell at alerce.com (George Hartzell)
Date: Sat, 5 Mar 2011 13:18:50 -0800
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <19824.7810.437300.584113@gargle.gargle.HOWL>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
Message-ID: <19826.43194.173739.594355@gargle.gargle.HOWL>

George Hartzell writes:
 > 
 > Hi all,
 > 
 > I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
 > does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
 > seems to have it.  The only tarballs that end up in Chris' directory
 > are these:
 > 
 > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
 > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
 > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
 > 
 > It is listed in the 02packages.details.txt.gz file that is mirrored.
 > 

Here's the conclusion, for the list and posterity.

CPAN::Mini is excluding the BioPerl modules, as well as the perl
source distributions, because they're "too big".

You can get minicpan to mirror all this stuff by adding

 perl: 1

to your .minicpan, which causes the app to set its internal skip_perl
flag to 0, which in turn causes it to mirror the big stuff.

I'm running a few experiments to figure out how much add'l space gets
used if one allows bioperl without all of the other perl source
releases.  Maybe I can convince Ricard to do something less heavy
handed for us.

g.


From hlapp at drycafe.net  Sat Mar  5 21:58:04 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 5 Mar 2011 21:58:04 -0500
Subject: [Bioperl-l] Job opening for GMOD User Support Specialist
Message-ID: <814155D1-1CD5-4E66-B726-2CF7E33EF3CE@drycafe.net>

(Apologies if you receive multiple copies, and also if you are not  
interested in job opportunities. If you know someone who might be  
interested please forward.)

============================
GMOD User Support Specialist
============================

Are you fascinated by genomics and bioinformatics? Are you passionate  
about collaborative open-source software? Do you enjoy teaching and  
working with scientists?  If so, then this position is for you.

The Generic Model Organism Database project (GMOD) is a collection of  
open source software tools for creating and managing biological, and  
particularly genomic, databases.  GMOD has a large, highly  
distributed, and dynamic community of software users and developers.   
The University of North Carolina at Chapel Hill has an opening for a  
GMOD user support specialist, to be based at the US National  
Evolutionary Synthesis Center (NESCent, www.nescent.org) in Durham,  
North Carolina, while serving the international community of GMOD users.

Job Description:

The GMOD user support specialist will maintain online documentation;  
respond to mailing list help requests; present tutorials; organize  
short courses, conference sessions and other community building  
activities; survey user needs, and recruit members of the community to  
assist with these functions.   The incumbent will collaborate closely  
with the GMOD Coordinator (Scott Cain, The Ontario Institute for  
Cancer Research) and other distributed personnel.  See http://gmod.org/wiki/GMOD_Help_Desk 
  for more background on the activities of the user support  
specialist.  The salary range is $68,906 to $82,687, depending on  
qualifications, and the incumbent will receive a comprehensive  
benefits package as an SPA employee within the UNC system.

Qualifications:

Required qualifications include: excellent written and verbal  
communication skills; team orientation with strong interpersonal  
skills. Preferred qualifications include: an MS or PhD in biology,  
computer science or related field; three or more years of experience  
with web programming and relational database management systems; three  
or more years of experience with genome database administration or  
curation, preferably in a GMOD environment; at least one year of  
experience with web content management, ideally using MediaWiki;  
freedom to travel 5-15 weeks/yr.

To Apply:

Please provide a cover letter and CV, including contact information  
for three references, to Hilmar Lapp, Assistant Director of  
Informatics, NESCent, at hlapp at nescent.org, and submit materials  
through http://bit.ly/h9l74r.  Inquiries may be addressed to H. Lapp  
by email or by phone at 919.668.5288.

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From eigenrosen at gmail.com  Sun Mar  6 18:34:09 2011
From: eigenrosen at gmail.com (Michael Rosen)
Date: Sun, 6 Mar 2011 15:34:09 -0800
Subject: [Bioperl-l] bioperl-ext installation
Message-ID: <AANLkTinuaavEU4RwxZu=bmFpUVxpYBAisOv9wgKmQ9+9@mail.gmail.com>

Hi all,
Sorry in advance for a most likely trivial question: I did the standard
make/make test/make install of the bioperl-ext packages with no problems (I
can post the full output if useful). But when I try to run a simple program
that has no trouble on a different machine w bioperl-ext I get:

"The C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has
not been installed.
 Please install the bioperl-ext package"

Any ideas what might be happening? I don't know if the problem was with
installation (but I got "all tests successful during make test") or if I may
need to add the installed packages to some path variable? I'm relatively new
to both bioperl and perl generally so not sure where to start

Thanks


From rmb32 at cornell.edu  Mon Mar  7 11:26:28 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Mon, 07 Mar 2011 11:26:28 -0500
Subject: [Bioperl-l] call for project ideas - Google Summer of Code
Message-ID: <4D750734.4020002@cornell.edu>

Hi all,

Google's Summer of Code is coming round again, very soon now (mentoring 
organization applications are due this week).  We need to update our 
project ideas for prospective Summer of Code interns.  The rest of the 
page also needs updates, changing dates and such.

There's a page on the BioPerl wiki, please have a look and add your 
ideas for intern projects.

For more on Google Summer of Code, what it is and how it works, see 
their FAQ at 
http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2011/faqs

One of the summer intern ideas I have on the page so far is to help with 
the tough grunt work of breaking BioPerl into smaller, more easily 
managed distributions.  I'm sure you all can think of plenty more!

Here's the page: http://www.bioperl.org/wiki/Google_Summer_of_Code

Please have a look, add your project ideas, and delete ones that have 
already been done or are no longer relevant.

Rob



From tzhu at mail.bnu.edu.cn  Tue Mar  8 01:45:11 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Tue, 08 Mar 2011 14:45:11 +0800
Subject: [Bioperl-l] locate introns in a protein sequence
Message-ID: <1299566711.5243.11.camel@ubuntu>

Hello, everyone. For example, I have a GTF file annotating like this,

Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 start_codon 25009
25011 . + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 stop_codon 26003
26005 . + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 24828
25172 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25009 25172 .
+ 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 25245
25364 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25245 25364 .
+ 1 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 25414
26178 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25414 26002 .
+ 1 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";

Obviously this transcript "SPOG_00008T0" has two introns.

Also I have a corresponding protein sequence file like this( in fasta
format),

>SPOG_00008T0 | SPOG_00008 | Schizosaccharomyces cryophilus OY26 exosome
subunit Rrp45 (292 aa)
MSKSLEPSANNKGFIVNALKKELRLDGRSLTDFRDLKIEFGEDYGQVDISLGSTRVMARI
SAEITKPYSDRPFDGIFAITTELTPLASPAFETGRVSEQEVIISRLIEQAIRRSNALDTE
SLCIISGQKCWSVRASVHFINHDGNLVDAACIAVITGLCHFRRPEITVLGDEVTVHSIEE
RVPVPLSVLHTPICVTFSFFEDGSLSAIDASLEEEELRTGSMTVTLNKNREICQIFKAGG
VTIEASSVVACAHTAFQKTTSIISEIQRALDEDLSKKETQFFGGSAENQRS*

I hope to precisely locate these two introns into the protein
sequence(find their location among the amino acids). Please recommend a
relatively convenient method. Thank you!



-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)



From jason at bioperl.org  Tue Mar  8 02:42:54 2011
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 07 Mar 2011 23:42:54 -0800
Subject: [Bioperl-l] locate introns in a protein sequence
In-Reply-To: <1299566711.5243.11.camel@ubuntu>
References: <1299566711.5243.11.camel@ubuntu>
Message-ID: <4D75DDFE.9090602@bioperl.org>

I think there are several ways to do this, the easiest is to walk 
through each exon, and count up the codons, and print out the 
translation of the codons so far when you get to the end of an exon, 
keeping the overhang for the next exon.

That's basically what I do here in terms of counting, though I'm mapping 
introns into an alignment not a single peptide (though undocumented so 
it is a bit impenetrable)
  https://github.com/hyphaltip/thesis/blob/master/src/intron/map_introns_aln.pl

Use Bio::DB::SeqFeature::Store will make this much easier.  You will 
want to convert this Broad GTF to GFF3 with this script
https://github.com/hyphaltip/genome-scripts/blob/master/data_format/gtf2gff3_3level.pl

Then load the annotation along with a scaffold GFF3 (like one from this 
script run on your FASTA genome file
  https://github.com/hyphaltip/genome-scripts/blob/master/gbrowse_tools/fasta_to_gbrowse_scaffold.pl
  - just watch out -- the Broad is capitalizing the contig name 
(Supercontig_3.1) while the FASTA file will have it uncapped and 
truncated name (supercont_3.1) so you need to fix that in either of the 
files so it is consistent - a perl one liner will work here;
perl -i -p -e 's/^>supercont3\./>Supercontig_3./' GENOME.fasta

and load this in and you'll then be able to use the Bio::DB::SeqFeature 
to get all genes, walk through them a CDS for each gene, one a time, and 
then just keep count of the frame you are in and the exon length and 
you'll know where the introns go in the protein.

for my $gene ( $dbh->features(-type => 
"gene:S_cryophilus_OY26_V3_CALLGENES_FINAL_2
") ) {
  for my $mRNA ( $gene->get_SeqFeatures('mRNA') ) {
   for my $CDS ( $mRNA->get_SeqFeatures('CDS') ) {
    my $length = $CDS->length;
    # do some stuff to keep count or whatever you need to figure out 
where you are to put the intron
   }
  }
}

you can also see this code which converts folders of GFF3 + genomes into 
coding seqs, translated peps, etc.
  https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/gff3_to_cdspep.pl

It all depends on what you want to report from this type of query.

Tao Zhu wrote:
> Hello, everyone. For example, I have a GTF file annotating like this,
>
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 start_codon 25009
> 25011 . + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 stop_codon 26003
> 26005 . + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 24828
> 25172 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25009 25172 .
> + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 25245
> 25364 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25245 25364 .
> + 1 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 25414
> 26178 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25414 26002 .
> + 1 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
>
> Obviously this transcript "SPOG_00008T0" has two introns.
>
> Also I have a corresponding protein sequence file like this( in fasta
> format),
>
>> SPOG_00008T0 | SPOG_00008 | Schizosaccharomyces cryophilus OY26 exosome
> subunit Rrp45 (292 aa)
> MSKSLEPSANNKGFIVNALKKELRLDGRSLTDFRDLKIEFGEDYGQVDISLGSTRVMARI
> SAEITKPYSDRPFDGIFAITTELTPLASPAFETGRVSEQEVIISRLIEQAIRRSNALDTE
> SLCIISGQKCWSVRASVHFINHDGNLVDAACIAVITGLCHFRRPEITVLGDEVTVHSIEE
> RVPVPLSVLHTPICVTFSFFEDGSLSAIDASLEEEELRTGSMTVTLNKNREICQIFKAGG
> VTIEASSVVACAHTAFQKTTSIISEIQRALDEDLSKKETQFFGGSAENQRS*
>
> I hope to precisely locate these two introns into the protein
> sequence(find their location among the amino acids). Please recommend a
> relatively convenient method. Thank you!
>
>
>

-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki



From bio.justin100 at gmail.com  Tue Mar  8 17:31:42 2011
From: bio.justin100 at gmail.com (Justin Li)
Date: Tue, 8 Mar 2011 17:31:42 -0500
Subject: [Bioperl-l] Bio::Phylo vs Bio:TreeIO; interface to Fitch
Message-ID: <AANLkTik+HwSQNN3WCkaqQRPz3xqheaa0khmzdD5nndJa@mail.gmail.com>

Hi,

Both Bio::Phylo and Bio:TreeIO seem to be able to parse phylogenetic trees.

Could anyone having experience with both of them please comment on their
capability/robustness/ease of use?

Where can I find the documentation for
"Bio::Tools::Run::PiseApplication::fitch"?

Thanks,

Justin


From abhishek.vit at gmail.com  Tue Mar  8 17:42:03 2011
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Tue, 8 Mar 2011 14:42:03 -0800
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
	Sequences (reads)
Message-ID: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>

Hi All

I have results from different megablast of short reads(DNA sequences)
and after extracting the tophit for each read I want to bin them by
their lineage creating a tree.

For example.

If blast query hits the reference ->
gi|196110604|gb|CP001103.1|__Alteromonas_macleodii_'Deep_ecotype',_complete_genome

I want to get the lineage for this specie.

Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Alteromonas;Alteromona

The final goal is to do the above mapping as efficiently as possible.
Any pointers will be appreciated.


Thanks!
-Abhi


From miguel.pignatelli at uv.es  Wed Mar  9 04:20:47 2011
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Wed, 09 Mar 2011 09:20:47 +0000
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
Message-ID: <4D77466F.4040604@uv.es>

Hi Abhishek,

For a non bioperl related solution, take a look at Bio::LITE::Taxonomy.
It has been design to deal with great number of sequences (it is fast 
and efficient).

You may also find interesting the Blast2lca tool,

https://github.com/emepyc/Blast2lca

It currently works with the best hits for each query (calculates the 
lower common ancestor), but if you want to use only the best hit, please 
drop me a line.

Please, let me know if you need further help with any of these,

Cheers,

M;



On 08/03/11 22:42, Abhishek Pratap wrote:
> Hi All
>
> I have results from different megablast of short reads(DNA sequences)
> and after extracting the tophit for each read I want to bin them by
> their lineage creating a tree.
>
> For example.
>
> If blast query hits the reference ->
> gi|196110604|gb|CP001103.1|__Alteromonas_macleodii_'Deep_ecotype',_complete_genome
>
> I want to get the lineage for this specie.
>
> Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Alteromonas;Alteromona
>
> The final goal is to do the above mapping as efficiently as possible.
> Any pointers will be appreciated.
>
>
> Thanks!
> -Abhi
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From shalabh.sharma7 at gmail.com  Wed Mar  9 12:34:57 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 9 Mar 2011 12:34:57 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <4D77466F.4040604@uv.es>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
Message-ID: <AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>

Hey Abhishek:
                    The other way to deal with this that you can download
the gi_taxaid file from ncbi.
Convert all your GI's to taxaid and use Bio::DB:Taxanomy.
http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Taxon.html

I think there are lot of other options too, if you are interested you can
search for the thread which i started long time back.

Hope this helps.

-Shalabh Sharma
-----------------------------------------------
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636

On Wed, Mar 9, 2011 at 4:20 AM, Miguel Pignatelli
<miguel.pignatelli at uv.es>wrote:

> Hi Abhishek,
>
> For a non bioperl related solution, take a look at Bio::LITE::Taxonomy.
> It has been design to deal with great number of sequences (it is fast and
> efficient).
>
> You may also find interesting the Blast2lca tool,
>
> https://github.com/emepyc/Blast2lca
>
> It currently works with the best hits for each query (calculates the lower
> common ancestor), but if you want to use only the best hit, please drop me a
> line.
>
> Please, let me know if you need further help with any of these,
>
> Cheers,
>
> M;
>
>
>
>
> On 08/03/11 22:42, Abhishek Pratap wrote:
>
>> Hi All
>>
>> I have results from different megablast of short reads(DNA sequences)
>> and after extracting the tophit for each read I want to bin them by
>> their lineage creating a tree.
>>
>> For example.
>>
>> If blast query hits the reference ->
>>
>> gi|196110604|gb|CP001103.1|__Alteromonas_macleodii_'Deep_ecotype',_complete_genome
>>
>> I want to get the lineage for this specie.
>>
>>
>> Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Alteromonas;Alteromona
>>
>> The final goal is to do the above mapping as efficiently as possible.
>> Any pointers will be appreciated.
>>
>>
>> Thanks!
>> -Abhi
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From abhishek.vit at gmail.com  Wed Mar  9 22:25:58 2011
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Wed, 9 Mar 2011 19:25:58 -0800
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
Message-ID: <AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>

Thanks guys. I could not try either method today but will get back to
you if I face problem.

Best,
-Abhi

On Wed, Mar 9, 2011 at 9:34 AM, shalabh sharma
<shalabh.sharma7 at gmail.com> wrote:
> Hey Abhishek:
> ?? ? ? ? ? ? ? ? ? ?The other way to deal with this that you can download
> the gi_taxaid file from ncbi.
> Convert all your GI's to taxaid and use Bio::DB:Taxanomy.
> http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy
> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Taxon.html
> I think there are lot of other options too, if you are interested you can
> search for the thread which i started long time back.
> Hope this helps.
> -Shalabh Sharma
> -----------------------------------------------
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
>
> On Wed, Mar 9, 2011 at 4:20 AM, Miguel Pignatelli <miguel.pignatelli at uv.es>
> wrote:
>>
>> Hi Abhishek,
>>
>> For a non bioperl related solution, take a look at Bio::LITE::Taxonomy.
>> It has been design to deal with great number of sequences (it is fast and
>> efficient).
>>
>> You may also find interesting the Blast2lca tool,
>>
>> https://github.com/emepyc/Blast2lca
>>
>> It currently works with the best hits for each query (calculates the lower
>> common ancestor), but if you want to use only the best hit, please drop me a
>> line.
>>
>> Please, let me know if you need further help with any of these,
>>
>> Cheers,
>>
>> M;
>>
>>
>>
>> On 08/03/11 22:42, Abhishek Pratap wrote:
>>>
>>> Hi All
>>>
>>> I have results from different megablast of short reads(DNA sequences)
>>> and after extracting the tophit for each read I want to bin them by
>>> their lineage creating a tree.
>>>
>>> For example.
>>>
>>> If blast query hits the reference ->
>>>
>>> gi|196110604|gb|CP001103.1|__Alteromonas_macleodii_'Deep_ecotype',_complete_genome
>>>
>>> I want to get the lineage for this specie.
>>>
>>>
>>> Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Alteromonas;Alteromona
>>>
>>> The final goal is to do the above mapping as efficiently as possible.
>>> Any pointers will be appreciated.
>>>
>>>
>>> Thanks!
>>> -Abhi
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>



From ian.mcdowell at gmail.com  Thu Mar 10 12:11:50 2011
From: ian.mcdowell at gmail.com (Ian Mc Dowell)
Date: Thu, 10 Mar 2011 12:11:50 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
	<AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
Message-ID: <AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>

Hi all,

I would like to take local blast hit sequences, i.e. hsp_hseq, and extract
the full sequences of those hits from the original fasta file and put them
in a fasta file of all hits that I can use later.

This should be a widely performed task but I can't find any scripts that
directly address this issue.  I have not acquired the skills to make my own
scripts for this task.

Thanks so much if you have anything that can help me out,

Ian McDowell
Aquatic Pathology
University of Rhode Island


From ian.mcdowell at gmail.com  Thu Mar 10 12:13:01 2011
From: ian.mcdowell at gmail.com (Ian Mc Dowell)
Date: Thu, 10 Mar 2011 12:13:01 -0500
Subject: [Bioperl-l] Local blast hit (hsp_hseq) extracted from fasta file
Message-ID: <AANLkTinF-Ai-AvTPG6ET9xWW0NaeMQugYJpumm4g-7NH@mail.gmail.com>

Hi all,

I would like to take local blast hit sequences, i.e. hsp_hseq in blast xml
format, and extract the full sequences of those hits from the original fasta
file and put them in a fasta file of all hits that I can use later.

This should be a widely performed task but I can't find any scripts that
directly address this issue.  I have not acquired the skills to make my own
scripts for this task.

Thanks so much if you have anything that can help me out,

Ian McDowell
Aquatic Pathology
University of Rhode Island


From rmb32 at cornell.edu  Thu Mar 10 12:22:51 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 10 Mar 2011 12:22:51 -0500
Subject: [Bioperl-l] update Google Summer of Code project ideas
Message-ID: <4D7908EB.6050003@cornell.edu>

Hi all,

Please make sure the BioPerl information is up to date for 2011 on both 
the OBF and BioPerl wikis.  The current page looks pretty good, just be 
aware that Google will be looking at it in the next few days to evaluate 
whether OBF will be accepted again this year to GSoC.

OBF wiki page: http://www.open-bio.org/wiki/Google_Summer_of_Code
BioPerl wiki: http://bioperl.org/wiki/Google_Summer_of_Code

Rob

----
Robert Buels
(prospective) 2011 OBF GSoC Organization Admin


From shalabh.sharma7 at gmail.com  Thu Mar 10 12:24:04 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Thu, 10 Mar 2011 12:24:04 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
	<AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
	<AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>
Message-ID: <AANLkTik9jt9Pkrgng4zv4nRhDmK0_bRpnbGJe+i9Dark@mail.gmail.com>

Hey Ian,
            I am not sure if i understood your problem completely.
But if you have ids of blast hits you can use 'fastacmd' to fetch sequences
from the database you used for blast.

-Shalabh Sharma
-----------------------------------------
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636

On Thu, Mar 10, 2011 at 12:11 PM, Ian Mc Dowell <ian.mcdowell at gmail.com>wrote:

> Hi all,
>
> I would like to take local blast hit sequences, i.e. hsp_hseq, and extract
> the full sequences of those hits from the original fasta file and put them
> in a fasta file of all hits that I can use later.
>
> This should be a widely performed task but I can't find any scripts that
> directly address this issue.  I have not acquired the skills to make my own
> scripts for this task.
>
> Thanks so much if you have anything that can help me out,
>
> Ian McDowell
> Aquatic Pathology
> University of Rhode Island
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From ian.mcdowell at gmail.com  Thu Mar 10 12:31:29 2011
From: ian.mcdowell at gmail.com (Ian Mc Dowell)
Date: Thu, 10 Mar 2011 12:31:29 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTik9jt9Pkrgng4zv4nRhDmK0_bRpnbGJe+i9Dark@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
	<AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
	<AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>
	<AANLkTik9jt9Pkrgng4zv4nRhDmK0_bRpnbGJe+i9Dark@mail.gmail.com>
Message-ID: <AANLkTi=-12y0LWzV2gRgriE=z3=d_-OKwDRe2wSWkmwr@mail.gmail.com>

I have a deeply sequenced transcriptome so when I look for a gene of
interest in my short reads (108bp) I get thousands of hits, at very low E
values.  And I want to do this for many sequences of interest. That's why I
want a script to automate the process of grabbing the accession numbers from
the blast xml output, then searching in the fasta file which is equivalent
to my local database and pulling those relevant reads.

On Thu, Mar 10, 2011 at 12:24 PM, shalabh sharma
<shalabh.sharma7 at gmail.com>wrote:

> Hey Ian,
>             I am not sure if i understood your problem completely.
> But if you have ids of blast hits you can use 'fastacmd' to fetch sequences
> from the database you used for blast.
>
> -Shalabh Sharma
> -----------------------------------------
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
>
> On Thu, Mar 10, 2011 at 12:11 PM, Ian Mc Dowell <ian.mcdowell at gmail.com>wrote:
>
>> Hi all,
>>
>> I would like to take local blast hit sequences, i.e. hsp_hseq, and extract
>> the full sequences of those hits from the original fasta file and put them
>> in a fasta file of all hits that I can use later.
>>
>> This should be a widely performed task but I can't find any scripts that
>> directly address this issue.  I have not acquired the skills to make my
>> own
>> scripts for this task.
>>
>> Thanks so much if you have anything that can help me out,
>>
>> Ian McDowell
>> Aquatic Pathology
>> University of Rhode Island
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>


From hrh at fmi.ch  Thu Mar 10 12:37:07 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Thu, 10 Mar 2011 18:37:07 +0100
Subject: [Bioperl-l] Local blast hit (hsp_hseq) extracted from fasta file
In-Reply-To: <AANLkTinF-Ai-AvTPG6ET9xWW0NaeMQugYJpumm4g-7NH@mail.gmail.com>
References: <AANLkTinF-Ai-AvTPG6ET9xWW0NaeMQugYJpumm4g-7NH@mail.gmail.com>
Message-ID: <4D790C43.5080801@fmi.ch>



On 03/10/2011 06:13 PM, Ian Mc Dowell wrote:
> Hi all,
>
> I would like to take local blast hit sequences, i.e. hsp_hseq in blast xml
> format, and extract the full sequences of those hits from the original fasta
> file and put them in a fasta file of all hits that I can use later.
>
> This should be a widely performed task but I can't find any scripts that
> directly address this issue.  I have not acquired the skills to make my own
> scripts for this task.


Hi Ian

It is not a Bioperl solution, but a simple one:

Assuming, you are using the NCBI blast+ tools, make sure you create the 
BLAST indices with the "-parse_seqids" option. This will allow you to 
extract individual sequences (in fasta format) from the BLAST database 
with the command 'blastdbcmd' by providing a comma-delimited search 
string of sequence identifiers. Fore more details see:

http://tinyurl.com/5sq2ehg


Regards, Hans


> Thanks so much if you have anything that can help me out,
>
> Ian McDowell
> Aquatic Pathology
> University of Rhode Island
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From shalabh.sharma7 at gmail.com  Thu Mar 10 12:42:51 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Thu, 10 Mar 2011 12:42:51 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTi=-12y0LWzV2gRgriE=z3=d_-OKwDRe2wSWkmwr@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
	<AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
	<AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>
	<AANLkTik9jt9Pkrgng4zv4nRhDmK0_bRpnbGJe+i9Dark@mail.gmail.com>
	<AANLkTi=-12y0LWzV2gRgriE=z3=d_-OKwDRe2wSWkmwr@mail.gmail.com>
Message-ID: <AANLkTin13Uhj8ZgQ1-+c0SjXbRBvU8VHdGhUXyqea1FV@mail.gmail.com>

Hey Ian,
             Writing that kind of script would not take that much time. But
i am not very much familiar with xml format.
But still you can do without writing a complicated script.

once you get the output you can get all the ids (use grep or simple perl
script to parse ids).
Then use that list of ids to fetch sequences from your database by using
"fastacmd" .

-Shalabh


On Thu, Mar 10, 2011 at 12:31 PM, Ian Mc Dowell <ian.mcdowell at gmail.com>wrote:

> I have a deeply sequenced transcriptome so when I look for a gene of
> interest in my short reads (108bp) I get thousands of hits, at very low E
> values.  And I want to do this for many sequences of interest. That's why I
> want a script to automate the process of grabbing the accession numbers from
> the blast xml output, then searching in the fasta file which is equivalent
> to my local database and pulling those relevant reads.
>
> On Thu, Mar 10, 2011 at 12:24 PM, shalabh sharma <
> shalabh.sharma7 at gmail.com> wrote:
>
>> Hey Ian,
>>             I am not sure if i understood your problem completely.
>> But if you have ids of blast hits you can use 'fastacmd' to fetch
>> sequences from the database you used for blast.
>>
>> -Shalabh Sharma
>> -----------------------------------------
>> Shalabh Sharma
>> Scientific Computing Professional Associate (Bioinformatics Specialist)
>> Department of Marine Sciences
>> University of Georgia
>> Athens, GA 30602-3636
>>
>> On Thu, Mar 10, 2011 at 12:11 PM, Ian Mc Dowell <ian.mcdowell at gmail.com>wrote:
>>
>>> Hi all,
>>>
>>> I would like to take local blast hit sequences, i.e. hsp_hseq, and
>>> extract
>>> the full sequences of those hits from the original fasta file and put
>>> them
>>> in a fasta file of all hits that I can use later.
>>>
>>> This should be a widely performed task but I can't find any scripts that
>>> directly address this issue.  I have not acquired the skills to make my
>>> own
>>> scripts for this task.
>>>
>>> Thanks so much if you have anything that can help me out,
>>>
>>> Ian McDowell
>>> Aquatic Pathology
>>> University of Rhode Island
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


From cjfields at illinois.edu  Mon Mar 14 13:44:44 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 12:44:44 -0500
Subject: [Bioperl-l] bioperl wiki spam
Message-ID: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>

All,

We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:

http://www.mediawiki.org/wiki/Extension:ConfirmAccount

I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.  

Any thoughts?

chris


From cjfields at illinois.edu  Mon Mar 14 13:51:51 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 12:51:51 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Google Summer of Code
Message-ID: <42CCFB33-B9FC-41C2-987D-BF969F5111EC@illinois.edu>

All,

As Rob Buels previously mentioned, the Open Bioinformatics Foundation has again applied for the Google Summer of Code (GSoC).  BioPerl has been involved with GSoC over the last several years, most recently when Jun Yin refactored the alignment subsystem, code that will be incorporated into BioPerl after the 1.6.2 release:

http://www.bioperl.org/wiki/Google_Summer_of_Code#2010

We have several ideas for projects for the upcoming GSoC 2011 on the wiki, but we are open to just about anything BioPerl-related.  We are also looking for more potential mentors!  If you have ideas or would like to be a mentor, free to submit to the web page, discuss it on this list, or join us on IRC (#obf-soc on freenode).

chris

Christopher Fields
IGB Postdoctoral Fellow
Genomics of Neural & Behavioral Plasticity
University of Illinois Urbana-Champaign
Institute for Genomic Biology
1206 W. Gregory Dr. , MC-195
Urbana, IL 61801




From scott at scottcain.net  Mon Mar 14 14:12:55 2011
From: scott at scottcain.net (Scott Cain)
Date: Mon, 14 Mar 2011 14:12:55 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
Message-ID: <AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>

Hi Chris,

The GMOD wiki has been getting hit similarly.  I've been thinking
about the "vampire" model that EcoliWiki uses: once you have an
account, you have the ability to approve other people's accounts.  The
hope being to distribute the load.  I'm not thrilled about it though:
I want the barrier to entry to be as low as possible.  We already make
it so that you have to have an account to edit, passing a recaptcha on
the way.  Apparently that barrier is already a little too low :-/

Scott


On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
> All,
>
> We have been getting inundated on the wiki with spam lately. ?In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>
> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>
> I wanted to get everyone's opinion on this prior to enforcing it. ?The queue is pretty configurable, and one can set this to auto-delete old requests.
>
> Any thoughts?
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From cjfields at illinois.edu  Mon Mar 14 14:25:05 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 13:25:05 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
Message-ID: <5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>

On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):

"Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."

I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.

chris

On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:

> Hi Chris,
> 
> The GMOD wiki has been getting hit similarly.  I've been thinking
> about the "vampire" model that EcoliWiki uses: once you have an
> account, you have the ability to approve other people's accounts.  The
> hope being to distribute the load.  I'm not thrilled about it though:
> I want the barrier to entry to be as low as possible.  We already make
> it so that you have to have an account to edit, passing a recaptcha on
> the way.  Apparently that barrier is already a little too low :-/
> 
> Scott
> 
> 
> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> All,
>> 
>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>> 
>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>> 
>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>> 
>> Any thoughts?
>> 
>> chris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research




From David.Messina at sbc.su.se  Mon Mar 14 14:25:10 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 14 Mar 2011 19:25:10 +0100
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
Message-ID: <5650D7D3-11ED-4ABF-89E8-BE9175848196@sbc.su.se>

> Any thoughts?

Do it.



From hlapp at drycafe.net  Mon Mar 14 14:48:55 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Mon, 14 Mar 2011 14:48:55 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
Message-ID: <6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>

Any update on the OpenID extension?

	-hilmar

On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:

> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit 
> ):
>
> "Unfortunately, reCAPTCHA might be a victim of its own success - as  
> of 2011, some spammers appear to have figured out a way to bypass  
> it, either through character recognition or by using humans. For  
> that reason, it is not necessarily recommended."
>
> I agree about the barrier to entry issue, but unfortunately with the  
> wiki we're facing a reality check re: spam attacks.  We can probably  
> set up a new group for users that allows account approval, though,  
> which might alleviate the process somewhat.
>
> chris
>
> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>
>> Hi Chris,
>>
>> The GMOD wiki has been getting hit similarly.  I've been thinking
>> about the "vampire" model that EcoliWiki uses: once you have an
>> account, you have the ability to approve other people's accounts.   
>> The
>> hope being to distribute the load.  I'm not thrilled about it though:
>> I want the barrier to entry to be as low as possible.  We already  
>> make
>> it so that you have to have an account to edit, passing a recaptcha  
>> on
>> the way.  Apparently that barrier is already a little too low :-/
>>
>> Scott
>>
>>
>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields  
>> <cjfields at illinois.edu> wrote:
>>> All,
>>>
>>> We have been getting inundated on the wiki with spam lately.  In  
>>> order to get on top of this, I'm thinking about having the wiki  
>>> set up so wiki admins approve new user accounts, using the  
>>> ConfirmAccount plugin:
>>>
>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>
>>> I wanted to get everyone's opinion on this prior to enforcing it.   
>>> The queue is pretty configurable, and one can set this to auto- 
>>> delete old requests.
>>>
>>> Any thoughts?
>>>
>>> chris
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>>
>> -- 
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at  
>> scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From cjfields at illinois.edu  Mon Mar 14 14:55:31 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 13:55:31 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
Message-ID: <2EB73F6E-AAD3-46BD-BB57-AAB3AA1063F7@illinois.edu>

We can test that one out first.  Maybe that will help.

chris

On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:

> Any update on the OpenID extension?
> 
> 	-hilmar
> 
> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
> 
>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>> 
>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>> 
>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>> 
>> chris
>> 
>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>> 
>>> Hi Chris,
>>> 
>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>> about the "vampire" model that EcoliWiki uses: once you have an
>>> account, you have the ability to approve other people's accounts.  The
>>> hope being to distribute the load.  I'm not thrilled about it though:
>>> I want the barrier to entry to be as low as possible.  We already make
>>> it so that you have to have an account to edit, passing a recaptcha on
>>> the way.  Apparently that barrier is already a little too low :-/
>>> 
>>> Scott
>>> 
>>> 
>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>> All,
>>>> 
>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>> 
>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>> 
>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>> 
>>>> Any thoughts?
>>>> 
>>>> chris
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hartzell at alerce.com  Mon Mar 14 20:37:36 2011
From: hartzell at alerce.com (George Hartzell)
Date: Mon, 14 Mar 2011 17:37:36 -0700
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <5650D7D3-11ED-4ABF-89E8-BE9175848196@sbc.su.se>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<5650D7D3-11ED-4ABF-89E8-BE9175848196@sbc.su.se>
Message-ID: <19838.46288.715397.413627@gargle.gargle.HOWL>

Dave Messina writes:
 > > Any thoughts?
 > 
 > Do it.

Do it^2.  You have better things to do than waste time on spammers.

It's nice to not have the bar too high for new folks, but in this age
of spam I think people understand.

g.


From cjfields at illinois.edu  Mon Mar 14 23:01:45 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 22:01:45 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
Message-ID: <84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>

Okay, we have bioperl.org set up to use OpenID, works well:  

http://www.bioperl.org/wiki/Special:OpenIDLogin

I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.

chris

On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:

> Any update on the OpenID extension?
> 
> 	-hilmar
> 
> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
> 
>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>> 
>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>> 
>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>> 
>> chris
>> 
>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>> 
>>> Hi Chris,
>>> 
>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>> about the "vampire" model that EcoliWiki uses: once you have an
>>> account, you have the ability to approve other people's accounts.  The
>>> hope being to distribute the load.  I'm not thrilled about it though:
>>> I want the barrier to entry to be as low as possible.  We already make
>>> it so that you have to have an account to edit, passing a recaptcha on
>>> the way.  Apparently that barrier is already a little too low :-/
>>> 
>>> Scott
>>> 
>>> 
>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>> All,
>>>> 
>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>> 
>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>> 
>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>> 
>>>> Any thoughts?
>>>> 
>>>> chris
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Mon Mar 14 23:12:16 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 22:12:16 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <19838.46288.715397.413627@gargle.gargle.HOWL>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<5650D7D3-11ED-4ABF-89E8-BE9175848196@sbc.su.se>
	<19838.46288.715397.413627@gargle.gargle.HOWL>
Message-ID: <D49A790C-E30D-4587-B9B6-0D5E99B84D97@illinois.edu>

On Mar 14, 2011, at 7:37 PM, George Hartzell wrote:

> Dave Messina writes:
>>> Any thoughts?
>> 
>> Do it.
> 
> Do it^2.  You have better things to do than waste time on spammers.
> 
> It's nice to not have the bar too high for new folks, but in this age
> of spam I think people understand.
> 
> g.

I've disabled new account creation unless OpenID is used; apparently this has worked elsewhere to cut down on spam.  All old accounts are still active, but I think new users will be prompted to tie an OpenID to the account.  

Anyway, if that doesn't work we'll go to the next step (account verification).

chris




From ross at cuhk.edu.hk  Tue Mar 15 01:54:35 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Tue, 15 Mar 2011 13:54:35 +0800
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
Message-ID: <004001cbe2d5$76598200$630c8600$@edu.hk>

$gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
'Fasta');            
$allseqobj = $gb->get_Stream_by_acc("A3ZI37");        
                l
print "HEELO";                                           
while ($seqobj = $allseqobj->next_seq) {             
                        #$seqobj = $allseqobj->next_seq;

                        $seq=$seqobj->seq;

                        }

                    print "222   HEELO";



I find that the 1st HEELO can be printed while the 2nd one can't. Google
does not return checking success/failure or null/exist of the Seq Object. As
the 1st HEELO can be executed, so no throw/exception occurs for the
get_Stream_by_acc. So what can I do? The real case is not hard-coding this
A3ZI37 but reading a file that may contain a lot of these "illegitimate"
accession numbers.



From David.Messina at sbc.su.se  Tue Mar 15 05:02:05 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 15 Mar 2011 10:02:05 +0100
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <004001cbe2d5$76598200$630c8600$@edu.hk>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
Message-ID: <AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>

Hi Ross,

Your code is incomplete and you didn't provide the output from running it,
so it's not easy to figure out where you're going wrong.

Try copying the example code directly from here


http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html

and making sure that works first before modifying it.


More documentation and examples here:
http://www.bioperl.org/wiki/HOWTO:Beginners
http://www.bioperl.org/wiki/Bioperl_scripts


Dave




On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:

> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
> 'Fasta');
> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>                l
> print "HEELO";
> while ($seqobj = $allseqobj->next_seq) {
>                        #$seqobj = $allseqobj->next_seq;
>
>                        $seq=$seqobj->seq;
>
>                        }
>
>                    print "222   HEELO";
>
>
>
> I find that the 1st HEELO can be printed while the 2nd one can't. Google
> does not return checking success/failure or null/exist of the Seq Object.
> As
> the 1st HEELO can be executed, so no throw/exception occurs for the
> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
> accession numbers.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From ross at cuhk.edu.hk  Tue Mar 15 10:16:56 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Tue, 15 Mar 2011 22:16:56 +0800
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
Message-ID: <005301cbe31b$a3bee550$eb3caff0$@edu.hk>

While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...

 

 

#!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   

use Bio::DB::GenBank;

 

$gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');


$allseqobj = $gb->get_Stream_by_acc("A3ZI37");


 print "HEELO";

while ($seqobj = $allseqobj->next_seq) {
                       #$seqobj = $allseqobj->next_seq;
                       $seq=$seqobj->seq;
}
print "222   HEELO";




 

 

From: Dave Messina [mailto:David.Messina at sbc.su.se] 
Sent: 2011?3?15? 17:02
To: Ross KK Leung
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] how to prevent forced exit?

 

Hi Ross,

 

Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.

 

Try copying the example code directly from here

 

    http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html

 

and making sure that works first before modifying it.

 

 

More documentation and examples here:

http://www.bioperl.org/wiki/HOWTO:Beginners

http://www.bioperl.org/wiki/Bioperl_scripts

 

 

Dave

 

 

 

On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:

$gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
'Fasta');
$allseqobj = $gb->get_Stream_by_acc("A3ZI37");
               l
print "HEELO";
while ($seqobj = $allseqobj->next_seq) {
                       #$seqobj = $allseqobj->next_seq;

                       $seq=$seqobj->seq;

                       }

                   print "222   HEELO";



I find that the 1st HEELO can be printed while the 2nd one can't. Google
does not return checking success/failure or null/exist of the Seq Object. As
the 1st HEELO can be executed, so no throw/exception occurs for the
get_Stream_by_acc. So what can I do? The real case is not hard-coding this
A3ZI37 but reading a file that may contain a lot of these "illegitimate"
accession numbers.

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

 




From cjfields at illinois.edu  Tue Mar 15 10:44:23 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 15 Mar 2011 09:44:23 -0500
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <005301cbe31b$a3bee550$eb3caff0$@edu.hk>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
Message-ID: <DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>

Ross,

Hope you're exaggerating, you really shouldn't use this service for retrieving 1 million records as you'll likely find your IP banned by NCBI; they are starting to enforce stricter web-based access to their  server now.  Bio::DB::GenBank uses a GET HTTP request using URI-based parameters which effectively limits the length of the query to around 200-300 IDs per request, so you would have to split single one large request many.  Thousands of repeated requests, even with a timeout, may flag your IP as 'spam'.  You can use something like Bio::DB::EUtilities to grab larger groups of seqs (~1000 IDs) b/c the latest EUtilities uses POST requests vs GET for a large number of IDs, but you are still effectively limited by the number of requests.

Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?

chris

On Mar 15, 2011, at 9:16 AM, Ross KK Leung wrote:

> While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...
> 
> 
> 
> 
> 
> #!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   
> 
> use Bio::DB::GenBank;
> 
> 
> 
> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');
> 
> 
> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
> 
> 
> print "HEELO";
> 
> while ($seqobj = $allseqobj->next_seq) {
>                       #$seqobj = $allseqobj->next_seq;
>                       $seq=$seqobj->seq;
> }
> print "222   HEELO";
> 
> 
> 
> 
> 
> 
> 
> 
> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
> Sent: 2011?3?15? 17:02
> To: Ross KK Leung
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] how to prevent forced exit?
> 
> 
> 
> Hi Ross,
> 
> 
> 
> Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.
> 
> 
> 
> Try copying the example code directly from here
> 
> 
> 
>    http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html
> 
> 
> 
> and making sure that works first before modifying it.
> 
> 
> 
> 
> 
> More documentation and examples here:
> 
> http://www.bioperl.org/wiki/HOWTO:Beginners
> 
> http://www.bioperl.org/wiki/Bioperl_scripts
> 
> 
> 
> 
> 
> Dave
> 
> 
> 
> 
> 
> 
> 
> On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:
> 
> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
> 'Fasta');
> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>               l
> print "HEELO";
> while ($seqobj = $allseqobj->next_seq) {
>                       #$seqobj = $allseqobj->next_seq;
> 
>                       $seq=$seqobj->seq;
> 
>                       }
> 
>                   print "222   HEELO";
> 
> 
> 
> I find that the 1st HEELO can be printed while the 2nd one can't. Google
> does not return checking success/failure or null/exist of the Seq Object. As
> the 1st HEELO can be executed, so no throw/exception occurs for the
> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
> accession numbers.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From dvadell at clustering.com.ar  Tue Mar 15 10:59:20 2011
From: dvadell at clustering.com.ar (Diego M. Vadell)
Date: Tue, 15 Mar 2011 11:59:20 -0300
Subject: [Bioperl-l] advice about bioperl-ext -- defunct?
Message-ID: <38be317a0815ba7276d56e5a6c93d116@webmail.clustering.com.ar>

Hi,

 I have just downloaded bioperl-ext from github, and it says "XS-based
BioPerl extensions to C libraries (defunct) ? [Read more ->
https://github.com/bioperl/bioperl-ext#readme]" . I read the readme but it
looks alive ( i.e. no mention of an ending of the project ). 

 I installed it ( adding "-fPIC" in the 3 Makefile.PLs ) and I'm about to
start using it. But, does is it still maintained? Is it still in use?
Recommended for a new project? I don't mind fixing compilation errors, but
maybe there is a new package that superseded it. Maybe I'm downloading it
from the wrong place.

 Regards,
 -- Diego





From jimhu at tamu.edu  Tue Mar 15 11:25:36 2011
From: jimhu at tamu.edu (Jim Hu)
Date: Tue, 15 Mar 2011 10:25:36 -0500
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
	<DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
Message-ID: <9CD1455E-88B4-4E2A-B3BC-398C10D5AAA9@tamu.edu>

Hi Chris,

A version of this admonition should be on every wiki HOWTO that involves retrieving records from external sources, and in the docs for the relevant modules.  Speaking as someone who has used BioPerl intermittently for years, and who has Sysiphus-like relationship with the learning curve, I think the docs could use more discussion of when to use particular modules in addition to the details of how to use them provided in the perldocs. I realize this is hard, given the perl "more than one way to do it" world view, but that's my $0.02.

Since BioPerl.org is a wiki, I suppose I should do that admonition edit myself... especially since I already know the wiki markup to transclude the same text into multiple pages.

Jim

Sent from my iPad

On Mar 15, 2011, at 9:44 AM, Chris Fields <cjfields at illinois.edu> wrote:

> Ross,
> 
> Hope you're exaggerating, you really shouldn't use this service for retrieving 1 million records as you'll likely find your IP banned by NCBI; they are starting to enforce stricter web-based access to their  server now.  Bio::DB::GenBank uses a GET HTTP request using URI-based parameters which effectively limits the length of the query to around 200-300 IDs per request, so you would have to split single one large request many.  Thousands of repeated requests, even with a timeout, may flag your IP as 'spam'.  You can use something like Bio::DB::EUtilities to grab larger groups of seqs (~1000 IDs) b/c the latest EUtilities uses POST requests vs GET for a large number of IDs, but you are still effectively limited by the number of requests.
> 
> Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?
> 
> chris
> 
> On Mar 15, 2011, at 9:16 AM, Ross KK Leung wrote:
> 
>> While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...
>> 
>> 
>> 
>> 
>> 
>> #!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   
>> 
>> use Bio::DB::GenBank;
>> 
>> 
>> 
>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');
>> 
>> 
>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>> 
>> 
>> print "HEELO";
>> 
>> while ($seqobj = $allseqobj->next_seq) {
>>                      #$seqobj = $allseqobj->next_seq;
>>                      $seq=$seqobj->seq;
>> }
>> print "222   HEELO";
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
>> Sent: 2011?3?15? 17:02
>> To: Ross KK Leung
>> Cc: bioperl-l at lists.open-bio.org
>> Subject: Re: [Bioperl-l] how to prevent forced exit?
>> 
>> 
>> 
>> Hi Ross,
>> 
>> 
>> 
>> Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.
>> 
>> 
>> 
>> Try copying the example code directly from here
>> 
>> 
>> 
>>   http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html
>> 
>> 
>> 
>> and making sure that works first before modifying it.
>> 
>> 
>> 
>> 
>> 
>> More documentation and examples here:
>> 
>> http://www.bioperl.org/wiki/HOWTO:Beginners
>> 
>> http://www.bioperl.org/wiki/Bioperl_scripts
>> 
>> 
>> 
>> 
>> 
>> Dave
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:
>> 
>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
>> 'Fasta');
>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>              l
>> print "HEELO";
>> while ($seqobj = $allseqobj->next_seq) {
>>                      #$seqobj = $allseqobj->next_seq;
>> 
>>                      $seq=$seqobj->seq;
>> 
>>                      }
>> 
>>                  print "222   HEELO";
>> 
>> 
>> 
>> I find that the 1st HEELO can be printed while the 2nd one can't. Google
>> does not return checking success/failure or null/exist of the Seq Object. As
>> the 1st HEELO can be executed, so no throw/exception occurs for the
>> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
>> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
>> accession numbers.
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Tue Mar 15 11:45:20 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 15 Mar 2011 10:45:20 -0500
Subject: [Bioperl-l] advice about bioperl-ext -- defunct?
In-Reply-To: <38be317a0815ba7276d56e5a6c93d116@webmail.clustering.com.ar>
References: <38be317a0815ba7276d56e5a6c93d116@webmail.clustering.com.ar>
Message-ID: <3892F905-2D1F-43CF-8968-055C9F902504@illinois.edu>

On Mar 15, 2011, at 9:59 AM, Diego M. Vadell wrote:

> Hi,
> 
> I have just downloaded bioperl-ext from github, and it says "XS-based
> BioPerl extensions to C libraries (defunct) ? [Read more ->
> https://github.com/bioperl/bioperl-ext#readme]" . I read the readme but it
> looks alive ( i.e. no mention of an ending of the project ). 
> 
> I installed it ( adding "-fPIC" in the 3 Makefile.PLs ) and I'm about to
> start using it. But, does is it still maintained? Is it still in use?

Re: being maintained: No, except Bio::Tools::HMM (https://github.com/bioperl/Bio-Tools-HMM)

Re: in use: somewhat.  I think some still use Bio::SeqIO::staden::read and Bio::Ext::Align, but they haven't actively maintained in quite some time.

> Recommended for a new project? I don't mind fixing compilation errors, but
> maybe there is a new package that superseded it. Maybe I'm downloading it
> from the wrong place.
> 
> Regards,
> -- Diego

The code still works in some cases but is somewhat bit-rotted (I recall getting very inconsistent results from Bio::SearchUtils, not sure why).  

We (Bio* projects) are starting to consolidate around using BioLib for consistent bindings to C/C++ libraries, though that project is undergoing some changes:

http://biolib.open-bio.org/wiki/Main_Page

Pjotr Prins is the lead on that, worth talking to.  The next big step is to interface with EMBOSS libraries, which is very promising.

chris


From cjfields at illinois.edu  Tue Mar 15 11:54:38 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 15 Mar 2011 10:54:38 -0500
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <9CD1455E-88B4-4E2A-B3BC-398C10D5AAA9@tamu.edu>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
	<DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
	<9CD1455E-88B4-4E2A-B3BC-398C10D5AAA9@tamu.edu>
Message-ID: <3E73745F-A687-4229-B71E-5C56B2D1FBAE@illinois.edu>

Jim,

It's worth noting in something more prominent, like the tutorial, FAQ, and appropriate HOWTO's.  We've long considered whether it would be worth setting up a cookbook-like section that includes simple workflows, that would also be appropriate for something like this.

Also, I do think this is mentioned in the POD for several modules, but worth adding a prominent section on it if it's not present.  In Bio::DB::GenBank:

  WARNING: Please do NOT spam the Entrez web server with multiple requests.  NCBI offers Batch Entrez for this purpose.

That could be placed somewhere that is a bit more helpful.

chris


On Mar 15, 2011, at 10:25 AM, Jim Hu wrote:

> Hi Chris,
> 
> A version of this admonition should be on every wiki HOWTO that involves retrieving records from external sources, and in the docs for the relevant modules.  Speaking as someone who has used BioPerl intermittently for years, and who has Sysiphus-like relationship with the learning curve, I think the docs could use more discussion of when to use particular modules in addition to the details of how to use them provided in the perldocs. I realize this is hard, given the perl "more than one way to do it" world view, but that's my $0.02.
> 
> Since BioPerl.org is a wiki, I suppose I should do that admonition edit myself... especially since I already know the wiki markup to transclude the same text into multiple pages.
> 
> Jim
> 
> Sent from my iPad
> 
> On Mar 15, 2011, at 9:44 AM, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Ross,
>> 
>> Hope you're exaggerating, you really shouldn't use this service for retrieving 1 million records as you'll likely find your IP banned by NCBI; they are starting to enforce stricter web-based access to their  server now.  Bio::DB::GenBank uses a GET HTTP request using URI-based parameters which effectively limits the length of the query to around 200-300 IDs per request, so you would have to split single one large request many.  Thousands of repeated requests, even with a timeout, may flag your IP as 'spam'.  You can use something like Bio::DB::EUtilities to grab larger groups of seqs (~1000 IDs) b/c the latest EUtilities uses POST requests vs GET for a large number of IDs, but you are still effectively limited by the number of requests.
>> 
>> Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?
>> 
>> chris
>> 
>> On Mar 15, 2011, at 9:16 AM, Ross KK Leung wrote:
>> 
>>> While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...
>>> 
>>> 
>>> 
>>> 
>>> 
>>> #!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   
>>> 
>>> use Bio::DB::GenBank;
>>> 
>>> 
>>> 
>>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');
>>> 
>>> 
>>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>> 
>>> 
>>> print "HEELO";
>>> 
>>> while ($seqobj = $allseqobj->next_seq) {
>>>                     #$seqobj = $allseqobj->next_seq;
>>>                     $seq=$seqobj->seq;
>>> }
>>> print "222   HEELO";
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
>>> Sent: 2011?3?15? 17:02
>>> To: Ross KK Leung
>>> Cc: bioperl-l at lists.open-bio.org
>>> Subject: Re: [Bioperl-l] how to prevent forced exit?
>>> 
>>> 
>>> 
>>> Hi Ross,
>>> 
>>> 
>>> 
>>> Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.
>>> 
>>> 
>>> 
>>> Try copying the example code directly from here
>>> 
>>> 
>>> 
>>>  http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html
>>> 
>>> 
>>> 
>>> and making sure that works first before modifying it.
>>> 
>>> 
>>> 
>>> 
>>> 
>>> More documentation and examples here:
>>> 
>>> http://www.bioperl.org/wiki/HOWTO:Beginners
>>> 
>>> http://www.bioperl.org/wiki/Bioperl_scripts
>>> 
>>> 
>>> 
>>> 
>>> 
>>> Dave
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:
>>> 
>>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
>>> 'Fasta');
>>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>>             l
>>> print "HEELO";
>>> while ($seqobj = $allseqobj->next_seq) {
>>>                     #$seqobj = $allseqobj->next_seq;
>>> 
>>>                     $seq=$seqobj->seq;
>>> 
>>>                     }
>>> 
>>>                 print "222   HEELO";
>>> 
>>> 
>>> 
>>> I find that the 1st HEELO can be printed while the 2nd one can't. Google
>>> does not return checking success/failure or null/exist of the Seq Object. As
>>> the 1st HEELO can be executed, so no throw/exception occurs for the
>>> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
>>> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
>>> accession numbers.
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From dvadell at clustering.com.ar  Tue Mar 15 12:01:22 2011
From: dvadell at clustering.com.ar (Diego M. Vadell)
Date: Tue, 15 Mar 2011 13:01:22 -0300
Subject: [Bioperl-l] advice about bioperl-ext -- defunct?
In-Reply-To: <3892F905-2D1F-43CF-8968-055C9F902504@illinois.edu>
Message-ID: <218950b508a0e4a8ad07227974989e5f@webmail.clustering.com.ar>

Hi Chris,

 Thank you! I will align with bioperl-run then, and keep an eye on biolib.

Cheers,
 -- Diego


 
----------------original message-----------------
From: "Chris Fields" cjfields at illinois.edu
To: "Diego M. Vadell" dvadell at clustering.com.ar
CC: bioperl-l at lists.open-bio.org
Date: Tue, 15 Mar 2011 10:45:20 -0500
-------------------------------------------------
 
 
> On Mar 15, 2011, at 9:59 AM, Diego M. Vadell wrote:
> 
>> Hi,
>> 
>> I have just downloaded bioperl-ext from github, and it says "XS-based
>> BioPerl extensions to C libraries (defunct) ? [Read more ->
>> https://github.com/bioperl/bioperl-ext#readme]" . I read the readme but 
>> it
>> looks alive ( i.e. no mention of an ending of the project ). 
>> 
>> I installed it ( adding "-fPIC" in the 3 Makefile.PLs ) and I'm about to
>> start using it. But, does is it still maintained? Is it still in use?
> 
> Re: being maintained: No, except Bio::Tools::HMM 
> (https://github.com/bioperl/Bio-Tools-HMM)
> 
> Re: in use: somewhat. I think some still use Bio::SeqIO::staden::read and 
> Bio::Ext::Align, but they haven't actively maintained in quite some time.
> 
>> Recommended for a new project? I don't mind fixing compilation errors,
but
>> maybe there is a new package that superseded it. Maybe I'm downloading it
>> from the wrong place.
>> 
>> Regards,
>> -- Diego
> 
> The code still works in some cases but is somewhat bit-rotted (I recall
getting 
> very inconsistent results from Bio::SearchUtils, not sure why). 
> 
> We (Bio* projects) are starting to consolidate around using BioLib for 
> consistent bindings to C/C++ libraries, though that project is undergoing
some 
> changes:
> 
> http://biolib.open-bio.org/wiki/Main_Page
> 
> Pjotr Prins is the lead on that, worth talking to. The next big step is to
interface 
> with EMBOSS libraries, which is very promising.
> 
> chris
> 





From ross at cuhk.edu.hk  Tue Mar 15 20:55:42 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Wed, 16 Mar 2011 08:55:42 +0800
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
	<DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
Message-ID: <007201cbe374$dffa5eb0$9fef1c10$@edu.hk>

-----Original Message-----
From: Chris Fields [mailto:cjfields at illinois.edu] 
Sent: 2011?3?15? 22:44
To: Ross KK Leung
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] how to prevent forced exit?

Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?

chris


Dear Chris,

Thanks for your suggestion. The problem we encounter is that we don't know what database/genbank files we have to retrieve in order to accomplish the job. It seems that the nr database does not include all the records, and we don't know whether we have to concatenate all the genbank files into a very big one so to parse one by one. Any advice?

Gratefully, Ross




From jimhu at tamu.edu  Wed Mar 16 02:22:23 2011
From: jimhu at tamu.edu (Jim Hu)
Date: Wed, 16 Mar 2011 01:22:23 -0500
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <3E73745F-A687-4229-B71E-5C56B2D1FBAE@illinois.edu>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
	<DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
	<9CD1455E-88B4-4E2A-B3BC-398C10D5AAA9@tamu.edu>
	<3E73745F-A687-4229-B71E-5C56B2D1FBAE@illinois.edu>
Message-ID: <D714889D-D73C-4E45-87E3-FE921BFEBA48@tamu.edu>

I put a snippet at the end of:

	http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database

The snippet is on an independent page, and is included via 

	{{:Remote_database_admonition}}
 
which allows people to put it into other pages, and to edit it and have the changes update on all the pages where it's included.  So if someone wants to reword it, make it red text, put it in a box div or whatever, it just has to be done once.  Or, since it's a wiki,  others can just kill it altogether. ;)

Jim

On Mar 15, 2011, at 10:54 AM, Chris Fields wrote:

> Jim,
> 
> It's worth noting in something more prominent, like the tutorial, FAQ, and appropriate HOWTO's.  We've long considered whether it would be worth setting up a cookbook-like section that includes simple workflows, that would also be appropriate for something like this.
> 
> Also, I do think this is mentioned in the POD for several modules, but worth adding a prominent section on it if it's not present.  In Bio::DB::GenBank:
> 
>  WARNING: Please do NOT spam the Entrez web server with multiple requests.  NCBI offers Batch Entrez for this purpose.
> 
> That could be placed somewhere that is a bit more helpful.
> 
> chris
> 
> 
> On Mar 15, 2011, at 10:25 AM, Jim Hu wrote:
> 
>> Hi Chris,
>> 
>> A version of this admonition should be on every wiki HOWTO that involves retrieving records from external sources, and in the docs for the relevant modules.  Speaking as someone who has used BioPerl intermittently for years, and who has Sysiphus-like relationship with the learning curve, I think the docs could use more discussion of when to use particular modules in addition to the details of how to use them provided in the perldocs. I realize this is hard, given the perl "more than one way to do it" world view, but that's my $0.02.
>> 
>> Since BioPerl.org is a wiki, I suppose I should do that admonition edit myself... especially since I already know the wiki markup to transclude the same text into multiple pages.
>> 
>> Jim
>> 
>> Sent from my iPad
>> 
>> On Mar 15, 2011, at 9:44 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> 
>>> Ross,
>>> 
>>> Hope you're exaggerating, you really shouldn't use this service for retrieving 1 million records as you'll likely find your IP banned by NCBI; they are starting to enforce stricter web-based access to their  server now.  Bio::DB::GenBank uses a GET HTTP request using URI-based parameters which effectively limits the length of the query to around 200-300 IDs per request, so you would have to split single one large request many.  Thousands of repeated requests, even with a timeout, may flag your IP as 'spam'.  You can use something like Bio::DB::EUtilities to grab larger groups of seqs (~1000 IDs) b/c the latest EUtilities uses POST requests vs GET for a large number of IDs, but you are still effectively limited by the number of requests.
>>> 
>>> Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?
>>> 
>>> chris
>>> 
>>> On Mar 15, 2011, at 9:16 AM, Ross KK Leung wrote:
>>> 
>>>> While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> #!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   
>>>> 
>>>> use Bio::DB::GenBank;
>>>> 
>>>> 
>>>> 
>>>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');
>>>> 
>>>> 
>>>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>>> 
>>>> 
>>>> print "HEELO";
>>>> 
>>>> while ($seqobj = $allseqobj->next_seq) {
>>>>                    #$seqobj = $allseqobj->next_seq;
>>>>                    $seq=$seqobj->seq;
>>>> }
>>>> print "222   HEELO";
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
>>>> Sent: 2011?3?15? 17:02
>>>> To: Ross KK Leung
>>>> Cc: bioperl-l at lists.open-bio.org
>>>> Subject: Re: [Bioperl-l] how to prevent forced exit?
>>>> 
>>>> 
>>>> 
>>>> Hi Ross,
>>>> 
>>>> 
>>>> 
>>>> Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.
>>>> 
>>>> 
>>>> 
>>>> Try copying the example code directly from here
>>>> 
>>>> 
>>>> 
>>>> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html
>>>> 
>>>> 
>>>> 
>>>> and making sure that works first before modifying it.
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> More documentation and examples here:
>>>> 
>>>> http://www.bioperl.org/wiki/HOWTO:Beginners
>>>> 
>>>> http://www.bioperl.org/wiki/Bioperl_scripts
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> Dave
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:
>>>> 
>>>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
>>>> 'Fasta');
>>>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>>>            l
>>>> print "HEELO";
>>>> while ($seqobj = $allseqobj->next_seq) {
>>>>                    #$seqobj = $allseqobj->next_seq;
>>>> 
>>>>                    $seq=$seqobj->seq;
>>>> 
>>>>                    }
>>>> 
>>>>                print "222   HEELO";
>>>> 
>>>> 
>>>> 
>>>> I find that the 1st HEELO can be printed while the 2nd one can't. Google
>>>> does not return checking success/failure or null/exist of the Seq Object. As
>>>> the 1st HEELO can be executed, so no throw/exception occurs for the
>>>> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
>>>> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
>>>> accession numbers.
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054





From cjfields at illinois.edu  Wed Mar 16 13:58:23 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 12:58:23 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
Message-ID: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>

(apologies if you receive multiple copies of this)

All,

We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:

http://redmine.open-bio.org/

All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.

For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:

1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.

2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.

Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.

Let us know if you have any questions.  

chris

Christopher Fields
IGB Postdoctoral Fellow
Genomics of Neural & Behavioral Plasticity
University of Illinois Urbana-Champaign
Institute for Genomic Biology
1206 W. Gregory Dr. , MC-195
Urbana, IL 61801


From simon.noel.2 at ulaval.ca  Wed Mar 16 15:40:09 2011
From: simon.noel.2 at ulaval.ca (=?iso-8859-1?Q?Simon_No=EBl?=)
Date: Wed, 16 Mar 2011 15:40:09 -0400
Subject: [Bioperl-l]  Perl/BioPerl
Message-ID: <1C970CA8E580A84394CE5CF42FEC0046DF67A4FA81@EXCH-MBX-E.ulaval.ca>

 Hi, 
 
I don't know if I am on the right mailling list for this.
 
My director say that I should have a class of Perl or BioPerl.  Witch one should be better?  Do you know where I can find such class?


Simon No?l
CdeC


From cjfields at illinois.edu  Wed Mar 16 18:30:40 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 17:30:40 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
	<AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
Message-ID: <D6A1291F-898A-4563-8C19-FA2E92D48767@illinois.edu>

Huh, Dave Messina reported something similar earlier.  I actually tested this myself and couldn't reproduce it, maybe I'll try it on Firefox (I was using Chrome).

chris

On Mar 16, 2011, at 3:48 PM, Jonathan Duke Leto wrote:

> Howdy,
> 
> Thanks for working on this Chris!
> 
> I am not sure the password reset works properly.
> 
> Attached is a screenshot of it giving odd errors.
> 
> This was on Firefox 3.6.
> 
> Duke
> 
> On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> (apologies if you receive multiple copies of this)
>> 
>> All,
>> 
>> We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:
>> 
>> http://redmine.open-bio.org/
>> 
>> All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.
>> 
>> For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:
>> 
>> 1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.
>> 
>> 2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.
>> 
>> Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
>> 
>> Let us know if you have any questions.
>> 
>> chris
>> 
>> Christopher Fields
>> IGB Postdoctoral Fellow
>> Genomics of Neural & Behavioral Plasticity
>> University of Illinois Urbana-Champaign
>> Institute for Genomic Biology
>> 1206 W. Gregory Dr. , MC-195
>> Urbana, IL 61801
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> Jonathan "Duke" Leto
> jonathan at leto.net
> http://leto.net
> <obf_redmine.png>




From cjfields at illinois.edu  Wed Mar 16 18:50:18 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 17:50:18 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
	<AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
Message-ID: <F380825D-8F8B-4766-99C3-36FDD8E9C99D@illinois.edu>

I reset the plugins and reloaded the database.  Does that help?  I tested it out again using a test user (using the 'Lost password' link) and it seemed to work.

If not, I can manually reset and send the password to you.

chris

On Mar 16, 2011, at 3:48 PM, Jonathan Duke Leto wrote:

> Howdy,
> 
> Thanks for working on this Chris!
> 
> I am not sure the password reset works properly.
> 
> Attached is a screenshot of it giving odd errors.
> 
> This was on Firefox 3.6.
> 
> Duke
> 
> On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> (apologies if you receive multiple copies of this)
>> 
>> All,
>> 
>> We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:
>> 
>> http://redmine.open-bio.org/
>> 
>> All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.
>> 
>> For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:
>> 
>> 1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.
>> 
>> 2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.
>> 
>> Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
>> 
>> Let us know if you have any questions.
>> 
>> chris
>> 
>> Christopher Fields
>> IGB Postdoctoral Fellow
>> Genomics of Neural & Behavioral Plasticity
>> University of Illinois Urbana-Champaign
>> Institute for Genomic Biology
>> 1206 W. Gregory Dr. , MC-195
>> Urbana, IL 61801
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> Jonathan "Duke" Leto
> jonathan at leto.net
> http://leto.net
> <obf_redmine.png>




From hlapp at drycafe.net  Wed Mar 16 23:05:15 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 16 Mar 2011 23:05:15 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
Message-ID: <1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>


On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:

> Okay, we have bioperl.org set up to use OpenID, works well:

Seems to work mostly - there seems to be some odd small problem with  
ClaimID: typing in my username leads to an OpenID error, whereas  
entering my full ClaimID OpenID works.  Not sure why that would be.

Any chance this can be enabled for BioSQL too (and accordingly account  
creation disabled there, too)?

	-hilmar

>
>
> http://www.bioperl.org/wiki/Special:OpenIDLogin
>
> I have also temporarily shut down new user account creation (new  
> users must now use OpenID); old users can still use the login, but  
> they can also tie their account to an OpenID.  Let's see if it cuts  
> down on the spam.
>
> chris
>
> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>
>> Any update on the OpenID extension?
>>
>> 	-hilmar
>>
>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>
>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit 
>>> ):
>>>
>>> "Unfortunately, reCAPTCHA might be a victim of its own success -  
>>> as of 2011, some spammers appear to have figured out a way to  
>>> bypass it, either through character recognition or by using  
>>> humans. For that reason, it is not necessarily recommended."
>>>
>>> I agree about the barrier to entry issue, but unfortunately with  
>>> the wiki we're facing a reality check re: spam attacks.  We can  
>>> probably set up a new group for users that allows account  
>>> approval, though, which might alleviate the process somewhat.
>>>
>>> chris
>>>
>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>
>>>> Hi Chris,
>>>>
>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>> account, you have the ability to approve other people's  
>>>> accounts.  The
>>>> hope being to distribute the load.  I'm not thrilled about it  
>>>> though:
>>>> I want the barrier to entry to be as low as possible.  We already  
>>>> make
>>>> it so that you have to have an account to edit, passing a  
>>>> recaptcha on
>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu 
>>>> > wrote:
>>>>> All,
>>>>>
>>>>> We have been getting inundated on the wiki with spam lately.  In  
>>>>> order to get on top of this, I'm thinking about having the wiki  
>>>>> set up so wiki admins approve new user accounts, using the  
>>>>> ConfirmAccount plugin:
>>>>>
>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>
>>>>> I wanted to get everyone's opinion on this prior to enforcing  
>>>>> it.  The queue is pretty configurable, and one can set this to  
>>>>> auto-delete old requests.
>>>>>
>>>>> Any thoughts?
>>>>>
>>>>> chris
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>
>>>>
>>>>
>>>> -- 
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at  
>>>> scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                      
>>>> 216-392-3087
>>>> Ontario Institute for Cancer Research
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>> ===========================================================
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From cjfields at illinois.edu  Wed Mar 16 23:08:11 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 22:08:11 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
Message-ID: <E0AD66F8-13FE-4940-A0F5-2E4CC0C02755@illinois.edu>

I can work on that.  Peter, need this for biopython?

chris

On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:

> 
> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
> 
>> Okay, we have bioperl.org set up to use OpenID, works well:
> 
> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works.  Not sure why that would be.
> 
> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
> 
> 	-hilmar
> 
>> 
>> 
>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>> 
>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.
>> 
>> chris
>> 
>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>> 
>>> Any update on the OpenID extension?
>>> 
>>> 	-hilmar
>>> 
>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>> 
>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>> 
>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>> 
>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>> 
>>>> chris
>>>> 
>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>> 
>>>>> Hi Chris,
>>>>> 
>>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>> account, you have the ability to approve other people's accounts.  The
>>>>> hope being to distribute the load.  I'm not thrilled about it though:
>>>>> I want the barrier to entry to be as low as possible.  We already make
>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>> 
>>>>> Scott
>>>>> 
>>>>> 
>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>> All,
>>>>>> 
>>>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>> 
>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>> 
>>>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>> 
>>>>>> Any thoughts?
>>>>>> 
>>>>>> chris
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> -- 
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>> ===========================================================
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 




From cjfields at illinois.edu  Wed Mar 16 23:59:17 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 22:59:17 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
Message-ID: <B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>

Done, for BioSQL.  Let me know about Biopython and the others.

-c 

On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:

> 
> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
> 
>> Okay, we have bioperl.org set up to use OpenID, works well:
> 
> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works.  Not sure why that would be.
> 
> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
> 
> 	-hilmar
> 
>> 
>> 
>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>> 
>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.
>> 
>> chris
>> 
>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>> 
>>> Any update on the OpenID extension?
>>> 
>>> 	-hilmar
>>> 
>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>> 
>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>> 
>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>> 
>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>> 
>>>> chris
>>>> 
>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>> 
>>>>> Hi Chris,
>>>>> 
>>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>> account, you have the ability to approve other people's accounts.  The
>>>>> hope being to distribute the load.  I'm not thrilled about it though:
>>>>> I want the barrier to entry to be as low as possible.  We already make
>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>> 
>>>>> Scott
>>>>> 
>>>>> 
>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>> All,
>>>>>> 
>>>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>> 
>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>> 
>>>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>> 
>>>>>> Any thoughts?
>>>>>> 
>>>>>> chris
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> -- 
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>> ===========================================================
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 




From hlapp at drycafe.net  Thu Mar 17 00:07:45 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Thu, 17 Mar 2011 00:07:45 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
Message-ID: <6747C6EA-27BC-43C1-89B4-0F3AEF18BFA4@drycafe.net>


On Mar 16, 2011, at 11:59 PM, Chris Fields wrote:

> Done, for BioSQL.  Let me know about Biopython and the others.

Great, works! -hilmar


-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From p.j.a.cock at googlemail.com  Thu Mar 17 04:27:22 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 17 Mar 2011 08:27:22 +0000
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
Message-ID: <AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>

Yes please - thanks Chris!

Peter

On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu> wrote:
> Done, for BioSQL. ?Let me know about Biopython and the others.
>
> -c
>
> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>
>>
>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>
>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>
>> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works. ?Not sure why that would be.
>>
>> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
>>
>> ? ? ? -hilmar
>>
>>>
>>>
>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>
>>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID. ?Let's see if it cuts down on the spam.
>>>
>>> chris
>>>
>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>
>>>> Any update on the OpenID extension?
>>>>
>>>> ? ? -hilmar
>>>>
>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>
>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>>>
>>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>>>
>>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks. ?We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>>>
>>>>> chris
>>>>>
>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>
>>>>>> Hi Chris,
>>>>>>
>>>>>> The GMOD wiki has been getting hit similarly. ?I've been thinking
>>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>>> account, you have the ability to approve other people's accounts. ?The
>>>>>> hope being to distribute the load. ?I'm not thrilled about it though:
>>>>>> I want the barrier to entry to be as low as possible. ?We already make
>>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>>> the way. ?Apparently that barrier is already a little too low :-/
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>>> All,
>>>>>>>
>>>>>>> We have been getting inundated on the wiki with spam lately. ?In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>>>
>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>
>>>>>>> I wanted to get everyone's opinion on this prior to enforcing it. ?The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>>>
>>>>>>> Any thoughts?
>>>>>>>
>>>>>>> chris
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> ------------------------------------------------------------------------
>>>>>> Scott Cain, Ph. D.



From David.Messina at sbc.su.se  Thu Mar 17 04:51:21 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 17 Mar 2011 09:51:21 +0100
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <F380825D-8F8B-4766-99C3-36FDD8E9C99D@illinois.edu>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
	<AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
	<F380825D-8F8B-4766-99C3-36FDD8E9C99D@illinois.edu>
Message-ID: <AANLkTik8oYG1yJ7HdV119K08NsbqpDTUpDAtKUPSKUMF@mail.gmail.com>

Works for me now ? I was able to reset the password and log in.

Thanks, Chris!

Dave




On Wed, Mar 16, 2011 at 23:50, Chris Fields <cjfields at illinois.edu> wrote:

> I reset the plugins and reloaded the database.  Does that help?  I tested
> it out again using a test user (using the 'Lost password' link) and it
> seemed to work.
>
> If not, I can manually reset and send the password to you.
>
> chris
>
> On Mar 16, 2011, at 3:48 PM, Jonathan Duke Leto wrote:
>
> > Howdy,
> >
> > Thanks for working on this Chris!
> >
> > I am not sure the password reset works properly.
> >
> > Attached is a screenshot of it giving odd errors.
> >
> > This was on Firefox 3.6.
> >
> > Duke
> >
> > On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu>
> wrote:
> >> (apologies if you receive multiple copies of this)
> >>
> >> All,
> >>
> >> We are currently about 95% done with a transition over to our new
> Redmine tracking system, to the point where we feel comfortable in going
> ahead with opening it to developers:
> >>
> >> http://redmine.open-bio.org/
> >>
> >> All edits to bugzilla reports on our old system (
> http://bugzilla.open-bio.org/) are now disabled and the system is now
> read-only.  Any new bugs and comments to old ones should be reported on the
> new Redmine server.
> >>
> >> For current Bugzilla users, we have migrated login IDs to Redmine (this
> is normally an email address), but we have reset user passwords for security
> reasons.  There are two ways to access your account:
> >>
> >> 1) When logging in (http://redmine.open-bio.org/login), click on the
> 'Lost password' link.  You will be prompted for your email address (this
> should be the same as your bugzilla login).  An new email will be sent out
> containing directions for resetting your password and logging in.
> >>
> >> 2) It is possible the above may be automatically detected as spam.  If
> the above doesn't work or the reset email isn't received within a day,
> contact support at helpdesk.open-bio.org to receive your new password.
> >>
> >> Also, note that Redmine has a different syntax for those who want to add
> links to their reports; see
> http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
> >>
> >> Let us know if you have any questions.
> >>
> >> chris
> >>
> >> Christopher Fields
> >> IGB Postdoctoral Fellow
> >> Genomics of Neural & Behavioral Plasticity
> >> University of Illinois Urbana-Champaign
> >> Institute for Genomic Biology
> >> 1206 W. Gregory Dr. , MC-195
> >> Urbana, IL 61801
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> >
> >
> > --
> > Jonathan "Duke" Leto
> > jonathan at leto.net
> > http://leto.net
> > <obf_redmine.png>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From cjfields at illinois.edu  Thu Mar 17 07:36:05 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Mar 2011 06:36:05 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <AANLkTik8oYG1yJ7HdV119K08NsbqpDTUpDAtKUPSKUMF@mail.gmail.com>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
	<AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
	<F380825D-8F8B-4766-99C3-36FDD8E9C99D@illinois.edu>
	<AANLkTik8oYG1yJ7HdV119K08NsbqpDTUpDAtKUPSKUMF@mail.gmail.com>
Message-ID: <B8AB68C4-0DD8-408E-8C49-D33339E6C6ED@illinois.edu>

I did a little database cleansing; the email notification settings were screwy (why the warnings popped up).

chris

On Mar 17, 2011, at 3:51 AM, Dave Messina wrote:

> Works for me now ? I was able to reset the password and log in.
> 
> Thanks, Chris!
> 
> Dave
> 
> 
> 
> 
> On Wed, Mar 16, 2011 at 23:50, Chris Fields <cjfields at illinois.edu> wrote:
> I reset the plugins and reloaded the database.  Does that help?  I tested it out again using a test user (using the 'Lost password' link) and it seemed to work.
> 
> If not, I can manually reset and send the password to you.
> 
> chris
> 
> On Mar 16, 2011, at 3:48 PM, Jonathan Duke Leto wrote:
> 
> > Howdy,
> >
> > Thanks for working on this Chris!
> >
> > I am not sure the password reset works properly.
> >
> > Attached is a screenshot of it giving odd errors.
> >
> > This was on Firefox 3.6.
> >
> > Duke
> >
> > On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
> >> (apologies if you receive multiple copies of this)
> >>
> >> All,
> >>
> >> We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:
> >>
> >> http://redmine.open-bio.org/
> >>
> >> All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.
> >>
> >> For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:
> >>
> >> 1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.
> >>
> >> 2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.
> >>
> >> Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
> >>
> >> Let us know if you have any questions.
> >>
> >> chris
> >>
> >> Christopher Fields
> >> IGB Postdoctoral Fellow
> >> Genomics of Neural & Behavioral Plasticity
> >> University of Illinois Urbana-Champaign
> >> Institute for Genomic Biology
> >> 1206 W. Gregory Dr. , MC-195
> >> Urbana, IL 61801
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> >
> >
> > --
> > Jonathan "Duke" Leto
> > jonathan at leto.net
> > http://leto.net
> > <obf_redmine.png>
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From cjfields at illinois.edu  Thu Mar 17 12:16:19 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Mar 2011 11:16:19 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
	<AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
Message-ID: <B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>

Peter, 

It's set up for biopython.  Will make an announcement on open-bio-l and post something on the blog when I catch my breath (redmine and this in one week is a little tiring!).

Will also ping biojava and the other wiki groups about switching over.

chris

On Mar 17, 2011, at 3:27 AM, Peter Cock wrote:

> Yes please - thanks Chris!
> 
> Peter
> 
> On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu> wrote:
>> Done, for BioSQL.  Let me know about Biopython and the others.
>> 
>> -c
>> 
>> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>> 
>>> 
>>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>> 
>>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>> 
>>> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works.  Not sure why that would be.
>>> 
>>> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
>>> 
>>>       -hilmar
>>> 
>>>> 
>>>> 
>>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>> 
>>>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.
>>>> 
>>>> chris
>>>> 
>>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>> 
>>>>> Any update on the OpenID extension?
>>>>> 
>>>>>     -hilmar
>>>>> 
>>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>> 
>>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>>>> 
>>>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>>>> 
>>>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>>>> 
>>>>>> chris
>>>>>> 
>>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>> 
>>>>>>> Hi Chris,
>>>>>>> 
>>>>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>>>> account, you have the ability to approve other people's accounts.  The
>>>>>>> hope being to distribute the load.  I'm not thrilled about it though:
>>>>>>> I want the barrier to entry to be as low as possible.  We already make
>>>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>>>> 
>>>>>>> Scott
>>>>>>> 
>>>>>>> 
>>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>>>> All,
>>>>>>>> 
>>>>>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>>>> 
>>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>> 
>>>>>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>>>> 
>>>>>>>> Any thoughts?
>>>>>>>> 
>>>>>>>> chris
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> --
>>>>>>> ------------------------------------------------------------------------
>>>>>>> Scott Cain, Ph. D.




From adam at retchless.us  Thu Mar 17 12:32:37 2011
From: adam at retchless.us (Adam Retchless)
Date: Thu, 17 Mar 2011 12:32:37 -0400
Subject: [Bioperl-l] Wiki login with OpenId
Message-ID: <4D8237A5.4050706@retchless.us>

Greetings all,

First: A "thank you" to everyone who has developed BioPerl and the 
BioPerl Wiki -- I'm new to BioPerl, but have already benefited from its 
ability to simplify tasks that would otherwise be very tedious.

Anyway, I noticed some outdated information on the Wiki, and wanted to 
change it, but had a little trouble figuring out how to do so. 
Basically, it wasn't clear that the way to create an account was to 
click on the "Login with OpenId" button. As someone who doesn't use 
OpenID, I immediately went to the traditional "Login" page, but got 
stumped there. It did not occur to me that the OpenID page would be any 
different. Only after looking at the recent discussion on the mailing 
list did I figure out what I needed to do.

In the interest of eliminating any obstacle to participation, I think it 
would be helpful for the Wiki itself to clearly indicate how to create a 
new account. Either by changing the wording of the "login with OpenID 
link", or placing a message on the traditional "Log In" page telling 
people what they need to do to make an account.

Thanks, and I look forward to participating here.

-Adam

-- 

Adam Retchless
Center for Genomic Sciences
Allegheny-Singer Research Institute



From cjfields at illinois.edu  Thu Mar 17 13:13:14 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Mar 2011 12:13:14 -0500
Subject: [Bioperl-l] Wiki login with OpenId
In-Reply-To: <4D8237A5.4050706@retchless.us>
References: <4D8237A5.4050706@retchless.us>
Message-ID: <62E050E8-E567-4117-B14C-1F613CC81016@illinois.edu>

Adam, 

We're in the process of doing so; the addition of OpenID logins is a few days old.  I'm actually writing a blog post right now on the problems we've had and the use of OpenID, and will add a few things to the wiki pages so the login is clearer (including adding text to the normal login page).

chris

On Mar 17, 2011, at 11:32 AM, Adam Retchless wrote:

> Greetings all,
> 
> First: A "thank you" to everyone who has developed BioPerl and the BioPerl Wiki -- I'm new to BioPerl, but have already benefited from its ability to simplify tasks that would otherwise be very tedious.
> 
> Anyway, I noticed some outdated information on the Wiki, and wanted to change it, but had a little trouble figuring out how to do so. Basically, it wasn't clear that the way to create an account was to click on the "Login with OpenId" button. As someone who doesn't use OpenID, I immediately went to the traditional "Login" page, but got stumped there. It did not occur to me that the OpenID page would be any different. Only after looking at the recent discussion on the mailing list did I figure out what I needed to do.
> 
> In the interest of eliminating any obstacle to participation, I think it would be helpful for the Wiki itself to clearly indicate how to create a new account. Either by changing the wording of the "login with OpenID link", or placing a message on the traditional "Log In" page telling people what they need to do to make an account.
> 
> Thanks, and I look forward to participating here.
> 
> -Adam
> 
> -- 
> 
> Adam Retchless
> Center for Genomic Sciences
> Allegheny-Singer Research Institute
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hlapp at drycafe.net  Thu Mar 17 15:38:01 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Thu, 17 Mar 2011 15:38:01 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
	<AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
	<B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>
Message-ID: <A95A687E-25DD-4325-983D-BE9A5F45FA23@drycafe.net>

Just a thought towards the future - OpenIDs are so easy to obtain that  
the way it is right now (any OpenID will do) is built on the premise  
that it's not used widely enough (yet!) to make it worth the spammers'  
time.  Same story as with reCaptcha, probably. So once OpenID is used  
widely, we'll probably have to restrict the OpenID providers that we  
permit.

	-hilmar

On Mar 17, 2011, at 12:16 PM, Chris Fields wrote:

> Peter,
>
> It's set up for biopython.  Will make an announcement on open-bio-l  
> and post something on the blog when I catch my breath (redmine and  
> this in one week is a little tiring!).
>
> Will also ping biojava and the other wiki groups about switching over.
>
> chris
>
> On Mar 17, 2011, at 3:27 AM, Peter Cock wrote:
>
>> Yes please - thanks Chris!
>>
>> Peter
>>
>> On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu>  
>> wrote:
>>> Done, for BioSQL.  Let me know about Biopython and the others.
>>>
>>> -c
>>>
>>> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>>>
>>>>
>>>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>>>
>>>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>>>
>>>> Seems to work mostly - there seems to be some odd small problem  
>>>> with ClaimID: typing in my username leads to an OpenID error,  
>>>> whereas entering my full ClaimID OpenID works.  Not sure why that  
>>>> would be.
>>>>
>>>> Any chance this can be enabled for BioSQL too (and accordingly  
>>>> account creation disabled there, too)?
>>>>
>>>>      -hilmar
>>>>
>>>>>
>>>>>
>>>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>>>
>>>>> I have also temporarily shut down new user account creation (new  
>>>>> users must now use OpenID); old users can still use the login,  
>>>>> but they can also tie their account to an OpenID.  Let's see if  
>>>>> it cuts down on the spam.
>>>>>
>>>>> chris
>>>>>
>>>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>>>
>>>>>> Any update on the OpenID extension?
>>>>>>
>>>>>>    -hilmar
>>>>>>
>>>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>>>
>>>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit 
>>>>>>> ):
>>>>>>>
>>>>>>> "Unfortunately, reCAPTCHA might be a victim of its own success  
>>>>>>> - as of 2011, some spammers appear to have figured out a way  
>>>>>>> to bypass it, either through character recognition or by using  
>>>>>>> humans. For that reason, it is not necessarily recommended."
>>>>>>>
>>>>>>> I agree about the barrier to entry issue, but unfortunately  
>>>>>>> with the wiki we're facing a reality check re: spam attacks.   
>>>>>>> We can probably set up a new group for users that allows  
>>>>>>> account approval, though, which might alleviate the process  
>>>>>>> somewhat.
>>>>>>>
>>>>>>> chris
>>>>>>>
>>>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>>>
>>>>>>>> Hi Chris,
>>>>>>>>
>>>>>>>> The GMOD wiki has been getting hit similarly.  I've been  
>>>>>>>> thinking
>>>>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>>>>> account, you have the ability to approve other people's  
>>>>>>>> accounts.  The
>>>>>>>> hope being to distribute the load.  I'm not thrilled about it  
>>>>>>>> though:
>>>>>>>> I want the barrier to entry to be as low as possible.  We  
>>>>>>>> already make
>>>>>>>> it so that you have to have an account to edit, passing a  
>>>>>>>> recaptcha on
>>>>>>>> the way.  Apparently that barrier is already a little too  
>>>>>>>> low :-/
>>>>>>>>
>>>>>>>> Scott
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu 
>>>>>>>> > wrote:
>>>>>>>>> All,
>>>>>>>>>
>>>>>>>>> We have been getting inundated on the wiki with spam  
>>>>>>>>> lately.  In order to get on top of this, I'm thinking about  
>>>>>>>>> having the wiki set up so wiki admins approve new user  
>>>>>>>>> accounts, using the ConfirmAccount plugin:
>>>>>>>>>
>>>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>>>
>>>>>>>>> I wanted to get everyone's opinion on this prior to  
>>>>>>>>> enforcing it.  The queue is pretty configurable, and one can  
>>>>>>>>> set this to auto-delete old requests.
>>>>>>>>>
>>>>>>>>> Any thoughts?
>>>>>>>>>
>>>>>>>>> chris
>>>>>>>>> _______________________________________________
>>>>>>>>> Bioperl-l mailing list
>>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> Scott Cain, Ph. D.
>

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From cjfields at illinois.edu  Thu Mar 17 15:40:47 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Mar 2011 14:40:47 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <A95A687E-25DD-4325-983D-BE9A5F45FA23@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
	<AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
	<B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>
	<A95A687E-25DD-4325-983D-BE9A5F45FA23@drycafe.net>
Message-ID: <2E6327AD-4CD3-45CE-A105-66FA3A474294@illinois.edu>

That's easy enough to do with the OpenID plugin settings:

$wgOpenIDConsumerAllow
an array of regular expressions that match OpenIDs you want to allow to log in. For example, "@^(http://)?wikitravel.org/@" will allow OpenIDs from the Wikitravel domain.
$wgOpenIDConsumerDeny
an array of regular expressions that match OpenIDs you want to deny access to. This is mostly useful for servers that are known to be bad. Example: "#^(http://)?example.com/#".

chris

On Mar 17, 2011, at 2:38 PM, Hilmar Lapp wrote:

> Just a thought towards the future - OpenIDs are so easy to obtain that the way it is right now (any OpenID will do) is built on the premise that it's not used widely enough (yet!) to make it worth the spammers' time.  Same story as with reCaptcha, probably. So once OpenID is used widely, we'll probably have to restrict the OpenID providers that we permit.
> 
> 	-hilmar
> 
> On Mar 17, 2011, at 12:16 PM, Chris Fields wrote:
> 
>> Peter,
>> 
>> It's set up for biopython.  Will make an announcement on open-bio-l and post something on the blog when I catch my breath (redmine and this in one week is a little tiring!).
>> 
>> Will also ping biojava and the other wiki groups about switching over.
>> 
>> chris
>> 
>> On Mar 17, 2011, at 3:27 AM, Peter Cock wrote:
>> 
>>> Yes please - thanks Chris!
>>> 
>>> Peter
>>> 
>>> On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu> wrote:
>>>> Done, for BioSQL.  Let me know about Biopython and the others.
>>>> 
>>>> -c
>>>> 
>>>> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>>>> 
>>>>> 
>>>>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>>>> 
>>>>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>>>> 
>>>>> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works.  Not sure why that would be.
>>>>> 
>>>>> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
>>>>> 
>>>>>     -hilmar
>>>>> 
>>>>>> 
>>>>>> 
>>>>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>>>> 
>>>>>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.
>>>>>> 
>>>>>> chris
>>>>>> 
>>>>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>>>> 
>>>>>>> Any update on the OpenID extension?
>>>>>>> 
>>>>>>>   -hilmar
>>>>>>> 
>>>>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>>>> 
>>>>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>>>>>> 
>>>>>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>>>>>> 
>>>>>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>>>>>> 
>>>>>>>> chris
>>>>>>>> 
>>>>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>>>> 
>>>>>>>>> Hi Chris,
>>>>>>>>> 
>>>>>>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>>>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>>>>>> account, you have the ability to approve other people's accounts.  The
>>>>>>>>> hope being to distribute the load.  I'm not thrilled about it though:
>>>>>>>>> I want the barrier to entry to be as low as possible.  We already make
>>>>>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>>>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>>>>>> 
>>>>>>>>> Scott
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>>>>>> All,
>>>>>>>>>> 
>>>>>>>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>>>>>> 
>>>>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>>>> 
>>>>>>>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>>>>>> 
>>>>>>>>>> Any thoughts?
>>>>>>>>>> 
>>>>>>>>>> chris
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Bioperl-l mailing list
>>>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> --
>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>> Scott Cain, Ph. D.
>> 
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 




From hlapp at drycafe.net  Thu Mar 17 16:01:42 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Thu, 17 Mar 2011 16:01:42 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <2E6327AD-4CD3-45CE-A105-66FA3A474294@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
	<AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
	<B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>
	<A95A687E-25DD-4325-983D-BE9A5F45FA23@drycafe.net>
	<2E6327AD-4CD3-45CE-A105-66FA3A474294@illinois.edu>
Message-ID: <14304AC6-1AAA-44C3-A169-F0111BA59AC2@drycafe.net>

Indeed. And I guess we can add "bad" providers incrementally as we  
spam from them trickle in. I can imagine that at some point there'll  
also be a blacklist of spam OpenID providers.

	-hilmar

On Mar 17, 2011, at 3:40 PM, Chris Fields wrote:

> That's easy enough to do with the OpenID plugin settings:
>
> $wgOpenIDConsumerAllow
> an array of regular expressions that match OpenIDs you want to allow  
> to log in. For example, "@^(http://)?wikitravel.org/@" will allow  
> OpenIDs from the Wikitravel domain.
> $wgOpenIDConsumerDeny
> an array of regular expressions that match OpenIDs you want to deny  
> access to. This is mostly useful for servers that are known to be  
> bad. Example: "#^(http://)?example.com/#".
>
> chris
>
> On Mar 17, 2011, at 2:38 PM, Hilmar Lapp wrote:
>
>> Just a thought towards the future - OpenIDs are so easy to obtain  
>> that the way it is right now (any OpenID will do) is built on the  
>> premise that it's not used widely enough (yet!) to make it worth  
>> the spammers' time.  Same story as with reCaptcha, probably. So  
>> once OpenID is used widely, we'll probably have to restrict the  
>> OpenID providers that we permit.
>>
>> 	-hilmar
>>
>> On Mar 17, 2011, at 12:16 PM, Chris Fields wrote:
>>
>>> Peter,
>>>
>>> It's set up for biopython.  Will make an announcement on open-bio- 
>>> l and post something on the blog when I catch my breath (redmine  
>>> and this in one week is a little tiring!).
>>>
>>> Will also ping biojava and the other wiki groups about switching  
>>> over.
>>>
>>> chris
>>>
>>> On Mar 17, 2011, at 3:27 AM, Peter Cock wrote:
>>>
>>>> Yes please - thanks Chris!
>>>>
>>>> Peter
>>>>
>>>> On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu>  
>>>> wrote:
>>>>> Done, for BioSQL.  Let me know about Biopython and the others.
>>>>>
>>>>> -c
>>>>>
>>>>> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>>>>>
>>>>>>
>>>>>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>>>>>
>>>>>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>>>>>
>>>>>> Seems to work mostly - there seems to be some odd small problem  
>>>>>> with ClaimID: typing in my username leads to an OpenID error,  
>>>>>> whereas entering my full ClaimID OpenID works.  Not sure why  
>>>>>> that would be.
>>>>>>
>>>>>> Any chance this can be enabled for BioSQL too (and accordingly  
>>>>>> account creation disabled there, too)?
>>>>>>
>>>>>>    -hilmar
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>>>>>
>>>>>>> I have also temporarily shut down new user account creation  
>>>>>>> (new users must now use OpenID); old users can still use the  
>>>>>>> login, but they can also tie their account to an OpenID.   
>>>>>>> Let's see if it cuts down on the spam.
>>>>>>>
>>>>>>> chris
>>>>>>>
>>>>>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>>>>>
>>>>>>>> Any update on the OpenID extension?
>>>>>>>>
>>>>>>>>  -hilmar
>>>>>>>>
>>>>>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>>>>>
>>>>>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit 
>>>>>>>>> ):
>>>>>>>>>
>>>>>>>>> "Unfortunately, reCAPTCHA might be a victim of its own  
>>>>>>>>> success - as of 2011, some spammers appear to have figured  
>>>>>>>>> out a way to bypass it, either through character recognition  
>>>>>>>>> or by using humans. For that reason, it is not necessarily  
>>>>>>>>> recommended."
>>>>>>>>>
>>>>>>>>> I agree about the barrier to entry issue, but unfortunately  
>>>>>>>>> with the wiki we're facing a reality check re: spam  
>>>>>>>>> attacks.  We can probably set up a new group for users that  
>>>>>>>>> allows account approval, though, which might alleviate the  
>>>>>>>>> process somewhat.
>>>>>>>>>
>>>>>>>>> chris
>>>>>>>>>
>>>>>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>>>>>
>>>>>>>>>> Hi Chris,
>>>>>>>>>>
>>>>>>>>>> The GMOD wiki has been getting hit similarly.  I've been  
>>>>>>>>>> thinking
>>>>>>>>>> about the "vampire" model that EcoliWiki uses: once you  
>>>>>>>>>> have an
>>>>>>>>>> account, you have the ability to approve other people's  
>>>>>>>>>> accounts.  The
>>>>>>>>>> hope being to distribute the load.  I'm not thrilled about  
>>>>>>>>>> it though:
>>>>>>>>>> I want the barrier to entry to be as low as possible.  We  
>>>>>>>>>> already make
>>>>>>>>>> it so that you have to have an account to edit, passing a  
>>>>>>>>>> recaptcha on
>>>>>>>>>> the way.  Apparently that barrier is already a little too  
>>>>>>>>>> low :-/
>>>>>>>>>>
>>>>>>>>>> Scott
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu 
>>>>>>>>>> > wrote:
>>>>>>>>>>> All,
>>>>>>>>>>>
>>>>>>>>>>> We have been getting inundated on the wiki with spam  
>>>>>>>>>>> lately.  In order to get on top of this, I'm thinking  
>>>>>>>>>>> about having the wiki set up so wiki admins approve new  
>>>>>>>>>>> user accounts, using the ConfirmAccount plugin:
>>>>>>>>>>>
>>>>>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>>>>>
>>>>>>>>>>> I wanted to get everyone's opinion on this prior to  
>>>>>>>>>>> enforcing it.  The queue is pretty configurable, and one  
>>>>>>>>>>> can set this to auto-delete old requests.
>>>>>>>>>>>
>>>>>>>>>>> Any thoughts?
>>>>>>>>>>>
>>>>>>>>>>> chris
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Bioperl-l mailing list
>>>>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>> Scott Cain, Ph. D.
>>>
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>> ===========================================================
>>
>>
>>
>>
>

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From tzhu at mail.bnu.edu.cn  Fri Mar 18 00:33:32 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Fri, 18 Mar 2011 12:33:32 +0800
Subject: [Bioperl-l] What's wrong with the script about module
 Bio::SeqFeature::Gene::GeneStructure
Message-ID: <1300422812.12949.5.camel@ubuntu>

I wrote my script like this,

#!/usr/bin/perl -w
use Bio::SeqIO;
my $catch_seq = Bio::SeqIO -> new(-file => 'test.gbk',-format=>
'genbank');
while( my $seq_obj = $catch_seq -> next_seq)
{
	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
get_SeqFeatures;
	for my $mRNA_feature (@all_mRNA_features)
	{
			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
		{
			@exons=$mRNA_feature->exons;
			$exon_number = scalar(@exons);
			print "$exon_number\n";
		}
	}
}

I hope to count exon number in every mRNA. But it print nothing(You can
arbitrarily get a genbank file to test it). What's wrong?


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)




From hrh at fmi.ch  Fri Mar 18 05:17:30 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Fri, 18 Mar 2011 10:17:30 +0100
Subject: [Bioperl-l] What's wrong with the script about module
	Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300422812.12949.5.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu>
Message-ID: <4D83232A.9050502@fmi.ch>

Hi Tao

I don't fully understand your script, but I do see a major problem:

why do you select for "primary_tag eq 'mRNA'" first?


this simple loop will probably do what you want:

while( my $seq_obj = $catch_seq -> next_seq) {

	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
$seq_obj ->get_SeqFeatures;
	$exon_number = scalar(@all_exon_features);
	print "$exon_number\n";
}


Alternatively, I recommend to read the HOWTO page:

http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

which has a nice example to print out all 'primary_tag' (ie the 'feature 
keys' in a GenBank formated file)

I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
definition:
http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html


Regards, Hans



On 03/18/2011 05:33 AM, Tao Zhu wrote:
> I wrote my script like this,
>
> #!/usr/bin/perl -w
> use Bio::SeqIO;
> my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
> 'genbank');
> while( my $seq_obj = $catch_seq ->  next_seq)
> {
> 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
> get_SeqFeatures;
> 	for my $mRNA_feature (@all_mRNA_features)
> 	{
> 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
> 		{
> 			@exons=$mRNA_feature->exons;
> 			$exon_number = scalar(@exons);
> 			print "$exon_number\n";
> 		}
> 	}
> }
>
> I hope to count exon number in every mRNA. But it print nothing(You can
> arbitrarily get a genbank file to test it). What's wrong?
>
>


From tzhu at mail.bnu.edu.cn  Fri Mar 18 07:32:00 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Fri, 18 Mar 2011 19:32:00 +0800
Subject: [Bioperl-l] What's wrong with the script about module
 Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <4D83232A.9050502@fmi.ch>
References: <1300422812.12949.5.camel@ubuntu>  <4D83232A.9050502@fmi.ch>
Message-ID: <1300447920.16670.2.camel@ubuntu>

Of course that's OK. But what I really want to know is how to use module
Bio::SeqFeature::Gene::GeneStructure. 

? 2011-03-18?? 10:17 +0100?Hans-Rudolf Hotz???
> Hi Tao
> 
> I don't fully understand your script, but I do see a major problem:
> 
> why do you select for "primary_tag eq 'mRNA'" first?
> 
> 
> this simple loop will probably do what you want:
> 
> while( my $seq_obj = $catch_seq -> next_seq) {
> 
> 	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
> $seq_obj ->get_SeqFeatures;
> 	$exon_number = scalar(@all_exon_features);
> 	print "$exon_number\n";
> }
> 
> 
> Alternatively, I recommend to read the HOWTO page:
> 
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> 
> which has a nice example to print out all 'primary_tag' (ie the 'feature 
> keys' in a GenBank formated file)
> 
> I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
> definition:
> http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
> 
> 
> Regards, Hans
> 
> 
> 
> On 03/18/2011 05:33 AM, Tao Zhu wrote:
> > I wrote my script like this,
> >
> > #!/usr/bin/perl -w
> > use Bio::SeqIO;
> > my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
> > 'genbank');
> > while( my $seq_obj = $catch_seq ->  next_seq)
> > {
> > 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
> > get_SeqFeatures;
> > 	for my $mRNA_feature (@all_mRNA_features)
> > 	{
> > 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
> > 		{
> > 			@exons=$mRNA_feature->exons;
> > 			$exon_number = scalar(@exons);
> > 			print "$exon_number\n";
> > 		}
> > 	}
> > }
> >
> > I hope to count exon number in every mRNA. But it print nothing(You can
> > arbitrarily get a genbank file to test it). What's wrong?
> >
> >

-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)




From cjfields at illinois.edu  Fri Mar 18 09:04:34 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 18 Mar 2011 08:04:34 -0500
Subject: [Bioperl-l] What's wrong with the script about module
	Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300447920.16670.2.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu> <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
Message-ID: <2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>

The SeqFeatures derived from a GenBank file are simple Bio::SeqFeature::Generic instances.  I don't think there is a straightforward way to have the parser return Bio::SeqFeature::Gene::GeneStructure instances.

chris

On Mar 18, 2011, at 6:32 AM, Tao Zhu wrote:

> Of course that's OK. But what I really want to know is how to use module
> Bio::SeqFeature::Gene::GeneStructure. 
> 
> ? 2011-03-18?? 10:17 +0100?Hans-Rudolf Hotz???
>> Hi Tao
>> 
>> I don't fully understand your script, but I do see a major problem:
>> 
>> why do you select for "primary_tag eq 'mRNA'" first?
>> 
>> 
>> this simple loop will probably do what you want:
>> 
>> while( my $seq_obj = $catch_seq -> next_seq) {
>> 
>> 	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
>> $seq_obj ->get_SeqFeatures;
>> 	$exon_number = scalar(@all_exon_features);
>> 	print "$exon_number\n";
>> }
>> 
>> 
>> Alternatively, I recommend to read the HOWTO page:
>> 
>> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
>> 
>> which has a nice example to print out all 'primary_tag' (ie the 'feature 
>> keys' in a GenBank formated file)
>> 
>> I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
>> definition:
>> http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
>> 
>> 
>> Regards, Hans
>> 
>> 
>> 
>> On 03/18/2011 05:33 AM, Tao Zhu wrote:
>>> I wrote my script like this,
>>> 
>>> #!/usr/bin/perl -w
>>> use Bio::SeqIO;
>>> my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
>>> 'genbank');
>>> while( my $seq_obj = $catch_seq ->  next_seq)
>>> {
>>> 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
>>> get_SeqFeatures;
>>> 	for my $mRNA_feature (@all_mRNA_features)
>>> 	{
>>> 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
>>> 		{
>>> 			@exons=$mRNA_feature->exons;
>>> 			$exon_number = scalar(@exons);
>>> 			print "$exon_number\n";
>>> 		}
>>> 	}
>>> }
>>> 
>>> I hope to count exon number in every mRNA. But it print nothing(You can
>>> arbitrarily get a genbank file to test it). What's wrong?
>>> 
>>> 
> 
> -- 
> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> 100875, China
> Email: tzhu at mail.bnu.edu.cn
> Website: http://bnuzt.org (mainly written in Chinese)
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From ross at cuhk.edu.hk  Fri Mar 18 09:22:40 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Fri, 18 Mar 2011 21:22:40 +0800
Subject: [Bioperl-l]  failure in unsubscription
In-Reply-To: <1300447920.16670.2.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu> <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
Message-ID: <018101cbe56f$8ec755f0$ac5601d0$@edu.hk>

unable to unsubscribe bioperl mailing list, anybody can help? the web link, after clicking "unsubscribe", there is no confirmation email sent to my email account and I keep receiving emails from bioperl mailing list.




From tzhu at mail.bnu.edu.cn  Fri Mar 18 09:57:21 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Fri, 18 Mar 2011 21:57:21 +0800
Subject: [Bioperl-l] What's wrong with the script about module
 Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
References: <1300422812.12949.5.camel@ubuntu>  <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
	<2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
Message-ID: <1300456641.18688.4.camel@ubuntu>

Yes. But in the document
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
Bio::SeqFeature::Generic. I wonder how to do such inheritance.

? 2011-03-18?? 08:04 -0500?Chris Fields???
> The SeqFeatures derived from a GenBank file are simple Bio::SeqFeature::Generic instances.  I don't think there is a straightforward way to have the parser return Bio::SeqFeature::Gene::GeneStructure instances.
> 
> chris
> 
> On Mar 18, 2011, at 6:32 AM, Tao Zhu wrote:
> 
> > Of course that's OK. But what I really want to know is how to use module
> > Bio::SeqFeature::Gene::GeneStructure. 
> > 
> > ? 2011-03-18?? 10:17 +0100?Hans-Rudolf Hotz???
> >> Hi Tao
> >> 
> >> I don't fully understand your script, but I do see a major problem:
> >> 
> >> why do you select for "primary_tag eq 'mRNA'" first?
> >> 
> >> 
> >> this simple loop will probably do what you want:
> >> 
> >> while( my $seq_obj = $catch_seq -> next_seq) {
> >> 
> >> 	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
> >> $seq_obj ->get_SeqFeatures;
> >> 	$exon_number = scalar(@all_exon_features);
> >> 	print "$exon_number\n";
> >> }
> >> 
> >> 
> >> Alternatively, I recommend to read the HOWTO page:
> >> 
> >> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> >> 
> >> which has a nice example to print out all 'primary_tag' (ie the 'feature 
> >> keys' in a GenBank formated file)
> >> 
> >> I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
> >> definition:
> >> http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
> >> 
> >> 
> >> Regards, Hans
> >> 
> >> 
> >> 
> >> On 03/18/2011 05:33 AM, Tao Zhu wrote:
> >>> I wrote my script like this,
> >>> 
> >>> #!/usr/bin/perl -w
> >>> use Bio::SeqIO;
> >>> my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
> >>> 'genbank');
> >>> while( my $seq_obj = $catch_seq ->  next_seq)
> >>> {
> >>> 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
> >>> get_SeqFeatures;
> >>> 	for my $mRNA_feature (@all_mRNA_features)
> >>> 	{
> >>> 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
> >>> 		{
> >>> 			@exons=$mRNA_feature->exons;
> >>> 			$exon_number = scalar(@exons);
> >>> 			print "$exon_number\n";
> >>> 		}
> >>> 	}
> >>> }
> >>> 
> >>> I hope to count exon number in every mRNA. But it print nothing(You can
> >>> arbitrarily get a genbank file to test it). What's wrong?
> >>> 
> >>> 
> > 
> > -- 
> > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> > 100875, China
> > Email: tzhu at mail.bnu.edu.cn
> > Website: http://bnuzt.org (mainly written in Chinese)
> > 
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 





From fs5 at sanger.ac.uk  Fri Mar 18 11:05:29 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Fri, 18 Mar 2011 15:05:29 +0000
Subject: [Bioperl-l] What's wrong with the script about
	module	Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300456641.18688.4.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu>  <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
	<2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
	<1300456641.18688.4.camel@ubuntu>
Message-ID: <1300460730.12411.50.camel@deskpro15336.internal.sanger.ac.uk>

maybe I'm missing the point here but I think an "mRNA" feature should
not be a Bio::SeqFeature::Gene::GeneStructure and it should not have
exons - it would not make sense biologically.

Frank


On Fri, 2011-03-18 at 21:57 +0800, Tao Zhu wrote:
> Yes. But in the document
> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
> It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
> Bio::SeqFeature::Generic. I wonder how to do such inheritance.
> 
> ? 2011-03-18?? 08:04 -0500?Chris Fields???
> > The SeqFeatures derived from a GenBank file are simple Bio::SeqFeature::Generic instances.  I don't think there is a straightforward way to have the parser return Bio::SeqFeature::Gene::GeneStructure instances.
> > 
> > chris
> > 
> > On Mar 18, 2011, at 6:32 AM, Tao Zhu wrote:
> > 
> > > Of course that's OK. But what I really want to know is how to use module
> > > Bio::SeqFeature::Gene::GeneStructure. 
> > > 
> > > ? 2011-03-18?? 10:17 +0100?Hans-Rudolf Hotz???
> > >> Hi Tao
> > >> 
> > >> I don't fully understand your script, but I do see a major problem:
> > >> 
> > >> why do you select for "primary_tag eq 'mRNA'" first?
> > >> 
> > >> 
> > >> this simple loop will probably do what you want:
> > >> 
> > >> while( my $seq_obj = $catch_seq -> next_seq) {
> > >> 
> > >> 	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
> > >> $seq_obj ->get_SeqFeatures;
> > >> 	$exon_number = scalar(@all_exon_features);
> > >> 	print "$exon_number\n";
> > >> }
> > >> 
> > >> 
> > >> Alternatively, I recommend to read the HOWTO page:
> > >> 
> > >> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> > >> 
> > >> which has a nice example to print out all 'primary_tag' (ie the 'feature 
> > >> keys' in a GenBank formated file)
> > >> 
> > >> I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
> > >> definition:
> > >> http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
> > >> 
> > >> 
> > >> Regards, Hans
> > >> 
> > >> 
> > >> 
> > >> On 03/18/2011 05:33 AM, Tao Zhu wrote:
> > >>> I wrote my script like this,
> > >>> 
> > >>> #!/usr/bin/perl -w
> > >>> use Bio::SeqIO;
> > >>> my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
> > >>> 'genbank');
> > >>> while( my $seq_obj = $catch_seq ->  next_seq)
> > >>> {
> > >>> 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
> > >>> get_SeqFeatures;
> > >>> 	for my $mRNA_feature (@all_mRNA_features)
> > >>> 	{
> > >>> 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
> > >>> 		{
> > >>> 			@exons=$mRNA_feature->exons;
> > >>> 			$exon_number = scalar(@exons);
> > >>> 			print "$exon_number\n";
> > >>> 		}
> > >>> 	}
> > >>> }
> > >>> 
> > >>> I hope to count exon number in every mRNA. But it print nothing(You can
> > >>> arbitrarily get a genbank file to test it). What's wrong?
> > >>> 
> > >>> 
> > > 
> > > -- 
> > > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> > > 100875, China
> > > Email: tzhu at mail.bnu.edu.cn
> > > Website: http://bnuzt.org (mainly written in Chinese)
> > > 
> > > 
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 



From chapmanb at 50mail.com  Fri Mar  4 07:37:28 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Fri, 4 Mar 2011 07:37:28 -0500
Subject: [Bioperl-l] Bioinformatics Open Source Conference (BOSC 2011)--Call
 for Abstracts
Message-ID: <20110304123728.GD27839@sobchak>

We invite you to submit an abstract to BOSC 2011! Please forward this
message as appropriate, and forgive multiple postings.

Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference (BOSC 2011)
An ISMB 2011 Special Interest Group (SIG)

Dates: July 15-16, 2011
Location: Vienna, Austria
Web site: http://www.open-bio.org/wiki/BOSC_2011
Email: bosc at open-bio.org
BOSC announcements mailing list:  http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:
April 18, 2011: Deadline for submitting abstracts to BOSC 2011
May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors
July 13-14, 2011: Codefest 2011 programming session (see http://www.open-bio.org/wiki/Codefest_2011 for details)
July 15-16, 2011: BOSC 2011
July 17-19, 2011: ISMB 2011

The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.

We invite you to submit abstracts for talks and posters.  Sessions include:
- Approaches to parallel processing
- Cloud-based approaches to improving software and data accessibility
- The Semantic Web in open source bioinformatics
- Data visualization
- Tools for next-generation sequencing
- Other Open Source software

In addition to the above sessions, there will be a panel discussion
about "Meeting the challenges of inter-institutional collaboration". We
are also working to arrange a joint session with one of the other ISMB
SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student Travel
Awards for BOSC 2011. Each winner will be awarded $250 to defray the
costs of travel to BOSC 2011.
 
For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee:
Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor 


From bill_zt at sina.com  Thu Mar 17 20:48:19 2011
From: bill_zt at sina.com (Tao Zhu)
Date: Fri, 18 Mar 2011 08:48:19 +0800
Subject: [Bioperl-l] Perl/BioPerl (Simon No?l)
Message-ID: <1300409299.2349.5.camel@ubuntu>

In order to learn BioPerl, you should first learn and master Perl. If
you are not majoring in Bioinformatics, learning Perl is just OK.
Otherwise you should learn both Perl and BioPerl.


> Message: 2
> Date: Wed, 16 Mar 2011 15:40:09 -0400
> From: Simon No?l <simon.noel.2 at ulaval.ca>
> Subject: [Bioperl-l]  Perl/BioPerl
> To: "bioperl-l at lists.open-bio.org" <bioperl-l at lists.open-bio.org>
> Message-ID:
>         <1C970CA8E580A84394CE5CF42FEC0046DF67A4FA81 at EXCH-MBX-E.ulaval.ca>
> Content-Type: text/plain; charset="iso-8859-1"
> 
>  Hi, 
>  
> I don't know if I am on the right mailling list for this.
>  
> My director say that I should have a class of Perl or BioPerl.  Witch
> one should be better?  Do you know where I can find such class?
> 
> 
> Simon No?l
> CdeC
> 


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)



From bio.justin100 at gmail.com  Fri Mar  4 15:24:51 2011
From: bio.justin100 at gmail.com (justin100)
Date: Fri, 4 Mar 2011 12:24:51 -0800 (PST)
Subject: [Bioperl-l] Please recommend Perl module to parse phylogentic trees
Message-ID: <2e94f0bb-0282-4d53-b205-56ff895665de@w7g2000pre.googlegroups.com>

Hi,

I am writing a script to parse phylogenetic trees. The input will be
trees in Newick format for now (maybe NEXUS in the future).

Quite a few Perl modules can parse phylogenetic trees. For Newick
format, there are Bio::TreeIO and  Bio::Phylo::Parsers. For NEXUS
format, there is Bio::NEXUS. From my understanding, it's not difficult
to convert from Newick to NEXUS or vice versa, if only for the purpose
of parsing trees.

I'd to know the advantages and disadvantages of these modules when
compared with each other. Please recommend one that you think is the
most capable parser (and hopefully has the least bugs).

Thanks.

Justin


From jonathan at leto.net  Wed Mar 16 16:48:24 2011
From: jonathan at leto.net (Jonathan "Duke" Leto)
Date: Wed, 16 Mar 2011 13:48:24 -0700
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
Message-ID: <AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>

Howdy,

Thanks for working on this Chris!

I am not sure the password reset works properly.

Attached is a screenshot of it giving odd errors.

This was on Firefox 3.6.

Duke

On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
> (apologies if you receive multiple copies of this)
>
> All,
>
> We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:
>
> http://redmine.open-bio.org/
>
> All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only. ?Any new bugs and comments to old ones should be reported on the new Redmine server.
>
> For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons. ?There are two ways to access your account:
>
> 1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link. ?You will be prompted for your email address (this should be the same as your bugzilla login). ?An new email will be sent out containing directions for resetting your password and logging in.
>
> 2) It is possible the above may be automatically detected as spam. ?If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.
>
> Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
>
> Let us know if you have any questions.
>
> chris
>
> Christopher Fields
> IGB Postdoctoral Fellow
> Genomics of Neural & Behavioral Plasticity
> University of Illinois Urbana-Champaign
> Institute for Genomic Biology
> 1206 W. Gregory Dr. , MC-195
> Urbana, IL 61801
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Jonathan "Duke" Leto
jonathan at leto.net
http://leto.net
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From rutgeraldo at gmail.com  Fri Mar 18 10:16:25 2011
From: rutgeraldo at gmail.com (Rutger Vos)
Date: Fri, 18 Mar 2011 14:16:25 +0000
Subject: [Bioperl-l] Please forward: collecting support for Japanese
	scientists
Message-ID: <AANLkTiksWdna1MLpbBWk2nDv0LAyrXdU7xV3Fs5gSHkF@mail.gmail.com>

Dear colleagues,

A web page has been launched to collect support for Japanese
(bio-)scientists: http://biohelpathon.org - please forward this
address widely.

The purpose of the web page is to establish a knowledge base of
available support for our colleagues in Japan. You are invited to
submit any tips, ideas and offers including accommodation, funding
resources, exchange schemes, lab space, server space and open
positions for visiting students and research personnel from Japan.

We will collect your suggestions and offers and will share them with
whoever is best placed to disseminate them. This initiative originates
with the attendees of the BioHackathons (the Japanese website
http://hackathon.dbcls.jp is offline due to the earthquake), but
anyone is very welcome to contribute. To get in touch, join
http://groups.google.com/group/biohelpathon.

This initiative is no alternative to first responders who are helping
out in Japan right now. The rescue operation and food and shelter
support comes first. If you can only do one thing, it should be a
donation to something like the Red Cross. This comes later.

See also:
A different initiative, with which we're in touch:
http://www.nipponsciencesupport.net/
More info on Nature blogs:
http://blogs.nature.com/news/thegreatbeyond/2011/03/helping_hand_for_scientistrefu.html

PLEASE NOTE: WE ARE NOT HANDLING MONEY. This is simply a way to
crowdsource information about available resources.

Thank you.

Rutger Vos


From spotforever at tiscali.it  Sun Mar 13 14:15:54 2011
From: spotforever at tiscali.it (marcocirilli)
Date: Sun, 13 Mar 2011 11:15:54 -0700 (PDT)
Subject: [Bioperl-l]  slit sequence with BioPerl by ID-query
Message-ID: <31138653.post@talk.nabble.com>


Hello, I have 2 fasta file with similar sequences and I want to compare them
and eliminate sequences with the same IDquery (or extract only different
ID-query). How can I do it with BioPerl? Thanks 
-- 
View this message in context: http://old.nabble.com/slit-sequence-with-BioPerl-by-ID-query-tp31138653p31138653.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From suhail.mn12 at yahoo.co.uk  Fri Mar 18 12:18:49 2011
From: suhail.mn12 at yahoo.co.uk (Suhail M)
Date: Fri, 18 Mar 2011 16:18:49 +0000 (GMT)
Subject: [Bioperl-l] RemoteBlast
Message-ID: <988359.99459.qm@web132309.mail.ird.yahoo.com>

Dear Sir or Madam,
I am using a remote blast and encounter either a too many hsp or CPU overload 
problem with my specific gene. The gene itself is not that big so I was 
wondering is there a parameter I can pass when using the submit option to 
restrict number of hsp and to avoid the cpu and too many hsp problem? (I know I 
can use repeat masking and change the e-value but I need something that does not 
require those changes)

my $prog = 'blastn';
#my $db   = 'swissprot';
my $e_val= '1e-10';

my @params = ( '-prog'       => $prog,
#       '-data'       => $db,
               '-expect'     => $e_val,
               '-readmethod' => 'SearchIO'
            );

my $factory = Bio::Tools::Run::RemoteBlast->new(@params);

$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens [ORGN]';

delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};

my $str = Bio::SeqIO->new(-file            =>'temporary.fa' , 
 '-format'         => 'fasta');

my $r = $factory->submit_blast('temporary.fa');

Thank you for your help.
Suhail


      


From shalabh.sharma7 at gmail.com  Fri Mar 18 12:41:42 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Fri, 18 Mar 2011 12:41:42 -0400
Subject: [Bioperl-l] RemoteBlast
In-Reply-To: <988359.99459.qm@web132309.mail.ird.yahoo.com>
References: <988359.99459.qm@web132309.mail.ird.yahoo.com>
Message-ID: <AANLkTikLD+A9o0Nujg9ThGbFL3HvtaAGXaihoEX5OmTE@mail.gmail.com>

Suhail,
         You can restrict the number of hits by using "-v" and "-b"
parameters.

-Shalabh


On Fri, Mar 18, 2011 at 12:18 PM, Suhail M <suhail.mn12 at yahoo.co.uk> wrote:

> Dear Sir or Madam,
> I am using a remote blast and encounter either a too many hsp or CPU
> overload
> problem with my specific gene. The gene itself is not that big so I was
> wondering is there a parameter I can pass when using the submit option to
> restrict number of hsp and to avoid the cpu and too many hsp problem? (I
> know I
> can use repeat masking and change the e-value but I need something that
> does not
> require those changes)
>
> my $prog = 'blastn';
> #my $db   = 'swissprot';
> my $e_val= '1e-10';
>
> my @params = ( '-prog'       => $prog,
> #       '-data'       => $db,
>               '-expect'     => $e_val,
>               '-readmethod' => 'SearchIO'
>            );
>
> my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
>
> $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens
> [ORGN]';
>
> delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};
>
> my $str = Bio::SeqIO->new(-file            =>'temporary.fa' ,
>  '-format'         => 'fasta');
>
> my $r = $factory->submit_blast('temporary.fa');
>
> Thank you for your help.
> Suhail
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


From rmb32 at cornell.edu  Fri Mar 18 15:24:03 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Fri, 18 Mar 2011 15:24:03 -0400
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
Message-ID: <4D83B153.6010006@cornell.edu>

Hi all,

Great news: Google announced today that the Open Bioinformatics
Foundation has been accepted as a mentoring organization for this
summer's Google Summer of Code!

GSoC is a Google-sponsored student internship program for open-source
projects, open to students from around the world (not just US
residents).   Students are paid a $5000 USD stipend to work as a
developer on an open-source project for the summer. For more on GSoC,
see GSoC 2011 FAQ at http://bit.ly/hpoz8W

Student applications are due April 8, 2011 at 19:00 UTC.  Students who
are interested in participating should look at the OBF's GSoC page at
http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
ideas, and whom to contact about applying.

For current developers on OBF projects, please consider volunteering to
be a mentor if you have not already, and contribute project ideas.  Just
list your name and project ideas on OBF wiki and on the relevant
project's GSoC wiki page.

Thanks to all who helped make OBF's application to GSoC a success, and
let's have a great, productive summer of code!

Rob Buels
OBF GSoC 2011 Administrator




From cjfields at illinois.edu  Fri Mar 18 16:06:36 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 18 Mar 2011 15:06:36 -0500
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <4D83B153.6010006@cornell.edu>
References: <4D83B153.6010006@cornell.edu>
Message-ID: <AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>

Congrats Rob!

chris

On Mar 18, 2011, at 2:24 PM, Robert Buels wrote:

> Hi all,
> 
> Great news: Google announced today that the Open Bioinformatics
> Foundation has been accepted as a mentoring organization for this
> summer's Google Summer of Code!
> 
> GSoC is a Google-sponsored student internship program for open-source
> projects, open to students from around the world (not just US
> residents).   Students are paid a $5000 USD stipend to work as a
> developer on an open-source project for the summer. For more on GSoC,
> see GSoC 2011 FAQ at http://bit.ly/hpoz8W
> 
> Student applications are due April 8, 2011 at 19:00 UTC.  Students who
> are interested in participating should look at the OBF's GSoC page at
> http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
> ideas, and whom to contact about applying.
> 
> For current developers on OBF projects, please consider volunteering to
> be a mentor if you have not already, and contribute project ideas.  Just
> list your name and project ideas on OBF wiki and on the relevant
> project's GSoC wiki page.
> 
> Thanks to all who helped make OBF's application to GSoC a success, and
> let's have a great, productive summer of code!
> 
> Rob Buels
> OBF GSoC 2011 Administrator
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From ross at cuhk.edu.hk  Fri Mar 18 19:28:51 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Sat, 19 Mar 2011 07:28:51 +0800
Subject: [Bioperl-l]  failure in unsubscription
In-Reply-To: <AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
Message-ID: <018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>

unable to unsubscribe bioperl mailing list, can anybody help? the web link,
after clicking "unsubscribe" at
http://lists.open-bio.org/mailman/options/bioperl-announce-l, there is no
confirmation email sent to my email account and I keep receiving emails from
bioperl mailing list.



From Kevin.M.Brown at asu.edu  Fri Mar 18 19:35:37 2011
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Fri, 18 Mar 2011 16:35:37 -0700
Subject: [Bioperl-l] failure in unsubscription
In-Reply-To: <018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>
References: <4D83B153.6010006@cornell.edu><AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
	<018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>
Message-ID: <1A4207F8295607498283FE9E93B775B407816AC4@EX02.asurite.ad.asu.edu>

Looks like you're unsubscribing to the wrong list. That is for the
Bioperl ANNOUNCE list. See the signature at the bottom of the emails for
the correct link to remove yourself from the Bioperl-l list.

Kevin Brown
Center for Innovations in Medicine
Biodesign Institute
Arizona State University 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Ross KK Leung
> Sent: Friday, March 18, 2011 4:29 PM
> To: 'Chris Fields'; 'Robert Buels'
> Cc: 'BioPerl List'
> Subject: [Bioperl-l] failure in unsubscription
> 
> unable to unsubscribe bioperl mailing list, can anybody help? the web
> link,
> after clicking "unsubscribe" at
> http://lists.open-bio.org/mailman/options/bioperl-announce-l, there is
> no
> confirmation email sent to my email account and I keep receiving
emails
> from
> bioperl mailing list.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From David.Messina at sbc.su.se  Fri Mar 18 19:55:08 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Sat, 19 Mar 2011 00:55:08 +0100
Subject: [Bioperl-l] failure in unsubscription
In-Reply-To: <018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
	<018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>
Message-ID: <AANLkTin6k3AfwYFxgRKLGWbL5BhqxkQr7Vv6MebhObzY@mail.gmail.com>

Looks like you accidentally found the page for the wrong email list. This is
bioperl-l, not bioperl-announce-l.

Try clicking unsubscribe on this page:
http://lists.open-bio.org/mailman/listinfo/bioperl-l



On Sat, Mar 19, 2011 at 00:28, Ross KK Leung <ross at cuhk.edu.hk> wrote:

> unable to unsubscribe bioperl mailing list, can anybody help? the web link,
> after clicking "unsubscribe" at
> http://lists.open-bio.org/mailman/options/bioperl-announce-l, there is no
> confirmation email sent to my email account and I keep receiving emails
> from
> bioperl mailing list.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From David.Messina at sbc.su.se  Fri Mar 18 19:56:12 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Sat, 19 Mar 2011 00:56:12 +0100
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
Message-ID: <AANLkTikTsPeJvs0StBPzicxM55XgfvGbjrZMrwX9mwNo@mail.gmail.com>

Hear, hear! Thanks again Rob for leading this effort. You rock!

Dave



On Fri, Mar 18, 2011 at 21:06, Chris Fields <cjfields at illinois.edu> wrote:

> Congrats Rob!
>
> chris
>
> On Mar 18, 2011, at 2:24 PM, Robert Buels wrote:
>
> > Hi all,
> >
> > Great news: Google announced today that the Open Bioinformatics
> > Foundation has been accepted as a mentoring organization for this
> > summer's Google Summer of Code!
> >
> > GSoC is a Google-sponsored student internship program for open-source
> > projects, open to students from around the world (not just US
> > residents).   Students are paid a $5000 USD stipend to work as a
> > developer on an open-source project for the summer. For more on GSoC,
> > see GSoC 2011 FAQ at http://bit.ly/hpoz8W
> >
> > Student applications are due April 8, 2011 at 19:00 UTC.  Students who
> > are interested in participating should look at the OBF's GSoC page at
> > http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
> > ideas, and whom to contact about applying.
> >
> > For current developers on OBF projects, please consider volunteering to
> > be a mentor if you have not already, and contribute project ideas.  Just
> > list your name and project ideas on OBF wiki and on the relevant
> > project's GSoC wiki page.
> >
> > Thanks to all who helped make OBF's application to GSoC a success, and
> > let's have a great, productive summer of code!
> >
> > Rob Buels
> > OBF GSoC 2011 Administrator
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From hlapp at drycafe.net  Fri Mar 18 22:04:28 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Fri, 18 Mar 2011 22:04:28 -0400
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <AANLkTikTsPeJvs0StBPzicxM55XgfvGbjrZMrwX9mwNo@mail.gmail.com>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
	<AANLkTikTsPeJvs0StBPzicxM55XgfvGbjrZMrwX9mwNo@mail.gmail.com>
Message-ID: <19636599-D2B1-49E5-B557-3E406B405523@drycafe.net>

Yes! -hilmar

On Mar 18, 2011, at 7:56 PM, Dave Messina wrote:

> Hear, hear! Thanks again Rob for leading this effort. You rock!
>
> Dave
>
>
>
> On Fri, Mar 18, 2011 at 21:06, Chris Fields <cjfields at illinois.edu>  
> wrote:
>
>> Congrats Rob!
>>
>> chris
>>
>> On Mar 18, 2011, at 2:24 PM, Robert Buels wrote:
>>
>>> Hi all,
>>>
>>> Great news: Google announced today that the Open Bioinformatics
>>> Foundation has been accepted as a mentoring organization for this
>>> summer's Google Summer of Code!
>>>
>>> GSoC is a Google-sponsored student internship program for open- 
>>> source
>>> projects, open to students from around the world (not just US
>>> residents).   Students are paid a $5000 USD stipend to work as a
>>> developer on an open-source project for the summer. For more on  
>>> GSoC,
>>> see GSoC 2011 FAQ at http://bit.ly/hpoz8W
>>>
>>> Student applications are due April 8, 2011 at 19:00 UTC.  Students  
>>> who
>>> are interested in participating should look at the OBF's GSoC page  
>>> at
>>> http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
>>> ideas, and whom to contact about applying.
>>>
>>> For current developers on OBF projects, please consider  
>>> volunteering to
>>> be a mentor if you have not already, and contribute project  
>>> ideas.  Just
>>> list your name and project ideas on OBF wiki and on the relevant
>>> project's GSoC wiki page.
>>>
>>> Thanks to all who helped make OBF's application to GSoC a success,  
>>> and
>>> let's have a great, productive summer of code!
>>>
>>> Rob Buels
>>> OBF GSoC 2011 Administrator
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From chiragmatkarbioinfo at gmail.com  Fri Mar 18 23:44:32 2011
From: chiragmatkarbioinfo at gmail.com (Chirag Matkar)
Date: Sat, 19 Mar 2011 10:44:32 +0700
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <19636599-D2B1-49E5-B557-3E406B405523@drycafe.net>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
	<AANLkTikTsPeJvs0StBPzicxM55XgfvGbjrZMrwX9mwNo@mail.gmail.com>
	<19636599-D2B1-49E5-B557-3E406B405523@drycafe.net>
Message-ID: <AANLkTin6_H-T7Eq2jxU-SM4CuMF=nBZpXoM_n6joFfmn@mail.gmail.com>

Great News

On Sat, Mar 19, 2011 at 9:04 AM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> Yes! -hilmar
>
>
> On Mar 18, 2011, at 7:56 PM, Dave Messina wrote:
>
>  Hear, hear! Thanks again Rob for leading this effort. You rock!
>>
>> Dave
>>
>>
>>
>> On Fri, Mar 18, 2011 at 21:06, Chris Fields <cjfields at illinois.edu>
>> wrote:
>>
>>  Congrats Rob!
>>>
>>> chris
>>>
>>> On Mar 18, 2011, at 2:24 PM, Robert Buels wrote:
>>>
>>>  Hi all,
>>>>
>>>> Great news: Google announced today that the Open Bioinformatics
>>>> Foundation has been accepted as a mentoring organization for this
>>>> summer's Google Summer of Code!
>>>>
>>>> GSoC is a Google-sponsored student internship program for open-source
>>>> projects, open to students from around the world (not just US
>>>> residents).   Students are paid a $5000 USD stipend to work as a
>>>> developer on an open-source project for the summer. For more on GSoC,
>>>> see GSoC 2011 FAQ at http://bit.ly/hpoz8W
>>>>
>>>> Student applications are due April 8, 2011 at 19:00 UTC.  Students who
>>>> are interested in participating should look at the OBF's GSoC page at
>>>> http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
>>>> ideas, and whom to contact about applying.
>>>>
>>>> For current developers on OBF projects, please consider volunteering to
>>>> be a mentor if you have not already, and contribute project ideas.  Just
>>>> list your name and project ideas on OBF wiki and on the relevant
>>>> project's GSoC wiki page.
>>>>
>>>> Thanks to all who helped make OBF's application to GSoC a success, and
>>>> let's have a great, productive summer of code!
>>>>
>>>> Rob Buels
>>>> OBF GSoC 2011 Administrator
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>  _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Regards,
Chirag Matkar


From tzhu at mail.bnu.edu.cn  Sat Mar 19 05:49:22 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Sat, 19 Mar 2011 17:49:22 +0800
Subject: [Bioperl-l] What's wrong with the script about module
 Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300460730.12411.50.camel@deskpro15336.internal.sanger.ac.uk>
References: <1300422812.12949.5.camel@ubuntu>  <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
	<2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
	<1300456641.18688.4.camel@ubuntu>
	<1300460730.12411.50.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <1300528162.5998.4.camel@ubuntu>

But I think an "mRNA" feature should have exons. For example:


     mRNA            complement(join(1031434..1031901,1031940..1032269,
                     1032329..1032418,1032472..1032489))
                     /locus_tag="SPCC825.05c"
                     /transcript_id="NM_001023047.1"
                     /db_xref="GI:68021105"
                     /db_xref="GeneID:2539459"

Such mRNA should have 4 exons and 3 introns, right? And I just want to
calculate the lengths of every exons and introns quickly.

Besides, in the document of module Bio::SeqFeature::Gene::GeneStructure,
it writes like these:

@exons = $gene->exons();
@introns = $gene->introns();
@utr_sites = $gene->utrs();

Then where does the object "$gene" come from? I've searched through all
the google sites but found nothing.

? 2011-03-18?? 15:05 +0000?Frank Schwach??? 
> maybe I'm missing the point here but I think an "mRNA" feature should
> not be a Bio::SeqFeature::Gene::GeneStructure and it should not have
> exons - it would not make sense biologically.
> 
> Frank
> 
> 
> On Fri, 2011-03-18 at 21:57 +0800, Tao Zhu wrote:
> > Yes. But in the document
> > http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
> > It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
> > Bio::SeqFeature::Generic. I wonder how to do such inheritance.


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)





From manju.rawat2 at gmail.com  Sat Mar 19 06:29:32 2011
From: manju.rawat2 at gmail.com (manju rawat)
Date: Sat, 19 Mar 2011 15:59:32 +0530
Subject: [Bioperl-l] bio-scf installation error
Message-ID: <AANLkTikQwcqs0YyaHvddq9yjowOpoe_YDRj4Z03zXRdv@mail.gmail.com>

Hello ,

I want to install Bio-SCF module on windows..But i am unable to do this bcs
to install bio-scf i have to install io_lib oe zlib on windows..
I download both from the described url in install file of bio-scf....i also
indtalled MinGW ..but now i dont know how to install it???
pls help to install it..

Thanks in Advance
Manju Rawat


From jason.stajich at gmail.com  Sat Mar 19 14:19:23 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 19 Mar 2011 11:19:23 -0700
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <4D83B153.6010006@cornell.edu>
References: <4D83B153.6010006@cornell.edu>
Message-ID: <6387373A-E17F-4CE2-9B19-E296A2668018@gmail.com>

Nice work Rob. Thanks for leading the effort and thanks to those who agreed to mentor. 

Sent from my iPhone-please excuse typos

--
Jason Stajich

On Mar 18, 2011, at 12:24 PM, Robert Buels <rmb32 at cornell.edu> wrote:

> Hi all,
> 
> Great news: Google announced today that the Open Bioinformatics
> Foundation has been accepted as a mentoring organization for this
> summer's Google Summer of Code!
> 
> GSoC is a Google-sponsored student internship program for open-source
> projects, open to students from around the world (not just US
> residents).   Students are paid a $5000 USD stipend to work as a
> developer on an open-source project for the summer. For more on GSoC,
> see GSoC 2011 FAQ at http://bit.ly/hpoz8W
> 
> Student applications are due April 8, 2011 at 19:00 UTC.  Students who
> are interested in participating should look at the OBF's GSoC page at
> http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
> ideas, and whom to contact about applying.
> 
> For current developers on OBF projects, please consider volunteering to
> be a mentor if you have not already, and contribute project ideas.  Just
> list your name and project ideas on OBF wiki and on the relevant
> project's GSoC wiki page.
> 
> Thanks to all who helped make OBF's application to GSoC a success, and
> let's have a great, productive summer of code!
> 
> Rob Buels
> OBF GSoC 2011 Administrator
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jason.stajich at gmail.com  Sat Mar 19 14:31:17 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 19 Mar 2011 11:31:17 -0700
Subject: [Bioperl-l] What's wrong with the script about module
	Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300528162.5998.4.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu> <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
	<2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
	<1300456641.18688.4.camel@ubuntu>
	<1300460730.12411.50.camel@deskpro15336.internal.sanger.ac.uk>
	<1300528162.5998.4.camel@ubuntu>
Message-ID: <093660B8-458E-4617-8D12-228985CA88CD@gmail.com>

You have to instantiate the gene structure and copy the exon objects into the substructure. Unless you have specific methods in the GeneStructure I would just pull out the data from the generic objects. 

See the genbank to gff script and the Unflattener for ways to more simply destruct the mRNA feature into gene->mRNA->CDS,Exons 

If you are just wanting to count Exons 
You can see example on slide 27 or so. 

http://jason.open-bio.org/Bioperl_Tutorials/ProgrammingBiology2008/ProgBiology_BioPerl_I.pdf

Sent from my iPhone-please excuse typos

--
Jason Stajich

On Mar 19, 2011, at 2:49 AM, Tao Zhu <tzhu at mail.bnu.edu.cn> wrote:

> But I think an "mRNA" feature should have exons. For example:
> 
> 
>     mRNA            complement(join(1031434..1031901,1031940..1032269,
>                     1032329..1032418,1032472..1032489))
>                     /locus_tag="SPCC825.05c"
>                     /transcript_id="NM_001023047.1"
>                     /db_xref="GI:68021105"
>                     /db_xref="GeneID:2539459"
> 
> Such mRNA should have 4 exons and 3 introns, right? And I just want to
> calculate the lengths of every exons and introns quickly.
> 
> Besides, in the document of module Bio::SeqFeature::Gene::GeneStructure,
> it writes like these:
> 
> @exons = $gene->exons();
> @introns = $gene->introns();
> @utr_sites = $gene->utrs();
> 
> Then where does the object "$gene" come from? I've searched through all
> the google sites but found nothing.
> 
> ? 2011-03-18?? 15:05 +0000?Frank Schwach??? 
>> maybe I'm missing the point here but I think an "mRNA" feature should
>> not be a Bio::SeqFeature::Gene::GeneStructure and it should not have
>> exons - it would not make sense biologically.
>> 
>> Frank
>> 
>> 
>> On Fri, 2011-03-18 at 21:57 +0800, Tao Zhu wrote:
>>> Yes. But in the document
>>> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
>>> It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
>>> Bio::SeqFeature::Generic. I wonder how to do such inheritance.
> 
> 
> -- 
> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> 100875, China
> Email: tzhu at mail.bnu.edu.cn
> Website: http://bnuzt.org (mainly written in Chinese)
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jason.stajich at gmail.com  Sat Mar 19 14:36:49 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 19 Mar 2011 11:36:49 -0700
Subject: [Bioperl-l] Please recommend Perl module to parse phylogentic
	trees
In-Reply-To: <2e94f0bb-0282-4d53-b205-56ff895665de@w7g2000pre.googlegroups.com>
References: <2e94f0bb-0282-4d53-b205-56ff895665de@w7g2000pre.googlegroups.com>
Message-ID: <447BFFD2-06E6-41E0-81BF-B03EB919316C@gmail.com>

Nexus is richer and we only parse the trees from that format. Since the format is a newick tree embedded within it relies on the same code in the newick parser. 

Knowing what you want to do would more likely lead to better answer.  As for bugs - you can search the redmine big tracker to see whether they are reported issues that are unresolved and you can examine the tests in the t directory to see what compliance is tested. 

Jason
Sent from my iPhone-please excuse typos

--
Jason Stajich

On Mar 4, 2011, at 12:24 PM, justin100 <bio.justin100 at gmail.com> wrote:

> Hi,
> 
> I am writing a script to parse phylogenetic trees. The input will be
> trees in Newick format for now (maybe NEXUS in the future).
> 
> Quite a few Perl modules can parse phylogenetic trees. For Newick
> format, there are Bio::TreeIO and  Bio::Phylo::Parsers. For NEXUS
> format, there is Bio::NEXUS. From my understanding, it's not difficult
> to convert from Newick to NEXUS or vice versa, if only for the purpose
> of parsing trees.
> 
> I'd to know the advantages and disadvantages of these modules when
> compared with each other. Please recommend one that you think is the
> most capable parser (and hopefully has the least bugs).
> 
> Thanks.
> 
> Justin
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From veer_lovepune at yahoo.co.in  Sat Mar 19 16:56:06 2011
From: veer_lovepune at yahoo.co.in (virendra patil)
Date: Sun, 20 Mar 2011 02:26:06 +0530 (IST)
Subject: [Bioperl-l] Bioperl-l Digest, Vol 95, Issue 19
In-Reply-To: <mailman.21.1300550405.26148.bioperl-l@lists.open-bio.org>
Message-ID: <790813.91588.qm@web137312.mail.in.yahoo.com>

hi can some one help me i tried to install ?bioperl many time but it show message likeCan't locate Bio/Seq.pm in @INC (@INC contains: E:/JAVA1/.metadata/.plugins/org.epic.debug E:/JAVA1/PERL EXAM D:/Perl/site/lib D:/Perl/lib .) at E:/JAVA1/PERL EXAM/PERLEXAM.pl line 2.BEGIN failed--compilation aborted at E:/JAVA1/PERL EXAM/PERLEXAM.pl line 2.?

---i try with java perl intgration my perl is working but bioperl show upper message




From ngoodman at systemsbiology.org  Tue Mar 22 09:57:50 2011
From: ngoodman at systemsbiology.org (Nathan (Nat) Goodman)
Date: Tue, 22 Mar 2011 06:57:50 -0700
Subject: [Bioperl-l] Ensembl stable_id_event table
Message-ID: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>

With apologies, this is not technically a bioperl question, but hopefully close enough.  I'm trying to map old Ensembl IDs to current ones.  Table stable_id_event on their ftp site seems to be the place to get this information, but the data in that table (for human build 61) is cyclic, meaning that old IDs are sometimes mapped to new ones which in turn are mapped back to the old one.  This seems wrong...  And, it's not a rare occurrence: 18% of IDs in the table lie on cycles, the largest of which contains more than 6000 IDs!

To see one short cycle, run this query (against human build 61).

mysql> select * from stable_id_event where 
    ->     (old_stable_id='ENSP00000399673' or new_stable_id='ENSP00000399673')
    -> and (old_stable_id='ENSP00000365536' or new_stable_id='ENSP00000365536');

The results are

+-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
| old_stable_id   | old_version | new_stable_id   | new_version | mapping_session_id | type        | score |
+-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
| ENSP00000399673 |           2 | ENSP00000365536 |           3 |                380 | translation |     1 | 
| ENSP00000399673 |           2 | ENSP00000365536 |           3 |                381 | translation |     1 | 
| ENSP00000365536 |           3 | ENSP00000399673 |           2 |                381 | translation |     1 | 
| ENSP00000399673 |           2 | ENSP00000365536 |           3 |                382 | translation |     1 | 
| ENSP00000365536 |           3 | ENSP00000399673 |           2 |                382 | translation |     1 | 
+-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+

The first and last lines reveal the cycle:

line 1) ENSP00000399673-> ENSP00000365536
line 5) ENSP00000365536-> ENSP00000399673

If anyone can shed some light, I would be most grateful.

Thanks very much,
Nat Goodman




From molecules at cpan.org  Wed Mar 23 14:44:15 2011
From: molecules at cpan.org (Christopher Bottoms)
Date: Wed, 23 Mar 2011 13:44:15 -0500
Subject: [Bioperl-l] Ensembl stable_id_event table
In-Reply-To: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>
References: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>
Message-ID: <AANLkTi=acb_oG6-PiDLeh373LkYUz9K=XDhUimv922qz@mail.gmail.com>

Hi Nat,

Have you tried contacting someone at Ensembl about it? That is the
first place I would try.

--Christopher Bottoms


On Tue, Mar 22, 2011 at 8:57 AM, Nathan (Nat) Goodman
<ngoodman at systemsbiology.org> wrote:
> With apologies, this is not technically a bioperl question, but hopefully close enough. ?I'm trying to map old Ensembl IDs to current ones. ?Table stable_id_event on their ftp site seems to be the place to get this information, but the data in that table (for human build 61) is cyclic, meaning that old IDs are sometimes mapped to new ones which in turn are mapped back to the old one. ?This seems wrong... ?And, it's not a rare occurrence: 18% of IDs in the table lie on cycles, the largest of which contains more than 6000 IDs!
>
> To see one short cycle, run this query (against human build 61).
>
> mysql> select * from stable_id_event where
> ? ?-> ? ? (old_stable_id='ENSP00000399673' or new_stable_id='ENSP00000399673')
> ? ?-> and (old_stable_id='ENSP00000365536' or new_stable_id='ENSP00000365536');
>
> The results are
>
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> | old_stable_id ? | old_version | new_stable_id ? | new_version | mapping_session_id | type ? ? ? ?| score |
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> | ENSP00000399673 | ? ? ? ? ? 2 | ENSP00000365536 | ? ? ? ? ? 3 | ? ? ? ? ? ? ? ?380 | translation | ? ? 1 |
> | ENSP00000399673 | ? ? ? ? ? 2 | ENSP00000365536 | ? ? ? ? ? 3 | ? ? ? ? ? ? ? ?381 | translation | ? ? 1 |
> | ENSP00000365536 | ? ? ? ? ? 3 | ENSP00000399673 | ? ? ? ? ? 2 | ? ? ? ? ? ? ? ?381 | translation | ? ? 1 |
> | ENSP00000399673 | ? ? ? ? ? 2 | ENSP00000365536 | ? ? ? ? ? 3 | ? ? ? ? ? ? ? ?382 | translation | ? ? 1 |
> | ENSP00000365536 | ? ? ? ? ? 3 | ENSP00000399673 | ? ? ? ? ? 2 | ? ? ? ? ? ? ? ?382 | translation | ? ? 1 |
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
>
> The first and last lines reveal the cycle:
>
> line 1) ENSP00000399673-> ENSP00000365536
> line 5) ENSP00000365536-> ENSP00000399673
>
> If anyone can shed some light, I would be most grateful.
>
> Thanks very much,
> Nat Goodman
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From cjfields at illinois.edu  Wed Mar 23 18:23:47 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 23 Mar 2011 17:23:47 -0500
Subject: [Bioperl-l] Ensembl stable_id_event table
In-Reply-To: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>
References: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>
Message-ID: <890FA151-63D4-4EAF-8141-8975911126E4@illinois.edu>

Odd, wonder what the ensembl folks have to say about it.  Have you asked them?

chris

On Mar 22, 2011, at 8:57 AM, Nathan (Nat) Goodman wrote:

> With apologies, this is not technically a bioperl question, but hopefully close enough.  I'm trying to map old Ensembl IDs to current ones.  Table stable_id_event on their ftp site seems to be the place to get this information, but the data in that table (for human build 61) is cyclic, meaning that old IDs are sometimes mapped to new ones which in turn are mapped back to the old one.  This seems wrong...  And, it's not a rare occurrence: 18% of IDs in the table lie on cycles, the largest of which contains more than 6000 IDs!
> 
> To see one short cycle, run this query (against human build 61).
> 
> mysql> select * from stable_id_event where 
>    ->     (old_stable_id='ENSP00000399673' or new_stable_id='ENSP00000399673')
>    -> and (old_stable_id='ENSP00000365536' or new_stable_id='ENSP00000365536');
> 
> The results are
> 
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> | old_stable_id   | old_version | new_stable_id   | new_version | mapping_session_id | type        | score |
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> | ENSP00000399673 |           2 | ENSP00000365536 |           3 |                380 | translation |     1 | 
> | ENSP00000399673 |           2 | ENSP00000365536 |           3 |                381 | translation |     1 | 
> | ENSP00000365536 |           3 | ENSP00000399673 |           2 |                381 | translation |     1 | 
> | ENSP00000399673 |           2 | ENSP00000365536 |           3 |                382 | translation |     1 | 
> | ENSP00000365536 |           3 | ENSP00000399673 |           2 |                382 | translation |     1 | 
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> 
> The first and last lines reveal the cycle:
> 
> line 1) ENSP00000399673-> ENSP00000365536
> line 5) ENSP00000365536-> ENSP00000399673
> 
> If anyone can shed some light, I would be most grateful.
> 
> Thanks very much,
> Nat Goodman
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From roy.chaudhuri at gmail.com  Thu Mar 24 09:47:27 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Thu, 24 Mar 2011 13:47:27 +0000
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
Message-ID: <4D8B4B6F.7010407@gmail.com>

Hi all,

I have discovered a possible bug in Bioperl, although maybe it's my 
expectations that are wrong, not the code.

I noticed that when calculating molecular weights for a bunch of protein 
sequences using Bio::Tools::SeqStats->get_mol_wt, the values I was 
getting were slightly different from the ones given by Emboss pepstats. 
This was due to my protein sequences ending with *, since they were 
derived from translating annotated genes including the stop codon. 
Surprisingly (to me, at least) Bio::Seq->length gives a value that 
counts the terminal *, so one greater than the number of amino acids. 
SeqStats->get_mol_wt calls Bio::Seq->length to determine the number of 
water molecules to subtract from the total molecular weight, so the 
reported weights for my sequence were the weight of one water molecule 
less than they should have been. I'm not sure if this is a bug in 
get_mol_wt, in Bio::Seq->length, or if it's bad practice to use protein 
sequences with a terminal asterisk (I've never had a problem doing so 
before).

Cheers,
Roy.


From adsj at novozymes.com  Thu Mar 24 11:01:25 2011
From: adsj at novozymes.com (Adam =?utf-8?Q?Sj=C3=B8gren?=)
Date: Thu, 24 Mar 2011 16:01:25 +0100
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
In-Reply-To: <4D8B4B6F.7010407@gmail.com> (Roy Chaudhuri's message of "Thu, 24
	Mar 2011 13:47:27 +0000")
References: <4D8B4B6F.7010407@gmail.com>
Message-ID: <87mxkkbm0q.fsf@topper.koldfront.dk>

On Thu, 24 Mar 2011 13:47:27 +0000, Roy wrote:

> This was due to my protein sequences ending with *, since they were
> derived from translating annotated genes including the stop codon.

If you give ->translate() the -complete=>1 option, the stop codon will
not be included in the resulting protein sequence.

 * http://bioperl.org/cgi-bin/deob_detail.cgi?method=Bio::PrimarySeqI::translate


  Best regards,

    Adam

-- 
                                                          Adam Sj?gren
                                                    adsj at novozymes.com



From roy.chaudhuri at gmail.com  Thu Mar 24 11:27:36 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Thu, 24 Mar 2011 15:27:36 +0000
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
In-Reply-To: <87mxkkbm0q.fsf@topper.koldfront.dk>
References: <4D8B4B6F.7010407@gmail.com> <87mxkkbm0q.fsf@topper.koldfront.dk>
Message-ID: <4D8B62E8.2050902@gmail.com>

On 24/03/2011 15:01, Adam Sj?gren wrote:
> If you give ->translate() the -complete=>1 option, the stop codon will
> not be included in the resulting protein sequence.

Ah, that's useful to know, thanks Adam. I still think that get_mol_wt 
should deal with such sequences without giving an incorrect weight, though.


From cjfields at illinois.edu  Thu Mar 24 11:47:29 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 24 Mar 2011 10:47:29 -0500
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
In-Reply-To: <4D8B4B6F.7010407@gmail.com>
References: <4D8B4B6F.7010407@gmail.com>
Message-ID: <2F1303AE-4678-4901-A33C-A7811FF8F309@illinois.edu>


On Mar 24, 2011, at 8:47 AM, Roy Chaudhuri wrote:

> Hi all,
> 
> I have discovered a possible bug in Bioperl, although maybe it's my expectations that are wrong, not the code.
> 
> I noticed that when calculating molecular weights for a bunch of protein sequences using Bio::Tools::SeqStats->get_mol_wt, the values I was getting were slightly different from the ones given by Emboss pepstats. This was due to my protein sequences ending with *, since they were derived from translating annotated genes including the stop codon. Surprisingly (to me, at least) Bio::Seq->length gives a value that counts the terminal *, so one greater than the number of amino acids. SeqStats->get_mol_wt calls Bio::Seq->length to determine the number of water molecules to subtract from the total molecular weight, so the reported weights for my sequence were the weight of one water molecule less than they should have been. I'm not sure if this is a bug in get_mol_wt, in Bio::Seq->length, or if it's bad practice to use protein sequences with a terminal asterisk (I've never had a problem doing so before).

The method should account for the possibility that '*' is present; should be easy enough to fix with something like:

my $len = $seq =~ tr/A-Za-z/A-Za-z/;

I'm not able to do this right away (on fam vacation), can you file this on our new bug server?

http://redmine.open-bio.org

> Cheers,
> Roy.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

chris


From roy.chaudhuri at gmail.com  Thu Mar 24 12:08:22 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Thu, 24 Mar 2011 16:08:22 +0000
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
In-Reply-To: <2F1303AE-4678-4901-A33C-A7811FF8F309@illinois.edu>
References: <4D8B4B6F.7010407@gmail.com>
	<2F1303AE-4678-4901-A33C-A7811FF8F309@illinois.edu>
Message-ID: <4D8B6C76.6090401@gmail.com>

Done:
http://redmine.open-bio.org/issues/3185

Have a good break,
Roy.

On 24/03/2011 15:47, Chris Fields wrote:
>
> On Mar 24, 2011, at 8:47 AM, Roy Chaudhuri wrote:
>
>> Hi all,
>>
>> I have discovered a possible bug in Bioperl, although maybe it's my
>> expectations that are wrong, not the code.
>>
>> I noticed that when calculating molecular weights for a bunch of
>> protein sequences using Bio::Tools::SeqStats->get_mol_wt, the
>> values I was getting were slightly different from the ones given by
>> Emboss pepstats. This was due to my protein sequences ending with
>> *, since they were derived from translating annotated genes
>> including the stop codon. Surprisingly (to me, at least)
>> Bio::Seq->length gives a value that counts the terminal *, so one
>> greater than the number of amino acids. SeqStats->get_mol_wt calls
>> Bio::Seq->length to determine the number of water molecules to
>> subtract from the total molecular weight, so the reported weights
>> for my sequence were the weight of one water molecule less than
>> they should have been. I'm not sure if this is a bug in get_mol_wt,
>> in Bio::Seq->length, or if it's bad practice to use protein
>> sequences with a terminal asterisk (I've never had a problem doing
>> so before).
>
> The method should account for the possibility that '*' is present;
> should be easy enough to fix with something like:
>
> my $len = $seq =~ tr/A-Za-z/A-Za-z/;
>
> I'm not able to do this right away (on fam vacation), can you file
> this on our new bug server?
>
> http://redmine.open-bio.org
>
>> Cheers, Roy. _______________________________________________
>> Bioperl-l mailing list Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> chris



From rachitasharma at gmail.com  Thu Mar 24 13:12:43 2011
From: rachitasharma at gmail.com (Rachita Sharma)
Date: Thu, 24 Mar 2011 11:12:43 -0600
Subject: [Bioperl-l] Genbank to gff3 format
Message-ID: <AANLkTimarbmi3XnFZ9VjT2GMHUoS6COkVGnbtawYh2a+@mail.gmail.com>

I am having trouble using the perl script bp_genbank2gff3.pl for
converting my genbank file into gff3 format. Unique IDs are not
created by the Bioperl converter so I cannot get the gff3 file
validated on the official GFF validator I want to use the final gff3
file on Gbrowse without errors. Will appreciate your suggestions.

Thanks!
Rachita


From dan.bolser at gmail.com  Fri Mar 25 07:21:57 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Fri, 25 Mar 2011 11:21:57 +0000
Subject: [Bioperl-l] from SimpleAlign to SAM/BAM
In-Reply-To: <AANLkTinEo3Ac8h5Gh-l4aqiKE0C1-iPiP96XilazQ4Hd@mail.gmail.com>
References: <AANLkTilHpBojt1AoAR6qe8YgqXrt8vp_dl64GOblTH3h@mail.gmail.com>
	<CF66A9BB040D49189BB80C9E057422AC@NewLife>
	<AANLkTinEo3Ac8h5Gh-l4aqiKE0C1-iPiP96XilazQ4Hd@mail.gmail.com>
Message-ID: <AANLkTikk4jNjG203Lw764Exdb9VBoZPVkXki8n8jVwLO@mail.gmail.com>

On 19 May 2010 17:40, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Bio::Samtools, which is separate from bioperl but compatible with it,
> provides read/write access to SAM and BAM via Heng's C library.

If I understand correctly, Bio::Samtools is a meta package that
encompasses Bio::DB::Sam and friends. However, when I look at
Bio::DB::Sam, I only see "Read SAM/BAM database files", not write, and
I don't see how to write SAM files from the docs there.

I just looked at the pod for Bio::Assembly::IO::sam (how come this
isn't documented in CPAN?), and I read:

This is a (currently) read-only IO module designed to convert
Sequence/Alignment Map (SAM) ...

I guess this is what was being discussed on in this thread (the fact
that IO doesn't yet write, but XS can be used to get it writing).

Did I understand correctly, or is there some way to write SAM from BioPerl?


Cheers,
Dan..

> Lincoln
>
> On Wed, May 19, 2010 at 9:34 AM, Mark A. Jensen <maj at fortinbras.us> wrote:
>
>> Albert-- have a look at Bio::Tools::Run::Samtools which incorporates the
>> use of Bio::Assembly::IO::sam (I think). I know there is only read
>> capability for B:A:I:sam, but Samtools may give you the appropriate wrapper
>> for doing writes (some assembly (so to speak) required...)-- cheers MAJ
>> ----- Original Message ----- From: "Albert Vilella" <avilella at gmail.com>
>>
>> To: <bioperl-l at bioperl.org>
>> Sent: Wednesday, May 19, 2010 4:36 AM
>>
>> Subject: [Bioperl-l] from SimpleAlign to SAM/BAM
>>
>>
>> ?Hi,
>>>
>>> I would like to know what would be the best way to generate a SAM/BAM file
>>> with cDNA alignments against the human reference from a bunch of
>>> Bio::SimpleAlign
>>> cDNA multiple sequence alignment objects.
>>>
>>> Considering I've got a way to map the cDNAs to chromosome coordinates,
>>> how can I generate a SAM/BAM file with ~1,000,000 entries against ~23.000
>>> human
>>> coordinates?
>>>
>>> As far as I can see, there is an Bio::Assembly::IO::sam.pm which loads
>>> assemblies.
>>> Should I be using some other tool existing not in bioperl?
>>>
>>> Cheers,
>>>
>>> Albert.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From dan.bolser at gmail.com  Sat Mar 26 20:11:27 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Sun, 27 Mar 2011 00:11:27 +0000
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
Message-ID: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>

Hi all,

I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm uses:
    if (length $source_tag) {

within the '_types_sql' function to test if $source_tag is defined
(and has a length). This obviously fails when $source_tag it isn't
defined, and I see the above error message from my script when I call
the 'features' function (as shown below).

>From tests (thanks to rbuels in #bioperl) it seems the value of $type
is simply 'fwd link intensity', so:
      ($primary_tag,$source_tag) = split ':',$type,2;

on line 1047 leaves $source_tag undefined.

Here is my proposed fix:

diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
index 00103c2..dfc70c0 100644
--- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
+++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
@@ -1057,8 +1057,8 @@ sub _types_sql {
       ($primary_tag,$source_tag) = split ':',$type,2;
     }

-    if (length $source_tag) {
-      if (length($primary_tag)) {
+    if (defined $source_tag && length $source_tag) {
+      if (defined $primary_tag && length($primary_tag)) {
         push @matches,"tl.tag=?";
         push @args,"$primary_tag:$source_tag";
       }


which seems to work. I'd write some tests, but an old bug that I can't
track down prevents me from running tests on this package
(http://bugzilla.open-bio.org/show_bug.cgi?id=2899).

Cheers,
Dan.


Here are some snippets of code to give context:

my $intensities = Bio::DB::SeqFeature::Store->
  new( -adaptor => 'DBI::mysql',
	-dsn => 'db:mysql.server.ac.uk',
	-user => 'me',
	-pass => 'secret',
       -verbose => $verbose,
     );

my @fwd_intensity = $intensities->
    features( -seqid => 'some-id', -type => 'fwd link intensity',
              -start => 10,
              -end   => 200,
    );


From hufeiyc at gmail.com  Tue Mar 22 15:14:54 2011
From: hufeiyc at gmail.com (Fei Hu)
Date: Tue, 22 Mar 2011 15:14:54 -0400
Subject: [Bioperl-l] GSoC 2011
Message-ID: <AANLkTim6o3bJ6NkBRmoUC5e76GaGzpjP5+xE+ZrWcEdc@mail.gmail.com>

Hi, All.

My name is Fei Hu from U. of South Carolina. I am currently a second-year
Ph.D student in computer science focusing on gene order and sequence(DNA &
AA) phylogeny as well as whole genome alignment. I am instreseted in joining
bioperl project of GSoC 2011. I have two ideas that would like to share.

My first idea is to extend the bioperl so that it can process and analysis
gene order data using published package such as MGR, GRAPPA and distance
estimator. This is a relatively new type of data and many great researchers
have contributed to this type of phylogeny reconstruction (Dr. Pavel Penzer,
Dr. Bernard Moret and Dr. David Sankoff).

Secondly as maximum likelihood becomes more and more popular, especially
RAxML has been widely recognized and used(over 1000 citations). I think it's
time to integrate that as well as GARLI into the Bio::Tools. I extensively
used and explored RAxML in my last publication on gene order phylogeny.

Those are just my preliminary thoughts, not even a plan and any suggestion
is greatly appreciated!!! I use perl on daily bases for data processing and
composing testing scripts, but not much OOP involved.

PS: Rest api for CIPRES is no longer available. So this following task can't
be finished right now:
Development of a
Bio::Tools::Run::RemoteBlast<http://bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast>-like
interface to CIPRES remote analyses; for more see this
thread<http://thread.gmane.org/gmane.comp.lang.perl.bio.general/16524>
.

And Thank you all.
Best

Fei

-- 
*Fei Hu
Bioinformatics Lab
3D-11 Swearingen Building
U of South Carolina
Tel: 803-397-5240*


From Dallas.Thomas at AGR.GC.CA  Wed Mar 23 13:08:12 2011
From: Dallas.Thomas at AGR.GC.CA (Thomas, Dallas)
Date: Wed, 23 Mar 2011 11:08:12 -0600
Subject: [Bioperl-l] Bio::Tools::Protparam
Message-ID: <DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>

Need help.  I am trying to use the Bio::Tools::Protparam perl module.

 

For testing purposes I have copied and pasted the example in the module,
I have set:

 

use strict;

use Bio::Tools::Protparam;

use Bio::DB::GenBank;

 

Every time I try and run the script I get the following error:

                        

                              Can't locate object method "new" via
package "Protparam" (perhaps you forgot to load "Protparam"?) at ...

 

Do you have any ideas?  Any help would be very much appreciated.

 

Sincerely

Dallas Thomas

 




From ravimbt at gmail.com  Thu Mar 24 08:33:55 2011
From: ravimbt at gmail.com (=?UTF-8?B?wrbigKLil4/guYvigKLgrofgrrDgrrXgrr/Rj86xzr3OueKXj+C5i+KAouKAosK2?=)
Date: Thu, 24 Mar 2011 18:03:55 +0530
Subject: [Bioperl-l] Bioperl installation doubt
Message-ID: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>

Hi,

Could you please help me installing bioperl-db, bioperl-run & other packages
using ppm on windows 7? Please find the attachment for the error message I
get. I would really appreciate if you help me fix this issue.

Thanks,

With regards,
Ravi.
-------------- next part --------------
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From abualiga at gmail.com  Sun Mar 27 09:34:05 2011
From: abualiga at gmail.com (Galeb Abu-Ali)
Date: Sun, 27 Mar 2011 06:34:05 -0700 (PDT)
Subject: [Bioperl-l] CDS complement statements from GenBank
Message-ID: <cdf62961-ac89-4274-91ed-9a233d2de15c@k10g2000prh.googlegroups.com>

Hi,

I'm trying to parse CDS complement statements from GenBank files of
bacterial genomes. I know it works for 'join' statements with
Bio::Location::SplitLocationI, but there is no spliced genes in
bacterial annotations and therefore no 'join()' statements. When I
replace 'complement' with 'join' in the bacterial GenBank file,
Bio::Location::SplitLocationI gets the coordinates. I took a look at
SplitLocationI.pm and Split.pm to see if I could replace 'join' with
'complement' to get it to work but no luck. At your convenience,
please advise.

cheers,

galeb


From drinmontana at gmail.com  Sun Mar 27 10:37:17 2011
From: drinmontana at gmail.com (Drin)
Date: Sun, 27 Mar 2011 07:37:17 -0700 (PDT)
Subject: [Bioperl-l] Various bioperl build test errors
Message-ID: <799d8933-c2de-4c88-ac2c-03bb1b32dd78@z27g2000prz.googlegroups.com>

Hello BioPerl mailing list!

So I have been successfully building BioPerl (though I thought I was
failing), but have been getting some errors during said builds. I'm
running ubuntu 9.04 and I ran 'perl Build.PL', then './Build test'
using bash. If any other information is desired, please let me know.
And here are some gists to help with some context:
perl Build.PL - https://gist.github.com/e4be0891635463b07812
./Build test - https://gist.github.com/3e9a1cba10ca0e9b087d


From cjfields at illinois.edu  Sun Mar 27 12:43:11 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 27 Mar 2011 11:43:11 -0500
Subject: [Bioperl-l] Bio::Tools::Protparam
In-Reply-To: <DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>
References: <DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>
Message-ID: <851BC032-98F0-441D-9185-5079527CDA3E@illinois.edu>

Dallas,

Can you send a script example?  Hard to judge what is going wrong w/o code.

chris
 
On Mar 23, 2011, at 12:08 PM, Thomas, Dallas wrote:

> Need help.  I am trying to use the Bio::Tools::Protparam perl module.
> 
> 
> 
> For testing purposes I have copied and pasted the example in the module,
> I have set:
> 
> 
> 
> use strict;
> 
> use Bio::Tools::Protparam;
> 
> use Bio::DB::GenBank;
> 
> 
> 
> Every time I try and run the script I get the following error:
> 
> 
> 
>                              Can't locate object method "new" via
> package "Protparam" (perhaps you forgot to load "Protparam"?) at ...
> 
> 
> 
> Do you have any ideas?  Any help would be very much appreciated.
> 
> 
> 
> Sincerely
> 
> Dallas Thomas
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From David.Messina at sbc.su.se  Sun Mar 27 13:05:05 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Sun, 27 Mar 2011 19:05:05 +0200
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
Message-ID: <AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>

Hi Ravi,

The get_sequence and write_sequence methods are in the Bio::Perl module, not
Bio::Seq. So your first line

use Bio::Seq;

should be replaced with

use Bio::Perl;


More examples in the BioPerl Tutorial here:
http://www.bioperl.org/wiki/BioPerl_Tutorial


Dve



2011/3/24 ?????????????????? <ravimbt at gmail.com>

> Hi,
>
> Could you please help me installing bioperl-db, bioperl-run & other
> packages
> using ppm on windows 7? Please find the attachment for the error message I
> get. I would really appreciate if you help me fix this issue.
>
> Thanks,
>
> With regards,
> Ravi.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From jason at bioperl.org  Sun Mar 27 13:28:04 2011
From: jason at bioperl.org (Jason Stajich)
Date: Sun, 27 Mar 2011 10:28:04 -0700
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
Message-ID: <4D8F73A4.8050408@bioperl.org>

Dan - not sure why you would need to do this as length on an undef 
should still return false (an undef).

$ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} 
print "\n"'
no
$ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"} 
print "\n"'
no

Also, having no 'source' is probably not proper GFF3.

BTW bugzilla is dead so the bug that you refer to is here
   http://redmine.open-bio.org/issues/2899
I've assigned the bug to Lincoln to help figure out what should be done 
with it.

Thanks,
jason

Dan Bolser wrote:
> Hi all,
>
> I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm uses:
>      if (length $source_tag) {
>
> within the '_types_sql' function to test if $source_tag is defined
> (and has a length). This obviously fails when $source_tag it isn't
> defined, and I see the above error message from my script when I call
> the 'features' function (as shown below).
>
> > From tests (thanks to rbuels in #bioperl) it seems the value of $type
> is simply 'fwd link intensity', so:
>        ($primary_tag,$source_tag) = split ':',$type,2;
>
> on line 1047 leaves $source_tag undefined.
>
> Here is my proposed fix:
>
> diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
> index 00103c2..dfc70c0 100644
> --- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
> +++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
> @@ -1057,8 +1057,8 @@ sub _types_sql {
>         ($primary_tag,$source_tag) = split ':',$type,2;
>       }
>
> -    if (length $source_tag) {
> -      if (length($primary_tag)) {
> +    if (defined $source_tag&&  length $source_tag) {
> +      if (defined $primary_tag&&  length($primary_tag)) {
>           push @matches,"tl.tag=?";
>           push @args,"$primary_tag:$source_tag";
>         }
>
>
> which seems to work. I'd write some tests, but an old bug that I can't
> track down prevents me from running tests on this package
> (http://bugzilla.open-bio.org/show_bug.cgi?id=2899).
>
> Cheers,
> Dan.
>
>
> Here are some snippets of code to give context:
>
> my $intensities = Bio::DB::SeqFeature::Store->
>    new( -adaptor =>  'DBI::mysql',
> 	-dsn =>  'db:mysql.server.ac.uk',
> 	-user =>  'me',
> 	-pass =>  'secret',
>         -verbose =>  $verbose,
>       );
>
> my @fwd_intensity = $intensities->
>      features( -seqid =>  'some-id', -type =>  'fwd link intensity',
>                -start =>  10,
>                -end   =>  200,
>      );
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki



From dan.bolser at gmail.com  Sun Mar 27 13:55:02 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Sun, 27 Mar 2011 18:55:02 +0100
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <4D8F73A4.8050408@bioperl.org>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
	<4D8F73A4.8050408@bioperl.org>
Message-ID: <AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>

On 27 March 2011 18:28, Jason Stajich <jason at bioperl.org> wrote:
> Dan - not sure why you would need to do this as length on an undef should
> still return false (an undef).
>
> $ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} print
> "\n"'
> no
> $ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"}
> print "\n"'
> no

Doesn't the latter spew a warning? (The output before / after my 'bug
fix' is the same, I just don't see 100s of warnings about undefined
values).


> Also, having no 'source' is probably not proper GFF3.

I'm quite sure it is, but by GFF does have a source. I'm just calling
'features' with only a feature type and not a feature type and a
source (because I only care about source). My call is pretty similar
to the example here:

http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/DB/SeqFeature/Store.pm#features

 @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');


> BTW bugzilla is dead so the bug that you refer to is here
> ?http://redmine.open-bio.org/issues/2899
> I've assigned the bug to Lincoln to help figure out what should be done with
> it.
>
> Thanks,
> jason

Cheers Jason,
Dan.


> Dan Bolser wrote:
>>
>> Hi all,
>>
>> I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm
>> uses:
>> ? ? if (length $source_tag) {
>>
>> within the '_types_sql' function to test if $source_tag is defined
>> (and has a length). This obviously fails when $source_tag it isn't
>> defined, and I see the above error message from my script when I call
>> the 'features' function (as shown below).
>>
>> > From tests (thanks to rbuels in #bioperl) it seems the value of $type
>> is simply 'fwd link intensity', so:
>> ? ? ? ($primary_tag,$source_tag) = split ':',$type,2;
>>
>> on line 1047 leaves $source_tag undefined.
>>
>> Here is my proposed fix:
>>
>> diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
>> index 00103c2..dfc70c0 100644
>> --- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>> +++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>> @@ -1057,8 +1057,8 @@ sub _types_sql {
>> ? ? ? ?($primary_tag,$source_tag) = split ':',$type,2;
>> ? ? ?}
>>
>> - ? ?if (length $source_tag) {
>> - ? ? ?if (length($primary_tag)) {
>> + ? ?if (defined $source_tag&& ?length $source_tag) {
>> + ? ? ?if (defined $primary_tag&& ?length($primary_tag)) {
>> ? ? ? ? ?push @matches,"tl.tag=?";
>> ? ? ? ? ?push @args,"$primary_tag:$source_tag";
>> ? ? ? ?}
>>
>>
>> which seems to work. I'd write some tests, but an old bug that I can't
>> track down prevents me from running tests on this package
>> (http://bugzilla.open-bio.org/show_bug.cgi?id=2899).
>>
>> Cheers,
>> Dan.
>>
>>
>> Here are some snippets of code to give context:
>>
>> my $intensities = Bio::DB::SeqFeature::Store->
>> ? new( -adaptor => ?'DBI::mysql',
>> ? ? ? ?-dsn => ?'db:mysql.server.ac.uk',
>> ? ? ? ?-user => ?'me',
>> ? ? ? ?-pass => ?'secret',
>> ? ? ? ?-verbose => ?$verbose,
>> ? ? ?);
>>
>> my @fwd_intensity = $intensities->
>> ? ? features( -seqid => ?'some-id', -type => ?'fwd link intensity',
>> ? ? ? ? ? ? ? -start => ?10,
>> ? ? ? ? ? ? ? -end ? => ?200,
>> ? ? );
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> jason at bioperl.org
> http://bioperl.org/wiki
>
>



From jason at bioperl.org  Sun Mar 27 13:59:09 2011
From: jason at bioperl.org (Jason Stajich)
Date: Sun, 27 Mar 2011 10:59:09 -0700
Subject: [Bioperl-l] CDS complement statements from GenBank
In-Reply-To: <cdf62961-ac89-4274-91ed-9a233d2de15c@k10g2000prh.googlegroups.com>
References: <cdf62961-ac89-4274-91ed-9a233d2de15c@k10g2000prh.googlegroups.com>
Message-ID: <4D8F7AED.1070705@bioperl.org>

they won't be split locations they will be Bio::Location::Simple 
locations then - I don't understand if that is causing you problems?



Galeb Abu-Ali wrote:
> Hi,
>
> I'm trying to parse CDS complement statements from GenBank files of
> bacterial genomes. I know it works for 'join' statements with
> Bio::Location::SplitLocationI, but there is no spliced genes in
> bacterial annotations and therefore no 'join()' statements. When I
> replace 'complement' with 'join' in the bacterial GenBank file,
> Bio::Location::SplitLocationI gets the coordinates. I took a look at
> SplitLocationI.pm and Split.pm to see if I could replace 'join' with
> 'complement' to get it to work but no luck. At your convenience,
> please advise.
>
> cheers,
>
> galeb
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki



From dan.bolser at gmail.com  Sun Mar 27 14:00:40 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Sun, 27 Mar 2011 19:00:40 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
Message-ID: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>

Hello,

I'm trying to get Bio::DB::BigWig installed again, this time on a different box.

I installed kent from git as described here:
http://genome.ucsc.edu/admin/git.html


I made the following changes, similar to those described previously:

git diff
diff --git a/src/inc/common.mk b/src/inc/common.mk
index c7fc557..5187901 100644
--- a/src/inc/common.mk
+++ b/src/inc/common.mk
@@ -3,7 +3,7 @@ CC=gcc
 ifeq (${COPT},)
     COPT=-O -g
 endif
-CFLAGS=
+CFLAGS=-fPIC
 HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
-DMACHTYPE_${MACHTYPE}
 HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
-I../../../../../inc

diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
index fa2292b..acb97d2 100644
--- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
+++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
@@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
     /* Parse current line. */
     wordCount = chopLine(line, row);
     if (wordCount == ArraySize(row))
-         errAbort("Too many fields (%d max is %lu) line %d of %s",
wordCount, ArraySize(row),
+         errAbort("Too many fields (%d max is %u) line %d of %s",
wordCount, ArraySize(row),
             lf->lineIx, lf->fileName);
     char *chrom = row[0];
     unsigned int start = lineFileNeedNum(lf, row, 1);


After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
-lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
correctly after typing 'make' in kent/src (should I be building it
differently?)



Now when I try to install Bio::DB::BigWig via cpan, things look like this:

cpan

cpan shell -- CPAN exploration and modules installation (v1.9600)
Enter 'h' for help.

cpan[1]> install Bio::DB::BigWig
CPAN: Storable loaded ok (v2.25)
Going to read '/homes/dbolser/.cpan/Metadata'
  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
Running install for module 'Bio::DB::BigWig'
Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
CPAN: Digest::SHA loaded ok (v5.61)
CPAN: Compress::Zlib loaded ok (v2.03)
Checksum for /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
ok
CPAN: Archive::Tar loaded ok (v1.76)
Bio-BigFile-1.05
Bio-BigFile-1.05/Changes
Bio-BigFile-1.05/LICENSE
Bio-BigFile-1.05/DISCLAIMER
Bio-BigFile-1.05/Build.PL
Bio-BigFile-1.05/typemap
Bio-BigFile-1.05/META.yml
Bio-BigFile-1.05/README
Bio-BigFile-1.05/MANIFEST
Bio-BigFile-1.05/ExampleData
Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
Bio-BigFile-1.05/ExampleData/refSeqTest.as
Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
Bio-BigFile-1.05/bin
Bio-BigFile-1.05/bin/bigWigToWig.pl
Bio-BigFile-1.05/bin/wigToBigWig.pl
Bio-BigFile-1.05/bin/index_bigwigset.pl
Bio-BigFile-1.05/lib
Bio-BigFile-1.05/lib/Bio
Bio-BigFile-1.05/lib/Bio/DB
Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
Bio-BigFile-1.05/lib/Bio/DB/BigFile
Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
Bio-BigFile-1.05/t
Bio-BigFile-1.05/t/02.bigbed.t
Bio-BigFile-1.05/t/03.bigwig_high.t
Bio-BigFile-1.05/t/04.bigbed_high.t
Bio-BigFile-1.05/t/05.bigwig_set.t
/bin/tar: Read 9216 bytes from -
Bio-BigFile-1.05/t/01.bigwig.t
Bio-BigFile-1.05/patches
Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
CPAN: File::Temp loaded ok (v0.22)
CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
CPAN: CPAN::Meta loaded ok (v2.110580)
CPAN: Module::CoreList loaded ok (v2.46)
CPAN: Time::HiRes loaded ok (v1.9717)

  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz


This module requires the compiled jkweb.a library from Jim Kent's source tree.
If you haven't already done so, please download the source from
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
contents of the "kent/src/lib" subdirectory as directed in the README. Then
enter the location of the "kent/src" subdirectory at the prompt below.
To prevent
this message from appearing in the future, set the environment
variable KENT_SRC
to point to the "kent/src" subdirectory.

Please enter the location of Kent source tree: /homes/dbolser/build/src/kent/src

Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-BigFile' version '1.05'
Building Bio-BigFile
gcc -I/homes/dbolser/build/src/kent/src/inc
-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
-DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
-c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
-Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
lib/Bio/DB/BigFile.c
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be undefined
lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be undefined
lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be undefined
lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be undefined
lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
lib/Bio/DB/BigFile.xs: In function
?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be undefined
lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
lib/Bio/DB/BigFile.xs: In function
?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be undefined
lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
-mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
/homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
  LDS/Bio-BigFile-1.05.tar.gz
  ./Build -- OK
CPAN: YAML loaded ok (v0.72)
Running Build test
t/01.bigwig.t ....... Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at t/01.bigwig.t line 28
Compilation failed in require at t/01.bigwig.t line 28.
BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
Failed 29/29 subtests
t/02.bigbed.t ....... Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at t/02.bigbed.t line 28
Compilation failed in require at t/02.bigbed.t line 28.
BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
Failed 15/15 subtests
t/03.bigwig_high.t .. Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
Compilation failed in require at t/03.bigwig_high.t line 28.
BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 32/32 subtests
t/04.bigbed_high.t .. Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
line 7.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
line 7.
Compilation failed in require at t/04.bigbed_high.t line 28.
BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 35/35 subtests
t/05.bigwig_set.t ... Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
line 177.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
line 177.
Compilation failed in require at t/05.bigwig_set.t line 19.
BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
No subtests run

Test Summary Report
-------------------
t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 29 tests but ran 0.
t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 15 tests but ran 0.
t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 32 tests but ran 0.
t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 35 tests but ran 0.
t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
0.11 csys =  1.09 CPU)
Result: FAIL
Failed 5/5 test programs. 0/0 subtests failed.
  LDS/Bio-BigFile-1.05.tar.gz
  ./Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports LDS/Bio-BigFile-1.05.tar.gz
Running Build install
  make test had returned bad status, won't install without force
Failed during this command:
 LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO

cpan[2]>






Any hints?

Cheers,
Dan.



From roy.chaudhuri at gmail.com  Sun Mar 27 14:26:55 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Sun, 27 Mar 2011 19:26:55 +0100
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>	<4D8F73A4.8050408@bioperl.org>
	<AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
Message-ID: <4D8F816F.5010809@gmail.com>

Hi Dan,

I think your problem is that you are using the outdated -w flag, which 
reports warnings from inside modules that may not have been designed 
with warnings in mind. The "use warnings" pragma is preferred. See:
http://perldoc.perl.org/perllexwarn.html#What%27s-wrong-with-*-w*-and-$^W

Cheers,
Roy.

On 27/03/2011 18:55, Dan Bolser wrote:
> On 27 March 2011 18:28, Jason Stajich<jason at bioperl.org>  wrote:
>> Dan - not sure why you would need to do this as length on an undef should
>> still return false (an undef).
>>
>> $ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} print
>> "\n"'
>> no
>> $ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"}
>> print "\n"'
>> no
>
> Doesn't the latter spew a warning? (The output before / after my 'bug
> fix' is the same, I just don't see 100s of warnings about undefined
> values).
>
>
>> Also, having no 'source' is probably not proper GFF3.
>
> I'm quite sure it is, but by GFF does have a source. I'm just calling
> 'features' with only a feature type and not a feature type and a
> source (because I only care about source). My call is pretty similar
> to the example here:
>
> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/DB/SeqFeature/Store.pm#features
>
>   @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');
>
>
>> BTW bugzilla is dead so the bug that you refer to is here
>>   http://redmine.open-bio.org/issues/2899
>> I've assigned the bug to Lincoln to help figure out what should be done with
>> it.
>>
>> Thanks,
>> jason
>
> Cheers Jason,
> Dan.
>
>
>> Dan Bolser wrote:
>>>
>>> Hi all,
>>>
>>> I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> uses:
>>>      if (length $source_tag) {
>>>
>>> within the '_types_sql' function to test if $source_tag is defined
>>> (and has a length). This obviously fails when $source_tag it isn't
>>> defined, and I see the above error message from my script when I call
>>> the 'features' function (as shown below).
>>>
>>>>  From tests (thanks to rbuels in #bioperl) it seems the value of $type
>>> is simply 'fwd link intensity', so:
>>>        ($primary_tag,$source_tag) = split ':',$type,2;
>>>
>>> on line 1047 leaves $source_tag undefined.
>>>
>>> Here is my proposed fix:
>>>
>>> diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
>>> index 00103c2..dfc70c0 100644
>>> --- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> +++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> @@ -1057,8 +1057,8 @@ sub _types_sql {
>>>         ($primary_tag,$source_tag) = split ':',$type,2;
>>>       }
>>>
>>> -    if (length $source_tag) {
>>> -      if (length($primary_tag)) {
>>> +    if (defined $source_tag&&    length $source_tag) {
>>> +      if (defined $primary_tag&&    length($primary_tag)) {
>>>           push @matches,"tl.tag=?";
>>>           push @args,"$primary_tag:$source_tag";
>>>         }
>>>
>>>
>>> which seems to work. I'd write some tests, but an old bug that I can't
>>> track down prevents me from running tests on this package
>>> (http://bugzilla.open-bio.org/show_bug.cgi?id=2899).
>>>
>>> Cheers,
>>> Dan.
>>>
>>>
>>> Here are some snippets of code to give context:
>>>
>>> my $intensities = Bio::DB::SeqFeature::Store->
>>>    new( -adaptor =>    'DBI::mysql',
>>>         -dsn =>    'db:mysql.server.ac.uk',
>>>         -user =>    'me',
>>>         -pass =>    'secret',
>>>         -verbose =>    $verbose,
>>>       );
>>>
>>> my @fwd_intensity = $intensities->
>>>      features( -seqid =>    'some-id', -type =>    'fwd link intensity',
>>>                -start =>    10,
>>>                -end   =>    200,
>>>      );
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> --
>> Jason Stajich
>> jason at bioperl.org
>> http://bioperl.org/wiki
>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Sun Mar 27 16:13:14 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 27 Mar 2011 15:13:14 -0500
Subject: [Bioperl-l] Use of uninitialized value in length at
	Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
	<4D8F73A4.8050408@bioperl.org>
	<AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
Message-ID: <4960971A-8C61-49F2-B43A-E32BAFC4C59E@illinois.edu>

On Mar 27, 2011, at 12:55 PM, Dan Bolser wrote:

> On 27 March 2011 18:28, Jason Stajich <jason at bioperl.org> wrote:
>> Dan - not sure why you would need to do this as length on an undef should
>> still return false (an undef).
>> 
>> $ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} print
>> "\n"'
>> no
>> $ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"}
>> print "\n"'
>> no
> 
> Doesn't the latter spew a warning? (The output before / after my 'bug
> fix' is the same, I just don't see 100s of warnings about undefined
> values).

Only with later versions of perl (I think perl 5.12).

>> Also, having no 'source' is probably not proper GFF3.
> 
> I'm quite sure it is, but by GFF does have a source. I'm just calling
> 'features' with only a feature type and not a feature type and a
> source (because I only care about source). My call is pretty similar
> to the example here:
> 
> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/DB/SeqFeature/Store.pm#features
> 
> @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');

I think Jason is inferring that the GFF3 is invalid from your statement below re: $source_tag not being defined, which to me means the source attribute for the feature is not defined.

Note: b/c something works with SF::Store does NOT mean the source is proper GFF3; it is quite possible to have invalid GFF3 loaded into the database w/o a hiccup.  I think the loader assumes the data loaded has already been validated; IIRC there is very little validation done on GFF3 loaded into SF::Store, particularly the 'type'.

chris

>> BTW bugzilla is dead so the bug that you refer to is here
>>  http://redmine.open-bio.org/issues/2899
>> I've assigned the bug to Lincoln to help figure out what should be done with
>> it.
>> 
>> Thanks,
>> jason
> 
> Cheers Jason,
> Dan.
> 
> 
>> Dan Bolser wrote:
>>> 
>>> Hi all,
>>> 
>>> I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> uses:
>>>     if (length $source_tag) {
>>> 
>>> within the '_types_sql' function to test if $source_tag is defined
>>> (and has a length). This obviously fails when $source_tag it isn't
>>> defined, and I see the above error message from my script when I call
>>> the 'features' function (as shown below).
>>> 
>>>> From tests (thanks to rbuels in #bioperl) it seems the value of $type
>>> is simply 'fwd link intensity', so:
>>>       ($primary_tag,$source_tag) = split ':',$type,2;
>>> 
>>> on line 1047 leaves $source_tag undefined.
>>> 
>>> Here is my proposed fix:
>>> 
>>> diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
>>> index 00103c2..dfc70c0 100644
>>> --- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> +++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> @@ -1057,8 +1057,8 @@ sub _types_sql {
>>>        ($primary_tag,$source_tag) = split ':',$type,2;
>>>      }
>>> 
>>> -    if (length $source_tag) {
>>> -      if (length($primary_tag)) {
>>> +    if (defined $source_tag&&  length $source_tag) {
>>> +      if (defined $primary_tag&&  length($primary_tag)) {
>>>          push @matches,"tl.tag=?";
>>>          push @args,"$primary_tag:$source_tag";
>>>        }
>>> 
>>> 
>>> which seems to work. I'd write some tests, but an old bug that I can't
>>> track down prevents me from running tests on this package
>>> (http://bugzilla.open-bio.org/show_bug.cgi?id=2899).
>>> 
>>> Cheers,
>>> Dan.
>>> 
>>> 
>>> Here are some snippets of code to give context:
>>> 
>>> my $intensities = Bio::DB::SeqFeature::Store->
>>>   new( -adaptor =>  'DBI::mysql',
>>>        -dsn =>  'db:mysql.server.ac.uk',
>>>        -user =>  'me',
>>>        -pass =>  'secret',
>>>        -verbose =>  $verbose,
>>>      );
>>> 
>>> my @fwd_intensity = $intensities->
>>>     features( -seqid =>  'some-id', -type =>  'fwd link intensity',
>>>               -start =>  10,
>>>               -end   =>  200,
>>>     );
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> --
>> Jason Stajich
>> jason at bioperl.org
>> http://bioperl.org/wiki
>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Sun Mar 27 16:13:56 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 27 Mar 2011 15:13:56 -0500
Subject: [Bioperl-l] Various bioperl build test errors
In-Reply-To: <799d8933-c2de-4c88-ac2c-03bb1b32dd78@z27g2000prz.googlegroups.com>
References: <799d8933-c2de-4c88-ac2c-03bb1b32dd78@z27g2000prz.googlegroups.com>
Message-ID: <FFAB293A-555E-4F4B-90C4-A50458AB2B8C@illinois.edu>

Re: the two problems:

1) The build failures are a new one, haven't seen that before.  

2) The failed tests are all related to NeXML and Bio::Phylo; it appears that Bio::Phylo is having versioning problems.  

Feel free to report these on our bug tracker:

http://redmine.open-bio.org/

chris


On Mar 27, 2011, at 9:37 AM, Drin wrote:

> Hello BioPerl mailing list!
> 
> So I have been successfully building BioPerl (though I thought I was
> failing), but have been getting some errors during said builds. I'm
> running ubuntu 9.04 and I ran 'perl Build.PL', then './Build test'
> using bash. If any other information is desired, please let me know.
> And here are some gists to help with some context:
> perl Build.PL - https://gist.github.com/e4be0891635463b07812
> ./Build test - https://gist.github.com/3e9a1cba10ca0e9b087d
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From heikki.lehvaslaiho at gmail.com  Mon Mar 28 02:11:12 2011
From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho)
Date: Mon, 28 Mar 2011 09:11:12 +0300
Subject: [Bioperl-l] Bio::Tools::Protparam
In-Reply-To: <DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>
References: <AcvpfORY7lvf7BT4TLGDgl1oKgOEwg==>
	<DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>
Message-ID: <AANLkTi=3wtG+7HO4O8vUbdrnVEu-NXofwmZfVHvRLeVH@mail.gmail.com>

The synopsis code should read:

	my $pp = Bio::Tools::Protparam->new(seq=>$seq->seq);

Fixed in the repository.

? ?? -Heikki

Heikki Lehvaslaiho - skype:heikki_lehvaslaiho http://about.me/heikki
cell: +966 545 595 849? office: +966 2 808 2429

Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
4700 King Abdullah University of Science and Technology (KAUST)
Thuwal 23955-6900, Kingdom of Saudi Arabia




On 23 March 2011 20:08, Thomas, Dallas <Dallas.Thomas at agr.gc.ca> wrote:
> Need help. ?I am trying to use the Bio::Tools::Protparam perl module.
>
>
>
> For testing purposes I have copied and pasted the example in the module,
> I have set:
>
>
>
> use strict;
>
> use Bio::Tools::Protparam;
>
> use Bio::DB::GenBank;
>
>
>
> Every time I try and run the script I get the following error:
>
>
>
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?Can't locate object method "new" via
> package "Protparam" (perhaps you forgot to load "Protparam"?) at ...
>
>
>
> Do you have any ideas? ?Any help would be very much appreciated.
>
>
>
> Sincerely
>
> Dallas Thomas
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From David.Messina at sbc.su.se  Mon Mar 28 03:33:25 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 28 Mar 2011 09:33:25 +0200
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
Message-ID: <AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>

Hi Ravi,

Please make sure to "Reply All" so that everyone on the mailing list can
follow (and add to) the discussion.

If you read the first line of the exception, you'll see it states what the
error is:
"WebDBSeqI Error ? check query sequences!"

You'd have no way of knowing this, but that ID and database combination is
not functioning anymore, so that's why in this case you're getting an error.
Please try using the example in the tutorial here:

  http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts

which has been updated to a different ID which should work.

Sorry for the confusion! So that we can prevent other people from having the
same issue, could you tell me where you got that example code?

Dave






2011/3/28 ?????????????????? <ravimbt at gmail.com>

> Hi Dave,
>
> Thanks a lot for your reply. It is really helpful. Please find the
> screenshot after making the change you pointed out. But I am getting
> "Exception: Bio::Root::Exception" error. I think I have to set the
> environment variables but I am not sure how to do that. Could you please
> guide me on this too.
>
> I can go to the "Environment Variable" Window in my pc. But I dont know
> what to enter once I click "New" on that window.
>
> Thanks in advance.
>
> With regards,
> Ravi.
>
>
> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>
>> Hi Ravi,
>>
>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>> not Bio::Seq. So your first line
>>
>> use Bio::Seq;
>>
>> should be replaced with
>>
>> use Bio::Perl;
>>
>>
>> More examples in the BioPerl Tutorial here:
>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>
>>
>> Dve
>>
>>
>>
>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>
>>> Hi,
>>>
>>> Could you please help me installing bioperl-db, bioperl-run & other
>>> packages
>>> using ppm on windows 7? Please find the attachment for the error message
>>> I
>>> get. I would really appreciate if you help me fix this issue.
>>>
>>> Thanks,
>>>
>>> With regards,
>>> Ravi.
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>



From David.Messina at sbc.su.se  Mon Mar 28 07:51:41 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 28 Mar 2011 13:51:41 +0200
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
Message-ID: <AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>

>
> Thank you very much. It is working. I got the program code from the
> following link.
>
> http://www.bioperl.org/Core/Latest/bptutorial.html


Aha, okay. You got there from Google, I guess? That is *way* out of date.

To the other core devs, in order to prevent this confusion in the future,
I'd like to delete the Core/ directory from our website since it's been
superseded at this point by other docs and is not current. I intend to put
up a ticket at Redmine, but I will wait a bit before doing so to allow time
for people to see this and comment ? please do speak up if there's good
reason to keep it.


Could you please give me the link to join this forum to see other
> discussions, which would be more helpful to me?
>

Sure, you can sign up for the mailing list here:

 <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


And the archives are also searchable:

    http://news.gmane.org/gmane.comp.lang.perl.bio.general


Please let me know if you have any suggestion for me to keep learning the
> bioperl.


I would also suggest reading the (current) tutorial and HOWTOs at
www.bioperl.org . Lots of good links on the main page there, particularly
under the Documentation heading.


Dave





> With regards,
> Ravi.
>
>
> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>
>> Hi Ravi,
>>
>> Please make sure to "Reply All" so that everyone on the mailing list can
>> follow (and add to) the discussion.
>>
>> If you read the first line of the exception, you'll see it states what the
>> error is:
>> "WebDBSeqI Error ? check query sequences!"
>>
>> You'd have no way of knowing this, but that ID and database combination is
>> not functioning anymore, so that's why in this case you're getting an error.
>> Please try using the example in the tutorial here:
>>
>>
>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>
>> which has been updated to a different ID which should work.
>>
>> Sorry for the confusion! So that we can prevent other people from having
>> the same issue, could you tell me where you got that example code?
>>
>> Dave
>>
>>
>>
>>
>>
>>
>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>
>>> Hi Dave,
>>>
>>> Thanks a lot for your reply. It is really helpful. Please find the
>>> screenshot after making the change you pointed out. But I am getting
>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>> environment variables but I am not sure how to do that. Could you please
>>> guide me on this too.
>>>
>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>> what to enter once I click "New" on that window.
>>>
>>> Thanks in advance.
>>>
>>> With regards,
>>> Ravi.
>>>
>>>
>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>
>>>> Hi Ravi,
>>>>
>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>> not Bio::Seq. So your first line
>>>>
>>>> use Bio::Seq;
>>>>
>>>> should be replaced with
>>>>
>>>> use Bio::Perl;
>>>>
>>>>
>>>> More examples in the BioPerl Tutorial here:
>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>
>>>>
>>>> Dve
>>>>
>>>>
>>>>
>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>
>>>>> Hi,
>>>>>
>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>> packages
>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>> message I
>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> With regards,
>>>>> Ravi.
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>
>>>>
>>>
>>
>



From David.Messina at sbc.su.se  Mon Mar 28 08:45:34 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 28 Mar 2011 14:45:34 +0200
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTinhqidOd7VBDT+hr6E-VNKwOobtyZ1Zn=A1uPfy@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
	<AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
	<AANLkTinhqidOd7VBDT+hr6E-VNKwOobtyZ1Zn=A1uPfy@mail.gmail.com>
Message-ID: <AANLkTikiN9J28oNWWnQ5hJSWYB_DKTPHPegj+7wZ-ELr@mail.gmail.com>

Again, please "Reply All" so that your messages go to the mailing list.

Ravi, PLEASE read the documentation on the website first and try to figure
out how to solve your problem on your own. BioPerl is a complex system and
requires some effort to learn how to use. I and everyone on this list
volunteers our time answering questions, and we are happy to do so, but you
have to meet us halfway.


Dave




2011/3/28 ?????????????????? <ravimbt at gmail.com>

> Hi Dave,
>
> Thanks for the information. I have also signed up to join the forum.
>
> I could not retrieve the sequence from other databases other than Genbank.
> Could you please do the changes on the below programme to make it working so
> that I can try in my system.
> --------------------
> use Bio::Perl;
>
> $seq_object = get_sequence('genbank',"ECORHO");
>
> write_sequence(">ael.fasta",'fasta',$seq_object);
> ------------------
>
> Thanks once again.
>
> With regards,
> Ravi.
>
>
> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>
>> Thank you very much. It is working. I got the program code from the
>>> following link.
>>>
>>> http://www.bioperl.org/Core/Latest/bptutorial.html
>>
>>
>> Aha, okay. You got there from Google, I guess? That is *way* out of date.
>>
>> To the other core devs, in order to prevent this confusion in the future,
>> I'd like to delete the Core/ directory from our website since it's been
>> superseded at this point by other docs and is not current. I intend to put
>> up a ticket at Redmine, but I will wait a bit before doing so to allow time
>> for people to see this and comment ? please do speak up if there's good
>> reason to keep it.
>>
>>
>> Could you please give me the link to join this forum to see other
>>> discussions, which would be more helpful to me?
>>>
>>
>> Sure, you can sign up for the mailing list here:
>>
>>  <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> And the archives are also searchable:
>>
>>     http://news.gmane.org/gmane.comp.lang.perl.bio.general
>>
>>
>> Please let me know if you have any suggestion for me to keep learning the
>>> bioperl.
>>
>>
>> I would also suggest reading the (current) tutorial and HOWTOs at
>> www.bioperl.org . Lots of good links on the main page there, particularly
>> under the Documentation heading.
>>
>>
>> Dave
>>
>>
>>
>>
>>
>>> With regards,
>>> Ravi.
>>>
>>>
>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>>>
>>>> Hi Ravi,
>>>>
>>>> Please make sure to "Reply All" so that everyone on the mailing list can
>>>> follow (and add to) the discussion.
>>>>
>>>> If you read the first line of the exception, you'll see it states what
>>>> the error is:
>>>> "WebDBSeqI Error ? check query sequences!"
>>>>
>>>> You'd have no way of knowing this, but that ID and database combination
>>>> is not functioning anymore, so that's why in this case you're getting an
>>>> error. Please try using the example in the tutorial here:
>>>>
>>>>
>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>>>
>>>> which has been updated to a different ID which should work.
>>>>
>>>> Sorry for the confusion! So that we can prevent other people from having
>>>> the same issue, could you tell me where you got that example code?
>>>>
>>>> Dave
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>>>
>>>>> Hi Dave,
>>>>>
>>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>>> screenshot after making the change you pointed out. But I am getting
>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>>> environment variables but I am not sure how to do that. Could you please
>>>>> guide me on this too.
>>>>>
>>>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>>>> what to enter once I click "New" on that window.
>>>>>
>>>>> Thanks in advance.
>>>>>
>>>>> With regards,
>>>>> Ravi.
>>>>>
>>>>>
>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>>>
>>>>>> Hi Ravi,
>>>>>>
>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl
>>>>>> module, not Bio::Seq. So your first line
>>>>>>
>>>>>> use Bio::Seq;
>>>>>>
>>>>>> should be replaced with
>>>>>>
>>>>>> use Bio::Perl;
>>>>>>
>>>>>>
>>>>>> More examples in the BioPerl Tutorial here:
>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>>>
>>>>>>
>>>>>> Dve
>>>>>>
>>>>>>
>>>>>>
>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>>>> packages
>>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>>> message I
>>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> With regards,
>>>>>>> Ravi.
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>



From abualiga at gmail.com  Mon Mar 28 09:19:00 2011
From: abualiga at gmail.com (Galeb Abu-Ali)
Date: Mon, 28 Mar 2011 09:19:00 -0400
Subject: [Bioperl-l] CDS complement statements from GenBank
In-Reply-To: <4D8F7AED.1070705@bioperl.org>
References: <cdf62961-ac89-4274-91ed-9a233d2de15c@k10g2000prh.googlegroups.com>
	<4D8F7AED.1070705@bioperl.org>
Message-ID: <AANLkTimpN2sRvrkn86Ges7100ssRizHr5GU7rPhDvyUS@mail.gmail.com>

I was using the wrong module, Bio::Location::Simple was what I needed.
thanks much!

galeb

On Sun, Mar 27, 2011 at 1:59 PM, Jason Stajich <jason at bioperl.org> wrote:

> they won't be split locations they will be Bio::Location::Simple locations
> then - I don't understand if that is causing you problems?
>
>
>
> Galeb Abu-Ali wrote:
>
>> Hi,
>>
>> I'm trying to parse CDS complement statements from GenBank files of
>> bacterial genomes. I know it works for 'join' statements with
>> Bio::Location::SplitLocationI, but there is no spliced genes in
>> bacterial annotations and therefore no 'join()' statements. When I
>> replace 'complement' with 'join' in the bacterial GenBank file,
>> Bio::Location::SplitLocationI gets the coordinates. I took a look at
>> SplitLocationI.pm and Split.pm to see if I could replace 'join' with
>> 'complement' to get it to work but no luck. At your convenience,
>> please advise.
>>
>> cheers,
>>
>> galeb
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> --
> Jason Stajich
> jason at bioperl.org
> http://bioperl.org/wiki
>
>


From cjfields at illinois.edu  Mon Mar 28 09:27:38 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 28 Mar 2011 08:27:38 -0500
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
	<AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
Message-ID: <6CE8AACF-0D78-4BBA-8094-CC189B0FF872@illinois.edu>

Dave,

+1 on removing old docs to prevent confusion.  Or, alternatively, +1 to syncing those to current docs (though I think decreasing the replication effort in keeping docs up-to-date is probably the best tact).

chris

On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:

>> 
>> Thank you very much. It is working. I got the program code from the
>> following link.
>> 
>> http://www.bioperl.org/Core/Latest/bptutorial.html
> 
> 
> Aha, okay. You got there from Google, I guess? That is *way* out of date.
> 
> To the other core devs, in order to prevent this confusion in the future,
> I'd like to delete the Core/ directory from our website since it's been
> superseded at this point by other docs and is not current. I intend to put
> up a ticket at Redmine, but I will wait a bit before doing so to allow time
> for people to see this and comment ? please do speak up if there's good
> reason to keep it.
> 
> 
> Could you please give me the link to join this forum to see other
>> discussions, which would be more helpful to me?
>> 
> 
> Sure, you can sign up for the mailing list here:
> 
> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> And the archives are also searchable:
> 
>    http://news.gmane.org/gmane.comp.lang.perl.bio.general
> 
> 
> Please let me know if you have any suggestion for me to keep learning the
>> bioperl.
> 
> 
> I would also suggest reading the (current) tutorial and HOWTOs at
> www.bioperl.org . Lots of good links on the main page there, particularly
> under the Documentation heading.
> 
> 
> Dave
> 
> 
> 
> 
> 
>> With regards,
>> Ravi.
>> 
>> 
>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>> 
>>> Hi Ravi,
>>> 
>>> Please make sure to "Reply All" so that everyone on the mailing list can
>>> follow (and add to) the discussion.
>>> 
>>> If you read the first line of the exception, you'll see it states what the
>>> error is:
>>> "WebDBSeqI Error ? check query sequences!"
>>> 
>>> You'd have no way of knowing this, but that ID and database combination is
>>> not functioning anymore, so that's why in this case you're getting an error.
>>> Please try using the example in the tutorial here:
>>> 
>>> 
>>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>> 
>>> which has been updated to a different ID which should work.
>>> 
>>> Sorry for the confusion! So that we can prevent other people from having
>>> the same issue, could you tell me where you got that example code?
>>> 
>>> Dave
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>> 
>>>> Hi Dave,
>>>> 
>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>> screenshot after making the change you pointed out. But I am getting
>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>> environment variables but I am not sure how to do that. Could you please
>>>> guide me on this too.
>>>> 
>>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>>> what to enter once I click "New" on that window.
>>>> 
>>>> Thanks in advance.
>>>> 
>>>> With regards,
>>>> Ravi.
>>>> 
>>>> 
>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>> 
>>>>> Hi Ravi,
>>>>> 
>>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>>> not Bio::Seq. So your first line
>>>>> 
>>>>> use Bio::Seq;
>>>>> 
>>>>> should be replaced with
>>>>> 
>>>>> use Bio::Perl;
>>>>> 
>>>>> 
>>>>> More examples in the BioPerl Tutorial here:
>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>> 
>>>>> 
>>>>> Dve
>>>>> 
>>>>> 
>>>>> 
>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>>> packages
>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>> message I
>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>> 
>>>>>> Thanks,
>>>>>> 
>>>>>> With regards,
>>>>>> Ravi.
>>>>>> 
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>> 
>>>>> 
>>>>> 
>>>> 
>>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From dan.bolser at gmail.com  Mon Mar 28 13:15:32 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 28 Mar 2011 18:15:32 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
Message-ID: <AANLkTikQgn2-YU4-4JBdLkSopFFihhJ-=2KG25P0Ugv6@mail.gmail.com>

--- Build.PL~   2011-03-14 20:27:57.000000000 +0000
+++ Build.PL    2011-03-28 18:06:45.503757000 +0100
@@ -16,7 +16,7 @@
     dist_abstract      => "Manipulate Jim Kent's BigWig and BigBed
index files for genomic features.",
     license            => 'perl',
     include_dirs       => [$jk_include],
-    extra_linker_flags => ["$jk_lib/$LibFile",'-lz'],
+    extra_linker_flags => ["$jk_lib/$LibFile",'-lz','-lssl'],

     extra_compiler_flags=>[
        # turn off warnings originating in Perl's Newx* calls

On 27 March 2011 19:00, Dan Bolser <dan.bolser at gmail.com> wrote:
> Hello,
>
> I'm trying to get Bio::DB::BigWig installed again, this time on a different box.
>
> I installed kent from git as described here:
> http://genome.ucsc.edu/admin/git.html
>
>
> I made the following changes, similar to those described previously:
>
> git diff
> diff --git a/src/inc/common.mk b/src/inc/common.mk
> index c7fc557..5187901 100644
> --- a/src/inc/common.mk
> +++ b/src/inc/common.mk
> @@ -3,7 +3,7 @@ CC=gcc
> ?ifeq (${COPT},)
> ? ? COPT=-O -g
> ?endif
> -CFLAGS=
> +CFLAGS=-fPIC
> ?HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> -DMACHTYPE_${MACHTYPE}
> ?HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> -I../../../../../inc
>
> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> index fa2292b..acb97d2 100644
> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
> ? ? /* Parse current line. */
> ? ? wordCount = chopLine(line, row);
> ? ? if (wordCount == ArraySize(row))
> - ? ? ? ? errAbort("Too many fields (%d max is %lu) line %d of %s",
> wordCount, ArraySize(row),
> + ? ? ? ? errAbort("Too many fields (%d max is %u) line %d of %s",
> wordCount, ArraySize(row),
> ? ? ? ? ? ? lf->lineIx, lf->fileName);
> ? ? char *chrom = row[0];
> ? ? unsigned int start = lineFileNeedNum(lf, row, 1);
>
>
> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> correctly after typing 'make' in kent/src (should I be building it
> differently?)
>
>
>
> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>
> cpan
>
> cpan shell -- CPAN exploration and modules installation (v1.9600)
> Enter 'h' for help.
>
> cpan[1]> install Bio::DB::BigWig
> CPAN: Storable loaded ok (v2.25)
> Going to read '/homes/dbolser/.cpan/Metadata'
> ?Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> Running install for module 'Bio::DB::BigWig'
> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> CPAN: Digest::SHA loaded ok (v5.61)
> CPAN: Compress::Zlib loaded ok (v2.03)
> Checksum for /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> ok
> CPAN: Archive::Tar loaded ok (v1.76)
> Bio-BigFile-1.05
> Bio-BigFile-1.05/Changes
> Bio-BigFile-1.05/LICENSE
> Bio-BigFile-1.05/DISCLAIMER
> Bio-BigFile-1.05/Build.PL
> Bio-BigFile-1.05/typemap
> Bio-BigFile-1.05/META.yml
> Bio-BigFile-1.05/README
> Bio-BigFile-1.05/MANIFEST
> Bio-BigFile-1.05/ExampleData
> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> Bio-BigFile-1.05/bin
> Bio-BigFile-1.05/bin/bigWigToWig.pl
> Bio-BigFile-1.05/bin/wigToBigWig.pl
> Bio-BigFile-1.05/bin/index_bigwigset.pl
> Bio-BigFile-1.05/lib
> Bio-BigFile-1.05/lib/Bio
> Bio-BigFile-1.05/lib/Bio/DB
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> Bio-BigFile-1.05/t
> Bio-BigFile-1.05/t/02.bigbed.t
> Bio-BigFile-1.05/t/03.bigwig_high.t
> Bio-BigFile-1.05/t/04.bigbed_high.t
> Bio-BigFile-1.05/t/05.bigwig_set.t
> /bin/tar: Read 9216 bytes from -
> Bio-BigFile-1.05/t/01.bigwig.t
> Bio-BigFile-1.05/patches
> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> CPAN: File::Temp loaded ok (v0.22)
> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> CPAN: CPAN::Meta loaded ok (v2.110580)
> CPAN: Module::CoreList loaded ok (v2.46)
> CPAN: Time::HiRes loaded ok (v1.9717)
>
> ?CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>
>
> This module requires the compiled jkweb.a library from Jim Kent's source tree.
> If you haven't already done so, please download the source from
> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
> contents of the "kent/src/lib" subdirectory as directed in the README. Then
> enter the location of the "kent/src" subdirectory at the prompt below.
> To prevent
> this message from appearing in the future, set the environment
> variable KENT_SRC
> to point to the "kent/src" subdirectory.
>
> Please enter the location of Kent source tree: /homes/dbolser/build/src/kent/src
>
> Created MYMETA.yml and MYMETA.json
> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> Building Bio-BigFile
> gcc -I/homes/dbolser/build/src/kent/src/inc
> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> lib/Bio/DB/BigFile.c
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be undefined
> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be undefined
> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
> ?LDS/Bio-BigFile-1.05.tar.gz
> ?./Build -- OK
> CPAN: YAML loaded ok (v0.72)
> Running Build test
> t/01.bigwig.t ....... Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at t/01.bigwig.t line 28
> Compilation failed in require at t/01.bigwig.t line 28.
> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 29/29 subtests
> t/02.bigbed.t ....... Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at t/02.bigbed.t line 28
> Compilation failed in require at t/02.bigbed.t line 28.
> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 15/15 subtests
> t/03.bigwig_high.t .. Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at t/03.bigwig_high.t line 28.
> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 32/32 subtests
> t/04.bigbed_high.t .. Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> Compilation failed in require at t/04.bigbed_high.t line 28.
> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 35/35 subtests
> t/05.bigwig_set.t ... Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> Compilation failed in require at t/05.bigwig_set.t line 19.
> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> No subtests run
>
> Test Summary Report
> -------------------
> t/01.bigwig.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: Bad plan. ?You planned 29 tests but ran 0.
> t/02.bigbed.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: Bad plan. ?You planned 15 tests but ran 0.
> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: Bad plan. ?You planned 32 tests but ran 0.
> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: Bad plan. ?You planned 35 tests but ran 0.
> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: No plan found in TAP output
> Files=5, Tests=0, ?1 wallclock secs ( 0.04 usr ?0.01 sys + ?0.93 cusr
> 0.11 csys = ?1.09 CPU)
> Result: FAIL
> Failed 5/5 test programs. 0/0 subtests failed.
> ?LDS/Bio-BigFile-1.05.tar.gz
> ?./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module, try:
> ?reports LDS/Bio-BigFile-1.05.tar.gz
> Running Build install
> ?make test had returned bad status, won't install without force
> Failed during this command:
> ?LDS/Bio-BigFile-1.05.tar.gz ? ? ? ? ? ? ? ? ?: make_test NO
>
> cpan[2]>
>
>
>
>
>
>
> Any hints?
>
> Cheers,
> Dan.
>



From dan.bolser at gmail.com  Mon Mar 28 16:08:52 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 28 Mar 2011 21:08:52 +0100
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <4960971A-8C61-49F2-B43A-E32BAFC4C59E@illinois.edu>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
	<4D8F73A4.8050408@bioperl.org>
	<AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
	<4960971A-8C61-49F2-B43A-E32BAFC4C59E@illinois.edu>
Message-ID: <AANLkTi=H4opbLx+qv8XM5+VpQNy2Fhxtbyx54iumRcE5@mail.gmail.com>

On 27 March 2011 21:13, Chris Fields <cjfields at illinois.edu> wrote:
> On Mar 27, 2011, at 12:55 PM, Dan Bolser wrote:
>
>> On 27 March 2011 18:28, Jason Stajich <jason at bioperl.org> wrote:
>>> Dan - not sure why you would need to do this as length on an undef should
>>> still return false (an undef).
>>>
>>> $ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} print
>>> "\n"'
>>> no
>>> $ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"}
>>> print "\n"'
>>> no
>>
>> Doesn't the latter spew a warning? (The output before / after my 'bug
>> fix' is the same, I just don't see 100s of warnings about undefined
>> values).
>
> Only with later versions of perl (I think perl 5.12).
>
>>> Also, having no 'source' is probably not proper GFF3.
>>
>> I'm quite sure it is, but by GFF does have a source. I'm just calling
>> 'features' with only a feature type and not a feature type and a
>> source (because I only care about source). My call is pretty similar
>> to the example here:
>>
>> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/DB/SeqFeature/Store.pm#features
>>
>> @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');
>
> I think Jason is inferring that the GFF3 is invalid from your statement below re: $source_tag not being defined, which to me means the source attribute for the feature is not defined.
>
> Note: b/c something works with SF::Store does NOT mean the source is proper GFF3; it is quite possible to have invalid GFF3 loaded into the database w/o a hiccup. ?I think the loader assumes the data loaded has already been validated; IIRC there is very little validation done on GFF3 loaded into SF::Store, particularly the 'type'.

As I said, my GFF3 does have a source. I'll try to put together a test
script, as it seems like the value should not be undef (but thanks for
the tip Roy).

I had a feeling that this relatively trivial fix was a sticking
plaster on a larger problem.


> chris
Dan



From dan.bolser at gmail.com  Mon Mar 28 16:12:19 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 28 Mar 2011 21:12:19 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTikQgn2-YU4-4JBdLkSopFFihhJ-=2KG25P0Ugv6@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTikQgn2-YU4-4JBdLkSopFFihhJ-=2KG25P0Ugv6@mail.gmail.com>
Message-ID: <AANLkTikjJpMcFWvvAt+bJoXJHHaORfecYmz053RScFjn@mail.gmail.com>

Context, this patch in the distro's Build.PL fixes the errors with the
tests, but doesn't fix the warnings.

On 28 March 2011 18:15, Dan Bolser <dan.bolser at gmail.com> wrote:
> --- Build.PL~ ? 2011-03-14 20:27:57.000000000 +0000
> +++ Build.PL ? ?2011-03-28 18:06:45.503757000 +0100
> @@ -16,7 +16,7 @@
> ? ? dist_abstract ? ? ?=> "Manipulate Jim Kent's BigWig and BigBed
> index files for genomic features.",
> ? ? license ? ? ? ? ? ?=> 'perl',
> ? ? include_dirs ? ? ? => [$jk_include],
> - ? ?extra_linker_flags => ["$jk_lib/$LibFile",'-lz'],
> + ? ?extra_linker_flags => ["$jk_lib/$LibFile",'-lz','-lssl'],
>
> ? ? extra_compiler_flags=>[
> ? ? ? ?# turn off warnings originating in Perl's Newx* calls



From cjfields at illinois.edu  Mon Mar 28 16:23:38 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 28 Mar 2011 15:23:38 -0500
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTikjJpMcFWvvAt+bJoXJHHaORfecYmz053RScFjn@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTikQgn2-YU4-4JBdLkSopFFihhJ-=2KG25P0Ugv6@mail.gmail.com>
	<AANLkTikjJpMcFWvvAt+bJoXJHHaORfecYmz053RScFjn@mail.gmail.com>
Message-ID: <91759940-6457-460D-95F5-EF7098A7412C@illinois.edu>

Dan,

Was this using the latest kent src and Bio::DB::BigWig?

chris

PS : cc'ing gbrowse, which is where these seem to get answered a bit faster, context thread here: http://lists.open-bio.org/pipermail/bioperl-l/2011-March/034738.html

On Mar 28, 2011, at 3:12 PM, Dan Bolser wrote:

> Context, this patch in the distro's Build.PL fixes the errors with the
> tests, but doesn't fix the warnings.
> 
> On 28 March 2011 18:15, Dan Bolser <dan.bolser at gmail.com> wrote:
>> --- Build.PL~   2011-03-14 20:27:57.000000000 +0000
>> +++ Build.PL    2011-03-28 18:06:45.503757000 +0100
>> @@ -16,7 +16,7 @@
>>     dist_abstract      => "Manipulate Jim Kent's BigWig and BigBed
>> index files for genomic features.",
>>     license            => 'perl',
>>     include_dirs       => [$jk_include],
>> -    extra_linker_flags => ["$jk_lib/$LibFile",'-lz'],
>> +    extra_linker_flags => ["$jk_lib/$LibFile",'-lz','-lssl'],
>> 
>>     extra_compiler_flags=>[
>>        # turn off warnings originating in Perl's Newx* calls
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From lincoln.stein at gmail.com  Mon Mar 28 17:26:20 2011
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Mon, 28 Mar 2011 17:26:20 -0400
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
Message-ID: <AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>

Hi Dan,

There are two problems that I can see. One is a series of compiler warnings
when compiling the Perl .XS interface file. These are likely nothing to
worry about, but I should fix them. What versions of Perl and gcc do you
have installed? I don't see them when I compile on my system.

The second issue is that the SSL library is not being linked in. Previously
there was no dependency on SSL, but Jim may recently have added this to the
BigWig library in order to allow it to read bigwig files from https servers.
I see that you added a -lssl to Build.PL; does this make the tests work
again?

Lincoln


On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com> wrote:

> Hello,
>
> I'm trying to get Bio::DB::BigWig installed again, this time on a different
> box.
>
> I installed kent from git as described here:
> http://genome.ucsc.edu/admin/git.html
>
>
> I made the following changes, similar to those described previously:
>
> git diff
> diff --git a/src/inc/common.mk b/src/inc/common.mk
> index c7fc557..5187901 100644
> --- a/src/inc/common.mk
> +++ b/src/inc/common.mk
> @@ -3,7 +3,7 @@ CC=gcc
>  ifeq (${COPT},)
>     COPT=-O -g
>  endif
> -CFLAGS=
> +CFLAGS=-fPIC
>  HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> -DMACHTYPE_${MACHTYPE}
>  HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> -I../../../../../inc
>
> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> index fa2292b..acb97d2 100644
> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
>     /* Parse current line. */
>     wordCount = chopLine(line, row);
>     if (wordCount == ArraySize(row))
> -         errAbort("Too many fields (%d max is %lu) line %d of %s",
> wordCount, ArraySize(row),
> +         errAbort("Too many fields (%d max is %u) line %d of %s",
> wordCount, ArraySize(row),
>             lf->lineIx, lf->fileName);
>     char *chrom = row[0];
>     unsigned int start = lineFileNeedNum(lf, row, 1);
>
>
> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> correctly after typing 'make' in kent/src (should I be building it
> differently?)
>
>
>
> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>
> cpan
>
> cpan shell -- CPAN exploration and modules installation (v1.9600)
> Enter 'h' for help.
>
> cpan[1]> install Bio::DB::BigWig
> CPAN: Storable loaded ok (v2.25)
> Going to read '/homes/dbolser/.cpan/Metadata'
>  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> Running install for module 'Bio::DB::BigWig'
> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> CPAN: Digest::SHA loaded ok (v5.61)
> CPAN: Compress::Zlib loaded ok (v2.03)
> Checksum for
> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> ok
> CPAN: Archive::Tar loaded ok (v1.76)
> Bio-BigFile-1.05
> Bio-BigFile-1.05/Changes
> Bio-BigFile-1.05/LICENSE
> Bio-BigFile-1.05/DISCLAIMER
> Bio-BigFile-1.05/Build.PL
> Bio-BigFile-1.05/typemap
> Bio-BigFile-1.05/META.yml
> Bio-BigFile-1.05/README
> Bio-BigFile-1.05/MANIFEST
> Bio-BigFile-1.05/ExampleData
> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> Bio-BigFile-1.05/bin
> Bio-BigFile-1.05/bin/bigWigToWig.pl
> Bio-BigFile-1.05/bin/wigToBigWig.pl
> Bio-BigFile-1.05/bin/index_bigwigset.pl
> Bio-BigFile-1.05/lib
> Bio-BigFile-1.05/lib/Bio
> Bio-BigFile-1.05/lib/Bio/DB
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> Bio-BigFile-1.05/t
> Bio-BigFile-1.05/t/02.bigbed.t
> Bio-BigFile-1.05/t/03.bigwig_high.t
> Bio-BigFile-1.05/t/04.bigbed_high.t
> Bio-BigFile-1.05/t/05.bigwig_set.t
> /bin/tar: Read 9216 bytes from -
> Bio-BigFile-1.05/t/01.bigwig.t
> Bio-BigFile-1.05/patches
> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> CPAN: File::Temp loaded ok (v0.22)
> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> CPAN: CPAN::Meta loaded ok (v2.110580)
> CPAN: Module::CoreList loaded ok (v2.46)
> CPAN: Time::HiRes loaded ok (v1.9717)
>
>  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>
>
> This module requires the compiled jkweb.a library from Jim Kent's source
> tree.
> If you haven't already done so, please download the source from
> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
> contents of the "kent/src/lib" subdirectory as directed in the README. Then
> enter the location of the "kent/src" subdirectory at the prompt below.
> To prevent
> this message from appearing in the future, set the environment
> variable KENT_SRC
> to point to the "kent/src" subdirectory.
>
> Please enter the location of Kent source tree:
> /homes/dbolser/build/src/kent/src
>
> Created MYMETA.yml and MYMETA.json
> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> Building Bio-BigFile
> gcc -I/homes/dbolser/build/src/kent/src/inc
> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> lib/Bio/DB/BigFile.c
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
> undefined
> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
> undefined
> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
>
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build -- OK
> CPAN: YAML loaded ok (v0.72)
> Running Build test
> t/01.bigwig.t ....... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/01.bigwig.t line 28
> Compilation failed in require at t/01.bigwig.t line 28.
> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 29/29 subtests
> t/02.bigbed.t ....... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/02.bigbed.t line 28
> Compilation failed in require at t/02.bigbed.t line 28.
> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 15/15 subtests
> t/03.bigwig_high.t .. Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at t/03.bigwig_high.t line 28.
> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 32/32 subtests
> t/04.bigbed_high.t .. Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> Compilation failed in require at t/04.bigbed_high.t line 28.
> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 35/35 subtests
> t/05.bigwig_set.t ... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> Compilation failed in require at t/05.bigwig_set.t line 19.
> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> No subtests run
>
> Test Summary Report
> -------------------
> t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 29 tests but ran 0.
> t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 32 tests but ran 0.
> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 35 tests but ran 0.
> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: No plan found in TAP output
> Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
> 0.11 csys =  1.09 CPU)
> Result: FAIL
> Failed 5/5 test programs. 0/0 subtests failed.
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module, try:
>  reports LDS/Bio-BigFile-1.05.tar.gz
> Running Build install
>  make test had returned bad status, won't install without force
> Failed during this command:
>  LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO
>
> cpan[2]>
>
>
>
>
>
>
> Any hints?
>
> Cheers,
> Dan.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>



From lincoln.stein at gmail.com  Mon Mar 28 17:26:20 2011
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Mon, 28 Mar 2011 17:26:20 -0400
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
Message-ID: <AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>

Hi Dan,

There are two problems that I can see. One is a series of compiler warnings
when compiling the Perl .XS interface file. These are likely nothing to
worry about, but I should fix them. What versions of Perl and gcc do you
have installed? I don't see them when I compile on my system.

The second issue is that the SSL library is not being linked in. Previously
there was no dependency on SSL, but Jim may recently have added this to the
BigWig library in order to allow it to read bigwig files from https servers.
I see that you added a -lssl to Build.PL; does this make the tests work
again?

Lincoln


On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com> wrote:

> Hello,
>
> I'm trying to get Bio::DB::BigWig installed again, this time on a different
> box.
>
> I installed kent from git as described here:
> http://genome.ucsc.edu/admin/git.html
>
>
> I made the following changes, similar to those described previously:
>
> git diff
> diff --git a/src/inc/common.mk b/src/inc/common.mk
> index c7fc557..5187901 100644
> --- a/src/inc/common.mk
> +++ b/src/inc/common.mk
> @@ -3,7 +3,7 @@ CC=gcc
>  ifeq (${COPT},)
>     COPT=-O -g
>  endif
> -CFLAGS=
> +CFLAGS=-fPIC
>  HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> -DMACHTYPE_${MACHTYPE}
>  HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> -I../../../../../inc
>
> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> index fa2292b..acb97d2 100644
> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
>     /* Parse current line. */
>     wordCount = chopLine(line, row);
>     if (wordCount == ArraySize(row))
> -         errAbort("Too many fields (%d max is %lu) line %d of %s",
> wordCount, ArraySize(row),
> +         errAbort("Too many fields (%d max is %u) line %d of %s",
> wordCount, ArraySize(row),
>             lf->lineIx, lf->fileName);
>     char *chrom = row[0];
>     unsigned int start = lineFileNeedNum(lf, row, 1);
>
>
> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> correctly after typing 'make' in kent/src (should I be building it
> differently?)
>
>
>
> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>
> cpan
>
> cpan shell -- CPAN exploration and modules installation (v1.9600)
> Enter 'h' for help.
>
> cpan[1]> install Bio::DB::BigWig
> CPAN: Storable loaded ok (v2.25)
> Going to read '/homes/dbolser/.cpan/Metadata'
>  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> Running install for module 'Bio::DB::BigWig'
> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> CPAN: Digest::SHA loaded ok (v5.61)
> CPAN: Compress::Zlib loaded ok (v2.03)
> Checksum for
> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> ok
> CPAN: Archive::Tar loaded ok (v1.76)
> Bio-BigFile-1.05
> Bio-BigFile-1.05/Changes
> Bio-BigFile-1.05/LICENSE
> Bio-BigFile-1.05/DISCLAIMER
> Bio-BigFile-1.05/Build.PL
> Bio-BigFile-1.05/typemap
> Bio-BigFile-1.05/META.yml
> Bio-BigFile-1.05/README
> Bio-BigFile-1.05/MANIFEST
> Bio-BigFile-1.05/ExampleData
> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> Bio-BigFile-1.05/bin
> Bio-BigFile-1.05/bin/bigWigToWig.pl
> Bio-BigFile-1.05/bin/wigToBigWig.pl
> Bio-BigFile-1.05/bin/index_bigwigset.pl
> Bio-BigFile-1.05/lib
> Bio-BigFile-1.05/lib/Bio
> Bio-BigFile-1.05/lib/Bio/DB
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> Bio-BigFile-1.05/t
> Bio-BigFile-1.05/t/02.bigbed.t
> Bio-BigFile-1.05/t/03.bigwig_high.t
> Bio-BigFile-1.05/t/04.bigbed_high.t
> Bio-BigFile-1.05/t/05.bigwig_set.t
> /bin/tar: Read 9216 bytes from -
> Bio-BigFile-1.05/t/01.bigwig.t
> Bio-BigFile-1.05/patches
> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> CPAN: File::Temp loaded ok (v0.22)
> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> CPAN: CPAN::Meta loaded ok (v2.110580)
> CPAN: Module::CoreList loaded ok (v2.46)
> CPAN: Time::HiRes loaded ok (v1.9717)
>
>  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>
>
> This module requires the compiled jkweb.a library from Jim Kent's source
> tree.
> If you haven't already done so, please download the source from
> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
> contents of the "kent/src/lib" subdirectory as directed in the README. Then
> enter the location of the "kent/src" subdirectory at the prompt below.
> To prevent
> this message from appearing in the future, set the environment
> variable KENT_SRC
> to point to the "kent/src" subdirectory.
>
> Please enter the location of Kent source tree:
> /homes/dbolser/build/src/kent/src
>
> Created MYMETA.yml and MYMETA.json
> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> Building Bio-BigFile
> gcc -I/homes/dbolser/build/src/kent/src/inc
> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> lib/Bio/DB/BigFile.c
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
> undefined
> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
> undefined
> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
>
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build -- OK
> CPAN: YAML loaded ok (v0.72)
> Running Build test
> t/01.bigwig.t ....... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/01.bigwig.t line 28
> Compilation failed in require at t/01.bigwig.t line 28.
> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 29/29 subtests
> t/02.bigbed.t ....... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/02.bigbed.t line 28
> Compilation failed in require at t/02.bigbed.t line 28.
> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 15/15 subtests
> t/03.bigwig_high.t .. Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at t/03.bigwig_high.t line 28.
> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 32/32 subtests
> t/04.bigbed_high.t .. Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> Compilation failed in require at t/04.bigbed_high.t line 28.
> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 35/35 subtests
> t/05.bigwig_set.t ... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> Compilation failed in require at t/05.bigwig_set.t line 19.
> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> No subtests run
>
> Test Summary Report
> -------------------
> t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 29 tests but ran 0.
> t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 32 tests but ran 0.
> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 35 tests but ran 0.
> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: No plan found in TAP output
> Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
> 0.11 csys =  1.09 CPU)
> Result: FAIL
> Failed 5/5 test programs. 0/0 subtests failed.
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module, try:
>  reports LDS/Bio-BigFile-1.05.tar.gz
> Running Build install
>  make test had returned bad status, won't install without force
> Failed during this command:
>  LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO
>
> cpan[2]>
>
>
>
>
>
>
> Any hints?
>
> Cheers,
> Dan.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>



From bosborne11 at verizon.net  Mon Mar 28 16:43:51 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Mon, 28 Mar 2011 16:43:51 -0400
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <6CE8AACF-0D78-4BBA-8094-CC189B0FF872@illinois.edu>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
	<AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
	<6CE8AACF-0D78-4BBA-8094-CC189B0FF872@illinois.edu>
Message-ID: <63E35F39-D70C-4D6F-A792-D2738B850567@verizon.net>

Chris,

I'll get started on dissembling bptutorial. There's certainly useful text in there but there's also duplicated or outdated material. Looks like there are 3 options for any given section:

- put it into an existing HOWTO
- make it into a new HOWTO
- delete it

BIO

On Mar 28, 2011, at 9:27 AM, Chris Fields wrote:

> Dave,
> 
> +1 on removing old docs to prevent confusion.  Or, alternatively, +1 to syncing those to current docs (though I think decreasing the replication effort in keeping docs up-to-date is probably the best tact).
> 
> chris
> 
> On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:
> 
>>> 
>>> Thank you very much. It is working. I got the program code from the
>>> following link.
>>> 
>>> http://www.bioperl.org/Core/Latest/bptutorial.html
>> 
>> 
>> Aha, okay. You got there from Google, I guess? That is *way* out of date.
>> 
>> To the other core devs, in order to prevent this confusion in the future,
>> I'd like to delete the Core/ directory from our website since it's been
>> superseded at this point by other docs and is not current. I intend to put
>> up a ticket at Redmine, but I will wait a bit before doing so to allow time
>> for people to see this and comment ? please do speak up if there's good
>> reason to keep it.
>> 
>> 
>> Could you please give me the link to join this forum to see other
>>> discussions, which would be more helpful to me?
>>> 
>> 
>> Sure, you can sign up for the mailing list here:
>> 
>> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> And the archives are also searchable:
>> 
>>   http://news.gmane.org/gmane.comp.lang.perl.bio.general
>> 
>> 
>> Please let me know if you have any suggestion for me to keep learning the
>>> bioperl.
>> 
>> 
>> I would also suggest reading the (current) tutorial and HOWTOs at
>> www.bioperl.org . Lots of good links on the main page there, particularly
>> under the Documentation heading.
>> 
>> 
>> Dave
>> 
>> 
>> 
>> 
>> 
>>> With regards,
>>> Ravi.
>>> 
>>> 
>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>>> 
>>>> Hi Ravi,
>>>> 
>>>> Please make sure to "Reply All" so that everyone on the mailing list can
>>>> follow (and add to) the discussion.
>>>> 
>>>> If you read the first line of the exception, you'll see it states what the
>>>> error is:
>>>> "WebDBSeqI Error ? check query sequences!"
>>>> 
>>>> You'd have no way of knowing this, but that ID and database combination is
>>>> not functioning anymore, so that's why in this case you're getting an error.
>>>> Please try using the example in the tutorial here:
>>>> 
>>>> 
>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>>> 
>>>> which has been updated to a different ID which should work.
>>>> 
>>>> Sorry for the confusion! So that we can prevent other people from having
>>>> the same issue, could you tell me where you got that example code?
>>>> 
>>>> Dave
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>>> 
>>>>> Hi Dave,
>>>>> 
>>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>>> screenshot after making the change you pointed out. But I am getting
>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>>> environment variables but I am not sure how to do that. Could you please
>>>>> guide me on this too.
>>>>> 
>>>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>>>> what to enter once I click "New" on that window.
>>>>> 
>>>>> Thanks in advance.
>>>>> 
>>>>> With regards,
>>>>> Ravi.
>>>>> 
>>>>> 
>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>>> 
>>>>>> Hi Ravi,
>>>>>> 
>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>>>> not Bio::Seq. So your first line
>>>>>> 
>>>>>> use Bio::Seq;
>>>>>> 
>>>>>> should be replaced with
>>>>>> 
>>>>>> use Bio::Perl;
>>>>>> 
>>>>>> 
>>>>>> More examples in the BioPerl Tutorial here:
>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>>> 
>>>>>> 
>>>>>> Dve
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>>> 
>>>>>>> Hi,
>>>>>>> 
>>>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>>>> packages
>>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>>> message I
>>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>>> 
>>>>>>> Thanks,
>>>>>>> 
>>>>>>> With regards,
>>>>>>> Ravi.
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Mon Mar 28 18:40:39 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 28 Mar 2011 17:40:39 -0500
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <63E35F39-D70C-4D6F-A792-D2738B850567@verizon.net>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
	<AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
	<6CE8AACF-0D78-4BBA-8094-CC189B0FF872@illinois.edu>
	<63E35F39-D70C-4D6F-A792-D2738B850567@verizon.net>
Message-ID: <1569920B-D132-487F-BBC6-9A81A430E6E0@illinois.edu>

Brian,

I think this was started:

http://www.bioperl.org/wiki/Bptutorial.pl

It certainly could be cleaned up, organized, and updated (that and the FAQ).  Makes sense to have it as a HOWTO or maybe split it into several HOWTOs.  Maybe even combine it with the beginner's HOWTO into various sections?

chris

On Mar 28, 2011, at 3:43 PM, Brian Osborne wrote:

> Chris,
> 
> I'll get started on dissembling bptutorial. There's certainly useful text in there but there's also duplicated or outdated material. Looks like there are 3 options for any given section:
> 
> - put it into an existing HOWTO
> - make it into a new HOWTO
> - delete it
> 
> BIO
> 
> On Mar 28, 2011, at 9:27 AM, Chris Fields wrote:
> 
>> Dave,
>> 
>> +1 on removing old docs to prevent confusion.  Or, alternatively, +1 to syncing those to current docs (though I think decreasing the replication effort in keeping docs up-to-date is probably the best tact).
>> 
>> chris
>> 
>> On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:
>> 
>>>> 
>>>> Thank you very much. It is working. I got the program code from the
>>>> following link.
>>>> 
>>>> http://www.bioperl.org/Core/Latest/bptutorial.html
>>> 
>>> 
>>> Aha, okay. You got there from Google, I guess? That is *way* out of date.
>>> 
>>> To the other core devs, in order to prevent this confusion in the future,
>>> I'd like to delete the Core/ directory from our website since it's been
>>> superseded at this point by other docs and is not current. I intend to put
>>> up a ticket at Redmine, but I will wait a bit before doing so to allow time
>>> for people to see this and comment ? please do speak up if there's good
>>> reason to keep it.
>>> 
>>> 
>>> Could you please give me the link to join this forum to see other
>>>> discussions, which would be more helpful to me?
>>>> 
>>> 
>>> Sure, you can sign up for the mailing list here:
>>> 
>>> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>>> And the archives are also searchable:
>>> 
>>>  http://news.gmane.org/gmane.comp.lang.perl.bio.general
>>> 
>>> 
>>> Please let me know if you have any suggestion for me to keep learning the
>>>> bioperl.
>>> 
>>> 
>>> I would also suggest reading the (current) tutorial and HOWTOs at
>>> www.bioperl.org . Lots of good links on the main page there, particularly
>>> under the Documentation heading.
>>> 
>>> 
>>> Dave
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> With regards,
>>>> Ravi.
>>>> 
>>>> 
>>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>>>> 
>>>>> Hi Ravi,
>>>>> 
>>>>> Please make sure to "Reply All" so that everyone on the mailing list can
>>>>> follow (and add to) the discussion.
>>>>> 
>>>>> If you read the first line of the exception, you'll see it states what the
>>>>> error is:
>>>>> "WebDBSeqI Error ? check query sequences!"
>>>>> 
>>>>> You'd have no way of knowing this, but that ID and database combination is
>>>>> not functioning anymore, so that's why in this case you're getting an error.
>>>>> Please try using the example in the tutorial here:
>>>>> 
>>>>> 
>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>>>> 
>>>>> which has been updated to a different ID which should work.
>>>>> 
>>>>> Sorry for the confusion! So that we can prevent other people from having
>>>>> the same issue, could you tell me where you got that example code?
>>>>> 
>>>>> Dave
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>>>> 
>>>>>> Hi Dave,
>>>>>> 
>>>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>>>> screenshot after making the change you pointed out. But I am getting
>>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>>>> environment variables but I am not sure how to do that. Could you please
>>>>>> guide me on this too.
>>>>>> 
>>>>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>>>>> what to enter once I click "New" on that window.
>>>>>> 
>>>>>> Thanks in advance.
>>>>>> 
>>>>>> With regards,
>>>>>> Ravi.
>>>>>> 
>>>>>> 
>>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>>>> 
>>>>>>> Hi Ravi,
>>>>>>> 
>>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>>>>> not Bio::Seq. So your first line
>>>>>>> 
>>>>>>> use Bio::Seq;
>>>>>>> 
>>>>>>> should be replaced with
>>>>>>> 
>>>>>>> use Bio::Perl;
>>>>>>> 
>>>>>>> 
>>>>>>> More examples in the BioPerl Tutorial here:
>>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>>>> 
>>>>>>> 
>>>>>>> Dve
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>>>> 
>>>>>>>> Hi,
>>>>>>>> 
>>>>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>>>>> packages
>>>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>>>> message I
>>>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>>>> 
>>>>>>>> Thanks,
>>>>>>>> 
>>>>>>>> With regards,
>>>>>>>> Ravi.
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From dan.kortschak at adelaide.edu.au  Mon Mar 28 21:12:55 2011
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Tue, 29 Mar 2011 11:42:55 +1030
Subject: [Bioperl-l] GuessSeqFormat GFF vs VCF
Message-ID: <1301361175.4727.17.camel@sueno>

Hi All,

I'm going through the BEDTools wrapper to bring it up to date. A number
BEDTools executables now accept GFF and VCF as well as BED format input
files.

Part of the WrapperBase::CommandExts give acceptable input formats, so
I'm adding to GuessSeqFormat guessers for GFF and VCF, which from the
point of view of a stateless guesser, are indistinguishable unless (and
I don't like this idea), GFF is additionally defined as not VCF and VCF
is additionally defined as not VCF (these can be identified from the
##gff-version and ##fileformat=VCF lines).

Can people provide their thoughts on this?

cheers
Dan



From dan.bolser at gmail.com  Tue Mar 29 04:57:29 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 29 Mar 2011 09:57:29 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
Message-ID: <AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>

On 28 March 2011 22:26, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Hi Dan,
> There are two problems that I can see. One is a series of compiler warnings
> when compiling the Perl .XS interface file. These are likely nothing to
> worry about, but I should fix them. What versions of Perl and gcc do you
> have installed? I don't see them when I compile on my system.

gcc --version # gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
perl --version # v5.8.8 built for i386-linux-thread-multi

uname -a # Linux cricket 2.6.18-194.32.1.el5PAE #1 SMP Wed Jan 5
18:43:13 EST 2011 i686 i686 i386 GNU/Linux



I got kent from git and built it with the following commands:

cd kent/src/lib/
echo $MACHTYPE # i686-redhat-linux-gnu
export MACHTYPE=i686
make
cd ../
export KENT_SRC=`pwd`

# NOTE, both $MACHTYPE and $KENT_SRC should be defined here
cpan -i Bio::DB::BigWig # FAILS AS DESCRIBED

cd /tmp
wget http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
tar zxfv Bio-BigFile-1.05.tar.gz
cd Bio-BigFile-1.05
# PATCH  Build.PL AS DESCRIBED (add -lssl after -lz)
perl Build.PL
./Build # SEE WARNINGS AS BEFORE
./Build test # Files=5, Tests=135, Result: PASS
./Build install


Note, above I didn't patch kent to include -fPIC as suggested
previously. I don't see any noticeable difference if I do on this
arch.

It would be good if the instructions above could make it into the
Bio::DB::BigWig README, as a few people have expressed confusion about
the exact steps (the README in kent is a bit confusing, and mostly
unnecessary for the purposes of building Bio::DB::BigWig).


> The second issue is that the SSL library is not being linked in. Previously
> there was no dependency on SSL, but Jim may recently have added this to the
> BigWig library in order to allow it to read bigwig files from https servers.
> I see that you added a -lssl to Build.PL; does this make the tests work
> again?

Yup, when I add -lssl to Build.PL (as per the previous diff), the
tests pass, but I still see the warnings.

I'm sure I saw the warnings disappear when I was playing with
different versions of Bio::DB::BigWig, but now they occur without
fail... if you pardon the pun.

I have a seeking suspicion that it's related to my perl 'build kit'...
However, since I'm not sure what module versions to report, and since
you promised to fix these issues anyway, I won't dig into it.


Thanks for help, and thanks for the support on
irc://irc.freenode.net/#bioperl, without which I would have probably
give up!

Cheers,
Dan.

> Lincoln
>
> On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com> wrote:
>>
>> Hello,
>>
>> I'm trying to get Bio::DB::BigWig installed again, this time on a
>> different box.
>>
>> I installed kent from git as described here:
>> http://genome.ucsc.edu/admin/git.html
>>
>>
>> I made the following changes, similar to those described previously:
>>
>> git diff
>> diff --git a/src/inc/common.mk b/src/inc/common.mk
>> index c7fc557..5187901 100644
>> --- a/src/inc/common.mk
>> +++ b/src/inc/common.mk
>> @@ -3,7 +3,7 @@ CC=gcc
>> ?ifeq (${COPT},)
>> ? ? COPT=-O -g
>> ?endif
>> -CFLAGS=
>> +CFLAGS=-fPIC
>> ?HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
>> -DMACHTYPE_${MACHTYPE}
>> ?HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
>> -I../../../../../inc
>>
>> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> index fa2292b..acb97d2 100644
>> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
>> ? ? /* Parse current line. */
>> ? ? wordCount = chopLine(line, row);
>> ? ? if (wordCount == ArraySize(row))
>> - ? ? ? ? errAbort("Too many fields (%d max is %lu) line %d of %s",
>> wordCount, ArraySize(row),
>> + ? ? ? ? errAbort("Too many fields (%d max is %u) line %d of %s",
>> wordCount, ArraySize(row),
>> ? ? ? ? ? ? lf->lineIx, lf->fileName);
>> ? ? char *chrom = row[0];
>> ? ? unsigned int start = lineFileNeedNum(lf, row, 1);
>>
>>
>> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
>> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
>> correctly after typing 'make' in kent/src (should I be building it
>> differently?)
>>
>>
>>
>> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>>
>> cpan
>>
>> cpan shell -- CPAN exploration and modules installation (v1.9600)
>> Enter 'h' for help.
>>
>> cpan[1]> install Bio::DB::BigWig
>> CPAN: Storable loaded ok (v2.25)
>> Going to read '/homes/dbolser/.cpan/Metadata'
>> ?Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
>> Running install for module 'Bio::DB::BigWig'
>> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
>> CPAN: Digest::SHA loaded ok (v5.61)
>> CPAN: Compress::Zlib loaded ok (v2.03)
>> Checksum for
>> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
>> ok
>> CPAN: Archive::Tar loaded ok (v1.76)
>> Bio-BigFile-1.05
>> Bio-BigFile-1.05/Changes
>> Bio-BigFile-1.05/LICENSE
>> Bio-BigFile-1.05/DISCLAIMER
>> Bio-BigFile-1.05/Build.PL
>> Bio-BigFile-1.05/typemap
>> Bio-BigFile-1.05/META.yml
>> Bio-BigFile-1.05/README
>> Bio-BigFile-1.05/MANIFEST
>> Bio-BigFile-1.05/ExampleData
>> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
>> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
>> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
>> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
>> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
>> Bio-BigFile-1.05/ExampleData/refSeqTest.as
>> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
>> Bio-BigFile-1.05/bin
>> Bio-BigFile-1.05/bin/bigWigToWig.pl
>> Bio-BigFile-1.05/bin/wigToBigWig.pl
>> Bio-BigFile-1.05/bin/index_bigwigset.pl
>> Bio-BigFile-1.05/lib
>> Bio-BigFile-1.05/lib/Bio
>> Bio-BigFile-1.05/lib/Bio/DB
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
>> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
>> Bio-BigFile-1.05/t
>> Bio-BigFile-1.05/t/02.bigbed.t
>> Bio-BigFile-1.05/t/03.bigwig_high.t
>> Bio-BigFile-1.05/t/04.bigbed_high.t
>> Bio-BigFile-1.05/t/05.bigwig_set.t
>> /bin/tar: Read 9216 bytes from -
>> Bio-BigFile-1.05/t/01.bigwig.t
>> Bio-BigFile-1.05/patches
>> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
>> CPAN: File::Temp loaded ok (v0.22)
>> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
>> CPAN: CPAN::Meta loaded ok (v2.110580)
>> CPAN: Module::CoreList loaded ok (v2.46)
>> CPAN: Time::HiRes loaded ok (v1.9717)
>>
>> ?CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>>
>>
>> This module requires the compiled jkweb.a library from Jim Kent's source
>> tree.
>> If you haven't already done so, please download the source from
>> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
>> contents of the "kent/src/lib" subdirectory as directed in the README.
>> Then
>> enter the location of the "kent/src" subdirectory at the prompt below.
>> To prevent
>> this message from appearing in the future, set the environment
>> variable KENT_SRC
>> to point to the "kent/src" subdirectory.
>>
>> Please enter the location of Kent source tree:
>> /homes/dbolser/build/src/kent/src
>>
>> Created MYMETA.yml and MYMETA.json
>> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
>> Building Bio-BigFile
>> gcc -I/homes/dbolser/build/src/kent/src/inc
>> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
>> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
>> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
>> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
>> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
>> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
>> lib/Bio/DB/BigFile.c
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
>> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
>> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
>> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
>> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
>> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
>> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
>> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
>> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
>> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
>>
>> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
>> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
>> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
>> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
>> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
>> ?LDS/Bio-BigFile-1.05.tar.gz
>> ?./Build -- OK
>> CPAN: YAML loaded ok (v0.72)
>> Running Build test
>> t/01.bigwig.t ....... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at t/01.bigwig.t line 28
>> Compilation failed in require at t/01.bigwig.t line 28.
>> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
>> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 29/29 subtests
>> t/02.bigbed.t ....... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at t/02.bigbed.t line 28
>> Compilation failed in require at t/02.bigbed.t line 28.
>> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
>> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 15/15 subtests
>> t/03.bigwig_high.t .. Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at t/03.bigwig_high.t line 28.
>> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
>> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 32/32 subtests
>> t/04.bigbed_high.t .. Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
>> line 7.
>> Compilation failed in require at t/04.bigbed_high.t line 28.
>> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
>> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 35/35 subtests
>> t/05.bigwig_set.t ... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
>> line 177.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
>> line 177.
>> Compilation failed in require at t/05.bigwig_set.t line 19.
>> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
>> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
>> No subtests run
>>
>> Test Summary Report
>> -------------------
>> t/01.bigwig.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 29 tests but ran 0.
>> t/02.bigbed.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 15 tests but ran 0.
>> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 32 tests but ran 0.
>> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 35 tests but ran 0.
>> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: No plan found in TAP output
>> Files=5, Tests=0, ?1 wallclock secs ( 0.04 usr ?0.01 sys + ?0.93 cusr
>> 0.11 csys = ?1.09 CPU)
>> Result: FAIL
>> Failed 5/5 test programs. 0/0 subtests failed.
>> ?LDS/Bio-BigFile-1.05.tar.gz
>> ?./Build test -- NOT OK
>> //hint// to see the cpan-testers results for installing this module, try:
>> ?reports LDS/Bio-BigFile-1.05.tar.gz
>> Running Build install
>> ?make test had returned bad status, won't install without force
>> Failed during this command:
>> ?LDS/Bio-BigFile-1.05.tar.gz ? ? ? ? ? ? ? ? ?: make_test NO
>>
>> cpan[2]>
>>
>>
>>
>>
>>
>>
>> Any hints?
>>
>> Cheers,
>> Dan.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
>



From dan.bolser at gmail.com  Tue Mar 29 04:57:29 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 29 Mar 2011 09:57:29 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
Message-ID: <AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>

On 28 March 2011 22:26, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Hi Dan,
> There are two problems that I can see. One is a series of compiler warnings
> when compiling the Perl .XS interface file. These are likely nothing to
> worry about, but I should fix them. What versions of Perl and gcc do you
> have installed? I don't see them when I compile on my system.

gcc --version # gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
perl --version # v5.8.8 built for i386-linux-thread-multi

uname -a # Linux cricket 2.6.18-194.32.1.el5PAE #1 SMP Wed Jan 5
18:43:13 EST 2011 i686 i686 i386 GNU/Linux



I got kent from git and built it with the following commands:

cd kent/src/lib/
echo $MACHTYPE # i686-redhat-linux-gnu
export MACHTYPE=i686
make
cd ../
export KENT_SRC=`pwd`

# NOTE, both $MACHTYPE and $KENT_SRC should be defined here
cpan -i Bio::DB::BigWig # FAILS AS DESCRIBED

cd /tmp
wget http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
tar zxfv Bio-BigFile-1.05.tar.gz
cd Bio-BigFile-1.05
# PATCH  Build.PL AS DESCRIBED (add -lssl after -lz)
perl Build.PL
./Build # SEE WARNINGS AS BEFORE
./Build test # Files=5, Tests=135, Result: PASS
./Build install


Note, above I didn't patch kent to include -fPIC as suggested
previously. I don't see any noticeable difference if I do on this
arch.

It would be good if the instructions above could make it into the
Bio::DB::BigWig README, as a few people have expressed confusion about
the exact steps (the README in kent is a bit confusing, and mostly
unnecessary for the purposes of building Bio::DB::BigWig).


> The second issue is that the SSL library is not being linked in. Previously
> there was no dependency on SSL, but Jim may recently have added this to the
> BigWig library in order to allow it to read bigwig files from https servers.
> I see that you added a -lssl to Build.PL; does this make the tests work
> again?

Yup, when I add -lssl to Build.PL (as per the previous diff), the
tests pass, but I still see the warnings.

I'm sure I saw the warnings disappear when I was playing with
different versions of Bio::DB::BigWig, but now they occur without
fail... if you pardon the pun.

I have a seeking suspicion that it's related to my perl 'build kit'...
However, since I'm not sure what module versions to report, and since
you promised to fix these issues anyway, I won't dig into it.


Thanks for help, and thanks for the support on
irc://irc.freenode.net/#bioperl, without which I would have probably
give up!

Cheers,
Dan.

> Lincoln
>
> On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com> wrote:
>>
>> Hello,
>>
>> I'm trying to get Bio::DB::BigWig installed again, this time on a
>> different box.
>>
>> I installed kent from git as described here:
>> http://genome.ucsc.edu/admin/git.html
>>
>>
>> I made the following changes, similar to those described previously:
>>
>> git diff
>> diff --git a/src/inc/common.mk b/src/inc/common.mk
>> index c7fc557..5187901 100644
>> --- a/src/inc/common.mk
>> +++ b/src/inc/common.mk
>> @@ -3,7 +3,7 @@ CC=gcc
>> ?ifeq (${COPT},)
>> ? ? COPT=-O -g
>> ?endif
>> -CFLAGS=
>> +CFLAGS=-fPIC
>> ?HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
>> -DMACHTYPE_${MACHTYPE}
>> ?HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
>> -I../../../../../inc
>>
>> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> index fa2292b..acb97d2 100644
>> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
>> ? ? /* Parse current line. */
>> ? ? wordCount = chopLine(line, row);
>> ? ? if (wordCount == ArraySize(row))
>> - ? ? ? ? errAbort("Too many fields (%d max is %lu) line %d of %s",
>> wordCount, ArraySize(row),
>> + ? ? ? ? errAbort("Too many fields (%d max is %u) line %d of %s",
>> wordCount, ArraySize(row),
>> ? ? ? ? ? ? lf->lineIx, lf->fileName);
>> ? ? char *chrom = row[0];
>> ? ? unsigned int start = lineFileNeedNum(lf, row, 1);
>>
>>
>> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
>> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
>> correctly after typing 'make' in kent/src (should I be building it
>> differently?)
>>
>>
>>
>> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>>
>> cpan
>>
>> cpan shell -- CPAN exploration and modules installation (v1.9600)
>> Enter 'h' for help.
>>
>> cpan[1]> install Bio::DB::BigWig
>> CPAN: Storable loaded ok (v2.25)
>> Going to read '/homes/dbolser/.cpan/Metadata'
>> ?Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
>> Running install for module 'Bio::DB::BigWig'
>> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
>> CPAN: Digest::SHA loaded ok (v5.61)
>> CPAN: Compress::Zlib loaded ok (v2.03)
>> Checksum for
>> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
>> ok
>> CPAN: Archive::Tar loaded ok (v1.76)
>> Bio-BigFile-1.05
>> Bio-BigFile-1.05/Changes
>> Bio-BigFile-1.05/LICENSE
>> Bio-BigFile-1.05/DISCLAIMER
>> Bio-BigFile-1.05/Build.PL
>> Bio-BigFile-1.05/typemap
>> Bio-BigFile-1.05/META.yml
>> Bio-BigFile-1.05/README
>> Bio-BigFile-1.05/MANIFEST
>> Bio-BigFile-1.05/ExampleData
>> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
>> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
>> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
>> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
>> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
>> Bio-BigFile-1.05/ExampleData/refSeqTest.as
>> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
>> Bio-BigFile-1.05/bin
>> Bio-BigFile-1.05/bin/bigWigToWig.pl
>> Bio-BigFile-1.05/bin/wigToBigWig.pl
>> Bio-BigFile-1.05/bin/index_bigwigset.pl
>> Bio-BigFile-1.05/lib
>> Bio-BigFile-1.05/lib/Bio
>> Bio-BigFile-1.05/lib/Bio/DB
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
>> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
>> Bio-BigFile-1.05/t
>> Bio-BigFile-1.05/t/02.bigbed.t
>> Bio-BigFile-1.05/t/03.bigwig_high.t
>> Bio-BigFile-1.05/t/04.bigbed_high.t
>> Bio-BigFile-1.05/t/05.bigwig_set.t
>> /bin/tar: Read 9216 bytes from -
>> Bio-BigFile-1.05/t/01.bigwig.t
>> Bio-BigFile-1.05/patches
>> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
>> CPAN: File::Temp loaded ok (v0.22)
>> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
>> CPAN: CPAN::Meta loaded ok (v2.110580)
>> CPAN: Module::CoreList loaded ok (v2.46)
>> CPAN: Time::HiRes loaded ok (v1.9717)
>>
>> ?CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>>
>>
>> This module requires the compiled jkweb.a library from Jim Kent's source
>> tree.
>> If you haven't already done so, please download the source from
>> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
>> contents of the "kent/src/lib" subdirectory as directed in the README.
>> Then
>> enter the location of the "kent/src" subdirectory at the prompt below.
>> To prevent
>> this message from appearing in the future, set the environment
>> variable KENT_SRC
>> to point to the "kent/src" subdirectory.
>>
>> Please enter the location of Kent source tree:
>> /homes/dbolser/build/src/kent/src
>>
>> Created MYMETA.yml and MYMETA.json
>> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
>> Building Bio-BigFile
>> gcc -I/homes/dbolser/build/src/kent/src/inc
>> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
>> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
>> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
>> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
>> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
>> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
>> lib/Bio/DB/BigFile.c
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
>> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
>> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
>> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
>> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
>> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
>> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
>> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
>> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
>> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
>>
>> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
>> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
>> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
>> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
>> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
>> ?LDS/Bio-BigFile-1.05.tar.gz
>> ?./Build -- OK
>> CPAN: YAML loaded ok (v0.72)
>> Running Build test
>> t/01.bigwig.t ....... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at t/01.bigwig.t line 28
>> Compilation failed in require at t/01.bigwig.t line 28.
>> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
>> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 29/29 subtests
>> t/02.bigbed.t ....... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at t/02.bigbed.t line 28
>> Compilation failed in require at t/02.bigbed.t line 28.
>> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
>> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 15/15 subtests
>> t/03.bigwig_high.t .. Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at t/03.bigwig_high.t line 28.
>> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
>> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 32/32 subtests
>> t/04.bigbed_high.t .. Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
>> line 7.
>> Compilation failed in require at t/04.bigbed_high.t line 28.
>> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
>> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 35/35 subtests
>> t/05.bigwig_set.t ... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
>> line 177.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
>> line 177.
>> Compilation failed in require at t/05.bigwig_set.t line 19.
>> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
>> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
>> No subtests run
>>
>> Test Summary Report
>> -------------------
>> t/01.bigwig.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 29 tests but ran 0.
>> t/02.bigbed.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 15 tests but ran 0.
>> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 32 tests but ran 0.
>> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 35 tests but ran 0.
>> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: No plan found in TAP output
>> Files=5, Tests=0, ?1 wallclock secs ( 0.04 usr ?0.01 sys + ?0.93 cusr
>> 0.11 csys = ?1.09 CPU)
>> Result: FAIL
>> Failed 5/5 test programs. 0/0 subtests failed.
>> ?LDS/Bio-BigFile-1.05.tar.gz
>> ?./Build test -- NOT OK
>> //hint// to see the cpan-testers results for installing this module, try:
>> ?reports LDS/Bio-BigFile-1.05.tar.gz
>> Running Build install
>> ?make test had returned bad status, won't install without force
>> Failed during this command:
>> ?LDS/Bio-BigFile-1.05.tar.gz ? ? ? ? ? ? ? ? ?: make_test NO
>>
>> cpan[2]>
>>
>>
>>
>>
>>
>>
>> Any hints?
>>
>> Cheers,
>> Dan.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
>



From David.Messina at sbc.su.se  Tue Mar 29 05:11:26 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 29 Mar 2011 11:11:26 +0200
Subject: [Bioperl-l] GSoC 2011
In-Reply-To: <AANLkTim6o3bJ6NkBRmoUC5e76GaGzpjP5+xE+ZrWcEdc@mail.gmail.com>
References: <AANLkTim6o3bJ6NkBRmoUC5e76GaGzpjP5+xE+ZrWcEdc@mail.gmail.com>
Message-ID: <AANLkTi=OW4OYGwB1AWRe4TXZTXyLuENxZakArcVoAjHF@mail.gmail.com>

Hi Fei,

Glad to hear you're interested in working on BioPerl!

Just to throw in my two cents, I think it would be great to have a RAxML
wrapper in BioPerl. Although actually any of the projects you mentioned
sound like they're about the right size for a summer project.

I'm not directly involved with GSoC, so I think if you haven't already you
should take a look at our GsOC page here

    http://news.open-bio.org/news/2011/03/obf-gsoc-2011/

and get in touch with Rob Buels, our coordinator (rmb32 at cornell.edu)



Best,
Dave





On Tue, Mar 22, 2011 at 20:14, Fei Hu <hufeiyc at gmail.com> wrote:

> Hi, All.
>
> My name is Fei Hu from U. of South Carolina. I am currently a second-year
> Ph.D student in computer science focusing on gene order and sequence(DNA &
> AA) phylogeny as well as whole genome alignment. I am instreseted in
> joining
> bioperl project of GSoC 2011. I have two ideas that would like to share.
>
> My first idea is to extend the bioperl so that it can process and analysis
> gene order data using published package such as MGR, GRAPPA and distance
> estimator. This is a relatively new type of data and many great researchers
> have contributed to this type of phylogeny reconstruction (Dr. Pavel
> Penzer,
> Dr. Bernard Moret and Dr. David Sankoff).
>
> Secondly as maximum likelihood becomes more and more popular, especially
> RAxML has been widely recognized and used(over 1000 citations). I think
> it's
> time to integrate that as well as GARLI into the Bio::Tools. I extensively
> used and explored RAxML in my last publication on gene order phylogeny.
>
> Those are just my preliminary thoughts, not even a plan and any suggestion
> is greatly appreciated!!! I use perl on daily bases for data processing and
> composing testing scripts, but not much OOP involved.
>
> PS: Rest api for CIPRES is no longer available. So this following task
> can't
> be finished right now:
> Development of a
> Bio::Tools::Run::RemoteBlast<
> http://bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast>-like
> interface to CIPRES remote analyses; for more see this
> thread<http://thread.gmane.org/gmane.comp.lang.perl.bio.general/16524>
> .
>
> And Thank you all.
> Best
>
> Fei
>
> --
> *Fei Hu
> Bioinformatics Lab
> 3D-11 Swearingen Building
> U of South Carolina
> Tel: 803-397-5240*
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From tzhu at mail.bnu.edu.cn  Tue Mar 29 06:33:59 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Tue, 29 Mar 2011 18:33:59 +0800
Subject: [Bioperl-l] How to use module Bio::SeqFeature::Gene::GeneStructure?
Message-ID: <1301394839.6397.1.camel@ubuntu>

I've referred the ducument
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
It says, @transcripts = $gene->transcripts(); @exons = $gene->exons();
The object $gene should mean a Bio::SeqFeature::Gene::GeneStructure
object. But how could I get such object? I hope to see a good example.
Thank you! 


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)




From lincoln.stein at gmail.com  Tue Mar 29 09:59:22 2011
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Tue, 29 Mar 2011 09:59:22 -0400
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
	<AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>
Message-ID: <AANLkTi=Jrw3adAgigbAeG_-KT4VqLBsPBE08x_NQyOHD@mail.gmail.com>

I'll release a new version with a fixed Build.PL and README today.

Lincoln

On Tue, Mar 29, 2011 at 4:57 AM, Dan Bolser <dan.bolser at gmail.com> wrote:

> On 28 March 2011 22:26, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> > Hi Dan,
> > There are two problems that I can see. One is a series of compiler
> warnings
> > when compiling the Perl .XS interface file. These are likely nothing to
> > worry about, but I should fix them. What versions of Perl and gcc do you
> > have installed? I don't see them when I compile on my system.
>
> gcc --version # gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
> perl --version # v5.8.8 built for i386-linux-thread-multi
>
> uname -a # Linux cricket 2.6.18-194.32.1.el5PAE #1 SMP Wed Jan 5
> 18:43:13 EST 2011 i686 i686 i386 GNU/Linux
>
>
>
> I got kent from git and built it with the following commands:
>
> cd kent/src/lib/
> echo $MACHTYPE # i686-redhat-linux-gnu
> export MACHTYPE=i686
> make
> cd ../
> export KENT_SRC=`pwd`
>
> # NOTE, both $MACHTYPE and $KENT_SRC should be defined here
> cpan -i Bio::DB::BigWig # FAILS AS DESCRIBED
>
> cd /tmp
> wget
> http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> tar zxfv Bio-BigFile-1.05.tar.gz
> cd Bio-BigFile-1.05
> # PATCH  Build.PL AS DESCRIBED (add -lssl after -lz)
> perl Build.PL
> ./Build # SEE WARNINGS AS BEFORE
> ./Build test # Files=5, Tests=135, Result: PASS
> ./Build install
>
>
> Note, above I didn't patch kent to include -fPIC as suggested
> previously. I don't see any noticeable difference if I do on this
> arch.
>
> It would be good if the instructions above could make it into the
> Bio::DB::BigWig README, as a few people have expressed confusion about
> the exact steps (the README in kent is a bit confusing, and mostly
> unnecessary for the purposes of building Bio::DB::BigWig).
>
>
> > The second issue is that the SSL library is not being linked in.
> Previously
> > there was no dependency on SSL, but Jim may recently have added this to
> the
> > BigWig library in order to allow it to read bigwig files from https
> servers.
> > I see that you added a -lssl to Build.PL; does this make the tests work
> > again?
>
> Yup, when I add -lssl to Build.PL (as per the previous diff), the
> tests pass, but I still see the warnings.
>
> I'm sure I saw the warnings disappear when I was playing with
> different versions of Bio::DB::BigWig, but now they occur without
> fail... if you pardon the pun.
>
> I have a seeking suspicion that it's related to my perl 'build kit'...
> However, since I'm not sure what module versions to report, and since
> you promised to fix these issues anyway, I won't dig into it.
>
>
> Thanks for help, and thanks for the support on
> irc://irc.freenode.net/#bioperl, without which I would have probably
> give up!
>
> Cheers,
> Dan.
>
> > Lincoln
> >
> > On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com>
> wrote:
> >>
> >> Hello,
> >>
> >> I'm trying to get Bio::DB::BigWig installed again, this time on a
> >> different box.
> >>
> >> I installed kent from git as described here:
> >> http://genome.ucsc.edu/admin/git.html
> >>
> >>
> >> I made the following changes, similar to those described previously:
> >>
> >> git diff
> >> diff --git a/src/inc/common.mk b/src/inc/common.mk
> >> index c7fc557..5187901 100644
> >> --- a/src/inc/common.mk
> >> +++ b/src/inc/common.mk
> >> @@ -3,7 +3,7 @@ CC=gcc
> >>  ifeq (${COPT},)
> >>     COPT=-O -g
> >>  endif
> >> -CFLAGS=
> >> +CFLAGS=-fPIC
> >>  HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> >> -DMACHTYPE_${MACHTYPE}
> >>  HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> >> -I../../../../../inc
> >>
> >> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> index fa2292b..acb97d2 100644
> >> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
> >>     /* Parse current line. */
> >>     wordCount = chopLine(line, row);
> >>     if (wordCount == ArraySize(row))
> >> -         errAbort("Too many fields (%d max is %lu) line %d of %s",
> >> wordCount, ArraySize(row),
> >> +         errAbort("Too many fields (%d max is %u) line %d of %s",
> >> wordCount, ArraySize(row),
> >>             lf->lineIx, lf->fileName);
> >>     char *chrom = row[0];
> >>     unsigned int start = lineFileNeedNum(lf, row, 1);
> >>
> >>
> >> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> >> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> >> correctly after typing 'make' in kent/src (should I be building it
> >> differently?)
> >>
> >>
> >>
> >> Now when I try to install Bio::DB::BigWig via cpan, things look like
> this:
> >>
> >> cpan
> >>
> >> cpan shell -- CPAN exploration and modules installation (v1.9600)
> >> Enter 'h' for help.
> >>
> >> cpan[1]> install Bio::DB::BigWig
> >> CPAN: Storable loaded ok (v2.25)
> >> Going to read '/homes/dbolser/.cpan/Metadata'
> >>  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> >> Running install for module 'Bio::DB::BigWig'
> >> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >> CPAN: Digest::SHA loaded ok (v5.61)
> >> CPAN: Compress::Zlib loaded ok (v2.03)
> >> Checksum for
> >> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >> ok
> >> CPAN: Archive::Tar loaded ok (v1.76)
> >> Bio-BigFile-1.05
> >> Bio-BigFile-1.05/Changes
> >> Bio-BigFile-1.05/LICENSE
> >> Bio-BigFile-1.05/DISCLAIMER
> >> Bio-BigFile-1.05/Build.PL
> >> Bio-BigFile-1.05/typemap
> >> Bio-BigFile-1.05/META.yml
> >> Bio-BigFile-1.05/README
> >> Bio-BigFile-1.05/MANIFEST
> >> Bio-BigFile-1.05/ExampleData
> >> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> >> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> >> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> >> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> >> Bio-BigFile-1.05/bin
> >> Bio-BigFile-1.05/bin/bigWigToWig.pl
> >> Bio-BigFile-1.05/bin/wigToBigWig.pl
> >> Bio-BigFile-1.05/bin/index_bigwigset.pl
> >> Bio-BigFile-1.05/lib
> >> Bio-BigFile-1.05/lib/Bio
> >> Bio-BigFile-1.05/lib/Bio/DB
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> >> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> >> Bio-BigFile-1.05/t
> >> Bio-BigFile-1.05/t/02.bigbed.t
> >> Bio-BigFile-1.05/t/03.bigwig_high.t
> >> Bio-BigFile-1.05/t/04.bigbed_high.t
> >> Bio-BigFile-1.05/t/05.bigwig_set.t
> >> /bin/tar: Read 9216 bytes from -
> >> Bio-BigFile-1.05/t/01.bigwig.t
> >> Bio-BigFile-1.05/patches
> >> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> >> CPAN: File::Temp loaded ok (v0.22)
> >> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> >> CPAN: CPAN::Meta loaded ok (v2.110580)
> >> CPAN: Module::CoreList loaded ok (v2.46)
> >> CPAN: Time::HiRes loaded ok (v1.9717)
> >>
> >>  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >>
> >>
> >> This module requires the compiled jkweb.a library from Jim Kent's source
> >> tree.
> >> If you haven't already done so, please download the source from
> >> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build
> the
> >> contents of the "kent/src/lib" subdirectory as directed in the README.
> >> Then
> >> enter the location of the "kent/src" subdirectory at the prompt below.
> >> To prevent
> >> this message from appearing in the future, set the environment
> >> variable KENT_SRC
> >> to point to the "kent/src" subdirectory.
> >>
> >> Please enter the location of Kent source tree:
> >> /homes/dbolser/build/src/kent/src
> >>
> >> Created MYMETA.yml and MYMETA.json
> >> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> >> Building Bio-BigFile
> >> gcc -I/homes/dbolser/build/src/kent/src/inc
> >> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> >> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> >> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> >> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> >> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> >> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> >> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> >> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> >> lib/Bio/DB/BigFile.c
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> >> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> >> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> >> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> >> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> >> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> >> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> >> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> >> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> >> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
> >>
> >>
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> >> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> >> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> >> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> >> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> >> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
> >>  LDS/Bio-BigFile-1.05.tar.gz
> >>  ./Build -- OK
> >> CPAN: YAML loaded ok (v0.72)
> >> Running Build test
> >> t/01.bigwig.t ....... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at t/01.bigwig.t line 28
> >> Compilation failed in require at t/01.bigwig.t line 28.
> >> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> >> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 29/29 subtests
> >> t/02.bigbed.t ....... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at t/02.bigbed.t line 28
> >> Compilation failed in require at t/02.bigbed.t line 28.
> >> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> >> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 15/15 subtests
> >> t/03.bigwig_high.t .. Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at t/03.bigwig_high.t line 28.
> >> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> >> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 32/32 subtests
> >> t/04.bigbed_high.t .. Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> >> line 7.
> >> Compilation failed in require at t/04.bigbed_high.t line 28.
> >> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> >> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 35/35 subtests
> >> t/05.bigwig_set.t ... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> >> line 177.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> >> line 177.
> >> Compilation failed in require at t/05.bigwig_set.t line 19.
> >> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> >> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> >> No subtests run
> >>
> >> Test Summary Report
> >> -------------------
> >> t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 29 tests but ran 0.
> >> t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> >> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 32 tests but ran 0.
> >> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 35 tests but ran 0.
> >> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: No plan found in TAP output
> >> Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
> >> 0.11 csys =  1.09 CPU)
> >> Result: FAIL
> >> Failed 5/5 test programs. 0/0 subtests failed.
> >>  LDS/Bio-BigFile-1.05.tar.gz
> >>  ./Build test -- NOT OK
> >> //hint// to see the cpan-testers results for installing this module,
> try:
> >>  reports LDS/Bio-BigFile-1.05.tar.gz
> >> Running Build install
> >>  make test had returned bad status, won't install without force
> >> Failed during this command:
> >>  LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO
> >>
> >> cpan[2]>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Any hints?
> >>
> >> Cheers,
> >> Dan.
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
> > --
> > Lincoln D. Stein
> > Director, Informatics and Biocomputing Platform
> > Ontario Institute for Cancer Research
> > 101 College St., Suite 800
> > Toronto, ON, Canada M5G0A3
> > 416 673-8514
> > Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> >
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>



From lincoln.stein at gmail.com  Tue Mar 29 09:59:22 2011
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Tue, 29 Mar 2011 09:59:22 -0400
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
	<AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>
Message-ID: <AANLkTi=Jrw3adAgigbAeG_-KT4VqLBsPBE08x_NQyOHD@mail.gmail.com>

I'll release a new version with a fixed Build.PL and README today.

Lincoln

On Tue, Mar 29, 2011 at 4:57 AM, Dan Bolser <dan.bolser at gmail.com> wrote:

> On 28 March 2011 22:26, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> > Hi Dan,
> > There are two problems that I can see. One is a series of compiler
> warnings
> > when compiling the Perl .XS interface file. These are likely nothing to
> > worry about, but I should fix them. What versions of Perl and gcc do you
> > have installed? I don't see them when I compile on my system.
>
> gcc --version # gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
> perl --version # v5.8.8 built for i386-linux-thread-multi
>
> uname -a # Linux cricket 2.6.18-194.32.1.el5PAE #1 SMP Wed Jan 5
> 18:43:13 EST 2011 i686 i686 i386 GNU/Linux
>
>
>
> I got kent from git and built it with the following commands:
>
> cd kent/src/lib/
> echo $MACHTYPE # i686-redhat-linux-gnu
> export MACHTYPE=i686
> make
> cd ../
> export KENT_SRC=`pwd`
>
> # NOTE, both $MACHTYPE and $KENT_SRC should be defined here
> cpan -i Bio::DB::BigWig # FAILS AS DESCRIBED
>
> cd /tmp
> wget
> http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> tar zxfv Bio-BigFile-1.05.tar.gz
> cd Bio-BigFile-1.05
> # PATCH  Build.PL AS DESCRIBED (add -lssl after -lz)
> perl Build.PL
> ./Build # SEE WARNINGS AS BEFORE
> ./Build test # Files=5, Tests=135, Result: PASS
> ./Build install
>
>
> Note, above I didn't patch kent to include -fPIC as suggested
> previously. I don't see any noticeable difference if I do on this
> arch.
>
> It would be good if the instructions above could make it into the
> Bio::DB::BigWig README, as a few people have expressed confusion about
> the exact steps (the README in kent is a bit confusing, and mostly
> unnecessary for the purposes of building Bio::DB::BigWig).
>
>
> > The second issue is that the SSL library is not being linked in.
> Previously
> > there was no dependency on SSL, but Jim may recently have added this to
> the
> > BigWig library in order to allow it to read bigwig files from https
> servers.
> > I see that you added a -lssl to Build.PL; does this make the tests work
> > again?
>
> Yup, when I add -lssl to Build.PL (as per the previous diff), the
> tests pass, but I still see the warnings.
>
> I'm sure I saw the warnings disappear when I was playing with
> different versions of Bio::DB::BigWig, but now they occur without
> fail... if you pardon the pun.
>
> I have a seeking suspicion that it's related to my perl 'build kit'...
> However, since I'm not sure what module versions to report, and since
> you promised to fix these issues anyway, I won't dig into it.
>
>
> Thanks for help, and thanks for the support on
> irc://irc.freenode.net/#bioperl, without which I would have probably
> give up!
>
> Cheers,
> Dan.
>
> > Lincoln
> >
> > On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com>
> wrote:
> >>
> >> Hello,
> >>
> >> I'm trying to get Bio::DB::BigWig installed again, this time on a
> >> different box.
> >>
> >> I installed kent from git as described here:
> >> http://genome.ucsc.edu/admin/git.html
> >>
> >>
> >> I made the following changes, similar to those described previously:
> >>
> >> git diff
> >> diff --git a/src/inc/common.mk b/src/inc/common.mk
> >> index c7fc557..5187901 100644
> >> --- a/src/inc/common.mk
> >> +++ b/src/inc/common.mk
> >> @@ -3,7 +3,7 @@ CC=gcc
> >>  ifeq (${COPT},)
> >>     COPT=-O -g
> >>  endif
> >> -CFLAGS=
> >> +CFLAGS=-fPIC
> >>  HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> >> -DMACHTYPE_${MACHTYPE}
> >>  HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> >> -I../../../../../inc
> >>
> >> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> index fa2292b..acb97d2 100644
> >> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
> >>     /* Parse current line. */
> >>     wordCount = chopLine(line, row);
> >>     if (wordCount == ArraySize(row))
> >> -         errAbort("Too many fields (%d max is %lu) line %d of %s",
> >> wordCount, ArraySize(row),
> >> +         errAbort("Too many fields (%d max is %u) line %d of %s",
> >> wordCount, ArraySize(row),
> >>             lf->lineIx, lf->fileName);
> >>     char *chrom = row[0];
> >>     unsigned int start = lineFileNeedNum(lf, row, 1);
> >>
> >>
> >> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> >> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> >> correctly after typing 'make' in kent/src (should I be building it
> >> differently?)
> >>
> >>
> >>
> >> Now when I try to install Bio::DB::BigWig via cpan, things look like
> this:
> >>
> >> cpan
> >>
> >> cpan shell -- CPAN exploration and modules installation (v1.9600)
> >> Enter 'h' for help.
> >>
> >> cpan[1]> install Bio::DB::BigWig
> >> CPAN: Storable loaded ok (v2.25)
> >> Going to read '/homes/dbolser/.cpan/Metadata'
> >>  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> >> Running install for module 'Bio::DB::BigWig'
> >> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >> CPAN: Digest::SHA loaded ok (v5.61)
> >> CPAN: Compress::Zlib loaded ok (v2.03)
> >> Checksum for
> >> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >> ok
> >> CPAN: Archive::Tar loaded ok (v1.76)
> >> Bio-BigFile-1.05
> >> Bio-BigFile-1.05/Changes
> >> Bio-BigFile-1.05/LICENSE
> >> Bio-BigFile-1.05/DISCLAIMER
> >> Bio-BigFile-1.05/Build.PL
> >> Bio-BigFile-1.05/typemap
> >> Bio-BigFile-1.05/META.yml
> >> Bio-BigFile-1.05/README
> >> Bio-BigFile-1.05/MANIFEST
> >> Bio-BigFile-1.05/ExampleData
> >> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> >> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> >> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> >> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> >> Bio-BigFile-1.05/bin
> >> Bio-BigFile-1.05/bin/bigWigToWig.pl
> >> Bio-BigFile-1.05/bin/wigToBigWig.pl
> >> Bio-BigFile-1.05/bin/index_bigwigset.pl
> >> Bio-BigFile-1.05/lib
> >> Bio-BigFile-1.05/lib/Bio
> >> Bio-BigFile-1.05/lib/Bio/DB
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> >> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> >> Bio-BigFile-1.05/t
> >> Bio-BigFile-1.05/t/02.bigbed.t
> >> Bio-BigFile-1.05/t/03.bigwig_high.t
> >> Bio-BigFile-1.05/t/04.bigbed_high.t
> >> Bio-BigFile-1.05/t/05.bigwig_set.t
> >> /bin/tar: Read 9216 bytes from -
> >> Bio-BigFile-1.05/t/01.bigwig.t
> >> Bio-BigFile-1.05/patches
> >> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> >> CPAN: File::Temp loaded ok (v0.22)
> >> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> >> CPAN: CPAN::Meta loaded ok (v2.110580)
> >> CPAN: Module::CoreList loaded ok (v2.46)
> >> CPAN: Time::HiRes loaded ok (v1.9717)
> >>
> >>  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >>
> >>
> >> This module requires the compiled jkweb.a library from Jim Kent's source
> >> tree.
> >> If you haven't already done so, please download the source from
> >> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build
> the
> >> contents of the "kent/src/lib" subdirectory as directed in the README.
> >> Then
> >> enter the location of the "kent/src" subdirectory at the prompt below.
> >> To prevent
> >> this message from appearing in the future, set the environment
> >> variable KENT_SRC
> >> to point to the "kent/src" subdirectory.
> >>
> >> Please enter the location of Kent source tree:
> >> /homes/dbolser/build/src/kent/src
> >>
> >> Created MYMETA.yml and MYMETA.json
> >> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> >> Building Bio-BigFile
> >> gcc -I/homes/dbolser/build/src/kent/src/inc
> >> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> >> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> >> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> >> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> >> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> >> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> >> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> >> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> >> lib/Bio/DB/BigFile.c
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> >> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> >> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> >> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> >> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> >> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> >> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> >> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> >> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> >> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
> >>
> >>
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> >> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> >> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> >> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> >> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> >> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
> >>  LDS/Bio-BigFile-1.05.tar.gz
> >>  ./Build -- OK
> >> CPAN: YAML loaded ok (v0.72)
> >> Running Build test
> >> t/01.bigwig.t ....... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at t/01.bigwig.t line 28
> >> Compilation failed in require at t/01.bigwig.t line 28.
> >> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> >> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 29/29 subtests
> >> t/02.bigbed.t ....... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at t/02.bigbed.t line 28
> >> Compilation failed in require at t/02.bigbed.t line 28.
> >> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> >> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 15/15 subtests
> >> t/03.bigwig_high.t .. Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at t/03.bigwig_high.t line 28.
> >> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> >> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 32/32 subtests
> >> t/04.bigbed_high.t .. Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> >> line 7.
> >> Compilation failed in require at t/04.bigbed_high.t line 28.
> >> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> >> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 35/35 subtests
> >> t/05.bigwig_set.t ... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> >> line 177.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> >> line 177.
> >> Compilation failed in require at t/05.bigwig_set.t line 19.
> >> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> >> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> >> No subtests run
> >>
> >> Test Summary Report
> >> -------------------
> >> t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 29 tests but ran 0.
> >> t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> >> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 32 tests but ran 0.
> >> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 35 tests but ran 0.
> >> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: No plan found in TAP output
> >> Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
> >> 0.11 csys =  1.09 CPU)
> >> Result: FAIL
> >> Failed 5/5 test programs. 0/0 subtests failed.
> >>  LDS/Bio-BigFile-1.05.tar.gz
> >>  ./Build test -- NOT OK
> >> //hint// to see the cpan-testers results for installing this module,
> try:
> >>  reports LDS/Bio-BigFile-1.05.tar.gz
> >> Running Build install
> >>  make test had returned bad status, won't install without force
> >> Failed during this command:
> >>  LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO
> >>
> >> cpan[2]>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Any hints?
> >>
> >> Cheers,
> >> Dan.
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
> > --
> > Lincoln D. Stein
> > Director, Informatics and Biocomputing Platform
> > Ontario Institute for Cancer Research
> > 101 College St., Suite 800
> > Toronto, ON, Canada M5G0A3
> > 416 673-8514
> > Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> >
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>



From ravimbt at gmail.com  Mon Mar 28 05:56:58 2011
From: ravimbt at gmail.com (=?UTF-8?B?wrbigKLil4/guYvigKLgrofgrrDgrrXgrr/Rj86xzr3OueKXj+C5i+KAouKAosK2?=)
Date: Mon, 28 Mar 2011 15:26:58 +0530
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
Message-ID: <AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>

Hi Dave,

Thank you very much. It is working. I got the program code from the
following link.

http://www.bioperl.org/Core/Latest/bptutorial.html

I spent so much time on browsing, downloading and installing programs and
packages. But, it seems like the code error is the reason it dint work.
Thanks Dave.

Could you please give me the link to join this forum to see other
discussions, which would be more helpful to me? Please let me know if you
have any suggestion for me to keep learning the bioperl.

With regards,
Ravi.

2011/3/28 Dave Messina <David.Messina at sbc.su.se>

> Hi Ravi,
>
> Please make sure to "Reply All" so that everyone on the mailing list can
> follow (and add to) the discussion.
>
> If you read the first line of the exception, you'll see it states what the
> error is:
> "WebDBSeqI Error ? check query sequences!"
>
> You'd have no way of knowing this, but that ID and database combination is
> not functioning anymore, so that's why in this case you're getting an error.
> Please try using the example in the tutorial here:
>
>
> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>
> which has been updated to a different ID which should work.
>
> Sorry for the confusion! So that we can prevent other people from having
> the same issue, could you tell me where you got that example code?
>
> Dave
>
>
>
>
>
>
> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>
>> Hi Dave,
>>
>> Thanks a lot for your reply. It is really helpful. Please find the
>> screenshot after making the change you pointed out. But I am getting
>> "Exception: Bio::Root::Exception" error. I think I have to set the
>> environment variables but I am not sure how to do that. Could you please
>> guide me on this too.
>>
>> I can go to the "Environment Variable" Window in my pc. But I dont know
>> what to enter once I click "New" on that window.
>>
>> Thanks in advance.
>>
>> With regards,
>> Ravi.
>>
>>
>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>
>>> Hi Ravi,
>>>
>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>> not Bio::Seq. So your first line
>>>
>>> use Bio::Seq;
>>>
>>> should be replaced with
>>>
>>> use Bio::Perl;
>>>
>>>
>>> More examples in the BioPerl Tutorial here:
>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>
>>>
>>> Dve
>>>
>>>
>>>
>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>
>>>> Hi,
>>>>
>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>> packages
>>>> using ppm on windows 7? Please find the attachment for the error message
>>>> I
>>>> get. I would really appreciate if you help me fix this issue.
>>>>
>>>> Thanks,
>>>>
>>>> With regards,
>>>> Ravi.
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>>
>>
>



From rmb32 at cornell.edu  Tue Mar 29 17:20:41 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Tue, 29 Mar 2011 14:20:41 -0700
Subject: [Bioperl-l] Announcing OBF Summer of Code - please forward!
Message-ID: <4D924D29.3020707@cornell.edu>

Hi all,

Here's an advertising-ready announcement for OBF's Summer of Code, 
thanks to Christian Zmasek and Hilmar Lapp for their excellent writing.

Student applications are due April 8!  Please spread it widely, we need 
to reach lots of students with it!

Rob Buels
OBF GSoC 2011 Admin


============================================================

*** Please disseminate widely at your local institutions ***
*** including posting to message and job boards, so that ***
*** we reach as many students as possible.               ***

============================================================


OPEN BIOINFORMATICS FOUNDATION SUMMER OF CODE 2011

Applications due 19:00 UTC, April 8, 2010.
http://www.open-bio.org/wiki/Google_Summer_of_Code

The Open Bioinformatics Foundation Summer of Code program provides a 
unique opportunity for undergraduate, masters, and PhD students to 
obtain hands-on experience writing and extending open-source software 
for bioinformatics under the mentorship of experienced developers from 
around the world. The program is the participation of the Open 
Bioinformatics Foundation (OBF) as a mentoring organization in the 
Google Summer of Code(tm) (http://code.google.com/soc/).

Students successfully completing the 3 month program receive a $5,000 
USD stipend, and may work entirely from their home or home institution. 
  Participation is open to students from any country in the world except 
countries subject to US trade restrictions.  Each student will have at 
least one dedicated mentor to show them the ropes and help them complete 
their project.

The Open Bioinformatics Foundation is particularly seeking students 
interested in both bioinformatics (computational biology) and software 
development. Some initial project ideas are listed on the website. These 
range from Galaxy phylogenetics pipeline development in Biopython to 
lightweight sequence objects and lazy parsing in BioPerl, a DAS Server 
for large files on local filesystems, and mapping Java libraries to 
Perl/Ruby/Python using Biolib+SWIG+JNI.  All project ideas are flexible 
and many can be adjusted in scope to match the skills of the student. We 
also welcome and encourage students proposing their own project ideas; 
historically some of the most successful Summer of Code projects are 
ones proposed by the students themselves.

TO APPLY: Apply online at the Google Summer of Code website 
(http://socghop.appspot.com/), where you will also find GSoC program 
rules and eligibility requirements. The 12-day application period for 
students runs from Monday, March 28 through Friday, April 8th, 2011.

INQUIRIES:

We strongly encourage all interested students to get in touch with us 
with their ideas as early on as possible.  See the OBF GSoC page for 
contact details.

2011 OBF Summer of Code:
http://www.open-bio.org/wiki/Google_Summer_of_Code

Google Summer of Code FAQ:
http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs





From cjfields at illinois.edu  Wed Mar 30 09:58:00 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 30 Mar 2011 08:58:00 -0500
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
Message-ID: <9EDCB97E-3256-476C-AA40-EDE27BF96033@illinois.edu>

Ravi,

You can sign up for the email list here:

http://lists.open-bio.org/mailman/listinfo/bioperl-l

Once you are signed up, you should be able to post questions.

chris

On Mar 28, 2011, at 4:56 AM, ?????????????????? wrote:

> Hi Dave,
> 
> Thank you very much. It is working. I got the program code from the
> following link.
> 
> http://www.bioperl.org/Core/Latest/bptutorial.html
> 
> I spent so much time on browsing, downloading and installing programs and
> packages. But, it seems like the code error is the reason it dint work.
> Thanks Dave.
> 
> Could you please give me the link to join this forum to see other
> discussions, which would be more helpful to me? Please let me know if you
> have any suggestion for me to keep learning the bioperl.
> 
> With regards,
> Ravi.
> 
> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
> 
>> Hi Ravi,
>> 
>> Please make sure to "Reply All" so that everyone on the mailing list can
>> follow (and add to) the discussion.
>> 
>> If you read the first line of the exception, you'll see it states what the
>> error is:
>> "WebDBSeqI Error ? check query sequences!"
>> 
>> You'd have no way of knowing this, but that ID and database combination is
>> not functioning anymore, so that's why in this case you're getting an error.
>> Please try using the example in the tutorial here:
>> 
>> 
>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>> 
>> which has been updated to a different ID which should work.
>> 
>> Sorry for the confusion! So that we can prevent other people from having
>> the same issue, could you tell me where you got that example code?
>> 
>> Dave
>> 
>> 
>> 
>> 
>> 
>> 
>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>> 
>>> Hi Dave,
>>> 
>>> Thanks a lot for your reply. It is really helpful. Please find the
>>> screenshot after making the change you pointed out. But I am getting
>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>> environment variables but I am not sure how to do that. Could you please
>>> guide me on this too.
>>> 
>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>> what to enter once I click "New" on that window.
>>> 
>>> Thanks in advance.
>>> 
>>> With regards,
>>> Ravi.
>>> 
>>> 
>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>> 
>>>> Hi Ravi,
>>>> 
>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>> not Bio::Seq. So your first line
>>>> 
>>>> use Bio::Seq;
>>>> 
>>>> should be replaced with
>>>> 
>>>> use Bio::Perl;
>>>> 
>>>> 
>>>> More examples in the BioPerl Tutorial here:
>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>> 
>>>> 
>>>> Dve
>>>> 
>>>> 
>>>> 
>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>> 
>>>>> Hi,
>>>>> 
>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>> packages
>>>>> using ppm on windows 7? Please find the attachment for the error message
>>>>> I
>>>>> get. I would really appreciate if you help me fix this issue.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> With regards,
>>>>> Ravi.
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> 
>>>> 
>>>> 
>>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From dvadell at clustering.com.ar  Wed Mar 30 10:51:38 2011
From: dvadell at clustering.com.ar (Diego M. Vadell)
Date: Wed, 30 Mar 2011 11:51:38 -0300
Subject: [Bioperl-l] Newbie alert: Aligning and printing first position
Message-ID: <201103301151.38752.dvadell@clustering.com.ar>

Hi list,

    I have an alignment ( done with Bio::Tools::Run::Alignment::Clustalw ) 
that I can see ( printing $aln->match_line() along with the sequences ):

        ********* .:                                   (match_line)
.......TDDSFDTDVSSS.........[...].............   ($seq1)
SDKIIHLTDDSFDTDVLKADGA[...]EFLDANLA   ($seq2)

    It looks right ( that "[...]" is mine, it's larger ). Now I want to get 
the position of the match ( the first "T" ), which should be "7". I thought I 
needed to use something like:

my $seq = $aln->get_seq_by_pos(1);
my $loc = $seq->location_from_column(1);
say $loc;

And $loc would be 7, but it's undef. If I try to iterate from 1 to 10, I start 
getting Bio::Location::Simple objects at the 8th place. So, should I loop 
untill I location_from_column() gives me an object? Is it another way of 
finding the position of the match?

As you can see, I'm just starting with bioinformatics. Any pointer will be 
appreciated.

Thanks in advance,
 -- Diego 


From joshearl1 at hotmail.com  Wed Mar 30 11:23:21 2011
From: joshearl1 at hotmail.com (Josh Earl)
Date: Wed, 30 Mar 2011 11:23:21 -0400
Subject: [Bioperl-l] Difficulty downloading biosql schema
Message-ID: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>


Hello all,

I'm trying to download the schema for biosql, however, when I run the command:
svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql-schema

(as per the instructions @ https://github.com/biosql/biosql/blob/master/INSTALL)
I either get no response, or it times out.  I've tried this a couple of times, the last time was a few weeks ago.  Anyone know what's going on?

Here's an example error:
svn: Can't connect to host 'code.open-bio.org': Connection timed out

thanks,
~josh

Center for Genomic Sciences
(412)-359-8341

 		 	   		  


From hlapp at drycafe.net  Wed Mar 30 11:52:22 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 30 Mar 2011 11:52:22 -0400
Subject: [Bioperl-l] Difficulty downloading biosql schema
In-Reply-To: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
References: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
Message-ID: <4C1B95A9-0480-4B9B-91E2-1D35BCB568B4@drycafe.net>

(moving this to BioSQL list)
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From cjfields at illinois.edu  Wed Mar 30 11:54:00 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 30 Mar 2011 10:54:00 -0500
Subject: [Bioperl-l] Difficulty downloading biosql schema
In-Reply-To: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
References: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
Message-ID: <87CBA000-B964-40DA-BF35-BC229CF24BB6@illinois.edu>

BioSQL moved to github a while back:

https://github.com/biosql/biosql

(this might be better asked on the biosql-l list, which I've cc'd)

chris

On Mar 30, 2011, at 10:23 AM, Josh Earl wrote:

> 
> Hello all,
> 
> I'm trying to download the schema for biosql, however, when I run the command:
> svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql-schema
> 
> (as per the instructions @ https://github.com/biosql/biosql/blob/master/INSTALL)
> I either get no response, or it times out.  I've tried this a couple of times, the last time was a few weeks ago.  Anyone know what's going on?
> 
> Here's an example error:
> svn: Can't connect to host 'code.open-bio.org': Connection timed out
> 
> thanks,
> ~josh
> 
> Center for Genomic Sciences
> (412)-359-8341
> 
> 		 	   		  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From p.j.a.cock at googlemail.com  Wed Mar 30 11:55:49 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 30 Mar 2011 16:55:49 +0100
Subject: [Bioperl-l] Difficulty downloading biosql schema
In-Reply-To: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
References: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
Message-ID: <AANLkTi=v80WkLtJxiDu1MBLoyKD0RTR5eBhmb4NF5zO7@mail.gmail.com>

On Wed, Mar 30, 2011 at 4:23 PM, Josh Earl <joshearl1 at hotmail.com> wrote:
>
> Hello all,
>
> I'm trying to download the schema for biosql, however, when I run the command:
> svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql-schema
>
> (as per the instructions @ https://github.com/biosql/biosql/blob/master/INSTALL)
> I either get no response, or it times out. ?I've tried this a couple of times, the last
> time was a few weeks ago. ?Anyone know what's going on?
>
> Here's an example error:
> svn: Can't connect to host 'code.open-bio.org': Connection timed out
>
> thanks,
> ~josh

Hi Josh

First the code.open-bio.org has been having trouble and is being rebuilt.
Even if it did work, it would give you an out of date copy prior to the move
from SVN to git.

Secondly, the instructions you pointed to are out of date, we'll have to
fix that. Just use git:

git clone git://github.com/biosql/biosql.git

Thanks for the heads up!

Peter

P.S. There is a dedicated BioSQL mailing list.



From roy.chaudhuri at gmail.com  Wed Mar 30 11:43:35 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Wed, 30 Mar 2011 16:43:35 +0100
Subject: [Bioperl-l] Newbie alert: Aligning and printing first position
In-Reply-To: <201103301151.38752.dvadell@clustering.com.ar>
References: <201103301151.38752.dvadell@clustering.com.ar>
Message-ID: <4D934FA7.2080206@gmail.com>

Hi Diego,

Column refers to the position in the alignment, not the individual 
sequence. location_from_column therefore gives the position in the 
individual sequence that corresponds to the requested column (you get 
undef since there is a gap in the first column of the alignment for 
seq1). If I understand correctly, you want the reverse, the position in 
the alignment that corresponds to the first position in your sequence. 
For that you need the opposite function, column_from_residue_number:

my $loc=$seq->column_from_residue_number(1);

$loc will now contain 8 (not 7), since position 1 of your sequence is in 
column 8 of the alignment.

Hope this helps,
Roy.

On 30/03/2011 15:51, Diego M. Vadell wrote:
> Hi list,
>
>      I have an alignment ( done with Bio::Tools::Run::Alignment::Clustalw )
> that I can see ( printing $aln->match_line() along with the sequences ):
>
>          ********* .:                                   (match_line)
> .......TDDSFDTDVSSS.........[...].............   ($seq1)
> SDKIIHLTDDSFDTDVLKADGA[...]EFLDANLA   ($seq2)
>
>      It looks right ( that "[...]" is mine, it's larger ). Now I want to get
> the position of the match ( the first "T" ), which should be "7". I thought I
> needed to use something like:
>
> my $seq = $aln->get_seq_by_pos(1);
> my $loc = $seq->location_from_column(1);
> say $loc;
>
> And $loc would be 7, but it's undef. If I try to iterate from 1 to 10, I start
> getting Bio::Location::Simple objects at the 8th place. So, should I loop
> untill I location_from_column() gives me an object? Is it another way of
> finding the position of the match?
>
> As you can see, I'm just starting with bioinformatics. Any pointer will be
> appreciated.
>
> Thanks in advance,
>   -- Diego
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From zheboyang at gmail.com  Thu Mar 31 08:28:53 2011
From: zheboyang at gmail.com (boyang zhe)
Date: Thu, 31 Mar 2011 14:28:53 +0200
Subject: [Bioperl-l] blast best hit
Message-ID: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>

Hi,

I just want to parse the blast results ,and get the best hit.

One way is to parse the results as usual, then get the first hit and exit
the loop.

I checked the bioperl document, and find that there is a method
best_hit_only in Bio::SearchIO::blast.pm.
But it only return 1/0. So my question is how to use this method to get the
best hit.

Thank you very much!

Boyang


From dvadell at clustering.com.ar  Thu Mar 31 08:59:46 2011
From: dvadell at clustering.com.ar (Diego M. Vadell)
Date: Thu, 31 Mar 2011 09:59:46 -0300
Subject: [Bioperl-l] Newbie alert: Aligning and printing first position
In-Reply-To: <4D934FA7.2080206@gmail.com>
References: <201103301151.38752.dvadell@clustering.com.ar>
	<4D934FA7.2080206@gmail.com>
Message-ID: <201103311000.36567.dvadell@clustering.com.ar>

Hi Roy,

  Thanks!! I can't beleive I didn't see that method in the documentation. 
Thank you very much. It worked perfectly.

Cheers,
 -- Diego

On Wednesday, March 30, 2011 12:43:35 pm Roy Chaudhuri wrote:
> Hi Diego,
> 
> Column refers to the position in the alignment, not the individual
> sequence. location_from_column therefore gives the position in the
> individual sequence that corresponds to the requested column (you get
> undef since there is a gap in the first column of the alignment for
> seq1). If I understand correctly, you want the reverse, the position in
> the alignment that corresponds to the first position in your sequence.
> For that you need the opposite function, column_from_residue_number:
> 
> my $loc=$seq->column_from_residue_number(1);
> 
> $loc will now contain 8 (not 7), since position 1 of your sequence is in
> column 8 of the alignment.
> 
> Hope this helps,
> Roy.
> 
> On 30/03/2011 15:51, Diego M. Vadell wrote:
> > Hi list,
> > 
> >      I have an alignment ( done with Bio::Tools::Run::Alignment::Clustalw
> >      )
> > 
> > that I can see ( printing $aln->match_line() along with the sequences ):
> >          ********* .:                                   (match_line)
> > 
> > .......TDDSFDTDVSSS.........[...].............   ($seq1)
> > SDKIIHLTDDSFDTDVLKADGA[...]EFLDANLA   ($seq2)
> > 
> >      It looks right ( that "[...]" is mine, it's larger ). Now I want to
> >      get
> > 
> > the position of the match ( the first "T" ), which should be "7". I
> > thought I needed to use something like:
> > 
> > my $seq = $aln->get_seq_by_pos(1);
> > my $loc = $seq->location_from_column(1);
> > say $loc;
> > 
> > And $loc would be 7, but it's undef. If I try to iterate from 1 to 10, I
> > start getting Bio::Location::Simple objects at the 8th place. So, should
> > I loop untill I location_from_column() gives me an object? Is it another
> > way of finding the position of the match?
> > 
> > As you can see, I'm just starting with bioinformatics. Any pointer will
> > be appreciated.
> > 
> > Thanks in advance,
> > 
> >   -- Diego
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l


From bosborne11 at verizon.net  Thu Mar 31 09:04:22 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Thu, 31 Mar 2011 09:04:22 -0400
Subject: [Bioperl-l] blast best hit
In-Reply-To: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
References: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
Message-ID: <A29F9EB5-BEC6-4DF3-924F-F8F98F96C6F1@verizon.net>

Boyang,

You can sort the hits, by any criterion you want:

my @hits = $result->hits;
@hits = sort { $a-> bits <=> $b->bits } @hits;

BIO

On Mar 31, 2011, at 8:28 AM, boyang zhe wrote:

> Hi,
> 
> I just want to parse the blast results ,and get the best hit.
> 
> One way is to parse the results as usual, then get the first hit and exit
> the loop.
> 
> I checked the bioperl document, and find that there is a method
> best_hit_only in Bio::SearchIO::blast.pm.
> But it only return 1/0. So my question is how to use this method to get the
> best hit.
> 
> Thank you very much!
> 
> Boyang
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jordi.durban at gmail.com  Thu Mar 31 10:23:54 2011
From: jordi.durban at gmail.com (Jordi Durban)
Date: Thu, 31 Mar 2011 16:23:54 +0200
Subject: [Bioperl-l] blast best hit
In-Reply-To: <A29F9EB5-BEC6-4DF3-924F-F8F98F96C6F1@verizon.net>
References: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
	<A29F9EB5-BEC6-4DF3-924F-F8F98F96C6F1@verizon.net>
Message-ID: <AANLkTimiAanHL89eJ3uKgnGXKbcbJh+jBmw6MRs1VC1t@mail.gmail.com>

Hi,
I did a pair of scripts to parse a blastxml report. I'd like know your
opinion.
First I obtained a file with tab separated results (whatever you want) from
the blast results according to some Bioperl modules as SearchIO. That is:
hit_name    query_name    e-value    score
hit_name    query-name   e-value     score
.
.

Then, I parse that file as an array where:
foreach my $line ($array[0]){ ###### best hit
        next if $seen {$line}++; ##### non-repeated lines
        push @unique , $line[1]; ### best hit outcome in a new array
       }

I hope this helps and I look forward some opinions.






2011/3/31 Brian Osborne <bosborne11 at verizon.net>

> Boyang,
>
> You can sort the hits, by any criterion you want:
>
> my @hits = $result->hits;
> @hits = sort { $a-> bits <=> $b->bits } @hits;
>
> BIO
>
> On Mar 31, 2011, at 8:28 AM, boyang zhe wrote:
>
> > Hi,
> >
> > I just want to parse the blast results ,and get the best hit.
> >
> > One way is to parse the results as usual, then get the first hit and exit
> > the loop.
> >
> > I checked the bioperl document, and find that there is a method
> > best_hit_only in Bio::SearchIO::blast.pm.
> > But it only return 1/0. So my question is how to use this method to get
> the
> > best hit.
> >
> > Thank you very much!
> >
> > Boyang
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Jordi


From fs5 at sanger.ac.uk  Thu Mar 31 10:23:33 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 31 Mar 2011 15:23:33 +0100
Subject: [Bioperl-l] blast best hit
In-Reply-To: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
References: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
Message-ID: <1301581413.12411.188.camel@deskpro15336.internal.sanger.ac.uk>

Yes, best_hit_only is a boolean that can be set to true if you only want
one hit to be returned from the stream of hits (the best hit). I have
never actualyl used this one but you shoud be able to set it in the
constructor as in:
my $blast = Bio::SearchIO->new( ...., -best_hit_only => 1 )



Frank

On Thu, 2011-03-31 at 14:28 +0200, boyang zhe wrote:
> Hi,
> 
> I just want to parse the blast results ,and get the best hit.
> 
> One way is to parse the results as usual, then get the first hit and exit
> the loop.
> 
> I checked the bioperl document, and find that there is a method
> best_hit_only in Bio::SearchIO::blast.pm.
> But it only return 1/0. So my question is how to use this method to get the
> best hit.
> 
> Thank you very much!
> 
> Boyang
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From fs5 at sanger.ac.uk  Thu Mar 31 11:06:41 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 31 Mar 2011 16:06:41 +0100
Subject: [Bioperl-l] blast best hit
In-Reply-To: <AANLkTimXj+D8VQO_Mb4vpgfadXqFfgD1dHQL+fwCMsX5@mail.gmail.com>
References: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
	<1301581413.12411.188.camel@deskpro15336.internal.sanger.ac.uk>
	<AANLkTimXj+D8VQO_Mb4vpgfadXqFfgD1dHQL+fwCMsX5@mail.gmail.com>
Message-ID: <1301584001.12411.202.camel@deskpro15336.internal.sanger.ac.uk>

Hi Boyang,

With best_hit_only set to "true" (as you have done now) you should be
able to use the usual way of parsing the BLAST report with 

while (my $result = $blast_io->next_result) {
  my $hit = $result->next_hit;
  ... (do something with the hit)
}

Because there should be only one hit now. 'best_hit_only' is a flag, an
indicator that tells the parser to limit the output to the best hit. It
does not itself return any hits.

Even if you used the 

while (my $hit=$result->next_hit){..

inner loop (as in the BioPerl HOWTOs) you should now only ever get one
hit retunred from that loop, which is the best hit for the result. I
haven't tried this but it should work.

Personally, I'd not use this option and rather sort or filter the hits
because tomorrow you might want to find out what the next best hit
actually was and how close the e-values and bits were or something like
that. 

Hope this helps,

Frank


On Thu, 2011-03-31 at 16:43 +0200, boyang zhe wrote:
> I try this at the constructor
> 
> my $blast_io = Bio::SearchIO->new(-file => 'test', -format => 'blast',
> -best_hit_only => 1);
> 
> What I need to do in the following steps? It seems that setting
> best_hit_only or not does not change the way of blast parser working.
> 
> In my opinion, if we can use it as a similar way following, it will be
> much better.
> 
> my $blast_io = Bio::SearchIO->new(-file => 'test', -format => 'blast',
> -best_hit_only => 1);
> 
> while (my $blast_result = $blast_io->next_result()) {
>       my $best_hit = $blast_result->best_hit_only();  # just assume it
> working here; in fact, it does not work
>       my $best_hit_name = $best_hit->name();
>       ...................................
> }
> 
> thank you !
> 
> On Thu, Mar 31, 2011 at 4:23 PM, Frank Schwach <fs5 at sanger.ac.uk>
> wrote:
>         Yes, best_hit_only is a boolean that can be set to true if you
>         only want
>         one hit to be returned from the stream of hits (the best hit).
>         I have
>         never actualyl used this one but you shoud be able to set it
>         in the
>         constructor as in:
>         my $blast = Bio::SearchIO->new( ...., -best_hit_only => 1 )
>         
>         
>         
>         Frank
>         
>         
>         On Thu, 2011-03-31 at 14:28 +0200, boyang zhe wrote:
>         > Hi,
>         >
>         > I just want to parse the blast results ,and get the best
>         hit.
>         >
>         > One way is to parse the results as usual, then get the first
>         hit and exit
>         > the loop.
>         >
>         > I checked the bioperl document, and find that there is a
>         method
>         > best_hit_only in Bio::SearchIO::blast.pm.
>         > But it only return 1/0. So my question is how to use this
>         method to get the
>         > best hit.
>         >
>         > Thank you very much!
>         >
>         > Boyang
>         
>         
>         > _______________________________________________
>         > Bioperl-l mailing list
>         > Bioperl-l at lists.open-bio.org
>         > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>         
>         
>         
>         
>         --
>          The Wellcome Trust Sanger Institute is operated by Genome
>         Research
>          Limited, a charity registered in England with number 1021457
>         and a
>          company registered in England with number 2742969, whose
>         registered
>          office is 215 Euston Road, London, NW1 2BE.
> 



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From suy at big.ac.cn  Thu Mar 31 03:24:55 2011
From: suy at big.ac.cn (suy)
Date: Thu, 31 Mar 2011 15:24:55 +0800
Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
Message-ID: <201103311524549534382@big.ac.cn>

I want to use Bio::Tools::HMM, but I can not find it in bioperl 1.6.1. Could anyone tell me how to do it ? 

2011-03-31 



suy 


From cjfields at illinois.edu  Thu Mar 31 13:01:13 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 31 Mar 2011 12:01:13 -0500
Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
In-Reply-To: <201103311524549534382@big.ac.cn>
References: <201103311524549534382@big.ac.cn>
Message-ID: <93E13DE0-5888-4B5C-AC9D-F68623D0D891@illinois.edu>

It's now in it's own distribution, along with the related C code.  See:

https://github.com/bioperl/Bio-Tools-HMM

It hasn't been released to CPAN yet, and (IIRC) it may be failing some tests.

chris

On Mar 31, 2011, at 2:24 AM, suy wrote:

> I want to use Bio::Tools::HMM, but I can not find it in bioperl 1.6.1. Could anyone tell me how to do it ? 
> 
> 2011-03-31 
> 
> 
> 
> suy 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From David.Messina at sbc.su.se  Thu Mar 31 13:07:54 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 31 Mar 2011 19:07:54 +0200
Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
In-Reply-To: <201103311524549534382@big.ac.cn>
References: <201103311524549534382@big.ac.cn>
Message-ID: <AANLkTin2qe1V=2swW1qd8O=s8eQTi5p1LDHc-=sViKPT@mail.gmail.com>

It's distributed separately from BioPerl now. You can get it here:

https://github.com/bioperl/Bio-Tools-HMM


Dave



On Thu, Mar 31, 2011 at 09:24, suy <suy at big.ac.cn> wrote:

> I want to use Bio::Tools::HMM, but I can not find it in bioperl 1.6.1.
> Could anyone tell me how to do it ?
>
> 2011-03-31
>
>
>
> suy
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From Kevin.M.Brown at asu.edu  Thu Mar 31 14:22:06 2011
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Thu, 31 Mar 2011 11:22:06 -0700
Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
In-Reply-To: <201103311524549534382@big.ac.cn>
References: <201103311524549534382@big.ac.cn>
Message-ID: <1A4207F8295607498283FE9E93B775B40781779B@EX02.asurite.ad.asu.edu>

https://github.com/bioperl/Bio-Tools-HMM

"moved Bio::Tools::HMM and Bio::Ext::HMM into their own distro, got them
compiling cleanly. tests not passing yet
svn path=/Bio-Tools-HMM/trunk/; revision=15966"

Kevin Brown
Center for Innovations in Medicine
Biodesign Institute
Arizona State University 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of suy
> Sent: Thursday, March 31, 2011 12:25 AM
> To: bioperl-l
> Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
> 
> I want to use Bio::Tools::HMM, but I can not find it in bioperl 1.6.1.
> Could anyone tell me how to do it ?
> 
> 2011-03-31
> 
> 
> 
> suy
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From David.Messina at sbc.su.se  Thu Mar 31 15:43:14 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 31 Mar 2011 21:43:14 +0200
Subject: [Bioperl-l] Old docs cleanup (was Re: Bioperl installation doubt)
Message-ID: <AANLkTikzx+iP6ws0CpwEEA2USiLwYVHTHjZU8KO+3vMo@mail.gmail.com>

Hi,

Just to clarify:

Brian, is it okay with you if I go ahead and remove the Core/ directory from
the website? (and okay with everyone else, too, for that matter? I haven't
heard any nays so far.)


Dave



On Tue, Mar 29, 2011 at 00:40, Chris Fields <cjfields at illinois.edu> wrote:

> Brian,
>
> I think this was started:
>
> http://www.bioperl.org/wiki/Bptutorial.pl
>
> It certainly could be cleaned up, organized, and updated (that and the
> FAQ).  Makes sense to have it as a HOWTO or maybe split it into several
> HOWTOs.  Maybe even combine it with the beginner's HOWTO into various
> sections?
>
> chris
>
> On Mar 28, 2011, at 3:43 PM, Brian Osborne wrote:
>
> > Chris,
> >
> > I'll get started on dissembling bptutorial. There's certainly useful text
> in there but there's also duplicated or outdated material. Looks like there
> are 3 options for any given section:
> >
> > - put it into an existing HOWTO
> > - make it into a new HOWTO
> > - delete it
> >
> > BIO
> >
> > On Mar 28, 2011, at 9:27 AM, Chris Fields wrote:
> >
> >> Dave,
> >>
> >> +1 on removing old docs to prevent confusion.  Or, alternatively, +1 to
> syncing those to current docs (though I think decreasing the replication
> effort in keeping docs up-to-date is probably the best tact).
> >>
> >> chris
> >>
> >> On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:
> >>
> >>>>
> >>>> Thank you very much. It is working. I got the program code from the
> >>>> following link.
> >>>>
> >>>> http://www.bioperl.org/Core/Latest/bptutorial.html
> >>>
> >>>
> >>> Aha, okay. You got there from Google, I guess? That is *way* out of
> date.
> >>>
> >>> To the other core devs, in order to prevent this confusion in the
> future,
> >>> I'd like to delete the Core/ directory from our website since it's been
> >>> superseded at this point by other docs and is not current. I intend to
> put
> >>> up a ticket at Redmine, but I will wait a bit before doing so to allow
> time
> >>> for people to see this and comment ? please do speak up if there's good
> >>> reason to keep it.
> >>>
> >>>
> >>> Could you please give me the link to join this forum to see other
> >>>> discussions, which would be more helpful to me?
> >>>>
> >>>
> >>> Sure, you can sign up for the mailing list here:
> >>>
> >>> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
> >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>>
> >>> And the archives are also searchable:
> >>>
> >>>  http://news.gmane.org/gmane.comp.lang.perl.bio.general
> >>>
> >>>
> >>> Please let me know if you have any suggestion for me to keep learning
> the
> >>>> bioperl.
> >>>
> >>>
> >>> I would also suggest reading the (current) tutorial and HOWTOs at
> >>> www.bioperl.org . Lots of good links on the main page there,
> particularly
> >>> under the Documentation heading.
> >>>
> >>>
> >>> Dave
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>> With regards,
> >>>> Ravi.
> >>>>
> >>>>
> >>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
> >>>>
> >>>>> Hi Ravi,
> >>>>>
> >>>>> Please make sure to "Reply All" so that everyone on the mailing list
> can
> >>>>> follow (and add to) the discussion.
> >>>>>
> >>>>> If you read the first line of the exception, you'll see it states
> what the
> >>>>> error is:
> >>>>> "WebDBSeqI Error ? check query sequences!"
> >>>>>
> >>>>> You'd have no way of knowing this, but that ID and database
> combination is
> >>>>> not functioning anymore, so that's why in this case you're getting an
> error.
> >>>>> Please try using the example in the tutorial here:
> >>>>>
> >>>>>
> >>>>>
> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
> >>>>>
> >>>>> which has been updated to a different ID which should work.
> >>>>>
> >>>>> Sorry for the confusion! So that we can prevent other people from
> having
> >>>>> the same issue, could you tell me where you got that example code?
> >>>>>
> >>>>> Dave
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
> >>>>>
> >>>>>> Hi Dave,
> >>>>>>
> >>>>>> Thanks a lot for your reply. It is really helpful. Please find the
> >>>>>> screenshot after making the change you pointed out. But I am getting
> >>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
> >>>>>> environment variables but I am not sure how to do that. Could you
> please
> >>>>>> guide me on this too.
> >>>>>>
> >>>>>> I can go to the "Environment Variable" Window in my pc. But I dont
> know
> >>>>>> what to enter once I click "New" on that window.
> >>>>>>
> >>>>>> Thanks in advance.
> >>>>>>
> >>>>>> With regards,
> >>>>>> Ravi.
> >>>>>>
> >>>>>>
> >>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
> >>>>>>
> >>>>>>> Hi Ravi,
> >>>>>>>
> >>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl
> module,
> >>>>>>> not Bio::Seq. So your first line
> >>>>>>>
> >>>>>>> use Bio::Seq;
> >>>>>>>
> >>>>>>> should be replaced with
> >>>>>>>
> >>>>>>> use Bio::Perl;
> >>>>>>>
> >>>>>>>
> >>>>>>> More examples in the BioPerl Tutorial here:
> >>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
> >>>>>>>
> >>>>>>>
> >>>>>>> Dve
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
> >>>>>>>
> >>>>>>>> Hi,
> >>>>>>>>
> >>>>>>>> Could you please help me installing bioperl-db, bioperl-run &
> other
> >>>>>>>> packages
> >>>>>>>> using ppm on windows 7? Please find the attachment for the error
> >>>>>>>> message I
> >>>>>>>> get. I would really appreciate if you help me fix this issue.
> >>>>>>>>
> >>>>>>>> Thanks,
> >>>>>>>>
> >>>>>>>> With regards,
> >>>>>>>> Ravi.
> >>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> Bioperl-l mailing list
> >>>>>>>> Bioperl-l at lists.open-bio.org
> >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>



From cjfields at illinois.edu  Thu Mar 31 15:49:08 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 31 Mar 2011 14:49:08 -0500
Subject: [Bioperl-l] Old docs cleanup (was Re: Bioperl installation
	doubt)
In-Reply-To: <AANLkTikzx+iP6ws0CpwEEA2USiLwYVHTHjZU8KO+3vMo@mail.gmail.com>
References: <AANLkTikzx+iP6ws0CpwEEA2USiLwYVHTHjZU8KO+3vMo@mail.gmail.com>
Message-ID: <1D3D2910-F1F9-40A1-9A39-656D3DF17847@illinois.edu>

+1 from me.  Go ahead.  Old misleading documentation is bad to have around.

chris

On Mar 31, 2011, at 2:43 PM, Dave Messina wrote:

> Hi,
> 
> Just to clarify:
> 
> Brian, is it okay with you if I go ahead and remove the Core/ directory from
> the website? (and okay with everyone else, too, for that matter? I haven't
> heard any nays so far.)
> 
> 
> Dave
> 
> 
> 
> On Tue, Mar 29, 2011 at 00:40, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Brian,
>> 
>> I think this was started:
>> 
>> http://www.bioperl.org/wiki/Bptutorial.pl
>> 
>> It certainly could be cleaned up, organized, and updated (that and the
>> FAQ).  Makes sense to have it as a HOWTO or maybe split it into several
>> HOWTOs.  Maybe even combine it with the beginner's HOWTO into various
>> sections?
>> 
>> chris
>> 
>> On Mar 28, 2011, at 3:43 PM, Brian Osborne wrote:
>> 
>>> Chris,
>>> 
>>> I'll get started on dissembling bptutorial. There's certainly useful text
>> in there but there's also duplicated or outdated material. Looks like there
>> are 3 options for any given section:
>>> 
>>> - put it into an existing HOWTO
>>> - make it into a new HOWTO
>>> - delete it
>>> 
>>> BIO
>>> 
>>> On Mar 28, 2011, at 9:27 AM, Chris Fields wrote:
>>> 
>>>> Dave,
>>>> 
>>>> +1 on removing old docs to prevent confusion.  Or, alternatively, +1 to
>> syncing those to current docs (though I think decreasing the replication
>> effort in keeping docs up-to-date is probably the best tact).
>>>> 
>>>> chris
>>>> 
>>>> On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:
>>>> 
>>>>>> 
>>>>>> Thank you very much. It is working. I got the program code from the
>>>>>> following link.
>>>>>> 
>>>>>> http://www.bioperl.org/Core/Latest/bptutorial.html
>>>>> 
>>>>> 
>>>>> Aha, okay. You got there from Google, I guess? That is *way* out of
>> date.
>>>>> 
>>>>> To the other core devs, in order to prevent this confusion in the
>> future,
>>>>> I'd like to delete the Core/ directory from our website since it's been
>>>>> superseded at this point by other docs and is not current. I intend to
>> put
>>>>> up a ticket at Redmine, but I will wait a bit before doing so to allow
>> time
>>>>> for people to see this and comment ? please do speak up if there's good
>>>>> reason to keep it.
>>>>> 
>>>>> 
>>>>> Could you please give me the link to join this forum to see other
>>>>>> discussions, which would be more helpful to me?
>>>>>> 
>>>>> 
>>>>> Sure, you can sign up for the mailing list here:
>>>>> 
>>>>> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> 
>>>>> 
>>>>> And the archives are also searchable:
>>>>> 
>>>>> http://news.gmane.org/gmane.comp.lang.perl.bio.general
>>>>> 
>>>>> 
>>>>> Please let me know if you have any suggestion for me to keep learning
>> the
>>>>>> bioperl.
>>>>> 
>>>>> 
>>>>> I would also suggest reading the (current) tutorial and HOWTOs at
>>>>> www.bioperl.org . Lots of good links on the main page there,
>> particularly
>>>>> under the Documentation heading.
>>>>> 
>>>>> 
>>>>> Dave
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> With regards,
>>>>>> Ravi.
>>>>>> 
>>>>>> 
>>>>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>>>>>> 
>>>>>>> Hi Ravi,
>>>>>>> 
>>>>>>> Please make sure to "Reply All" so that everyone on the mailing list
>> can
>>>>>>> follow (and add to) the discussion.
>>>>>>> 
>>>>>>> If you read the first line of the exception, you'll see it states
>> what the
>>>>>>> error is:
>>>>>>> "WebDBSeqI Error ? check query sequences!"
>>>>>>> 
>>>>>>> You'd have no way of knowing this, but that ID and database
>> combination is
>>>>>>> not functioning anymore, so that's why in this case you're getting an
>> error.
>>>>>>> Please try using the example in the tutorial here:
>>>>>>> 
>>>>>>> 
>>>>>>> 
>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>>>>>> 
>>>>>>> which has been updated to a different ID which should work.
>>>>>>> 
>>>>>>> Sorry for the confusion! So that we can prevent other people from
>> having
>>>>>>> the same issue, could you tell me where you got that example code?
>>>>>>> 
>>>>>>> Dave
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>>>>>> 
>>>>>>>> Hi Dave,
>>>>>>>> 
>>>>>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>>>>>> screenshot after making the change you pointed out. But I am getting
>>>>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>>>>>> environment variables but I am not sure how to do that. Could you
>> please
>>>>>>>> guide me on this too.
>>>>>>>> 
>>>>>>>> I can go to the "Environment Variable" Window in my pc. But I dont
>> know
>>>>>>>> what to enter once I click "New" on that window.
>>>>>>>> 
>>>>>>>> Thanks in advance.
>>>>>>>> 
>>>>>>>> With regards,
>>>>>>>> Ravi.
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>>>>>> 
>>>>>>>>> Hi Ravi,
>>>>>>>>> 
>>>>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl
>> module,
>>>>>>>>> not Bio::Seq. So your first line
>>>>>>>>> 
>>>>>>>>> use Bio::Seq;
>>>>>>>>> 
>>>>>>>>> should be replaced with
>>>>>>>>> 
>>>>>>>>> use Bio::Perl;
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> More examples in the BioPerl Tutorial here:
>>>>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> Dve
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>>>>>> 
>>>>>>>>>> Hi,
>>>>>>>>>> 
>>>>>>>>>> Could you please help me installing bioperl-db, bioperl-run &
>> other
>>>>>>>>>> packages
>>>>>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>>>>>> message I
>>>>>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>>>>>> 
>>>>>>>>>> Thanks,
>>>>>>>>>> 
>>>>>>>>>> With regards,
>>>>>>>>>> Ravi.
>>>>>>>>>> 
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Bioperl-l mailing list
>>>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From rmb32 at cornell.edu  Thu Mar 31 17:58:52 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 31 Mar 2011 14:58:52 -0700
Subject: [Bioperl-l] Reminder: GSoC proposals due in 1 week
Message-ID: <4D94F91C.1080005@cornell.edu>

Hi all,

Just a reminder, Google Summer of Code student applications are due April 8!

If you're a student planning to apply to GSoC with OBF, it's very much 
in your best interest to write your proposal *early*, like now, and get 
it into the hands of the developers and mentors on your subproject 
(BioPerl/Ruby/Python/etc) so that they can give you some feedback on it.

The final proposals must, of course, still be submitted to Google 
through the GSoC web application, as described on the main GSoC site 
(http://www.google-melange.com/gsoc/homepage/google/gsoc2011).

Rob Buels
OBF GSoC 2011 Administrator




From rmb32 at cornell.edu  Thu Mar 31 18:04:49 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 31 Mar 2011 15:04:49 -0700
Subject: [Bioperl-l] GSoC call for mentors
Message-ID: <4D94FA81.5090701@cornell.edu>

Hi all,

For current developers on OBF projects:

If you would not mind being a mentor to a Summer of Code student this 
summer, please make sure you sign up as an OBF mentor in the GSoC web 
app.  There's a link under "mentors: apply now!" midway down the page at 
http://www.google-melange.com/.  If you didn't do last year's summer of 
code, it would be a good idea to drop me an email introducing yourself, 
as well, or I won't know whether to approve your request. :-)

Being signed up as an OBF GSoC mentor will give you access to the 
student proposals, as they come in, and the ability to comment on them 
and assign scores to the ones you think show the most promise.

If you sign up as a mentor, please also add yourself to the two OBF GSoC 
mailing lists: OBF-GSoC and OBF-GSoC-mentors

OBF-GSoC list: http://lists.open-bio.org/mailman/listinfo/gsoc
OBF mentors:   http://lists.open-bio.org/mailman/listinfo/gsoc-mentors


Thanks in advance!

Rob

---
Robert Buels
OBF GSoC 2011 Administrator



From zuz17 at psu.edu  Thu Mar 31 18:18:59 2011
From: zuz17 at psu.edu (Zhenguo Zhang)
Date: Thu, 31 Mar 2011 18:18:59 -0400
Subject: [Bioperl-l] FW: How to specify color for each feature in a track?
In-Reply-To: 1301604855l.1593384l.0l@psu.edu
References: <1301604855l.1593384l.0l@psu.edu>
Message-ID: <1301609939l.901330l.0l@psu.edu>

Dear Dr. Stein,

Sorry for interruption. I found the problems, I used
$f->get_tag_values('color'); to return the tag value, it is not correct. The
list context should be provided. It is my mistake. Thanks.

Best wishes!

Zhenguo

---------------- Forwarded Message ----------------
From: "Zhenguo Zhang" <zuz17 at psu.edu>
Date: Thu, Mar 31, 2011 04:54 PM
Subject: How to specify color for each feature in a track?
To: lstein at cshl.edu, bioperl-l at lists.open-bio.org

Dear Dr. Stein,

I am using your excellent module Bio::Graphics for
programming to show protein domains. I want to put all the domains for a
sequence into one track, and give each domain (one feature here) one designated
color. The following is the cold to add_track:


 75        
$panel->add_track($seq,
 78                 -glyph    =>  'segments',
 81                 -bgcolor  => sub {
 82                     my $f = shift;
 87                     return $f->get_tag_values('color');
 88                 },
 89                 -fgcolor  => 'black',
 90                 -font2color => 'red',
 91                 -key      => "$seq",
 92                 -label    => 1,
 93                 -bump     => +1,
 94                 -height   => 8,
 95                 -description => 1,
 96 #               -part_label_merge => 1
 97                 );

Here $seq is an array reference, each element being one domain feature. I
specify the -bgcolor based on the tag 'color'  defined when domain feature was
constructed. However, it does not work. All the domains in all sequences show
the same color. Based on the document, the -glyph can be changed by calling
back the anonymous functions (I have not tried this). The color might be
changed in a similar way. Thank you in advance!

Best regards!

Zhenguo

**************************************************************
Zhenguo Zhang
Postdoctoral Scholar
Institute of Molecular Evolutionary Genetics
Penn State University
312 Mueller Lab
University Park, PA 16802
Tel: 814-865-2796
Homepage: <http://www.personal.psu.edu/zuz17/>
Lab page:  <http://homes.bio.psu.edu/people/Faculty/Nei/>




**************************************************************
Zhenguo Zhang
Postdoctoral Scholar
Institute of Molecular Evolutionary Genetics
Penn State University
312 Mueller Lab
University Park, PA 16802
Tel: 814-865-2796
Homepage: <http://www.personal.psu.edu/zuz17/>
Lab page:  <http://homes.bio.psu.edu/people/Faculty/Nei/>





From scott at scottcain.net  Thu Mar 31 19:13:06 2011
From: scott at scottcain.net (Scott Cain)
Date: Thu, 31 Mar 2011 19:13:06 -0400
Subject: [Bioperl-l] git help
Message-ID: <AANLkTin9BRdaSY_p-5rKSCFvpUr+rfCSZ8hjVTgyhxC5@mail.gmail.com>

Hi all,

I just want to know if it is safe for me to commit.  Here is what git
said to me:

scott-cains-macbook-pro:bioperl-live cain$ git commit
# On branch master
# Your branch is behind 'origin/master' by 47 commits, and can be
fast-forwarded.
#
# Changed but not updated:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#	modified:   Bio/DB/GFF.pm
#	modified:   Bio/FeatureIO/gff.pm
#	modified:   scripts/Bio-DB-GFF/bulk_load_gff.PLS
#	modified:   scripts/Bio-DB-GFF/fast_load_gff.PLS
#	modified:   t/SeqFeature/FeatureIO.t
#	modified:   t/data/knownGene.gff3
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#	scripts/Bio-DB-GFF/genbank2gff3.diff
no changes added to commit (use "git add" and/or "git commit -a")
----------------------

so should I do a git commit -a?

Also, when I try a git pull, this is what it tells me:

scott-cains-macbook-pro:bioperl-live cain$ git pull
Updating 1c2cf24..d5de022
error: Your local changes to 'Bio/FeatureIO/gff.pm' would be
overwritten by merge.  Aborting.
Please, commit your changes or stash them before you can merge.

Thanks,
Scott



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From dan.kortschak at adelaide.edu.au  Thu Mar 31 19:24:25 2011
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Fri, 01 Apr 2011 09:54:25 +1030
Subject: [Bioperl-l] BEDTools.pm update
Message-ID: <1301613865.3334.35.camel@sueno>

Hi All,

I have completed a revision of the BEDTools module that makes use of the
v2.10.1 BEDTools additions, including the ability to read GFF and VCF
file formats.

Because of the interactions between CommandExts/Config and the way
BEDTools executables can receive input files, I have had to change the
parameter names for a number of the filespecs from -bed* to -bvg* (for
BED/GFF/VCF). The alternative, though possible was much more involved
for little gain in my view.

This change will break BEDTools.pm-using scripts that use the -bed[12]?
filespecs (except for those wrapping genomeCoverageBed which cannot read
bgv and so which see no change).

I just wanted to get an idea if this is going to be a significant
problem for people before I push the changes to bioperl-run.

cheers
Dan



From scott at scottcain.net  Thu Mar 31 20:19:33 2011
From: scott at scottcain.net (Scott Cain)
Date: Thu, 31 Mar 2011 20:19:33 -0400
Subject: [Bioperl-l] git help
In-Reply-To: <AANLkTin9BRdaSY_p-5rKSCFvpUr+rfCSZ8hjVTgyhxC5@mail.gmail.com>
References: <AANLkTin9BRdaSY_p-5rKSCFvpUr+rfCSZ8hjVTgyhxC5@mail.gmail.com>
Message-ID: <AANLkTimaOpkH1+S3Yn-14uLj+OVy5T=PBH3KGPi6gjnN@mail.gmail.com>

I just went a head and:

  git commit -a
  git pull --rebase
  git push

as suggested by rbuels.  That appeared to work.

Scott


On Thu, Mar 31, 2011 at 7:13 PM, Scott Cain <scott at scottcain.net> wrote:
> Hi all,
>
> I just want to know if it is safe for me to commit. ?Here is what git
> said to me:
>
> scott-cains-macbook-pro:bioperl-live cain$ git commit
> # On branch master
> # Your branch is behind 'origin/master' by 47 commits, and can be
> fast-forwarded.
> #
> # Changed but not updated:
> # ? (use "git add <file>..." to update what will be committed)
> # ? (use "git checkout -- <file>..." to discard changes in working directory)
> #
> # ? ? ? modified: ? Bio/DB/GFF.pm
> # ? ? ? modified: ? Bio/FeatureIO/gff.pm
> # ? ? ? modified: ? scripts/Bio-DB-GFF/bulk_load_gff.PLS
> # ? ? ? modified: ? scripts/Bio-DB-GFF/fast_load_gff.PLS
> # ? ? ? modified: ? t/SeqFeature/FeatureIO.t
> # ? ? ? modified: ? t/data/knownGene.gff3
> #
> # Untracked files:
> # ? (use "git add <file>..." to include in what will be committed)
> #
> # ? ? ? scripts/Bio-DB-GFF/genbank2gff3.diff
> no changes added to commit (use "git add" and/or "git commit -a")
> ----------------------
>
> so should I do a git commit -a?
>
> Also, when I try a git pull, this is what it tells me:
>
> scott-cains-macbook-pro:bioperl-live cain$ git pull
> Updating 1c2cf24..d5de022
> error: Your local changes to 'Bio/FeatureIO/gff.pm' would be
> overwritten by merge. ?Aborting.
> Please, commit your changes or stash them before you can merge.
>
> Thanks,
> Scott
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
> Ontario Institute for Cancer Research
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From cjfields at illinois.edu  Thu Mar 31 20:43:33 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 31 Mar 2011 19:43:33 -0500
Subject: [Bioperl-l] BEDTools.pm update
In-Reply-To: <1301613865.3334.35.camel@sueno>
References: <1301613865.3334.35.camel@sueno>
Message-ID: <557CDC9D-E16D-4DF2-A27A-1DFD7092A926@illinois.edu>

I would say push away, I don't think this will be a problem. 

chris

On Mar 31, 2011, at 6:24 PM, Dan Kortschak wrote:

> Hi All,
> 
> I have completed a revision of the BEDTools module that makes use of the
> v2.10.1 BEDTools additions, including the ability to read GFF and VCF
> file formats.
> 
> Because of the interactions between CommandExts/Config and the way
> BEDTools executables can receive input files, I have had to change the
> parameter names for a number of the filespecs from -bed* to -bvg* (for
> BED/GFF/VCF). The alternative, though possible was much more involved
> for little gain in my view.
> 
> This change will break BEDTools.pm-using scripts that use the -bed[12]?
> filespecs (except for those wrapping genomeCoverageBed which cannot read
> bgv and so which see no change).
> 
> I just wanted to get an idea if this is going to be a significant
> problem for people before I push the changes to bioperl-run.
> 
> cheers
> Dan
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Thu Mar 31 20:44:38 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 31 Mar 2011 19:44:38 -0500
Subject: [Bioperl-l] git help
In-Reply-To: <AANLkTimaOpkH1+S3Yn-14uLj+OVy5T=PBH3KGPi6gjnN@mail.gmail.com>
References: <AANLkTin9BRdaSY_p-5rKSCFvpUr+rfCSZ8hjVTgyhxC5@mail.gmail.com>
	<AANLkTimaOpkH1+S3Yn-14uLj+OVy5T=PBH3KGPi6gjnN@mail.gmail.com>
Message-ID: <27E55B19-4795-4F41-88DC-824CC9A9C3C4@illinois.edu>

Yep, that's generally the way to do it, though you sometimes have to be careful with the '--rebase' if there are changes in the same code (I think git will catch this if it occurs).

chris

On Mar 31, 2011, at 7:19 PM, Scott Cain wrote:

> I just went a head and:
> 
>  git commit -a
>  git pull --rebase
>  git push
> 
> as suggested by rbuels.  That appeared to work.
> 
> Scott
> 
> 
> On Thu, Mar 31, 2011 at 7:13 PM, Scott Cain <scott at scottcain.net> wrote:
>> Hi all,
>> 
>> I just want to know if it is safe for me to commit.  Here is what git
>> said to me:
>> 
>> scott-cains-macbook-pro:bioperl-live cain$ git commit
>> # On branch master
>> # Your branch is behind 'origin/master' by 47 commits, and can be
>> fast-forwarded.
>> #
>> # Changed but not updated:
>> #   (use "git add <file>..." to update what will be committed)
>> #   (use "git checkout -- <file>..." to discard changes in working directory)
>> #
>> #       modified:   Bio/DB/GFF.pm
>> #       modified:   Bio/FeatureIO/gff.pm
>> #       modified:   scripts/Bio-DB-GFF/bulk_load_gff.PLS
>> #       modified:   scripts/Bio-DB-GFF/fast_load_gff.PLS
>> #       modified:   t/SeqFeature/FeatureIO.t
>> #       modified:   t/data/knownGene.gff3
>> #
>> # Untracked files:
>> #   (use "git add <file>..." to include in what will be committed)
>> #
>> #       scripts/Bio-DB-GFF/genbank2gff3.diff
>> no changes added to commit (use "git add" and/or "git commit -a")
>> ----------------------
>> 
>> so should I do a git commit -a?
>> 
>> Also, when I try a git pull, this is what it tells me:
>> 
>> scott-cains-macbook-pro:bioperl-live cain$ git pull
>> Updating 1c2cf24..d5de022
>> error: Your local changes to 'Bio/FeatureIO/gff.pm' would be
>> overwritten by merge.  Aborting.
>> Please, commit your changes or stash them before you can merge.
>> 
>> Thanks,
>> Scott
>> 
>> 
>> 
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Thu Mar 31 20:47:49 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 31 Mar 2011 19:47:49 -0500
Subject: [Bioperl-l] git help
In-Reply-To: <AANLkTimaOpkH1+S3Yn-14uLj+OVy5T=PBH3KGPi6gjnN@mail.gmail.com>
References: <AANLkTin9BRdaSY_p-5rKSCFvpUr+rfCSZ8hjVTgyhxC5@mail.gmail.com>
	<AANLkTimaOpkH1+S3Yn-14uLj+OVy5T=PBH3KGPi6gjnN@mail.gmail.com>
Message-ID: <9E536349-3EA4-43FC-B4C9-665BC81D68F8@illinois.edu>

Also, forgot to mention but we've moved FeatureIO out to it's own repo to reorganize it somewhat, so I'll likely migrate your changes over there.  We're eschewing Bio::SeqFeature::Annotated for simpler features and a few other bits that should allow for more flexibility in the future.  

chris

On Mar 31, 2011, at 7:19 PM, Scott Cain wrote:

> I just went a head and:
> 
>  git commit -a
>  git pull --rebase
>  git push
> 
> as suggested by rbuels.  That appeared to work.
> 
> Scott
> 
> 
> On Thu, Mar 31, 2011 at 7:13 PM, Scott Cain <scott at scottcain.net> wrote:
>> Hi all,
>> 
>> I just want to know if it is safe for me to commit.  Here is what git
>> said to me:
>> 
>> scott-cains-macbook-pro:bioperl-live cain$ git commit
>> # On branch master
>> # Your branch is behind 'origin/master' by 47 commits, and can be
>> fast-forwarded.
>> #
>> # Changed but not updated:
>> #   (use "git add <file>..." to update what will be committed)
>> #   (use "git checkout -- <file>..." to discard changes in working directory)
>> #
>> #       modified:   Bio/DB/GFF.pm
>> #       modified:   Bio/FeatureIO/gff.pm
>> #       modified:   scripts/Bio-DB-GFF/bulk_load_gff.PLS
>> #       modified:   scripts/Bio-DB-GFF/fast_load_gff.PLS
>> #       modified:   t/SeqFeature/FeatureIO.t
>> #       modified:   t/data/knownGene.gff3
>> #
>> # Untracked files:
>> #   (use "git add <file>..." to include in what will be committed)
>> #
>> #       scripts/Bio-DB-GFF/genbank2gff3.diff
>> no changes added to commit (use "git add" and/or "git commit -a")
>> ----------------------
>> 
>> so should I do a git commit -a?
>> 
>> Also, when I try a git pull, this is what it tells me:
>> 
>> scott-cains-macbook-pro:bioperl-live cain$ git pull
>> Updating 1c2cf24..d5de022
>> error: Your local changes to 'Bio/FeatureIO/gff.pm' would be
>> overwritten by merge.  Aborting.
>> Please, commit your changes or stash them before you can merge.
>> 
>> Thanks,
>> Scott
>> 
>> 
>> 
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From armendarez77 at hotmail.com  Thu Mar 31 20:45:11 2011
From: armendarez77 at hotmail.com (Veronica A.)
Date: Thu, 31 Mar 2011 17:45:11 -0700
Subject: [Bioperl-l] StandAloneBlastPlus Question
Message-ID: <BLU156-w251B5A50D1CFF47EE8CA4ED2BE0@phx.gbl>





Hello,

I'm trying to create a Perl script using StandAloneBlastPlus that can either create a new database or update it with new FASTA sequences.  However, I can only find information on the creation of a new database.  I've checked the information on doc.bioperl.org but a lot of the Methods don't have descriptions yet.


Is it possible to use StandAloneBlastPlus or is there another/a better way?

Thank you,

Veronica




 		 	   		  


From zuz17 at psu.edu  Thu Mar 31 16:54:15 2011
From: zuz17 at psu.edu (Zhenguo Zhang)
Date: Thu, 31 Mar 2011 16:54:15 -0400
Subject: [Bioperl-l] How to specify color for each feature in a track?
Message-ID: <1301604855l.1593384l.0l@psu.edu>

Dear Dr. Stein,

I am using your excellent module Bio::Graphics for programming to show protein
domains. I want to put all the domains for a sequence into one track, and give
each domain (one feature here) one designated color. The following is the cold
to add_track: 

 75         $panel->add_track($seq,
 78                 -glyph    =>  'segments',
 81                 -bgcolor  => sub {
 82                     my $f = shift;
 87                     return $f->get_tag_values('color');
 88                 },
 89                 -fgcolor  => 'black',
 90                 -font2color => 'red',
 91                 -key      => "$seq",
 92                 -label    => 1,
 93                 -bump     => +1,
 94                 -height   => 8,
 95                 -description => 1,
 96 #               -part_label_merge => 1
 97                 );

Here $seq is an array reference, each element being one domain feature. I
specify the -bgcolor based on the tag 'color'  defined when domain feature was
constructed. However, it does not work. All the domains in all sequences show
the same color. Based on the document, the -glyph can be changed by calling
back the anonymous functions (I have not tried this). The color might be
changed in a similar way. Thank you in advance!

Best regards!

Zhenguo

**************************************************************
Zhenguo Zhang
Postdoctoral Scholar
Institute of Molecular Evolutionary Genetics
Penn State University
312 Mueller Lab
University Park, PA 16802
Tel: 814-865-2796
Homepage: <http://www.personal.psu.edu/zuz17/>
Lab page:  <http://homes.bio.psu.edu/people/Faculty/Nei/>





From David.Messina at sbc.su.se  Tue Mar  1 09:02:59 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 1 Mar 2011 15:02:59 +0100
Subject: [Bioperl-l] Plans for the next release (and beyond)
In-Reply-To: <11F5BA8C-D4F4-419B-870B-D4B5180F4D7D@illinois.edu>
References: <11F5BA8C-D4F4-419B-870B-D4B5180F4D7D@illinois.edu>
Message-ID: <AANLkTinSR+RwUrvTeyund+CoxDzgEEqrGP0F2RW0_666@mail.gmail.com>

Hi Chris and everyone,

The plans sound great.

My only concern would be on point 3, moving some of the wiki docs into the
distros.

- In what format would the docs be in the distros?

Would it be POD? There is rich markup (URLs, code blocks, syntax coloring,
font sizes, etc) available on the wiki that I'd hate to lose.


- Are there discordant versions now?

I agree that we shouldn't maintain separate versions of these, but I thought
the tutorial had been moved completely to the wiki a while ago, and AFAIK,
the HOWTOs are only present on the wiki. I admit, though, I haven't looked
into this extensively.


- Tying the docs to the version of the code they came with

This could be beneficial if we expect people to have a (good) reason to be
using different (read: OLD) versions of the code. But in practice we're
pretty much always going to recommend people use the latest version, right?
In which case having the docs on the wiki (in sync with the latest, greatest
version) would be fairly practical.

Even if there is a good case for supporting older versions of the code and
docs, I don't know that that's enough of an asset to outweigh the downsides
such as loss of rich formatting and having to have some POD->wiki bridge and
keep it in sync.


I raise all the above mostly to ask for more information on that part of the
plan ? I suspect you've considered most of my concerns already, so I'm quite
open to seeing a different point of view on this.


Dave








3) I would like to work on moving the HOWTO's and other relevant
> documentation (Tutorial) back into the distributions, maybe in a particular
> namespace (Bio::Manual or similar).  The reason is simple: maintaining
> possibly discordant versions of documentation is unsustainable.  We could
> possibly set up a way of converting POD->wiki for on-line documentation, but
> I would like the documentation be tied to the version of the code it comes
> with, and the only easy way to do so is to package them all together.
>



From awitney at sgul.ac.uk  Tue Mar  1 12:08:12 2011
From: awitney at sgul.ac.uk (Adam Witney)
Date: Tue, 1 Mar 2011 17:08:12 +0000
Subject: [Bioperl-l] building NGS pipeline
In-Reply-To: <0FF71A5D-F5F6-4AAD-9501-4F4911DB40D8@illinois.edu>
References: <86D567CE-1735-4D85-B40F-B67823749FB7@sgul.ac.uk>
	<AANLkTi=eU0f=GuHE=zLfLoc5LhaiHBG_A2mjmMybQeNH@mail.gmail.com>
	<0FF71A5D-F5F6-4AAD-9501-4F4911DB40D8@illinois.edu>
Message-ID: <066A6A2B-05F7-4523-8A22-A91209953BB7@sgul.ac.uk>


On 28 Feb 2011, at 15:03, Chris Fields wrote:

> On Feb 28, 2011, at 6:04 AM, Sean Davis wrote:
> 
>> On Mon, Feb 28, 2011 at 6:06 AM, Adam Witney <awitney at sgul.ac.uk> wrote:
>> 
>>> Hi,
>>> 
>>> I'm trying to put together a set of steps to runs some analysis on NGS data
>>> we have. I have found modules that wrap alignment software such as
>>> bowtie/bwa/maq, but are there any packages to calculate RPKM's etc? what are
>>> people using for this?
>>> 
>>> 
>> scripture, cufflinks/cuffdiff, bioconductor (GenomicFeatures package, for
>> example), ERANGE (wold lab), and several others.  I don't know of perl
>> wrappers for these, but they are all command-line applications, generally
>> speaking.
>> 
>> This is an interesting site to follow for RNA-seq analysis and applications:
>> 
>> http://rna-seqblog.com/
>> 
>> Sean
> 
> BioPerl does have wrappers and interfaces for some packages, particularly Lincoln's Bio::DB::Sam (samtools package) and wrappers for bowtie, tophat, and bwa.  Locally, for comparative gene expression analyses we use bioconductor (many packages to choose from) as well as the command-line tools Sean mentions.
> 
> chris 

Thanks Sean, Chris,

the bowtie/tophat/cufflinks set of tools seem to work well. I have also come across myrna also but I am still getting that setup.

Thanks again

adam




From cjfields at illinois.edu  Tue Mar  1 12:37:29 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 1 Mar 2011 11:37:29 -0600
Subject: [Bioperl-l] Plans for the next release (and beyond)
In-Reply-To: <AANLkTinSR+RwUrvTeyund+CoxDzgEEqrGP0F2RW0_666@mail.gmail.com>
References: <11F5BA8C-D4F4-419B-870B-D4B5180F4D7D@illinois.edu>
	<AANLkTinSR+RwUrvTeyund+CoxDzgEEqrGP0F2RW0_666@mail.gmail.com>
Message-ID: <90D9611F-0DFA-43A6-A3C4-65948DF3F071@illinois.edu>

On Mar 1, 2011, at 8:02 AM, Dave Messina wrote:

> Hi Chris and everyone,
> 
> The plans sound great.
> 
> My only concern would be on point 3, moving some of the wiki docs into the distros.
> 
> - In what format would the docs be in the distros?
> 
> Would it be POD? There is rich markup (URLs, code blocks, syntax coloring, font sizes, etc) available on the wiki that I'd hate to lose.

It would very likely be POD, though I believe there are POD extensions for adding additional markup in CPAN.  We wouldn't necessarily lose the wiki HOWTOs, but they would be only editable via changes to the official docs in github.  My thought is to have wiki pages tied to the latest version in github via POD->wiki, with additional markup added in for syntax highlighting, etc.  Lots of CPAN modules that could help with this, but it needs further investigation.  Might need a HOWTO unto itself :)

One other point: inclusion of docs may also allow easier implementation of inline testing, where synopsis or HOWTO code can be directly tested from POD when specific directives allow for it.  I believe Dist::Zilla has plugins for this, and of course there is Test::Inline:

http://search.cpan.org/dist/Test-Inline/lib/Test/Inline.pm

This pushes the developers a bit to make sure code examples actually pass tests.  In particular I have thought about using this with the eutils cookbook, just to catch any changes on NCBI's end, but then realized it's broadly applicable to other areas as well.  

> - Are there discordant versions now?
> 
> I agree that we shouldn't maintain separate versions of these, but I thought the tutorial had been moved completely to the wiki a while ago, and AFAIK, the HOWTOs are only present on the wiki. I admit, though, I haven't looked into this extensively.

The original intent on moving docs to the wiki was somewhat correct: we wanted dynamic documentation that could be marked up for easier reading, better annotation, etc.  Wiki markup and templates has proved more useful than simple POD (HOWTO for Bio::Graphics, for example).  

However, at least to me there seems to be a fundamental disconnect between the code being developed in one repository (github) and the documentation being maintained elsewhere (wiki).  In many cases, once docs are placed on the wiki they seem to be largely forgotten by the devs once they have reached 'completeness'.  Our focus tends to be the code itself, not the documentation.  I'm basically looking for ways to resolve that and have documentation evolve along with the code, if possible making it testable.

Lastly, access to critical documentation is now reliant on access to the wiki, which may not always be possible.  We've had several wiki outages over the years and have recently talked about (off-list) migrating some resource away from open bio servers, wikis being one due to maintenance overhead and spam.  We'll always have a centralized website of some sort, I just want to make sure that one has means to access good documentation all the time.  Installing it with the code seems the best way currently, but I'm open to suggestions.

> - Tying the docs to the version of the code they came with
> 
> This could be beneficial if we expect people to have a (good) reason to be using different (read: OLD) versions of the code. But in practice we're pretty much always going to recommend people use the latest version, right? In which case having the docs on the wiki (in sync with the latest, greatest version) would be fairly practical.

Right, I agree, and I believe the wikis should only contain a very specific version of the docs, probably either the latest CPAN release or master.  However, I'm thinking of cases where users might not be able to get the latest/greatest, perhaps b/c they are constrained in using a specific version: with Ensembl (v. 1.2.3) or via sysadmin restrictions. 

If we consistently point to the official documentation as being on the wiki, we're not tying it to any specific version (unless it's explicitly stated), only what should work with the current version.    The only history is via the edits on the wiki page, which is not associated with anything, just the edits made.  

We should be able to demonstrate via tests that code and examples released with a specific version of BioPerl, including those in the HOWTOs and the tutorial, should work with that version of the software; anything else is a documentation error or a bug.  We can't do that currently.

> Even if there is a good case for supporting older versions of the code and docs, I don't know that that's enough of an asset to outweigh the downsides such as loss of rich formatting and having to have some POD->wiki bridge and keep it in sync.

The actual process of including documentation with the code works as the archival process itself (v 1.7 docs go with v 1.7 code, v 2 with v2 code, etc).  And I think there are ways around the lack of rich formatting with POD, just need to look into it more.

> I raise all the above mostly to ask for more information on that part of the plan ? I suspect you've considered most of my concerns already, so I'm quite open to seeing a different point of view on this.
> 
> 
> Dave

I've thought about it (as you can probably tell) but I think thought is needed about how to approach it.  It might require testing things out a bit first.

chris




From moitrayee at mbu.iisc.ernet.in  Tue Mar  1 06:22:54 2011
From: moitrayee at mbu.iisc.ernet.in (moitrayee at mbu.iisc.ernet.in)
Date: Tue, 1 Mar 2011 16:52:54 +0530 (IST)
Subject: [Bioperl-l] clustering trees obtained from phylip neighbor
Message-ID: <57675.10.128.10.17.1298978574.squirrel@mbu.iisc.ernet.in>

Dear BioPerl Users/Developers,

I have obtained a tree using a very large number of nodes
(1000 nodes) using the neighbor joining in PHYLIP. A small
test output looks like the following:

  +------------------------------------------------Bovine
--6
  !    +-------------------------------------------Mouse
  +----5
       !                        +------------------Gibbon
       +------------------------4
                                !    +-------------Orang
                                +----3
                                     !   +---------Gorilla
                                     +---2
                                         ! +-------Chimp
                                         +-1
                                           +-------Human

The outtree in Newick format is:

(Bovine:0.81551,(Mouse:0.73556,(Gibbon:0.31044,(Orang:0.24003,
(Gorilla:0.16418,(Chimp:0.13460,Human:0.13460):0.02958):0.07586):0.07040):0.42512):0.07995);


I am trying to obtain the cluster at different fork level of this tree.

The fork level goes as an user input. I looked into the link

http://www.bioperl.org/wiki/HOWTO:Trees#Related_Modules

But the Node connectivity methods described there does not apply
to the tree I have pasted above.

Any help / suggestions would be thankfully appreciated.

Thanks a lot in advance and looking forward to hear from you.

Sincere Regards,
Moitrayee Bhattacharyya
Molecular Biophysics Unit,
Indian Institute of Science
Bangalore-560012
India



-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.



From lskatz at gmail.com  Wed Mar  2 09:32:24 2011
From: lskatz at gmail.com (Lee Katz)
Date: Wed, 2 Mar 2011 09:32:24 -0500
Subject: [Bioperl-l] GuessSeqFormat
Message-ID: <AANLkTi=Aa=a-gs4shAM3yxk7w=h5MVqPy0VKKhLYoDah@mail.gmail.com>

Hi,
I noticed that even though there is a GuessSeqFormat module, SeqIO and
probably other modules first rely on the extension of a filename rather than
the content.  Could the behavior be altered so that it first checks the
content of the file, and if it turns up nothing then check the file
extension?


From daniel.standage at gmail.com  Wed Mar  2 11:01:12 2011
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 2 Mar 2011 10:01:12 -0600
Subject: [Bioperl-l] BioPerl POD
Message-ID: <AANLkTi=tfUzD78O-mA0tq84sFrtsCnaN4ZYD7Y0T+xnk@mail.gmail.com>

BioPerl,

I've been writing Perl (and BioPerl) for several years now, but I have
little to know experience using POD. I've added some POD to a module I wrote
and now I am trying to create an HTML page from it. I was able to do so with
*pod2html*, but the output is...underwhelming. The docs at
http://doc.bioperl.org aren't the essence of beauty themselves, but they do
have a bit of color and really nice features (like links to the code, etc).

Which tool(s) was/were used to generate the BioPerl HTML docs?

--
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University


From cjfields at illinois.edu  Wed Mar  2 11:26:58 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 2 Mar 2011 10:26:58 -0600
Subject: [Bioperl-l] GuessSeqFormat
In-Reply-To: <AANLkTi=Aa=a-gs4shAM3yxk7w=h5MVqPy0VKKhLYoDah@mail.gmail.com>
References: <AANLkTi=Aa=a-gs4shAM3yxk7w=h5MVqPy0VKKhLYoDah@mail.gmail.com>
Message-ID: <4F41B8DA-93D6-4442-95DC-D0EA24322351@illinois.edu>

On Mar 2, 2011, at 8:32 AM, Lee Katz wrote:

> Hi,
> I noticed that even though there is a GuessSeqFormat module, SeqIO and
> probably other modules first rely on the extension of a filename rather than
> the content.  Could the behavior be altered so that it first checks the
> content of the file, and if it turns up nothing then check the file
> extension?

The current behavior is the most common use case; stipulating the format with the file extension is pretty common and a surer way to get the correct format beyond explicitly setting it.  

If you want the opposite you can manually run the file through GuessSeqFormat and then (using the guess) use SeqIO with the guessed format, but I'm curious as to why you would want this behavior.  If it's for validation, I would highly recommend NOT using that module for validation purposes...

chris




From cjfields at illinois.edu  Wed Mar  2 11:40:22 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 2 Mar 2011 10:40:22 -0600
Subject: [Bioperl-l] BioPerl POD
In-Reply-To: <AANLkTi=tfUzD78O-mA0tq84sFrtsCnaN4ZYD7Y0T+xnk@mail.gmail.com>
References: <AANLkTi=tfUzD78O-mA0tq84sFrtsCnaN4ZYD7Y0T+xnk@mail.gmail.com>
Message-ID: <26289423-6B39-418C-B16B-1CECA73B5983@illinois.edu>

pdoc, I believe, is used for the doc.bioperl.org site:

http://pdoc.sourceforge.net/

Most POD->HTML converters are simple for a reason, sites generally use CSS to deal with formatting.  You could get around that with a few tools that embed the formatting with the HTML elements (see below link for examples), but I highly suggest using CSS if possible.  

Here's a stackoverflow article on the search.cpan.org HTML output:

http://stackoverflow.com/questions/4996684/modern-pod-to-html-converter-to-produce-results-like-search-cpan-org

Also, ActiveState has another one that generates their custom HTML (pretty nice), it comes with their perl dist I think.

chris

On Mar 2, 2011, at 10:01 AM, Daniel Standage wrote:

> BioPerl,
> 
> I've been writing Perl (and BioPerl) for several years now, but I have
> little to know experience using POD. I've added some POD to a module I wrote
> and now I am trying to create an HTML page from it. I was able to do so with
> *pod2html*, but the output is...underwhelming. The docs at
> http://doc.bioperl.org aren't the essence of beauty themselves, but they do
> have a bit of color and really nice features (like links to the code, etc).
> 
> Which tool(s) was/were used to generate the BioPerl HTML docs?
> 
> --
> Daniel S. Standage
> Graduate Research Assistant
> Bioinformatics and Computational Biology Program
> Iowa State University
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From lskatz at gmail.com  Wed Mar  2 11:53:52 2011
From: lskatz at gmail.com (Lee Katz)
Date: Wed, 2 Mar 2011 11:53:52 -0500
Subject: [Bioperl-l] GuessSeqFormat
In-Reply-To: <4F41B8DA-93D6-4442-95DC-D0EA24322351@illinois.edu>
References: <AANLkTi=Aa=a-gs4shAM3yxk7w=h5MVqPy0VKKhLYoDah@mail.gmail.com>
	<4F41B8DA-93D6-4442-95DC-D0EA24322351@illinois.edu>
Message-ID: <AANLkTimNeG4+n21mAVQfN3PS10snVStD6WTwAqT1EMhm@mail.gmail.com>

>
> The current behavior is the most common use case; stipulating the format
> with the file extension is pretty common and a surer way to get the correct
> format beyond explicitly setting it.
>
> If you want the opposite you can manually run the file through
> GuessSeqFormat and then (using the guess) use SeqIO with the guessed format,
> but I'm curious as to why you would want this behavior.  If it's for
> validation, I would highly recommend NOT using that module for validation
> purposes...
>
> chris
>


I understand your reasoning that checking a file extension is almost like a
user setting for providing the correct format.  Also I understand that I can
use the guessing module to discover the format on my own if I should choose
to do so.

However for your curiosity I'll try to explain why I would want this.
 Occasionally I get an error that I gave the wrong format for an input file.
 This could be quickly remedied by BioPerl figuring out the format by the
contents of the file rather than the extension.

Although now that I think about it--perhaps it is not a very fast method for
discovering the format and that it only looks at the first numbers of lines
before making a decision.  This would make it error-prone and slow I
suppose.


From daniel.standage at gmail.com  Wed Mar  2 11:55:46 2011
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 2 Mar 2011 10:55:46 -0600
Subject: [Bioperl-l] BioPerl POD
In-Reply-To: <26289423-6B39-418C-B16B-1CECA73B5983@illinois.edu>
References: <AANLkTi=tfUzD78O-mA0tq84sFrtsCnaN4ZYD7Y0T+xnk@mail.gmail.com>
	<26289423-6B39-418C-B16B-1CECA73B5983@illinois.edu>
Message-ID: <AANLkTikyhzULFY9foc5rOQ4yxMEpwS-4=RxFSBjfSioD@mail.gmail.com>

Great! Thanks!

--
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University



On Wed, Mar 2, 2011 at 10:40 AM, Chris Fields <cjfields at illinois.edu> wrote:

> pdoc, I believe, is used for the doc.bioperl.org site:
>
> http://pdoc.sourceforge.net/
>
> Most POD->HTML converters are simple for a reason, sites generally use CSS
> to deal with formatting.  You could get around that with a few tools that
> embed the formatting with the HTML elements (see below link for examples),
> but I highly suggest using CSS if possible.
>
> Here's a stackoverflow article on the search.cpan.org HTML output:
>
>
> http://stackoverflow.com/questions/4996684/modern-pod-to-html-converter-to-produce-results-like-search-cpan-org
>
> Also, ActiveState has another one that generates their custom HTML (pretty
> nice), it comes with their perl dist I think.
>
> chris
>
> On Mar 2, 2011, at 10:01 AM, Daniel Standage wrote:
>
> > BioPerl,
> >
> > I've been writing Perl (and BioPerl) for several years now, but I have
> > little to know experience using POD. I've added some POD to a module I
> wrote
> > and now I am trying to create an HTML page from it. I was able to do so
> with
> > *pod2html*, but the output is...underwhelming. The docs at
> > http://doc.bioperl.org aren't the essence of beauty themselves, but they
> do
> > have a bit of color and really nice features (like links to the code,
> etc).
> >
> > Which tool(s) was/were used to generate the BioPerl HTML docs?
> >
> > --
> > Daniel S. Standage
> > Graduate Research Assistant
> > Bioinformatics and Computational Biology Program
> > Iowa State University
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From roy.chaudhuri at gmail.com  Wed Mar  2 13:06:48 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Wed, 02 Mar 2011 18:06:48 +0000
Subject: [Bioperl-l] clustering trees obtained from phylip neighbor
In-Reply-To: <57675.10.128.10.17.1298978574.squirrel@mbu.iisc.ernet.in>
References: <57675.10.128.10.17.1298978574.squirrel@mbu.iisc.ernet.in>
Message-ID: <4D6E8738.7010103@gmail.com>

Hi Moitrayee,

I know a fair amount about phylogenetics, but I have no idea what you 
mean by the "fork level" of a tree. Perhaps you could use your example 
tree to explain what input you want the user to specify, and what output 
you want to produce?

Roy.

On 01/03/2011 11:22, moitrayee at mbu.iisc.ernet.in wrote:
> Dear BioPerl Users/Developers,
>
> I have obtained a tree using a very large number of nodes
> (1000 nodes) using the neighbor joining in PHYLIP. A small
> test output looks like the following:
>
>    +------------------------------------------------Bovine
> --6
>    !    +-------------------------------------------Mouse
>    +----5
>         !                        +------------------Gibbon
>         +------------------------4
>                                  !    +-------------Orang
>                                  +----3
>                                       !   +---------Gorilla
>                                       +---2
>                                           ! +-------Chimp
>                                           +-1
>                                             +-------Human
>
> The outtree in Newick format is:
>
> (Bovine:0.81551,(Mouse:0.73556,(Gibbon:0.31044,(Orang:0.24003,
> (Gorilla:0.16418,(Chimp:0.13460,Human:0.13460):0.02958):0.07586):0.07040):0.42512):0.07995);
>
>
> I am trying to obtain the cluster at different fork level of this tree.
>
> The fork level goes as an user input. I looked into the link
>
> http://www.bioperl.org/wiki/HOWTO:Trees#Related_Modules
>
> But the Node connectivity methods described there does not apply
> to the tree I have pasted above.
>
> Any help / suggestions would be thankfully appreciated.
>
> Thanks a lot in advance and looking forward to hear from you.
>
> Sincere Regards,
> Moitrayee Bhattacharyya
> Molecular Biophysics Unit,
> Indian Institute of Science
> Bangalore-560012
> India
>
>
>



From David.Messina at sbc.su.se  Thu Mar  3 10:52:44 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 3 Mar 2011 16:52:44 +0100
Subject: [Bioperl-l] Plans for the next release (and beyond)
In-Reply-To: <90D9611F-0DFA-43A6-A3C4-65948DF3F071@illinois.edu>
References: <11F5BA8C-D4F4-419B-870B-D4B5180F4D7D@illinois.edu>
	<AANLkTinSR+RwUrvTeyund+CoxDzgEEqrGP0F2RW0_666@mail.gmail.com>
	<90D9611F-0DFA-43A6-A3C4-65948DF3F071@illinois.edu>
Message-ID: <AANLkTikiWXv9yhVDYiPcAZ9D_12=d5TrKWcCMvsir0P4@mail.gmail.com>

Thanks, Chris.


> [re inline testing]
>


> This pushes the developers a bit to make sure code examples actually pass
> tests.  In particular I have thought about using this with the eutils
> cookbook, just to catch any changes on NCBI's end, but then realized it's
> broadly applicable to other areas as well.


This is a great idea, and goes well with the docs being version controlled
(your point below) along with the code itself.



> However, at least to me there seems to be a fundamental disconnect between
> the code being developed in one repository (github) and the documentation
> being maintained elsewhere (wiki).  In many cases, once docs are placed on
> the wiki they seem to be largely forgotten by the devs once they have
> reached 'completeness'.  Our focus tends to be the code itself, not the
> documentation.  I'm basically looking for ways to resolve that and have
> documentation evolve along with the code, if possible making it testable.
>

Yes, I can't argue. This has been a problem.



>   We should be able to demonstrate via tests that code and examples
> released with a specific version of BioPerl, including those in the HOWTOs
> and the tutorial, should work with that version of the software; anything
> else is a documentation error or a bug.  We can't do that currently.


That would be great.

In the end I'd have to say correct, up-to-date, and testable documentation
is the most important thing. Hopefully, we can find a way to keep the
readability/usability high ? which I think pretty much requires richer
formatting ? at the same time. Certainly worth trying in any case!


Dave



From p.j.a.cock at googlemail.com  Thu Mar  3 15:35:29 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 3 Mar 2011 20:35:29 +0000
Subject: [Bioperl-l] Fwd: [Bosc] Bioinformatics Open Source Conference (BOSC
 2011)--Call for Abstracts
In-Reply-To: <3922D2BE-5A99-4CDE-91AB-B311C42E10CE@lbl.gov>
References: <3922D2BE-5A99-4CDE-91AB-B311C42E10CE@lbl.gov>
Message-ID: <AANLkTinwgazvb5WPV-tiS41tO8wVkQ65NT0m75TPUVVw@mail.gmail.com>

Dear all,

I hope some of you will consider coming to BOSC 2011 in Vienna, and
maybe even submitting a talk or poster abstract.

Thank you,

Peter
(Biopython)


---------- Forwarded message ----------
From: Nomi Harris <nlharris at lbl.gov>
Date: Thu, Mar 3, 2011 at 7:37 PM
Subject: [Bosc] Bioinformatics Open Source Conference (BOSC
2011)--Call for Abstracts
To: bosc-announce at lists.open-bio.org, members at open-bio.org, GMOD
Announcements List <gmod-announce at lists.sourceforge.net>, GMOD
Developers List <gmod-devel at lists.sourceforge.net>
Cc: Nomi Harris <nlharris at lbl.gov>


We invite you to submit an abstract to BOSC 2011! ?Please forward this
message as appropriate, and forgive multiple postings.

Call for Abstracts for the 12th Annual Bioinformatics Open Source
Conference (BOSC 2011)
An ISMB 2011 Special Interest Group (SIG)

Dates: July 15-16, 2011
Location: Vienna, Austria
Web site: http://www.open-bio.org/wiki/BOSC_2011
Email: bosc at open-bio.org
BOSC announcements mailing list:
http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:
April 18, 2011: Deadline for submitting abstracts to BOSC 2011
May 9, 2011: Notifications of accepted abstracts emailed to
corresponding authors
July 13-14, 2011: Codefest 2011 programming session (see
http://www.open-bio.org/wiki/Codefest_2011 for details)
July 15-16, 2011: BOSC 2011
July 17-19, 2011: ISMB 2011

The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.

We invite you to submit abstracts for talks and posters. ?Sessions include:
- Approaches to parallel processing
- Cloud-based approaches to improving software and data accessibility
- The Semantic Web in open source bioinformatics
- Data visualization
- Tools for next-generation sequencing
- Other Open Source software

In addition to the above sessions, there will be a panel discussion
about "Meeting the challenges of inter-institutional collaboration".
We are also working to arrange a joint session with one of the other
ISMB SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student
Travel Awards for BOSC 2011. Each winner will be awarded $250 to
defray the costs of travel to BOSC 2011.

For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee:
Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock,
Erwin Frise, Darin London, Ron Taylor


_______________________________________________
BOSC mailing list
BOSC at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bosc



From sac at bioperl.org  Thu Mar  3 16:45:27 2011
From: sac at bioperl.org (Steve Chervitz)
Date: Thu, 3 Mar 2011 13:45:27 -0800
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
Message-ID: <AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>

Good catch, Elia. Looks like an legitimate edge case. Your fix looks
reasonable to me, but I haven't tried running it through the regression
tests to see if it breaks anything else.

Would be good to get this fix into the upcoming release.

Cheers,
Steve


On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:

> Hi Steve and Rob,
>
> it's been sometime since I last plunged my head into the code, but today we
> nailed a bug in Bio::Restriction::Analysis.
>
> Basically if a sequence has a restriction site which is exactly at the
> start of the sequence, it fails to produce any sites. The  culprits is this
> line (536 of Analysis.pm)
>
> unless ($cut_positions[0]) {
>
> where if the position is zero, it will fail to execute the rest of the
> code, so I changed it to:
>
> unless (defined($cut_positions[0])) {
>
> Also, for similar reasons a bit further down this line:
>
> my $start=1; my $stop; my %seq; my %stop;
>
> needs to change to:
> my $start=0; my $stop; my %seq; my %stop;
>
> I didn't commit the changes because I wanted to check if it makes sense,
> etc.
>
> The bug seems reproducible also in older, stable versions of bioperl, such
> as 1.4 and 1.6...
>
> best
>
> Elia
>
>
>
> ---
> Scientific Director - Bioinformatics, UCL Genomics
> Senior Lecturer, Bioinformatics
>
> UCL Cancer Institute
> Paul O' Gorman Building
> University College London
> 72, Huntley Street
> WC1E 6BT
> London
> UK
>
> Institute of Cell and Molecular Science
> Barts and The London School of Medicine and Dentistry
> 4 Newark Street
> Whitechapel
> London
> E1 2AT
>
> Office (UCL): +44 207 679 6493
> Fax: +44 0207 6796817
> Office (ICMS): +44 0207 8822374
>
> Mobile: +44 787 6478912
>
>
>
>
-- 
Steve Chervitz, Ph.D.
Omicia Inc. |  Senior Computational Biologist
2200 Powell Street, Ste 525, Emeryville CA 94608
T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com

Omicia.com: Unlocking Individualized Medicine.


From cjfields at illinois.edu  Thu Mar  3 17:42:41 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 3 Mar 2011 16:42:41 -0600
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
Message-ID: <E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>

Elia, Steve,

Any tests we can add for this?  I ran tests with the changes below and had several failing ones, but when only implementing the first fix ('unless (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate issue (string-based positions are 0-based, bioperl coords are 1-based).

chris

On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:

> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
> reasonable to me, but I haven't tried running it through the regression
> tests to see if it breaks anything else.
> 
> Would be good to get this fix into the upcoming release.
> 
> Cheers,
> Steve
> 
> 
> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
> 
>> Hi Steve and Rob,
>> 
>> it's been sometime since I last plunged my head into the code, but today we
>> nailed a bug in Bio::Restriction::Analysis.
>> 
>> Basically if a sequence has a restriction site which is exactly at the
>> start of the sequence, it fails to produce any sites. The  culprits is this
>> line (536 of Analysis.pm)
>> 
>> unless ($cut_positions[0]) {
>> 
>> where if the position is zero, it will fail to execute the rest of the
>> code, so I changed it to:
>> 
>> unless (defined($cut_positions[0])) {
>> 
>> Also, for similar reasons a bit further down this line:
>> 
>> my $start=1; my $stop; my %seq; my %stop;
>> 
>> needs to change to:
>> my $start=0; my $stop; my %seq; my %stop;
>> 
>> I didn't commit the changes because I wanted to check if it makes sense,
>> etc.
>> 
>> The bug seems reproducible also in older, stable versions of bioperl, such
>> as 1.4 and 1.6...
>> 
>> best
>> 
>> Elia
>> 
>> 
>> 
>> ---
>> Scientific Director - Bioinformatics, UCL Genomics
>> Senior Lecturer, Bioinformatics
>> 
>> UCL Cancer Institute
>> Paul O' Gorman Building
>> University College London
>> 72, Huntley Street
>> WC1E 6BT
>> London
>> UK
>> 
>> Institute of Cell and Molecular Science
>> Barts and The London School of Medicine and Dentistry
>> 4 Newark Street
>> Whitechapel
>> London
>> E1 2AT
>> 
>> Office (UCL): +44 207 679 6493
>> Fax: +44 0207 6796817
>> Office (ICMS): +44 0207 8822374
>> 
>> Mobile: +44 787 6478912
>> 
>> 
>> 
>> 
> -- 
> Steve Chervitz, Ph.D.
> Omicia Inc. |  Senior Computational Biologist
> 2200 Powell Street, Ste 525, Emeryville CA 94608
> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
> 
> Omicia.com: Unlocking Individualized Medicine.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Thu Mar  3 17:57:57 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 3 Mar 2011 16:57:57 -0600
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
	<E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
Message-ID: <CADBF252-9F51-4C7C-8062-C98B0E8E3B13@illinois.edu>

Forgot to add the summary, just for completeness. lots of errors like this that are halting tests:

------------- EXCEPTION -------------
MSG: Bad start parameter (0). Start must be positive.
STACK Bio::PrimarySeq::subseq /Users/cjfields/bioperl/bioperl-live/blib/lib/Bio/PrimarySeq.pm:400
STACK Bio::Restriction::Analysis::fragment_maps Bio/Restriction/Analysis.pm:556
STACK toplevel t/Restriction/Analysis-refac.t:143
-------------------------------------

Test Summary Report
-------------------
t/Restriction/Analysis-refac.t (Wstat: 65280 Tests: 26 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 91 tests but ran 26.
t/Restriction/Analysis.t      (Wstat: 65280 Tests: 118 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 177 tests but ran 118.
t/Restriction/Gel.t           (Wstat: 65280 Tests: 3 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 9 tests but ran 3.
Files=4, Tests=165, 29 wallclock secs ( 0.05 usr  0.03 sys +  3.44 cusr  0.21 csys =  3.73 CPU)
Result: FAIL
Failed 3/4 test programs. 0/165 subtests failed.

-c

On Mar 3, 2011, at 4:42 PM, Chris Fields wrote:

> Elia, Steve,
> 
> Any tests we can add for this?  I ran tests with the changes below and had several failing ones, but when only implementing the first fix ('unless (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate issue (string-based positions are 0-based, bioperl coords are 1-based).
> 
> chris
> 
> On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:
> 
>> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
>> reasonable to me, but I haven't tried running it through the regression
>> tests to see if it breaks anything else.
>> 
>> Would be good to get this fix into the upcoming release.
>> 
>> Cheers,
>> Steve
>> 
>> 
>> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
>> 
>>> Hi Steve and Rob,
>>> 
>>> it's been sometime since I last plunged my head into the code, but today we
>>> nailed a bug in Bio::Restriction::Analysis.
>>> 
>>> Basically if a sequence has a restriction site which is exactly at the
>>> start of the sequence, it fails to produce any sites. The  culprits is this
>>> line (536 of Analysis.pm)
>>> 
>>> unless ($cut_positions[0]) {
>>> 
>>> where if the position is zero, it will fail to execute the rest of the
>>> code, so I changed it to:
>>> 
>>> unless (defined($cut_positions[0])) {
>>> 
>>> Also, for similar reasons a bit further down this line:
>>> 
>>> my $start=1; my $stop; my %seq; my %stop;
>>> 
>>> needs to change to:
>>> my $start=0; my $stop; my %seq; my %stop;
>>> 
>>> I didn't commit the changes because I wanted to check if it makes sense,
>>> etc.
>>> 
>>> The bug seems reproducible also in older, stable versions of bioperl, such
>>> as 1.4 and 1.6...
>>> 
>>> best
>>> 
>>> Elia
>>> 
>>> 
>>> 
>>> ---
>>> Scientific Director - Bioinformatics, UCL Genomics
>>> Senior Lecturer, Bioinformatics
>>> 
>>> UCL Cancer Institute
>>> Paul O' Gorman Building
>>> University College London
>>> 72, Huntley Street
>>> WC1E 6BT
>>> London
>>> UK
>>> 
>>> Institute of Cell and Molecular Science
>>> Barts and The London School of Medicine and Dentistry
>>> 4 Newark Street
>>> Whitechapel
>>> London
>>> E1 2AT
>>> 
>>> Office (UCL): +44 207 679 6493
>>> Fax: +44 0207 6796817
>>> Office (ICMS): +44 0207 8822374
>>> 
>>> Mobile: +44 787 6478912
>>> 
>>> 
>>> 
>>> 
>> -- 
>> Steve Chervitz, Ph.D.
>> Omicia Inc. |  Senior Computational Biologist
>> 2200 Powell Street, Ste 525, Emeryville CA 94608
>> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
>> 
>> Omicia.com: Unlocking Individualized Medicine.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From sac at bioperl.org  Thu Mar  3 18:07:52 2011
From: sac at bioperl.org (Steve Chervitz)
Date: Thu, 3 Mar 2011 15:07:52 -0800
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <CADBF252-9F51-4C7C-8062-C98B0E8E3B13@illinois.edu>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
	<E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
	<CADBF252-9F51-4C7C-8062-C98B0E8E3B13@illinois.edu>
Message-ID: <AANLkTik7CGWADGzJvenQt7kbmOoMGij4u6Q5U9NOP_rd@mail.gmail.com>

Chris: Thanks or checking. I'm not sure about this.

Elia: Can you send an example sequence + enzyme name that causes the issue
you found?

Steve

On Thu, Mar 3, 2011 at 2:57 PM, Chris Fields <cjfields at illinois.edu> wrote:

> Forgot to add the summary, just for completeness. lots of errors like this
> that are halting tests:
>
> ------------- EXCEPTION -------------
> MSG: Bad start parameter (0). Start must be positive.
> STACK Bio::PrimarySeq::subseq
> /Users/cjfields/bioperl/bioperl-live/blib/lib/Bio/PrimarySeq.pm:400
> STACK Bio::Restriction::Analysis::fragment_maps
> Bio/Restriction/Analysis.pm:556
> STACK toplevel t/Restriction/Analysis-refac.t:143
> -------------------------------------
>
> Test Summary Report
> -------------------
> t/Restriction/Analysis-refac.t (Wstat: 65280 Tests: 26 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 91 tests but ran 26.
> t/Restriction/Analysis.t      (Wstat: 65280 Tests: 118 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 177 tests but ran 118.
> t/Restriction/Gel.t           (Wstat: 65280 Tests: 3 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 9 tests but ran 3.
> Files=4, Tests=165, 29 wallclock secs ( 0.05 usr  0.03 sys +  3.44 cusr
>  0.21 csys =  3.73 CPU)
> Result: FAIL
> Failed 3/4 test programs. 0/165 subtests failed.
>
> -c
>
> On Mar 3, 2011, at 4:42 PM, Chris Fields wrote:
>
> > Elia, Steve,
> >
> > Any tests we can add for this?  I ran tests with the changes below and
> had several failing ones, but when only implementing the first fix ('unless
> (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate
> issue (string-based positions are 0-based, bioperl coords are 1-based).
> >
> > chris
> >
> > On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:
> >
> >> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
> >> reasonable to me, but I haven't tried running it through the regression
> >> tests to see if it breaks anything else.
> >>
> >> Would be good to get this fix into the upcoming release.
> >>
> >> Cheers,
> >> Steve
> >>
> >>
> >> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
> >>
> >>> Hi Steve and Rob,
> >>>
> >>> it's been sometime since I last plunged my head into the code, but
> today we
> >>> nailed a bug in Bio::Restriction::Analysis.
> >>>
> >>> Basically if a sequence has a restriction site which is exactly at the
> >>> start of the sequence, it fails to produce any sites. The  culprits is
> this
> >>> line (536 of Analysis.pm)
> >>>
> >>> unless ($cut_positions[0]) {
> >>>
> >>> where if the position is zero, it will fail to execute the rest of the
> >>> code, so I changed it to:
> >>>
> >>> unless (defined($cut_positions[0])) {
> >>>
> >>> Also, for similar reasons a bit further down this line:
> >>>
> >>> my $start=1; my $stop; my %seq; my %stop;
> >>>
> >>> needs to change to:
> >>> my $start=0; my $stop; my %seq; my %stop;
> >>>
> >>> I didn't commit the changes because I wanted to check if it makes
> sense,
> >>> etc.
> >>>
> >>> The bug seems reproducible also in older, stable versions of bioperl,
> such
> >>> as 1.4 and 1.6...
> >>>
> >>> best
> >>>
> >>> Elia
> >>>
> >>>
> >>>
> >>> ---
> >>> Scientific Director - Bioinformatics, UCL Genomics
> >>> Senior Lecturer, Bioinformatics
> >>>
> >>> UCL Cancer Institute
> >>> Paul O' Gorman Building
> >>> University College London
> >>> 72, Huntley Street
> >>> WC1E 6BT
> >>> London
> >>> UK
> >>>
> >>> Institute of Cell and Molecular Science
> >>> Barts and The London School of Medicine and Dentistry
> >>> 4 Newark Street
> >>> Whitechapel
> >>> London
> >>> E1 2AT
> >>>
> >>> Office (UCL): +44 207 679 6493
> >>> Fax: +44 0207 6796817
> >>> Office (ICMS): +44 0207 8822374
> >>>
> >>> Mobile: +44 787 6478912
> >>>
> >>>
> >>>
> >>>
> >> --
> >> Steve Chervitz, Ph.D.
> >> Omicia Inc. |  Senior Computational Biologist
> >> 2200 Powell Street, Ste 525, Emeryville CA 94608
> >> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
> >>
> >> Omicia.com: Unlocking Individualized Medicine.
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From hartzell at alerce.com  Thu Mar  3 18:04:34 2011
From: hartzell at alerce.com (George Hartzell)
Date: Thu, 3 Mar 2011 15:04:34 -0800
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
Message-ID: <19824.7810.437300.584113@gargle.gargle.HOWL>


Hi all,

I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
seems to have it.  The only tarballs that end up in Chris' directory
are these:

/Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
/Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
/Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz

It is listed in the 02packages.details.txt.gz file that is mirrored.

Thoughts, suggestions?

Thanks,

g.


From cjfields at illinois.edu  Thu Mar  3 21:24:05 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 3 Mar 2011 20:24:05 -0600
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <19824.7810.437300.584113@gargle.gargle.HOWL>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
Message-ID: <5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>

On Mar 3, 2011, at 5:04 PM, George Hartzell wrote:

> Hi all,
> 
> I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
> does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
> seems to have it.  The only tarballs that end up in Chris' directory
> are these:
> 
> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
> 
> It is listed in the 02packages.details.txt.gz file that is mirrored.
> 
> Thoughts, suggestions?
> 
> Thanks,
> 
> g.

That's odd; could it be the repo you created the mirror from?

This is my PAUSE account:

 BioPerl-1.6.0.meta                                   78518  Sun, 25 Jan 2009 05:19:20 GMT
 BioPerl-1.6.0.readme                                 12174  Sun, 25 Jan 2009 05:19:41 GMT
 BioPerl-1.6.0.tar.gz                               6813396  Sun, 25 Jan 2009 17:14:12 GMT
 BioPerl-1.6.1.meta                                   82231  Tue, 29 Sep 2009 16:33:52 GMT
 BioPerl-1.6.1.readme                                 12174  Tue, 29 Sep 2009 16:33:49 GMT
 BioPerl-1.6.1.tar.gz                               10462526  Tue, 29 Sep 2009 16:43:11 GMT
 BioPerl-DB-1.6.0_001.tar.gz                         494106  Wed, 30 Sep 2009 20:49:59 GMT
 BioPerl-Network-1.6.0_001.tar.gz                   2198338  Wed, 30 Sep 2009 20:50:18 GMT
 BioPerl-Run-1.6.1_001.tar.gz                       4289239  Wed, 30 Sep 2009 21:07:38 GMT
 BioPerl-db-1.6.0.meta                                 7728  Tue, 24 Feb 2009 02:58:05 GMT
 BioPerl-db-1.6.0.readme                               7066  Tue, 24 Feb 2009 02:58:05 GMT
 BioPerl-db-1.6.0.tar.gz                             392773  Tue, 24 Feb 2009 15:33:05 GMT
 BioPerl-network-1.6.0.meta                            1268  Tue, 24 Feb 2009 03:00:26 GMT
 BioPerl-network-1.6.0.readme                          3669  Tue, 24 Feb 2009 03:00:28 GMT
 BioPerl-network-1.6.0.tar.gz                       1410782  Tue, 24 Feb 2009 15:33:16 GMT
 BioPerl-run-1.6.0.meta                               10289  Tue, 24 Feb 2009 02:59:26 GMT
 BioPerl-run-1.6.0.readme                               576  Tue, 24 Feb 2009 02:59:26 GMT
 BioPerl-run-1.6.0.tar.gz                           4082430  Tue, 24 Feb 2009 15:34:43 GMT
 BioPerl-run-1.6.1.meta                               10289  Wed, 25 Feb 2009 16:07:06 GMT
 BioPerl-run-1.6.1.readme                               576  Wed, 25 Feb 2009 16:07:06 GMT
 BioPerl-run-1.6.1.tar.gz                           4082463  Wed, 25 Feb 2009 16:14:37 GMT
 CHECKSUMS                                             5035  Sun, 03 Oct 2010 19:21:56 GMT

chris


From hartzell at alerce.com  Fri Mar  4 00:50:49 2011
From: hartzell at alerce.com (George Hartzell)
Date: Thu, 3 Mar 2011 21:50:49 -0800
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
	<5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
Message-ID: <19824.32185.570232.624286@gargle.gargle.HOWL>

Chris Fields writes:
 > On Mar 3, 2011, at 5:04 PM, George Hartzell wrote:
 > 
 > > Hi all,
 > > 
 > > I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
 > > does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
 > > seems to have it.  The only tarballs that end up in Chris' directory
 > > are these:
 > > 
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
 > > 
 > > It is listed in the 02packages.details.txt.gz file that is mirrored.
 > > 
 > > Thoughts, suggestions?
 > > 
 > > Thanks,
 > > 
 > > g.
 > 
 > That's odd; could it be the repo you created the mirror from?
 > 
 > This is my PAUSE account:
 > 
 >  BioPerl-1.6.0.meta                                   78518  Sun, 25 Jan 2009 05:19:20 GMT
 >  BioPerl-1.6.0.readme                                 12174  Sun, 25 Jan 2009 05:19:41 GMT
 >  BioPerl-1.6.0.tar.gz                               6813396  Sun, 25 Jan 2009 17:14:12 GMT
 >  BioPerl-1.6.1.meta                                   82231  Tue, 29 Sep 2009 16:33:52 GMT
 >  BioPerl-1.6.1.readme                                 12174  Tue, 29 Sep 2009 16:33:49 GMT
 >  BioPerl-1.6.1.tar.gz                               10462526  Tue, 29 Sep 2009 16:43:11 GMT
 >  BioPerl-DB-1.6.0_001.tar.gz                         494106  Wed, 30 Sep 2009 20:49:59 GMT
 >  BioPerl-Network-1.6.0_001.tar.gz                   2198338  Wed, 30 Sep 2009 20:50:18 GMT
 >  BioPerl-Run-1.6.1_001.tar.gz                       4289239  Wed, 30 Sep 2009 21:07:38 GMT
 >  BioPerl-db-1.6.0.meta                                 7728  Tue, 24 Feb 2009 02:58:05 GMT
 >  BioPerl-db-1.6.0.readme                               7066  Tue, 24 Feb 2009 02:58:05 GMT
 >  BioPerl-db-1.6.0.tar.gz                             392773  Tue, 24 Feb 2009 15:33:05 GMT
 >  BioPerl-network-1.6.0.meta                            1268  Tue, 24 Feb 2009 03:00:26 GMT
 >  BioPerl-network-1.6.0.readme                          3669  Tue, 24 Feb 2009 03:00:28 GMT
 >  BioPerl-network-1.6.0.tar.gz                       1410782  Tue, 24 Feb 2009 15:33:16 GMT
 >  BioPerl-run-1.6.0.meta                               10289  Tue, 24 Feb 2009 02:59:26 GMT
 >  BioPerl-run-1.6.0.readme                               576  Tue, 24 Feb 2009 02:59:26 GMT
 >  BioPerl-run-1.6.0.tar.gz                           4082430  Tue, 24 Feb 2009 15:34:43 GMT
 >  BioPerl-run-1.6.1.meta                               10289  Wed, 25 Feb 2009 16:07:06 GMT
 >  BioPerl-run-1.6.1.readme                               576  Wed, 25 Feb 2009 16:07:06 GMT
 >  BioPerl-run-1.6.1.tar.gz                           4082463  Wed, 25 Feb 2009 16:14:37 GMT
 >  CHECKSUMS                                             5035  Sun, 03 Oct 2010 19:21:56 GMT
 > 
 > chris
 > 
 > 

I've tried a couple of them, a couple of times.  Wouldn't surprise me
if it's something on my end.  I'll peek under the minicpan kilt over
the weekend and see if I can see what's going on.

g.


From e.stupka at ucl.ac.uk  Fri Mar  4 04:30:17 2011
From: e.stupka at ucl.ac.uk (Elia Stupka)
Date: Fri, 4 Mar 2011 09:30:17 +0000
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
	<E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
Message-ID: <535DCA0E-A74D-483B-96FB-544387EF08C3@ucl.ac.uk>

Ignore the second fix, the first one is the useful and correct one. The 2nd one was an oversight.

Elia


---
Scientific Director - Bioinformatics, UCL Genomics
Senior Lecturer, Bioinformatics

UCL Cancer Institute
Paul O' Gorman Building
University College London
Gower Street
WC1E 6BT
London
UK

Institute of Cell and Molecular Science
Barts and The London School of Medicine and Dentistry
4 Newark Street
Whitechapel
London
E1 2AT

Office (UCL): +44 207 679 6493
Fax: +44 0207 6796817 
Office (ICMS): +44 0207 8822374

On 3 Mar 2011, at 22:42, Chris Fields <cjfields at illinois.edu> wrote:

> Elia, Steve,
> 
> Any tests we can add for this?  I ran tests with the changes below and had several failing ones, but when only implementing the first fix ('unless (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate issue (string-based positions are 0-based, bioperl coords are 1-based).
> 
> chris
> 
> On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:
> 
>> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
>> reasonable to me, but I haven't tried running it through the regression
>> tests to see if it breaks anything else.
>> 
>> Would be good to get this fix into the upcoming release.
>> 
>> Cheers,
>> Steve
>> 
>> 
>> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
>> 
>>> Hi Steve and Rob,
>>> 
>>> it's been sometime since I last plunged my head into the code, but today we
>>> nailed a bug in Bio::Restriction::Analysis.
>>> 
>>> Basically if a sequence has a restriction site which is exactly at the
>>> start of the sequence, it fails to produce any sites. The  culprits is this
>>> line (536 of Analysis.pm)
>>> 
>>> unless ($cut_positions[0]) {
>>> 
>>> where if the position is zero, it will fail to execute the rest of the
>>> code, so I changed it to:
>>> 
>>> unless (defined($cut_positions[0])) {
>>> 
>>> Also, for similar reasons a bit further down this line:
>>> 
>>> my $start=1; my $stop; my %seq; my %stop;
>>> 
>>> needs to change to:
>>> my $start=0; my $stop; my %seq; my %stop;
>>> 
>>> I didn't commit the changes because I wanted to check if it makes sense,
>>> etc.
>>> 
>>> The bug seems reproducible also in older, stable versions of bioperl, such
>>> as 1.4 and 1.6...
>>> 
>>> best
>>> 
>>> Elia
>>> 
>>> 
>>> 
>>> ---
>>> Scientific Director - Bioinformatics, UCL Genomics
>>> Senior Lecturer, Bioinformatics
>>> 
>>> UCL Cancer Institute
>>> Paul O' Gorman Building
>>> University College London
>>> 72, Huntley Street
>>> WC1E 6BT
>>> London
>>> UK
>>> 
>>> Institute of Cell and Molecular Science
>>> Barts and The London School of Medicine and Dentistry
>>> 4 Newark Street
>>> Whitechapel
>>> London
>>> E1 2AT
>>> 
>>> Office (UCL): +44 207 679 6493
>>> Fax: +44 0207 6796817
>>> Office (ICMS): +44 0207 8822374
>>> 
>>> Mobile: +44 787 6478912
>>> 
>>> 
>>> 
>>> 
>> -- 
>> Steve Chervitz, Ph.D.
>> Omicia Inc. |  Senior Computational Biologist
>> 2200 Powell Street, Ste 525, Emeryville CA 94608
>> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
>> 
>> Omicia.com: Unlocking Individualized Medicine.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From cjfields at illinois.edu  Fri Mar  4 11:09:42 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 4 Mar 2011 10:09:42 -0600
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <535DCA0E-A74D-483B-96FB-544387EF08C3@ucl.ac.uk>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
	<E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
	<535DCA0E-A74D-483B-96FB-544387EF08C3@ucl.ac.uk>
Message-ID: <243A2900-C5D3-4772-AC88-69A3ABF238E6@illinois.edu>

Committed to github, should be in the next release.  I'll see if I can add a simple test for this.

chris


On Mar 4, 2011, at 3:30 AM, Elia Stupka wrote:

> Ignore the second fix, the first one is the useful and correct one. The 2nd one was an oversight.
> 
> Elia
> 
> 
> ---
> Scientific Director - Bioinformatics, UCL Genomics
> Senior Lecturer, Bioinformatics
> 
> UCL Cancer Institute
> Paul O' Gorman Building
> University College London
> Gower Street
> WC1E 6BT
> London
> UK
> 
> Institute of Cell and Molecular Science
> Barts and The London School of Medicine and Dentistry
> 4 Newark Street
> Whitechapel
> London
> E1 2AT
> 
> Office (UCL): +44 207 679 6493
> Fax: +44 0207 6796817 
> Office (ICMS): +44 0207 8822374
> 
> On 3 Mar 2011, at 22:42, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Elia, Steve,
>> 
>> Any tests we can add for this?  I ran tests with the changes below and had several failing ones, but when only implementing the first fix ('unless (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate issue (string-based positions are 0-based, bioperl coords are 1-based).
>> 
>> chris
>> 
>> On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:
>> 
>>> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
>>> reasonable to me, but I haven't tried running it through the regression
>>> tests to see if it breaks anything else.
>>> 
>>> Would be good to get this fix into the upcoming release.
>>> 
>>> Cheers,
>>> Steve
>>> 
>>> 
>>> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
>>> 
>>>> Hi Steve and Rob,
>>>> 
>>>> it's been sometime since I last plunged my head into the code, but today we
>>>> nailed a bug in Bio::Restriction::Analysis.
>>>> 
>>>> Basically if a sequence has a restriction site which is exactly at the
>>>> start of the sequence, it fails to produce any sites. The  culprits is this
>>>> line (536 of Analysis.pm)
>>>> 
>>>> unless ($cut_positions[0]) {
>>>> 
>>>> where if the position is zero, it will fail to execute the rest of the
>>>> code, so I changed it to:
>>>> 
>>>> unless (defined($cut_positions[0])) {
>>>> 
>>>> Also, for similar reasons a bit further down this line:
>>>> 
>>>> my $start=1; my $stop; my %seq; my %stop;
>>>> 
>>>> needs to change to:
>>>> my $start=0; my $stop; my %seq; my %stop;
>>>> 
>>>> I didn't commit the changes because I wanted to check if it makes sense,
>>>> etc.
>>>> 
>>>> The bug seems reproducible also in older, stable versions of bioperl, such
>>>> as 1.4 and 1.6...
>>>> 
>>>> best
>>>> 
>>>> Elia
>>>> 
>>>> 
>>>> 
>>>> ---
>>>> Scientific Director - Bioinformatics, UCL Genomics
>>>> Senior Lecturer, Bioinformatics
>>>> 
>>>> UCL Cancer Institute
>>>> Paul O' Gorman Building
>>>> University College London
>>>> 72, Huntley Street
>>>> WC1E 6BT
>>>> London
>>>> UK
>>>> 
>>>> Institute of Cell and Molecular Science
>>>> Barts and The London School of Medicine and Dentistry
>>>> 4 Newark Street
>>>> Whitechapel
>>>> London
>>>> E1 2AT
>>>> 
>>>> Office (UCL): +44 207 679 6493
>>>> Fax: +44 0207 6796817
>>>> Office (ICMS): +44 0207 8822374
>>>> 
>>>> Mobile: +44 787 6478912
>>>> 
>>>> 
>>>> 
>>>> 
>>> -- 
>>> Steve Chervitz, Ph.D.
>>> Omicia Inc. |  Senior Computational Biologist
>>> 2200 Powell Street, Ste 525, Emeryville CA 94608
>>> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
>>> 
>>> Omicia.com: Unlocking Individualized Medicine.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 




From hartzell at alerce.com  Fri Mar  4 13:16:03 2011
From: hartzell at alerce.com (George Hartzell)
Date: Fri, 4 Mar 2011 10:16:03 -0800
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
	<5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
Message-ID: <19825.11363.446731.724414@gargle.gargle.HOWL>

Chris Fields writes:
 > On Mar 3, 2011, at 5:04 PM, George Hartzell wrote:
 > 
 > > Hi all,
 > > 
 > > I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
 > > does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
 > > seems to have it.  The only tarballs that end up in Chris' directory
 > > are these:
 > > 
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
 > > 
 > > It is listed in the 02packages.details.txt.gz file that is mirrored.
 > > 
 > > Thoughts, suggestions?
 > > 
 > > Thanks,
 > > 
 > > g.
 > 
 > That's odd; could it be the repo you created the mirror from?
 > 
 > This is my PAUSE account:
 > 
 >  BioPerl-1.6.0.meta                                   78518  Sun, 25 Jan 2009 05:19:20 GMT
 >  BioPerl-1.6.0.readme                                 12174  Sun, 25 Jan 2009 05:19:41 GMT
 >  BioPerl-1.6.0.tar.gz                               6813396  Sun, 25 Jan 2009 17:14:12 GMT
 >  BioPerl-1.6.1.meta                                   82231  Tue, 29 Sep 2009 16:33:52 GMT
 >  BioPerl-1.6.1.readme                                 12174  Tue, 29 Sep 2009 16:33:49 GMT
 >  BioPerl-1.6.1.tar.gz                               10462526  Tue, 29 Sep 2009 16:43:11 GMT
 >  BioPerl-DB-1.6.0_001.tar.gz                         494106  Wed, 30 Sep 2009 20:49:59 GMT
 >  BioPerl-Network-1.6.0_001.tar.gz                   2198338  Wed, 30 Sep 2009 20:50:18 GMT
 >  BioPerl-Run-1.6.1_001.tar.gz                       4289239  Wed, 30 Sep 2009 21:07:38 GMT
 >  BioPerl-db-1.6.0.meta                                 7728  Tue, 24 Feb 2009 02:58:05 GMT
 >  BioPerl-db-1.6.0.readme                               7066  Tue, 24 Feb 2009 02:58:05 GMT
 >  BioPerl-db-1.6.0.tar.gz                             392773  Tue, 24 Feb 2009 15:33:05 GMT
 >  BioPerl-network-1.6.0.meta                            1268  Tue, 24 Feb 2009 03:00:26 GMT
 >  BioPerl-network-1.6.0.readme                          3669  Tue, 24 Feb 2009 03:00:28 GMT
 >  BioPerl-network-1.6.0.tar.gz                       1410782  Tue, 24 Feb 2009 15:33:16 GMT
 >  BioPerl-run-1.6.0.meta                               10289  Tue, 24 Feb 2009 02:59:26 GMT
 >  BioPerl-run-1.6.0.readme                               576  Tue, 24 Feb 2009 02:59:26 GMT
 >  BioPerl-run-1.6.0.tar.gz                           4082430  Tue, 24 Feb 2009 15:34:43 GMT
 >  BioPerl-run-1.6.1.meta                               10289  Wed, 25 Feb 2009 16:07:06 GMT
 >  BioPerl-run-1.6.1.readme                               576  Wed, 25 Feb 2009 16:07:06 GMT
 >  BioPerl-run-1.6.1.tar.gz                           4082463  Wed, 25 Feb 2009 16:14:37 GMT
 >  CHECKSUMS                                             5035  Sun, 03 Oct 2010 19:21:56 GMT
 > 
 > chris
 > 
 > 

Ok, apparently we've earned a reputation, and it has preceeded us....
Here's the code that Ricardo uses to filter the list of things to mirror:

  sub _filter_module {
    my $self = shift;
    my $args = shift;
  
    if ($self->{skip_perl}) {
      return 1 if $args->{path} =~ m{/(?:emb|syb|bio)?perl-\d}i;
      return 1 if $args->{path} =~ m{/(?:parrot|ponie)-\d}i;
      return 1 if $args->{path} =~ m{/(?:kurila)-\d}i;
      return 1 if $args->{path} =~ m{/\bperl-?5\.004}i;
      return 1 if $args->{path} =~ m{/\bperl_mlb\.zip}i;
    }
  
    return 1 if $self->__do_filter($self->{path_filters},   $args->{path});
    return 1 if $self->__do_filter($self->{module_filters}, $args->{module});
    return 0;
  }

I'll ask him why he's filtering bioperl out and we can see if we can
fix it.  I'm hoping that it's just an over-eager cut-n-paste of stuff
that he thinks of as the "perl" source (which is why it's within the
skip_perl test) and not that we've done something egregious.

g.


From cjfields at illinois.edu  Fri Mar  4 13:24:05 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 4 Mar 2011 12:24:05 -0600
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <19825.11363.446731.724414@gargle.gargle.HOWL>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
	<5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
	<19825.11363.446731.724414@gargle.gargle.HOWL>
Message-ID: <F8DFAE16-FE59-4EDF-80D0-4FE60620FFF8@illinois.edu>

On Mar 4, 2011, at 12:16 PM, George Hartzell wrote:

> Chris Fields writes:
>> On Mar 3, 2011, at 5:04 PM, George Hartzell wrote:
>> 
>>> Hi all,
>>> 
>>> I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
>>> does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
>>> seems to have it.  The only tarballs that end up in Chris' directory
>>> are these:
>>> 
>>> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
>>> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
>>> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
>>> 
>>> It is listed in the 02packages.details.txt.gz file that is mirrored.
>>> 
>>> Thoughts, suggestions?
>>> 
>>> Thanks,
>>> 
>>> g.
>> 
>> That's odd; could it be the repo you created the mirror from?
>> 
>> This is my PAUSE account:
>> 
>> BioPerl-1.6.0.meta                                   78518  Sun, 25 Jan 2009 05:19:20 GMT
>> BioPerl-1.6.0.readme                                 12174  Sun, 25 Jan 2009 05:19:41 GMT
>> BioPerl-1.6.0.tar.gz                               6813396  Sun, 25 Jan 2009 17:14:12 GMT
>> BioPerl-1.6.1.meta                                   82231  Tue, 29 Sep 2009 16:33:52 GMT
>> BioPerl-1.6.1.readme                                 12174  Tue, 29 Sep 2009 16:33:49 GMT
>> BioPerl-1.6.1.tar.gz                               10462526  Tue, 29 Sep 2009 16:43:11 GMT
>> BioPerl-DB-1.6.0_001.tar.gz                         494106  Wed, 30 Sep 2009 20:49:59 GMT
>> BioPerl-Network-1.6.0_001.tar.gz                   2198338  Wed, 30 Sep 2009 20:50:18 GMT
>> BioPerl-Run-1.6.1_001.tar.gz                       4289239  Wed, 30 Sep 2009 21:07:38 GMT
>> BioPerl-db-1.6.0.meta                                 7728  Tue, 24 Feb 2009 02:58:05 GMT
>> BioPerl-db-1.6.0.readme                               7066  Tue, 24 Feb 2009 02:58:05 GMT
>> BioPerl-db-1.6.0.tar.gz                             392773  Tue, 24 Feb 2009 15:33:05 GMT
>> BioPerl-network-1.6.0.meta                            1268  Tue, 24 Feb 2009 03:00:26 GMT
>> BioPerl-network-1.6.0.readme                          3669  Tue, 24 Feb 2009 03:00:28 GMT
>> BioPerl-network-1.6.0.tar.gz                       1410782  Tue, 24 Feb 2009 15:33:16 GMT
>> BioPerl-run-1.6.0.meta                               10289  Tue, 24 Feb 2009 02:59:26 GMT
>> BioPerl-run-1.6.0.readme                               576  Tue, 24 Feb 2009 02:59:26 GMT
>> BioPerl-run-1.6.0.tar.gz                           4082430  Tue, 24 Feb 2009 15:34:43 GMT
>> BioPerl-run-1.6.1.meta                               10289  Wed, 25 Feb 2009 16:07:06 GMT
>> BioPerl-run-1.6.1.readme                               576  Wed, 25 Feb 2009 16:07:06 GMT
>> BioPerl-run-1.6.1.tar.gz                           4082463  Wed, 25 Feb 2009 16:14:37 GMT
>> CHECKSUMS                                             5035  Sun, 03 Oct 2010 19:21:56 GMT
>> 
>> chris
>> 
>> 
> 
> Ok, apparently we've earned a reputation, and it has preceeded us....
> Here's the code that Ricardo uses to filter the list of things to mirror:
> 
>  sub _filter_module {
>    my $self = shift;
>    my $args = shift;
> 
>    if ($self->{skip_perl}) {
>      return 1 if $args->{path} =~ m{/(?:emb|syb|bio)?perl-\d}i;
>      return 1 if $args->{path} =~ m{/(?:parrot|ponie)-\d}i;
>      return 1 if $args->{path} =~ m{/(?:kurila)-\d}i;
>      return 1 if $args->{path} =~ m{/\bperl-?5\.004}i;
>      return 1 if $args->{path} =~ m{/\bperl_mlb\.zip}i;
>    }
> 
>    return 1 if $self->__do_filter($self->{path_filters},   $args->{path});
>    return 1 if $self->__do_filter($self->{module_filters}, $args->{module});
>    return 0;
>  }
> 
> I'll ask him why he's filtering bioperl out and we can see if we can
> fix it.  I'm hoping that it's just an over-eager cut-n-paste of stuff
> that he thinks of as the "perl" source (which is why it's within the
> skip_perl test) and not that we've done something egregious.
> 
> g.

Could be the size of the distribution was considered egregious (we're at 10 MB compressed I think).  Most of the other dists that appear to be filtered are fairly large as well.  That's nothing really these days; would be interested to hear what Ricardo says.

chris




From hlapp at drycafe.net  Fri Mar  4 18:26:25 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Fri, 4 Mar 2011 18:26:25 -0500
Subject: [Bioperl-l] Informatics job opportunity at NESCent
Message-ID: <1878F27F-000D-4C80-B9EA-A83F7887828F@drycafe.net>

(Apologies if you receive multiple copies, and also if you are not  
interested in job opportunities.  In my defense, quite a few people on  
Bio* lists might qualify for (let alone enjoy) the position. And if  
you know someone who might be interested please forward.)

===================================================
User Interface Design and Web Application Developer
===================================================

The National Evolutionary Synthesis Center (NESCent) seeks a creative  
and enthusiastic individual to design user interfaces and web  
applications for scientific applications. The incumbent will work as  
part of a small informatics team in close collaboration with domain  
scientists.

NESCent is an NSF-funded center dedicated to cross-disciplinary  
research in evolutionary science. Our informatics team works closely  
with visiting and resident scientists to support their custom software  
and database development needs. All NESCent software products are open- 
source, and the Center has a number of initiatives to actively promote  
collaborative development of community software resources  
(informatics.nescent.org). Above all, we are enthusiastic about our  
work, about the mission of the Center, and about the contribution of  
informatics to that mission.

Job description: The incumbent will design and develop user interfaces  
and web applications for databases and other software tools for  
sponsored scientists and staff. The job responsibilities include all  
stages of the software development process, including requirements  
gathering, design, implementation, release packaging and  
documentation, as part of a small team (typically 2-3 individuals)  
following project management best practices. We expect the incumbent  
to present their work at conferences and contribute to publications  
with scientific collaborators; interact regularly with visiting and  
resident scientists, other members of the informatics team and Center  
staff; and generally serve as an expert resource for Center personnel.  
The position provides opportunities for professional development. Most  
informatics staff work at our Durham NC offices, located adjacent to  
Duke University, but we do support a wide range of technologies for  
virtual communication with off-site staff and collaborators.

Required Qualifications:
* Demonstrated success collaborating with clients on custom software  
solutions
* Experience with various stages of the software development cycle
* Expertise in development and testing of user interface designs
* Excellent communication skills, both virtual and face-to-face
* A four-year college degree in Computer Science, Bioinformatics or a  
related field

Preferred Qualifications:
* M.S. or Ph.D. in Computer Science, Bioinformatics or related field  
along with demonstrated interest in science, particularly biology
* Expertise in rapid application development and respective  
programming technologies and languages (e.g., modern scripting  
languages and web-application frameworks such as Python/Django, Ruby/ 
Ruby-on-Rails, and Perl/Catalyst), fluency in Java programming, and  
prior experience in relational database programming (PostgreSQL or  
MySQL)
* Expertise in dynamic and interactive web technologies (JavaScript,  
CGI), web service (SOAP, REST, XML, JSON) and semantic web technologies
* Experience with open-source, and collaborative, software  
development, software usability design and assessment
* Expertise in graphic design, data visualization and/or scientific  
data integration

How to apply: Please send cover letter, resume and contact information  
for three references to Dr. Karen Cranston, Training Coordinator and  
Bioinformatics Project Manager (karen.cranston at nescent.org). Review of  
applications will begin March 21, 2011. Informal inquires or requests  
for additional information may be directed to Dr. Cranston by email or  
phone (+1-919-613-2275).

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From hartzell at alerce.com  Sat Mar  5 16:18:50 2011
From: hartzell at alerce.com (George Hartzell)
Date: Sat, 5 Mar 2011 13:18:50 -0800
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <19824.7810.437300.584113@gargle.gargle.HOWL>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
Message-ID: <19826.43194.173739.594355@gargle.gargle.HOWL>

George Hartzell writes:
 > 
 > Hi all,
 > 
 > I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
 > does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
 > seems to have it.  The only tarballs that end up in Chris' directory
 > are these:
 > 
 > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
 > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
 > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
 > 
 > It is listed in the 02packages.details.txt.gz file that is mirrored.
 > 

Here's the conclusion, for the list and posterity.

CPAN::Mini is excluding the BioPerl modules, as well as the perl
source distributions, because they're "too big".

You can get minicpan to mirror all this stuff by adding

 perl: 1

to your .minicpan, which causes the app to set its internal skip_perl
flag to 0, which in turn causes it to mirror the big stuff.

I'm running a few experiments to figure out how much add'l space gets
used if one allows bioperl without all of the other perl source
releases.  Maybe I can convince Ricard to do something less heavy
handed for us.

g.


From hlapp at drycafe.net  Sat Mar  5 21:58:04 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 5 Mar 2011 21:58:04 -0500
Subject: [Bioperl-l] Job opening for GMOD User Support Specialist
Message-ID: <814155D1-1CD5-4E66-B726-2CF7E33EF3CE@drycafe.net>

(Apologies if you receive multiple copies, and also if you are not  
interested in job opportunities. If you know someone who might be  
interested please forward.)

============================
GMOD User Support Specialist
============================

Are you fascinated by genomics and bioinformatics? Are you passionate  
about collaborative open-source software? Do you enjoy teaching and  
working with scientists?  If so, then this position is for you.

The Generic Model Organism Database project (GMOD) is a collection of  
open source software tools for creating and managing biological, and  
particularly genomic, databases.  GMOD has a large, highly  
distributed, and dynamic community of software users and developers.   
The University of North Carolina at Chapel Hill has an opening for a  
GMOD user support specialist, to be based at the US National  
Evolutionary Synthesis Center (NESCent, www.nescent.org) in Durham,  
North Carolina, while serving the international community of GMOD users.

Job Description:

The GMOD user support specialist will maintain online documentation;  
respond to mailing list help requests; present tutorials; organize  
short courses, conference sessions and other community building  
activities; survey user needs, and recruit members of the community to  
assist with these functions.   The incumbent will collaborate closely  
with the GMOD Coordinator (Scott Cain, The Ontario Institute for  
Cancer Research) and other distributed personnel.  See http://gmod.org/wiki/GMOD_Help_Desk 
  for more background on the activities of the user support  
specialist.  The salary range is $68,906 to $82,687, depending on  
qualifications, and the incumbent will receive a comprehensive  
benefits package as an SPA employee within the UNC system.

Qualifications:

Required qualifications include: excellent written and verbal  
communication skills; team orientation with strong interpersonal  
skills. Preferred qualifications include: an MS or PhD in biology,  
computer science or related field; three or more years of experience  
with web programming and relational database management systems; three  
or more years of experience with genome database administration or  
curation, preferably in a GMOD environment; at least one year of  
experience with web content management, ideally using MediaWiki;  
freedom to travel 5-15 weeks/yr.

To Apply:

Please provide a cover letter and CV, including contact information  
for three references, to Hilmar Lapp, Assistant Director of  
Informatics, NESCent, at hlapp at nescent.org, and submit materials  
through http://bit.ly/h9l74r.  Inquiries may be addressed to H. Lapp  
by email or by phone at 919.668.5288.

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From eigenrosen at gmail.com  Sun Mar  6 18:34:09 2011
From: eigenrosen at gmail.com (Michael Rosen)
Date: Sun, 6 Mar 2011 15:34:09 -0800
Subject: [Bioperl-l] bioperl-ext installation
Message-ID: <AANLkTinuaavEU4RwxZu=bmFpUVxpYBAisOv9wgKmQ9+9@mail.gmail.com>

Hi all,
Sorry in advance for a most likely trivial question: I did the standard
make/make test/make install of the bioperl-ext packages with no problems (I
can post the full output if useful). But when I try to run a simple program
that has no trouble on a different machine w bioperl-ext I get:

"The C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has
not been installed.
 Please install the bioperl-ext package"

Any ideas what might be happening? I don't know if the problem was with
installation (but I got "all tests successful during make test") or if I may
need to add the installed packages to some path variable? I'm relatively new
to both bioperl and perl generally so not sure where to start

Thanks


From rmb32 at cornell.edu  Mon Mar  7 11:26:28 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Mon, 07 Mar 2011 11:26:28 -0500
Subject: [Bioperl-l] call for project ideas - Google Summer of Code
Message-ID: <4D750734.4020002@cornell.edu>

Hi all,

Google's Summer of Code is coming round again, very soon now (mentoring 
organization applications are due this week).  We need to update our 
project ideas for prospective Summer of Code interns.  The rest of the 
page also needs updates, changing dates and such.

There's a page on the BioPerl wiki, please have a look and add your 
ideas for intern projects.

For more on Google Summer of Code, what it is and how it works, see 
their FAQ at 
http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2011/faqs

One of the summer intern ideas I have on the page so far is to help with 
the tough grunt work of breaking BioPerl into smaller, more easily 
managed distributions.  I'm sure you all can think of plenty more!

Here's the page: http://www.bioperl.org/wiki/Google_Summer_of_Code

Please have a look, add your project ideas, and delete ones that have 
already been done or are no longer relevant.

Rob



From tzhu at mail.bnu.edu.cn  Tue Mar  8 01:45:11 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Tue, 08 Mar 2011 14:45:11 +0800
Subject: [Bioperl-l] locate introns in a protein sequence
Message-ID: <1299566711.5243.11.camel@ubuntu>

Hello, everyone. For example, I have a GTF file annotating like this,

Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 start_codon 25009
25011 . + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 stop_codon 26003
26005 . + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 24828
25172 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25009 25172 .
+ 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 25245
25364 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25245 25364 .
+ 1 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 25414
26178 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25414 26002 .
+ 1 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";

Obviously this transcript "SPOG_00008T0" has two introns.

Also I have a corresponding protein sequence file like this( in fasta
format),

>SPOG_00008T0 | SPOG_00008 | Schizosaccharomyces cryophilus OY26 exosome
subunit Rrp45 (292 aa)
MSKSLEPSANNKGFIVNALKKELRLDGRSLTDFRDLKIEFGEDYGQVDISLGSTRVMARI
SAEITKPYSDRPFDGIFAITTELTPLASPAFETGRVSEQEVIISRLIEQAIRRSNALDTE
SLCIISGQKCWSVRASVHFINHDGNLVDAACIAVITGLCHFRRPEITVLGDEVTVHSIEE
RVPVPLSVLHTPICVTFSFFEDGSLSAIDASLEEEELRTGSMTVTLNKNREICQIFKAGG
VTIEASSVVACAHTAFQKTTSIISEIQRALDEDLSKKETQFFGGSAENQRS*

I hope to precisely locate these two introns into the protein
sequence(find their location among the amino acids). Please recommend a
relatively convenient method. Thank you!



-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)



From jason at bioperl.org  Tue Mar  8 02:42:54 2011
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 07 Mar 2011 23:42:54 -0800
Subject: [Bioperl-l] locate introns in a protein sequence
In-Reply-To: <1299566711.5243.11.camel@ubuntu>
References: <1299566711.5243.11.camel@ubuntu>
Message-ID: <4D75DDFE.9090602@bioperl.org>

I think there are several ways to do this, the easiest is to walk 
through each exon, and count up the codons, and print out the 
translation of the codons so far when you get to the end of an exon, 
keeping the overhang for the next exon.

That's basically what I do here in terms of counting, though I'm mapping 
introns into an alignment not a single peptide (though undocumented so 
it is a bit impenetrable)
  https://github.com/hyphaltip/thesis/blob/master/src/intron/map_introns_aln.pl

Use Bio::DB::SeqFeature::Store will make this much easier.  You will 
want to convert this Broad GTF to GFF3 with this script
https://github.com/hyphaltip/genome-scripts/blob/master/data_format/gtf2gff3_3level.pl

Then load the annotation along with a scaffold GFF3 (like one from this 
script run on your FASTA genome file
  https://github.com/hyphaltip/genome-scripts/blob/master/gbrowse_tools/fasta_to_gbrowse_scaffold.pl
  - just watch out -- the Broad is capitalizing the contig name 
(Supercontig_3.1) while the FASTA file will have it uncapped and 
truncated name (supercont_3.1) so you need to fix that in either of the 
files so it is consistent - a perl one liner will work here;
perl -i -p -e 's/^>supercont3\./>Supercontig_3./' GENOME.fasta

and load this in and you'll then be able to use the Bio::DB::SeqFeature 
to get all genes, walk through them a CDS for each gene, one a time, and 
then just keep count of the frame you are in and the exon length and 
you'll know where the introns go in the protein.

for my $gene ( $dbh->features(-type => 
"gene:S_cryophilus_OY26_V3_CALLGENES_FINAL_2
") ) {
  for my $mRNA ( $gene->get_SeqFeatures('mRNA') ) {
   for my $CDS ( $mRNA->get_SeqFeatures('CDS') ) {
    my $length = $CDS->length;
    # do some stuff to keep count or whatever you need to figure out 
where you are to put the intron
   }
  }
}

you can also see this code which converts folders of GFF3 + genomes into 
coding seqs, translated peps, etc.
  https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/gff3_to_cdspep.pl

It all depends on what you want to report from this type of query.

Tao Zhu wrote:
> Hello, everyone. For example, I have a GTF file annotating like this,
>
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 start_codon 25009
> 25011 . + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 stop_codon 26003
> 26005 . + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 24828
> 25172 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25009 25172 .
> + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 25245
> 25364 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25245 25364 .
> + 1 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 25414
> 26178 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25414 26002 .
> + 1 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
>
> Obviously this transcript "SPOG_00008T0" has two introns.
>
> Also I have a corresponding protein sequence file like this( in fasta
> format),
>
>> SPOG_00008T0 | SPOG_00008 | Schizosaccharomyces cryophilus OY26 exosome
> subunit Rrp45 (292 aa)
> MSKSLEPSANNKGFIVNALKKELRLDGRSLTDFRDLKIEFGEDYGQVDISLGSTRVMARI
> SAEITKPYSDRPFDGIFAITTELTPLASPAFETGRVSEQEVIISRLIEQAIRRSNALDTE
> SLCIISGQKCWSVRASVHFINHDGNLVDAACIAVITGLCHFRRPEITVLGDEVTVHSIEE
> RVPVPLSVLHTPICVTFSFFEDGSLSAIDASLEEEELRTGSMTVTLNKNREICQIFKAGG
> VTIEASSVVACAHTAFQKTTSIISEIQRALDEDLSKKETQFFGGSAENQRS*
>
> I hope to precisely locate these two introns into the protein
> sequence(find their location among the amino acids). Please recommend a
> relatively convenient method. Thank you!
>
>
>

-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki



From bio.justin100 at gmail.com  Tue Mar  8 17:31:42 2011
From: bio.justin100 at gmail.com (Justin Li)
Date: Tue, 8 Mar 2011 17:31:42 -0500
Subject: [Bioperl-l] Bio::Phylo vs Bio:TreeIO; interface to Fitch
Message-ID: <AANLkTik+HwSQNN3WCkaqQRPz3xqheaa0khmzdD5nndJa@mail.gmail.com>

Hi,

Both Bio::Phylo and Bio:TreeIO seem to be able to parse phylogenetic trees.

Could anyone having experience with both of them please comment on their
capability/robustness/ease of use?

Where can I find the documentation for
"Bio::Tools::Run::PiseApplication::fitch"?

Thanks,

Justin


From abhishek.vit at gmail.com  Tue Mar  8 17:42:03 2011
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Tue, 8 Mar 2011 14:42:03 -0800
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
	Sequences (reads)
Message-ID: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>

Hi All

I have results from different megablast of short reads(DNA sequences)
and after extracting the tophit for each read I want to bin them by
their lineage creating a tree.

For example.

If blast query hits the reference ->
gi|196110604|gb|CP001103.1|__Alteromonas_macleodii_'Deep_ecotype',_complete_genome

I want to get the lineage for this specie.

Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Alteromonas;Alteromona

The final goal is to do the above mapping as efficiently as possible.
Any pointers will be appreciated.


Thanks!
-Abhi


From miguel.pignatelli at uv.es  Wed Mar  9 04:20:47 2011
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Wed, 09 Mar 2011 09:20:47 +0000
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
Message-ID: <4D77466F.4040604@uv.es>

Hi Abhishek,

For a non bioperl related solution, take a look at Bio::LITE::Taxonomy.
It has been design to deal with great number of sequences (it is fast 
and efficient).

You may also find interesting the Blast2lca tool,

https://github.com/emepyc/Blast2lca

It currently works with the best hits for each query (calculates the 
lower common ancestor), but if you want to use only the best hit, please 
drop me a line.

Please, let me know if you need further help with any of these,

Cheers,

M;



On 08/03/11 22:42, Abhishek Pratap wrote:
> Hi All
>
> I have results from different megablast of short reads(DNA sequences)
> and after extracting the tophit for each read I want to bin them by
> their lineage creating a tree.
>
> For example.
>
> If blast query hits the reference ->
> gi|196110604|gb|CP001103.1|__Alteromonas_macleodii_'Deep_ecotype',_complete_genome
>
> I want to get the lineage for this specie.
>
> Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Alteromonas;Alteromona
>
> The final goal is to do the above mapping as efficiently as possible.
> Any pointers will be appreciated.
>
>
> Thanks!
> -Abhi
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From shalabh.sharma7 at gmail.com  Wed Mar  9 12:34:57 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 9 Mar 2011 12:34:57 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <4D77466F.4040604@uv.es>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
Message-ID: <AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>

Hey Abhishek:
                    The other way to deal with this that you can download
the gi_taxaid file from ncbi.
Convert all your GI's to taxaid and use Bio::DB:Taxanomy.
http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Taxon.html

I think there are lot of other options too, if you are interested you can
search for the thread which i started long time back.

Hope this helps.

-Shalabh Sharma
-----------------------------------------------
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636

On Wed, Mar 9, 2011 at 4:20 AM, Miguel Pignatelli
<miguel.pignatelli at uv.es>wrote:

> Hi Abhishek,
>
> For a non bioperl related solution, take a look at Bio::LITE::Taxonomy.
> It has been design to deal with great number of sequences (it is fast and
> efficient).
>
> You may also find interesting the Blast2lca tool,
>
> https://github.com/emepyc/Blast2lca
>
> It currently works with the best hits for each query (calculates the lower
> common ancestor), but if you want to use only the best hit, please drop me a
> line.
>
> Please, let me know if you need further help with any of these,
>
> Cheers,
>
> M;
>
>
>
>
> On 08/03/11 22:42, Abhishek Pratap wrote:
>
>> Hi All
>>
>> I have results from different megablast of short reads(DNA sequences)
>> and after extracting the tophit for each read I want to bin them by
>> their lineage creating a tree.
>>
>> For example.
>>
>> If blast query hits the reference ->
>>
>> gi|196110604|gb|CP001103.1|__Alteromonas_macleodii_'Deep_ecotype',_complete_genome
>>
>> I want to get the lineage for this specie.
>>
>>
>> Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Alteromonas;Alteromona
>>
>> The final goal is to do the above mapping as efficiently as possible.
>> Any pointers will be appreciated.
>>
>>
>> Thanks!
>> -Abhi
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From abhishek.vit at gmail.com  Wed Mar  9 22:25:58 2011
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Wed, 9 Mar 2011 19:25:58 -0800
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
Message-ID: <AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>

Thanks guys. I could not try either method today but will get back to
you if I face problem.

Best,
-Abhi

On Wed, Mar 9, 2011 at 9:34 AM, shalabh sharma
<shalabh.sharma7 at gmail.com> wrote:
> Hey Abhishek:
> ?? ? ? ? ? ? ? ? ? ?The other way to deal with this that you can download
> the gi_taxaid file from ncbi.
> Convert all your GI's to taxaid and use Bio::DB:Taxanomy.
> http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy
> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Taxon.html
> I think there are lot of other options too, if you are interested you can
> search for the thread which i started long time back.
> Hope this helps.
> -Shalabh Sharma
> -----------------------------------------------
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
>
> On Wed, Mar 9, 2011 at 4:20 AM, Miguel Pignatelli <miguel.pignatelli at uv.es>
> wrote:
>>
>> Hi Abhishek,
>>
>> For a non bioperl related solution, take a look at Bio::LITE::Taxonomy.
>> It has been design to deal with great number of sequences (it is fast and
>> efficient).
>>
>> You may also find interesting the Blast2lca tool,
>>
>> https://github.com/emepyc/Blast2lca
>>
>> It currently works with the best hits for each query (calculates the lower
>> common ancestor), but if you want to use only the best hit, please drop me a
>> line.
>>
>> Please, let me know if you need further help with any of these,
>>
>> Cheers,
>>
>> M;
>>
>>
>>
>> On 08/03/11 22:42, Abhishek Pratap wrote:
>>>
>>> Hi All
>>>
>>> I have results from different megablast of short reads(DNA sequences)
>>> and after extracting the tophit for each read I want to bin them by
>>> their lineage creating a tree.
>>>
>>> For example.
>>>
>>> If blast query hits the reference ->
>>>
>>> gi|196110604|gb|CP001103.1|__Alteromonas_macleodii_'Deep_ecotype',_complete_genome
>>>
>>> I want to get the lineage for this specie.
>>>
>>>
>>> Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Alteromonas;Alteromona
>>>
>>> The final goal is to do the above mapping as efficiently as possible.
>>> Any pointers will be appreciated.
>>>
>>>
>>> Thanks!
>>> -Abhi
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>



From ian.mcdowell at gmail.com  Thu Mar 10 12:11:50 2011
From: ian.mcdowell at gmail.com (Ian Mc Dowell)
Date: Thu, 10 Mar 2011 12:11:50 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
	<AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
Message-ID: <AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>

Hi all,

I would like to take local blast hit sequences, i.e. hsp_hseq, and extract
the full sequences of those hits from the original fasta file and put them
in a fasta file of all hits that I can use later.

This should be a widely performed task but I can't find any scripts that
directly address this issue.  I have not acquired the skills to make my own
scripts for this task.

Thanks so much if you have anything that can help me out,

Ian McDowell
Aquatic Pathology
University of Rhode Island


From ian.mcdowell at gmail.com  Thu Mar 10 12:13:01 2011
From: ian.mcdowell at gmail.com (Ian Mc Dowell)
Date: Thu, 10 Mar 2011 12:13:01 -0500
Subject: [Bioperl-l] Local blast hit (hsp_hseq) extracted from fasta file
Message-ID: <AANLkTinF-Ai-AvTPG6ET9xWW0NaeMQugYJpumm4g-7NH@mail.gmail.com>

Hi all,

I would like to take local blast hit sequences, i.e. hsp_hseq in blast xml
format, and extract the full sequences of those hits from the original fasta
file and put them in a fasta file of all hits that I can use later.

This should be a widely performed task but I can't find any scripts that
directly address this issue.  I have not acquired the skills to make my own
scripts for this task.

Thanks so much if you have anything that can help me out,

Ian McDowell
Aquatic Pathology
University of Rhode Island


From rmb32 at cornell.edu  Thu Mar 10 12:22:51 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 10 Mar 2011 12:22:51 -0500
Subject: [Bioperl-l] update Google Summer of Code project ideas
Message-ID: <4D7908EB.6050003@cornell.edu>

Hi all,

Please make sure the BioPerl information is up to date for 2011 on both 
the OBF and BioPerl wikis.  The current page looks pretty good, just be 
aware that Google will be looking at it in the next few days to evaluate 
whether OBF will be accepted again this year to GSoC.

OBF wiki page: http://www.open-bio.org/wiki/Google_Summer_of_Code
BioPerl wiki: http://bioperl.org/wiki/Google_Summer_of_Code

Rob

----
Robert Buels
(prospective) 2011 OBF GSoC Organization Admin


From shalabh.sharma7 at gmail.com  Thu Mar 10 12:24:04 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Thu, 10 Mar 2011 12:24:04 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
	<AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
	<AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>
Message-ID: <AANLkTik9jt9Pkrgng4zv4nRhDmK0_bRpnbGJe+i9Dark@mail.gmail.com>

Hey Ian,
            I am not sure if i understood your problem completely.
But if you have ids of blast hits you can use 'fastacmd' to fetch sequences
from the database you used for blast.

-Shalabh Sharma
-----------------------------------------
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636

On Thu, Mar 10, 2011 at 12:11 PM, Ian Mc Dowell <ian.mcdowell at gmail.com>wrote:

> Hi all,
>
> I would like to take local blast hit sequences, i.e. hsp_hseq, and extract
> the full sequences of those hits from the original fasta file and put them
> in a fasta file of all hits that I can use later.
>
> This should be a widely performed task but I can't find any scripts that
> directly address this issue.  I have not acquired the skills to make my own
> scripts for this task.
>
> Thanks so much if you have anything that can help me out,
>
> Ian McDowell
> Aquatic Pathology
> University of Rhode Island
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From ian.mcdowell at gmail.com  Thu Mar 10 12:31:29 2011
From: ian.mcdowell at gmail.com (Ian Mc Dowell)
Date: Thu, 10 Mar 2011 12:31:29 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTik9jt9Pkrgng4zv4nRhDmK0_bRpnbGJe+i9Dark@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
	<AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
	<AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>
	<AANLkTik9jt9Pkrgng4zv4nRhDmK0_bRpnbGJe+i9Dark@mail.gmail.com>
Message-ID: <AANLkTi=-12y0LWzV2gRgriE=z3=d_-OKwDRe2wSWkmwr@mail.gmail.com>

I have a deeply sequenced transcriptome so when I look for a gene of
interest in my short reads (108bp) I get thousands of hits, at very low E
values.  And I want to do this for many sequences of interest. That's why I
want a script to automate the process of grabbing the accession numbers from
the blast xml output, then searching in the fasta file which is equivalent
to my local database and pulling those relevant reads.

On Thu, Mar 10, 2011 at 12:24 PM, shalabh sharma
<shalabh.sharma7 at gmail.com>wrote:

> Hey Ian,
>             I am not sure if i understood your problem completely.
> But if you have ids of blast hits you can use 'fastacmd' to fetch sequences
> from the database you used for blast.
>
> -Shalabh Sharma
> -----------------------------------------
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
>
> On Thu, Mar 10, 2011 at 12:11 PM, Ian Mc Dowell <ian.mcdowell at gmail.com>wrote:
>
>> Hi all,
>>
>> I would like to take local blast hit sequences, i.e. hsp_hseq, and extract
>> the full sequences of those hits from the original fasta file and put them
>> in a fasta file of all hits that I can use later.
>>
>> This should be a widely performed task but I can't find any scripts that
>> directly address this issue.  I have not acquired the skills to make my
>> own
>> scripts for this task.
>>
>> Thanks so much if you have anything that can help me out,
>>
>> Ian McDowell
>> Aquatic Pathology
>> University of Rhode Island
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>


From hrh at fmi.ch  Thu Mar 10 12:37:07 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Thu, 10 Mar 2011 18:37:07 +0100
Subject: [Bioperl-l] Local blast hit (hsp_hseq) extracted from fasta file
In-Reply-To: <AANLkTinF-Ai-AvTPG6ET9xWW0NaeMQugYJpumm4g-7NH@mail.gmail.com>
References: <AANLkTinF-Ai-AvTPG6ET9xWW0NaeMQugYJpumm4g-7NH@mail.gmail.com>
Message-ID: <4D790C43.5080801@fmi.ch>



On 03/10/2011 06:13 PM, Ian Mc Dowell wrote:
> Hi all,
>
> I would like to take local blast hit sequences, i.e. hsp_hseq in blast xml
> format, and extract the full sequences of those hits from the original fasta
> file and put them in a fasta file of all hits that I can use later.
>
> This should be a widely performed task but I can't find any scripts that
> directly address this issue.  I have not acquired the skills to make my own
> scripts for this task.


Hi Ian

It is not a Bioperl solution, but a simple one:

Assuming, you are using the NCBI blast+ tools, make sure you create the 
BLAST indices with the "-parse_seqids" option. This will allow you to 
extract individual sequences (in fasta format) from the BLAST database 
with the command 'blastdbcmd' by providing a comma-delimited search 
string of sequence identifiers. Fore more details see:

http://tinyurl.com/5sq2ehg


Regards, Hans


> Thanks so much if you have anything that can help me out,
>
> Ian McDowell
> Aquatic Pathology
> University of Rhode Island
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From shalabh.sharma7 at gmail.com  Thu Mar 10 12:42:51 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Thu, 10 Mar 2011 12:42:51 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTi=-12y0LWzV2gRgriE=z3=d_-OKwDRe2wSWkmwr@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
	<AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
	<AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>
	<AANLkTik9jt9Pkrgng4zv4nRhDmK0_bRpnbGJe+i9Dark@mail.gmail.com>
	<AANLkTi=-12y0LWzV2gRgriE=z3=d_-OKwDRe2wSWkmwr@mail.gmail.com>
Message-ID: <AANLkTin13Uhj8ZgQ1-+c0SjXbRBvU8VHdGhUXyqea1FV@mail.gmail.com>

Hey Ian,
             Writing that kind of script would not take that much time. But
i am not very much familiar with xml format.
But still you can do without writing a complicated script.

once you get the output you can get all the ids (use grep or simple perl
script to parse ids).
Then use that list of ids to fetch sequences from your database by using
"fastacmd" .

-Shalabh


On Thu, Mar 10, 2011 at 12:31 PM, Ian Mc Dowell <ian.mcdowell at gmail.com>wrote:

> I have a deeply sequenced transcriptome so when I look for a gene of
> interest in my short reads (108bp) I get thousands of hits, at very low E
> values.  And I want to do this for many sequences of interest. That's why I
> want a script to automate the process of grabbing the accession numbers from
> the blast xml output, then searching in the fasta file which is equivalent
> to my local database and pulling those relevant reads.
>
> On Thu, Mar 10, 2011 at 12:24 PM, shalabh sharma <
> shalabh.sharma7 at gmail.com> wrote:
>
>> Hey Ian,
>>             I am not sure if i understood your problem completely.
>> But if you have ids of blast hits you can use 'fastacmd' to fetch
>> sequences from the database you used for blast.
>>
>> -Shalabh Sharma
>> -----------------------------------------
>> Shalabh Sharma
>> Scientific Computing Professional Associate (Bioinformatics Specialist)
>> Department of Marine Sciences
>> University of Georgia
>> Athens, GA 30602-3636
>>
>> On Thu, Mar 10, 2011 at 12:11 PM, Ian Mc Dowell <ian.mcdowell at gmail.com>wrote:
>>
>>> Hi all,
>>>
>>> I would like to take local blast hit sequences, i.e. hsp_hseq, and
>>> extract
>>> the full sequences of those hits from the original fasta file and put
>>> them
>>> in a fasta file of all hits that I can use later.
>>>
>>> This should be a widely performed task but I can't find any scripts that
>>> directly address this issue.  I have not acquired the skills to make my
>>> own
>>> scripts for this task.
>>>
>>> Thanks so much if you have anything that can help me out,
>>>
>>> Ian McDowell
>>> Aquatic Pathology
>>> University of Rhode Island
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


From cjfields at illinois.edu  Mon Mar 14 13:44:44 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 12:44:44 -0500
Subject: [Bioperl-l] bioperl wiki spam
Message-ID: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>

All,

We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:

http://www.mediawiki.org/wiki/Extension:ConfirmAccount

I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.  

Any thoughts?

chris


From cjfields at illinois.edu  Mon Mar 14 13:51:51 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 12:51:51 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Google Summer of Code
Message-ID: <42CCFB33-B9FC-41C2-987D-BF969F5111EC@illinois.edu>

All,

As Rob Buels previously mentioned, the Open Bioinformatics Foundation has again applied for the Google Summer of Code (GSoC).  BioPerl has been involved with GSoC over the last several years, most recently when Jun Yin refactored the alignment subsystem, code that will be incorporated into BioPerl after the 1.6.2 release:

http://www.bioperl.org/wiki/Google_Summer_of_Code#2010

We have several ideas for projects for the upcoming GSoC 2011 on the wiki, but we are open to just about anything BioPerl-related.  We are also looking for more potential mentors!  If you have ideas or would like to be a mentor, free to submit to the web page, discuss it on this list, or join us on IRC (#obf-soc on freenode).

chris

Christopher Fields
IGB Postdoctoral Fellow
Genomics of Neural & Behavioral Plasticity
University of Illinois Urbana-Champaign
Institute for Genomic Biology
1206 W. Gregory Dr. , MC-195
Urbana, IL 61801




From scott at scottcain.net  Mon Mar 14 14:12:55 2011
From: scott at scottcain.net (Scott Cain)
Date: Mon, 14 Mar 2011 14:12:55 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
Message-ID: <AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>

Hi Chris,

The GMOD wiki has been getting hit similarly.  I've been thinking
about the "vampire" model that EcoliWiki uses: once you have an
account, you have the ability to approve other people's accounts.  The
hope being to distribute the load.  I'm not thrilled about it though:
I want the barrier to entry to be as low as possible.  We already make
it so that you have to have an account to edit, passing a recaptcha on
the way.  Apparently that barrier is already a little too low :-/

Scott


On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
> All,
>
> We have been getting inundated on the wiki with spam lately. ?In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>
> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>
> I wanted to get everyone's opinion on this prior to enforcing it. ?The queue is pretty configurable, and one can set this to auto-delete old requests.
>
> Any thoughts?
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From cjfields at illinois.edu  Mon Mar 14 14:25:05 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 13:25:05 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
Message-ID: <5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>

On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):

"Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."

I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.

chris

On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:

> Hi Chris,
> 
> The GMOD wiki has been getting hit similarly.  I've been thinking
> about the "vampire" model that EcoliWiki uses: once you have an
> account, you have the ability to approve other people's accounts.  The
> hope being to distribute the load.  I'm not thrilled about it though:
> I want the barrier to entry to be as low as possible.  We already make
> it so that you have to have an account to edit, passing a recaptcha on
> the way.  Apparently that barrier is already a little too low :-/
> 
> Scott
> 
> 
> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> All,
>> 
>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>> 
>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>> 
>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>> 
>> Any thoughts?
>> 
>> chris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research




From David.Messina at sbc.su.se  Mon Mar 14 14:25:10 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 14 Mar 2011 19:25:10 +0100
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
Message-ID: <5650D7D3-11ED-4ABF-89E8-BE9175848196@sbc.su.se>

> Any thoughts?

Do it.



From hlapp at drycafe.net  Mon Mar 14 14:48:55 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Mon, 14 Mar 2011 14:48:55 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
Message-ID: <6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>

Any update on the OpenID extension?

	-hilmar

On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:

> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit 
> ):
>
> "Unfortunately, reCAPTCHA might be a victim of its own success - as  
> of 2011, some spammers appear to have figured out a way to bypass  
> it, either through character recognition or by using humans. For  
> that reason, it is not necessarily recommended."
>
> I agree about the barrier to entry issue, but unfortunately with the  
> wiki we're facing a reality check re: spam attacks.  We can probably  
> set up a new group for users that allows account approval, though,  
> which might alleviate the process somewhat.
>
> chris
>
> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>
>> Hi Chris,
>>
>> The GMOD wiki has been getting hit similarly.  I've been thinking
>> about the "vampire" model that EcoliWiki uses: once you have an
>> account, you have the ability to approve other people's accounts.   
>> The
>> hope being to distribute the load.  I'm not thrilled about it though:
>> I want the barrier to entry to be as low as possible.  We already  
>> make
>> it so that you have to have an account to edit, passing a recaptcha  
>> on
>> the way.  Apparently that barrier is already a little too low :-/
>>
>> Scott
>>
>>
>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields  
>> <cjfields at illinois.edu> wrote:
>>> All,
>>>
>>> We have been getting inundated on the wiki with spam lately.  In  
>>> order to get on top of this, I'm thinking about having the wiki  
>>> set up so wiki admins approve new user accounts, using the  
>>> ConfirmAccount plugin:
>>>
>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>
>>> I wanted to get everyone's opinion on this prior to enforcing it.   
>>> The queue is pretty configurable, and one can set this to auto- 
>>> delete old requests.
>>>
>>> Any thoughts?
>>>
>>> chris
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>>
>> -- 
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at  
>> scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From cjfields at illinois.edu  Mon Mar 14 14:55:31 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 13:55:31 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
Message-ID: <2EB73F6E-AAD3-46BD-BB57-AAB3AA1063F7@illinois.edu>

We can test that one out first.  Maybe that will help.

chris

On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:

> Any update on the OpenID extension?
> 
> 	-hilmar
> 
> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
> 
>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>> 
>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>> 
>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>> 
>> chris
>> 
>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>> 
>>> Hi Chris,
>>> 
>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>> about the "vampire" model that EcoliWiki uses: once you have an
>>> account, you have the ability to approve other people's accounts.  The
>>> hope being to distribute the load.  I'm not thrilled about it though:
>>> I want the barrier to entry to be as low as possible.  We already make
>>> it so that you have to have an account to edit, passing a recaptcha on
>>> the way.  Apparently that barrier is already a little too low :-/
>>> 
>>> Scott
>>> 
>>> 
>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>> All,
>>>> 
>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>> 
>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>> 
>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>> 
>>>> Any thoughts?
>>>> 
>>>> chris
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hartzell at alerce.com  Mon Mar 14 20:37:36 2011
From: hartzell at alerce.com (George Hartzell)
Date: Mon, 14 Mar 2011 17:37:36 -0700
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <5650D7D3-11ED-4ABF-89E8-BE9175848196@sbc.su.se>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<5650D7D3-11ED-4ABF-89E8-BE9175848196@sbc.su.se>
Message-ID: <19838.46288.715397.413627@gargle.gargle.HOWL>

Dave Messina writes:
 > > Any thoughts?
 > 
 > Do it.

Do it^2.  You have better things to do than waste time on spammers.

It's nice to not have the bar too high for new folks, but in this age
of spam I think people understand.

g.


From cjfields at illinois.edu  Mon Mar 14 23:01:45 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 22:01:45 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
Message-ID: <84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>

Okay, we have bioperl.org set up to use OpenID, works well:  

http://www.bioperl.org/wiki/Special:OpenIDLogin

I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.

chris

On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:

> Any update on the OpenID extension?
> 
> 	-hilmar
> 
> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
> 
>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>> 
>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>> 
>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>> 
>> chris
>> 
>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>> 
>>> Hi Chris,
>>> 
>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>> about the "vampire" model that EcoliWiki uses: once you have an
>>> account, you have the ability to approve other people's accounts.  The
>>> hope being to distribute the load.  I'm not thrilled about it though:
>>> I want the barrier to entry to be as low as possible.  We already make
>>> it so that you have to have an account to edit, passing a recaptcha on
>>> the way.  Apparently that barrier is already a little too low :-/
>>> 
>>> Scott
>>> 
>>> 
>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>> All,
>>>> 
>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>> 
>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>> 
>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>> 
>>>> Any thoughts?
>>>> 
>>>> chris
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Mon Mar 14 23:12:16 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 22:12:16 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <19838.46288.715397.413627@gargle.gargle.HOWL>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<5650D7D3-11ED-4ABF-89E8-BE9175848196@sbc.su.se>
	<19838.46288.715397.413627@gargle.gargle.HOWL>
Message-ID: <D49A790C-E30D-4587-B9B6-0D5E99B84D97@illinois.edu>

On Mar 14, 2011, at 7:37 PM, George Hartzell wrote:

> Dave Messina writes:
>>> Any thoughts?
>> 
>> Do it.
> 
> Do it^2.  You have better things to do than waste time on spammers.
> 
> It's nice to not have the bar too high for new folks, but in this age
> of spam I think people understand.
> 
> g.

I've disabled new account creation unless OpenID is used; apparently this has worked elsewhere to cut down on spam.  All old accounts are still active, but I think new users will be prompted to tie an OpenID to the account.  

Anyway, if that doesn't work we'll go to the next step (account verification).

chris




From ross at cuhk.edu.hk  Tue Mar 15 01:54:35 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Tue, 15 Mar 2011 13:54:35 +0800
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
Message-ID: <004001cbe2d5$76598200$630c8600$@edu.hk>

$gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
'Fasta');            
$allseqobj = $gb->get_Stream_by_acc("A3ZI37");        
                l
print "HEELO";                                           
while ($seqobj = $allseqobj->next_seq) {             
                        #$seqobj = $allseqobj->next_seq;

                        $seq=$seqobj->seq;

                        }

                    print "222   HEELO";



I find that the 1st HEELO can be printed while the 2nd one can't. Google
does not return checking success/failure or null/exist of the Seq Object. As
the 1st HEELO can be executed, so no throw/exception occurs for the
get_Stream_by_acc. So what can I do? The real case is not hard-coding this
A3ZI37 but reading a file that may contain a lot of these "illegitimate"
accession numbers.



From David.Messina at sbc.su.se  Tue Mar 15 05:02:05 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 15 Mar 2011 10:02:05 +0100
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <004001cbe2d5$76598200$630c8600$@edu.hk>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
Message-ID: <AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>

Hi Ross,

Your code is incomplete and you didn't provide the output from running it,
so it's not easy to figure out where you're going wrong.

Try copying the example code directly from here


http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html

and making sure that works first before modifying it.


More documentation and examples here:
http://www.bioperl.org/wiki/HOWTO:Beginners
http://www.bioperl.org/wiki/Bioperl_scripts


Dave




On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:

> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
> 'Fasta');
> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>                l
> print "HEELO";
> while ($seqobj = $allseqobj->next_seq) {
>                        #$seqobj = $allseqobj->next_seq;
>
>                        $seq=$seqobj->seq;
>
>                        }
>
>                    print "222   HEELO";
>
>
>
> I find that the 1st HEELO can be printed while the 2nd one can't. Google
> does not return checking success/failure or null/exist of the Seq Object.
> As
> the 1st HEELO can be executed, so no throw/exception occurs for the
> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
> accession numbers.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From ross at cuhk.edu.hk  Tue Mar 15 10:16:56 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Tue, 15 Mar 2011 22:16:56 +0800
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
Message-ID: <005301cbe31b$a3bee550$eb3caff0$@edu.hk>

While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...

 

 

#!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   

use Bio::DB::GenBank;

 

$gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');


$allseqobj = $gb->get_Stream_by_acc("A3ZI37");


 print "HEELO";

while ($seqobj = $allseqobj->next_seq) {
                       #$seqobj = $allseqobj->next_seq;
                       $seq=$seqobj->seq;
}
print "222   HEELO";




 

 

From: Dave Messina [mailto:David.Messina at sbc.su.se] 
Sent: 2011?3?15? 17:02
To: Ross KK Leung
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] how to prevent forced exit?

 

Hi Ross,

 

Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.

 

Try copying the example code directly from here

 

    http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html

 

and making sure that works first before modifying it.

 

 

More documentation and examples here:

http://www.bioperl.org/wiki/HOWTO:Beginners

http://www.bioperl.org/wiki/Bioperl_scripts

 

 

Dave

 

 

 

On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:

$gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
'Fasta');
$allseqobj = $gb->get_Stream_by_acc("A3ZI37");
               l
print "HEELO";
while ($seqobj = $allseqobj->next_seq) {
                       #$seqobj = $allseqobj->next_seq;

                       $seq=$seqobj->seq;

                       }

                   print "222   HEELO";



I find that the 1st HEELO can be printed while the 2nd one can't. Google
does not return checking success/failure or null/exist of the Seq Object. As
the 1st HEELO can be executed, so no throw/exception occurs for the
get_Stream_by_acc. So what can I do? The real case is not hard-coding this
A3ZI37 but reading a file that may contain a lot of these "illegitimate"
accession numbers.

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

 




From cjfields at illinois.edu  Tue Mar 15 10:44:23 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 15 Mar 2011 09:44:23 -0500
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <005301cbe31b$a3bee550$eb3caff0$@edu.hk>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
Message-ID: <DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>

Ross,

Hope you're exaggerating, you really shouldn't use this service for retrieving 1 million records as you'll likely find your IP banned by NCBI; they are starting to enforce stricter web-based access to their  server now.  Bio::DB::GenBank uses a GET HTTP request using URI-based parameters which effectively limits the length of the query to around 200-300 IDs per request, so you would have to split single one large request many.  Thousands of repeated requests, even with a timeout, may flag your IP as 'spam'.  You can use something like Bio::DB::EUtilities to grab larger groups of seqs (~1000 IDs) b/c the latest EUtilities uses POST requests vs GET for a large number of IDs, but you are still effectively limited by the number of requests.

Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?

chris

On Mar 15, 2011, at 9:16 AM, Ross KK Leung wrote:

> While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...
> 
> 
> 
> 
> 
> #!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   
> 
> use Bio::DB::GenBank;
> 
> 
> 
> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');
> 
> 
> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
> 
> 
> print "HEELO";
> 
> while ($seqobj = $allseqobj->next_seq) {
>                       #$seqobj = $allseqobj->next_seq;
>                       $seq=$seqobj->seq;
> }
> print "222   HEELO";
> 
> 
> 
> 
> 
> 
> 
> 
> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
> Sent: 2011?3?15? 17:02
> To: Ross KK Leung
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] how to prevent forced exit?
> 
> 
> 
> Hi Ross,
> 
> 
> 
> Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.
> 
> 
> 
> Try copying the example code directly from here
> 
> 
> 
>    http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html
> 
> 
> 
> and making sure that works first before modifying it.
> 
> 
> 
> 
> 
> More documentation and examples here:
> 
> http://www.bioperl.org/wiki/HOWTO:Beginners
> 
> http://www.bioperl.org/wiki/Bioperl_scripts
> 
> 
> 
> 
> 
> Dave
> 
> 
> 
> 
> 
> 
> 
> On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:
> 
> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
> 'Fasta');
> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>               l
> print "HEELO";
> while ($seqobj = $allseqobj->next_seq) {
>                       #$seqobj = $allseqobj->next_seq;
> 
>                       $seq=$seqobj->seq;
> 
>                       }
> 
>                   print "222   HEELO";
> 
> 
> 
> I find that the 1st HEELO can be printed while the 2nd one can't. Google
> does not return checking success/failure or null/exist of the Seq Object. As
> the 1st HEELO can be executed, so no throw/exception occurs for the
> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
> accession numbers.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From dvadell at clustering.com.ar  Tue Mar 15 10:59:20 2011
From: dvadell at clustering.com.ar (Diego M. Vadell)
Date: Tue, 15 Mar 2011 11:59:20 -0300
Subject: [Bioperl-l] advice about bioperl-ext -- defunct?
Message-ID: <38be317a0815ba7276d56e5a6c93d116@webmail.clustering.com.ar>

Hi,

 I have just downloaded bioperl-ext from github, and it says "XS-based
BioPerl extensions to C libraries (defunct) ? [Read more ->
https://github.com/bioperl/bioperl-ext#readme]" . I read the readme but it
looks alive ( i.e. no mention of an ending of the project ). 

 I installed it ( adding "-fPIC" in the 3 Makefile.PLs ) and I'm about to
start using it. But, does is it still maintained? Is it still in use?
Recommended for a new project? I don't mind fixing compilation errors, but
maybe there is a new package that superseded it. Maybe I'm downloading it
from the wrong place.

 Regards,
 -- Diego





From jimhu at tamu.edu  Tue Mar 15 11:25:36 2011
From: jimhu at tamu.edu (Jim Hu)
Date: Tue, 15 Mar 2011 10:25:36 -0500
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
	<DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
Message-ID: <9CD1455E-88B4-4E2A-B3BC-398C10D5AAA9@tamu.edu>

Hi Chris,

A version of this admonition should be on every wiki HOWTO that involves retrieving records from external sources, and in the docs for the relevant modules.  Speaking as someone who has used BioPerl intermittently for years, and who has Sysiphus-like relationship with the learning curve, I think the docs could use more discussion of when to use particular modules in addition to the details of how to use them provided in the perldocs. I realize this is hard, given the perl "more than one way to do it" world view, but that's my $0.02.

Since BioPerl.org is a wiki, I suppose I should do that admonition edit myself... especially since I already know the wiki markup to transclude the same text into multiple pages.

Jim

Sent from my iPad

On Mar 15, 2011, at 9:44 AM, Chris Fields <cjfields at illinois.edu> wrote:

> Ross,
> 
> Hope you're exaggerating, you really shouldn't use this service for retrieving 1 million records as you'll likely find your IP banned by NCBI; they are starting to enforce stricter web-based access to their  server now.  Bio::DB::GenBank uses a GET HTTP request using URI-based parameters which effectively limits the length of the query to around 200-300 IDs per request, so you would have to split single one large request many.  Thousands of repeated requests, even with a timeout, may flag your IP as 'spam'.  You can use something like Bio::DB::EUtilities to grab larger groups of seqs (~1000 IDs) b/c the latest EUtilities uses POST requests vs GET for a large number of IDs, but you are still effectively limited by the number of requests.
> 
> Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?
> 
> chris
> 
> On Mar 15, 2011, at 9:16 AM, Ross KK Leung wrote:
> 
>> While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...
>> 
>> 
>> 
>> 
>> 
>> #!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   
>> 
>> use Bio::DB::GenBank;
>> 
>> 
>> 
>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');
>> 
>> 
>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>> 
>> 
>> print "HEELO";
>> 
>> while ($seqobj = $allseqobj->next_seq) {
>>                      #$seqobj = $allseqobj->next_seq;
>>                      $seq=$seqobj->seq;
>> }
>> print "222   HEELO";
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
>> Sent: 2011?3?15? 17:02
>> To: Ross KK Leung
>> Cc: bioperl-l at lists.open-bio.org
>> Subject: Re: [Bioperl-l] how to prevent forced exit?
>> 
>> 
>> 
>> Hi Ross,
>> 
>> 
>> 
>> Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.
>> 
>> 
>> 
>> Try copying the example code directly from here
>> 
>> 
>> 
>>   http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html
>> 
>> 
>> 
>> and making sure that works first before modifying it.
>> 
>> 
>> 
>> 
>> 
>> More documentation and examples here:
>> 
>> http://www.bioperl.org/wiki/HOWTO:Beginners
>> 
>> http://www.bioperl.org/wiki/Bioperl_scripts
>> 
>> 
>> 
>> 
>> 
>> Dave
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:
>> 
>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
>> 'Fasta');
>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>              l
>> print "HEELO";
>> while ($seqobj = $allseqobj->next_seq) {
>>                      #$seqobj = $allseqobj->next_seq;
>> 
>>                      $seq=$seqobj->seq;
>> 
>>                      }
>> 
>>                  print "222   HEELO";
>> 
>> 
>> 
>> I find that the 1st HEELO can be printed while the 2nd one can't. Google
>> does not return checking success/failure or null/exist of the Seq Object. As
>> the 1st HEELO can be executed, so no throw/exception occurs for the
>> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
>> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
>> accession numbers.
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Tue Mar 15 11:45:20 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 15 Mar 2011 10:45:20 -0500
Subject: [Bioperl-l] advice about bioperl-ext -- defunct?
In-Reply-To: <38be317a0815ba7276d56e5a6c93d116@webmail.clustering.com.ar>
References: <38be317a0815ba7276d56e5a6c93d116@webmail.clustering.com.ar>
Message-ID: <3892F905-2D1F-43CF-8968-055C9F902504@illinois.edu>

On Mar 15, 2011, at 9:59 AM, Diego M. Vadell wrote:

> Hi,
> 
> I have just downloaded bioperl-ext from github, and it says "XS-based
> BioPerl extensions to C libraries (defunct) ? [Read more ->
> https://github.com/bioperl/bioperl-ext#readme]" . I read the readme but it
> looks alive ( i.e. no mention of an ending of the project ). 
> 
> I installed it ( adding "-fPIC" in the 3 Makefile.PLs ) and I'm about to
> start using it. But, does is it still maintained? Is it still in use?

Re: being maintained: No, except Bio::Tools::HMM (https://github.com/bioperl/Bio-Tools-HMM)

Re: in use: somewhat.  I think some still use Bio::SeqIO::staden::read and Bio::Ext::Align, but they haven't actively maintained in quite some time.

> Recommended for a new project? I don't mind fixing compilation errors, but
> maybe there is a new package that superseded it. Maybe I'm downloading it
> from the wrong place.
> 
> Regards,
> -- Diego

The code still works in some cases but is somewhat bit-rotted (I recall getting very inconsistent results from Bio::SearchUtils, not sure why).  

We (Bio* projects) are starting to consolidate around using BioLib for consistent bindings to C/C++ libraries, though that project is undergoing some changes:

http://biolib.open-bio.org/wiki/Main_Page

Pjotr Prins is the lead on that, worth talking to.  The next big step is to interface with EMBOSS libraries, which is very promising.

chris


From cjfields at illinois.edu  Tue Mar 15 11:54:38 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 15 Mar 2011 10:54:38 -0500
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <9CD1455E-88B4-4E2A-B3BC-398C10D5AAA9@tamu.edu>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
	<DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
	<9CD1455E-88B4-4E2A-B3BC-398C10D5AAA9@tamu.edu>
Message-ID: <3E73745F-A687-4229-B71E-5C56B2D1FBAE@illinois.edu>

Jim,

It's worth noting in something more prominent, like the tutorial, FAQ, and appropriate HOWTO's.  We've long considered whether it would be worth setting up a cookbook-like section that includes simple workflows, that would also be appropriate for something like this.

Also, I do think this is mentioned in the POD for several modules, but worth adding a prominent section on it if it's not present.  In Bio::DB::GenBank:

  WARNING: Please do NOT spam the Entrez web server with multiple requests.  NCBI offers Batch Entrez for this purpose.

That could be placed somewhere that is a bit more helpful.

chris


On Mar 15, 2011, at 10:25 AM, Jim Hu wrote:

> Hi Chris,
> 
> A version of this admonition should be on every wiki HOWTO that involves retrieving records from external sources, and in the docs for the relevant modules.  Speaking as someone who has used BioPerl intermittently for years, and who has Sysiphus-like relationship with the learning curve, I think the docs could use more discussion of when to use particular modules in addition to the details of how to use them provided in the perldocs. I realize this is hard, given the perl "more than one way to do it" world view, but that's my $0.02.
> 
> Since BioPerl.org is a wiki, I suppose I should do that admonition edit myself... especially since I already know the wiki markup to transclude the same text into multiple pages.
> 
> Jim
> 
> Sent from my iPad
> 
> On Mar 15, 2011, at 9:44 AM, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Ross,
>> 
>> Hope you're exaggerating, you really shouldn't use this service for retrieving 1 million records as you'll likely find your IP banned by NCBI; they are starting to enforce stricter web-based access to their  server now.  Bio::DB::GenBank uses a GET HTTP request using URI-based parameters which effectively limits the length of the query to around 200-300 IDs per request, so you would have to split single one large request many.  Thousands of repeated requests, even with a timeout, may flag your IP as 'spam'.  You can use something like Bio::DB::EUtilities to grab larger groups of seqs (~1000 IDs) b/c the latest EUtilities uses POST requests vs GET for a large number of IDs, but you are still effectively limited by the number of requests.
>> 
>> Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?
>> 
>> chris
>> 
>> On Mar 15, 2011, at 9:16 AM, Ross KK Leung wrote:
>> 
>>> While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...
>>> 
>>> 
>>> 
>>> 
>>> 
>>> #!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   
>>> 
>>> use Bio::DB::GenBank;
>>> 
>>> 
>>> 
>>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');
>>> 
>>> 
>>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>> 
>>> 
>>> print "HEELO";
>>> 
>>> while ($seqobj = $allseqobj->next_seq) {
>>>                     #$seqobj = $allseqobj->next_seq;
>>>                     $seq=$seqobj->seq;
>>> }
>>> print "222   HEELO";
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
>>> Sent: 2011?3?15? 17:02
>>> To: Ross KK Leung
>>> Cc: bioperl-l at lists.open-bio.org
>>> Subject: Re: [Bioperl-l] how to prevent forced exit?
>>> 
>>> 
>>> 
>>> Hi Ross,
>>> 
>>> 
>>> 
>>> Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.
>>> 
>>> 
>>> 
>>> Try copying the example code directly from here
>>> 
>>> 
>>> 
>>>  http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html
>>> 
>>> 
>>> 
>>> and making sure that works first before modifying it.
>>> 
>>> 
>>> 
>>> 
>>> 
>>> More documentation and examples here:
>>> 
>>> http://www.bioperl.org/wiki/HOWTO:Beginners
>>> 
>>> http://www.bioperl.org/wiki/Bioperl_scripts
>>> 
>>> 
>>> 
>>> 
>>> 
>>> Dave
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:
>>> 
>>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
>>> 'Fasta');
>>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>>             l
>>> print "HEELO";
>>> while ($seqobj = $allseqobj->next_seq) {
>>>                     #$seqobj = $allseqobj->next_seq;
>>> 
>>>                     $seq=$seqobj->seq;
>>> 
>>>                     }
>>> 
>>>                 print "222   HEELO";
>>> 
>>> 
>>> 
>>> I find that the 1st HEELO can be printed while the 2nd one can't. Google
>>> does not return checking success/failure or null/exist of the Seq Object. As
>>> the 1st HEELO can be executed, so no throw/exception occurs for the
>>> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
>>> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
>>> accession numbers.
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From dvadell at clustering.com.ar  Tue Mar 15 12:01:22 2011
From: dvadell at clustering.com.ar (Diego M. Vadell)
Date: Tue, 15 Mar 2011 13:01:22 -0300
Subject: [Bioperl-l] advice about bioperl-ext -- defunct?
In-Reply-To: <3892F905-2D1F-43CF-8968-055C9F902504@illinois.edu>
Message-ID: <218950b508a0e4a8ad07227974989e5f@webmail.clustering.com.ar>

Hi Chris,

 Thank you! I will align with bioperl-run then, and keep an eye on biolib.

Cheers,
 -- Diego


 
----------------original message-----------------
From: "Chris Fields" cjfields at illinois.edu
To: "Diego M. Vadell" dvadell at clustering.com.ar
CC: bioperl-l at lists.open-bio.org
Date: Tue, 15 Mar 2011 10:45:20 -0500
-------------------------------------------------
 
 
> On Mar 15, 2011, at 9:59 AM, Diego M. Vadell wrote:
> 
>> Hi,
>> 
>> I have just downloaded bioperl-ext from github, and it says "XS-based
>> BioPerl extensions to C libraries (defunct) ? [Read more ->
>> https://github.com/bioperl/bioperl-ext#readme]" . I read the readme but 
>> it
>> looks alive ( i.e. no mention of an ending of the project ). 
>> 
>> I installed it ( adding "-fPIC" in the 3 Makefile.PLs ) and I'm about to
>> start using it. But, does is it still maintained? Is it still in use?
> 
> Re: being maintained: No, except Bio::Tools::HMM 
> (https://github.com/bioperl/Bio-Tools-HMM)
> 
> Re: in use: somewhat. I think some still use Bio::SeqIO::staden::read and 
> Bio::Ext::Align, but they haven't actively maintained in quite some time.
> 
>> Recommended for a new project? I don't mind fixing compilation errors,
but
>> maybe there is a new package that superseded it. Maybe I'm downloading it
>> from the wrong place.
>> 
>> Regards,
>> -- Diego
> 
> The code still works in some cases but is somewhat bit-rotted (I recall
getting 
> very inconsistent results from Bio::SearchUtils, not sure why). 
> 
> We (Bio* projects) are starting to consolidate around using BioLib for 
> consistent bindings to C/C++ libraries, though that project is undergoing
some 
> changes:
> 
> http://biolib.open-bio.org/wiki/Main_Page
> 
> Pjotr Prins is the lead on that, worth talking to. The next big step is to
interface 
> with EMBOSS libraries, which is very promising.
> 
> chris
> 





From ross at cuhk.edu.hk  Tue Mar 15 20:55:42 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Wed, 16 Mar 2011 08:55:42 +0800
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
	<DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
Message-ID: <007201cbe374$dffa5eb0$9fef1c10$@edu.hk>

-----Original Message-----
From: Chris Fields [mailto:cjfields at illinois.edu] 
Sent: 2011?3?15? 22:44
To: Ross KK Leung
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] how to prevent forced exit?

Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?

chris


Dear Chris,

Thanks for your suggestion. The problem we encounter is that we don't know what database/genbank files we have to retrieve in order to accomplish the job. It seems that the nr database does not include all the records, and we don't know whether we have to concatenate all the genbank files into a very big one so to parse one by one. Any advice?

Gratefully, Ross




From jimhu at tamu.edu  Wed Mar 16 02:22:23 2011
From: jimhu at tamu.edu (Jim Hu)
Date: Wed, 16 Mar 2011 01:22:23 -0500
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <3E73745F-A687-4229-B71E-5C56B2D1FBAE@illinois.edu>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
	<DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
	<9CD1455E-88B4-4E2A-B3BC-398C10D5AAA9@tamu.edu>
	<3E73745F-A687-4229-B71E-5C56B2D1FBAE@illinois.edu>
Message-ID: <D714889D-D73C-4E45-87E3-FE921BFEBA48@tamu.edu>

I put a snippet at the end of:

	http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database

The snippet is on an independent page, and is included via 

	{{:Remote_database_admonition}}
 
which allows people to put it into other pages, and to edit it and have the changes update on all the pages where it's included.  So if someone wants to reword it, make it red text, put it in a box div or whatever, it just has to be done once.  Or, since it's a wiki,  others can just kill it altogether. ;)

Jim

On Mar 15, 2011, at 10:54 AM, Chris Fields wrote:

> Jim,
> 
> It's worth noting in something more prominent, like the tutorial, FAQ, and appropriate HOWTO's.  We've long considered whether it would be worth setting up a cookbook-like section that includes simple workflows, that would also be appropriate for something like this.
> 
> Also, I do think this is mentioned in the POD for several modules, but worth adding a prominent section on it if it's not present.  In Bio::DB::GenBank:
> 
>  WARNING: Please do NOT spam the Entrez web server with multiple requests.  NCBI offers Batch Entrez for this purpose.
> 
> That could be placed somewhere that is a bit more helpful.
> 
> chris
> 
> 
> On Mar 15, 2011, at 10:25 AM, Jim Hu wrote:
> 
>> Hi Chris,
>> 
>> A version of this admonition should be on every wiki HOWTO that involves retrieving records from external sources, and in the docs for the relevant modules.  Speaking as someone who has used BioPerl intermittently for years, and who has Sysiphus-like relationship with the learning curve, I think the docs could use more discussion of when to use particular modules in addition to the details of how to use them provided in the perldocs. I realize this is hard, given the perl "more than one way to do it" world view, but that's my $0.02.
>> 
>> Since BioPerl.org is a wiki, I suppose I should do that admonition edit myself... especially since I already know the wiki markup to transclude the same text into multiple pages.
>> 
>> Jim
>> 
>> Sent from my iPad
>> 
>> On Mar 15, 2011, at 9:44 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> 
>>> Ross,
>>> 
>>> Hope you're exaggerating, you really shouldn't use this service for retrieving 1 million records as you'll likely find your IP banned by NCBI; they are starting to enforce stricter web-based access to their  server now.  Bio::DB::GenBank uses a GET HTTP request using URI-based parameters which effectively limits the length of the query to around 200-300 IDs per request, so you would have to split single one large request many.  Thousands of repeated requests, even with a timeout, may flag your IP as 'spam'.  You can use something like Bio::DB::EUtilities to grab larger groups of seqs (~1000 IDs) b/c the latest EUtilities uses POST requests vs GET for a large number of IDs, but you are still effectively limited by the number of requests.
>>> 
>>> Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?
>>> 
>>> chris
>>> 
>>> On Mar 15, 2011, at 9:16 AM, Ross KK Leung wrote:
>>> 
>>>> While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> #!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   
>>>> 
>>>> use Bio::DB::GenBank;
>>>> 
>>>> 
>>>> 
>>>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');
>>>> 
>>>> 
>>>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>>> 
>>>> 
>>>> print "HEELO";
>>>> 
>>>> while ($seqobj = $allseqobj->next_seq) {
>>>>                    #$seqobj = $allseqobj->next_seq;
>>>>                    $seq=$seqobj->seq;
>>>> }
>>>> print "222   HEELO";
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
>>>> Sent: 2011?3?15? 17:02
>>>> To: Ross KK Leung
>>>> Cc: bioperl-l at lists.open-bio.org
>>>> Subject: Re: [Bioperl-l] how to prevent forced exit?
>>>> 
>>>> 
>>>> 
>>>> Hi Ross,
>>>> 
>>>> 
>>>> 
>>>> Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.
>>>> 
>>>> 
>>>> 
>>>> Try copying the example code directly from here
>>>> 
>>>> 
>>>> 
>>>> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html
>>>> 
>>>> 
>>>> 
>>>> and making sure that works first before modifying it.
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> More documentation and examples here:
>>>> 
>>>> http://www.bioperl.org/wiki/HOWTO:Beginners
>>>> 
>>>> http://www.bioperl.org/wiki/Bioperl_scripts
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> Dave
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:
>>>> 
>>>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
>>>> 'Fasta');
>>>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>>>            l
>>>> print "HEELO";
>>>> while ($seqobj = $allseqobj->next_seq) {
>>>>                    #$seqobj = $allseqobj->next_seq;
>>>> 
>>>>                    $seq=$seqobj->seq;
>>>> 
>>>>                    }
>>>> 
>>>>                print "222   HEELO";
>>>> 
>>>> 
>>>> 
>>>> I find that the 1st HEELO can be printed while the 2nd one can't. Google
>>>> does not return checking success/failure or null/exist of the Seq Object. As
>>>> the 1st HEELO can be executed, so no throw/exception occurs for the
>>>> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
>>>> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
>>>> accession numbers.
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054





From cjfields at illinois.edu  Wed Mar 16 13:58:23 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 12:58:23 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
Message-ID: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>

(apologies if you receive multiple copies of this)

All,

We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:

http://redmine.open-bio.org/

All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.

For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:

1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.

2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.

Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.

Let us know if you have any questions.  

chris

Christopher Fields
IGB Postdoctoral Fellow
Genomics of Neural & Behavioral Plasticity
University of Illinois Urbana-Champaign
Institute for Genomic Biology
1206 W. Gregory Dr. , MC-195
Urbana, IL 61801


From simon.noel.2 at ulaval.ca  Wed Mar 16 15:40:09 2011
From: simon.noel.2 at ulaval.ca (=?iso-8859-1?Q?Simon_No=EBl?=)
Date: Wed, 16 Mar 2011 15:40:09 -0400
Subject: [Bioperl-l]  Perl/BioPerl
Message-ID: <1C970CA8E580A84394CE5CF42FEC0046DF67A4FA81@EXCH-MBX-E.ulaval.ca>

 Hi, 
 
I don't know if I am on the right mailling list for this.
 
My director say that I should have a class of Perl or BioPerl.  Witch one should be better?  Do you know where I can find such class?


Simon No?l
CdeC


From cjfields at illinois.edu  Wed Mar 16 18:30:40 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 17:30:40 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
	<AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
Message-ID: <D6A1291F-898A-4563-8C19-FA2E92D48767@illinois.edu>

Huh, Dave Messina reported something similar earlier.  I actually tested this myself and couldn't reproduce it, maybe I'll try it on Firefox (I was using Chrome).

chris

On Mar 16, 2011, at 3:48 PM, Jonathan Duke Leto wrote:

> Howdy,
> 
> Thanks for working on this Chris!
> 
> I am not sure the password reset works properly.
> 
> Attached is a screenshot of it giving odd errors.
> 
> This was on Firefox 3.6.
> 
> Duke
> 
> On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> (apologies if you receive multiple copies of this)
>> 
>> All,
>> 
>> We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:
>> 
>> http://redmine.open-bio.org/
>> 
>> All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.
>> 
>> For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:
>> 
>> 1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.
>> 
>> 2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.
>> 
>> Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
>> 
>> Let us know if you have any questions.
>> 
>> chris
>> 
>> Christopher Fields
>> IGB Postdoctoral Fellow
>> Genomics of Neural & Behavioral Plasticity
>> University of Illinois Urbana-Champaign
>> Institute for Genomic Biology
>> 1206 W. Gregory Dr. , MC-195
>> Urbana, IL 61801
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> Jonathan "Duke" Leto
> jonathan at leto.net
> http://leto.net
> <obf_redmine.png>




From cjfields at illinois.edu  Wed Mar 16 18:50:18 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 17:50:18 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
	<AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
Message-ID: <F380825D-8F8B-4766-99C3-36FDD8E9C99D@illinois.edu>

I reset the plugins and reloaded the database.  Does that help?  I tested it out again using a test user (using the 'Lost password' link) and it seemed to work.

If not, I can manually reset and send the password to you.

chris

On Mar 16, 2011, at 3:48 PM, Jonathan Duke Leto wrote:

> Howdy,
> 
> Thanks for working on this Chris!
> 
> I am not sure the password reset works properly.
> 
> Attached is a screenshot of it giving odd errors.
> 
> This was on Firefox 3.6.
> 
> Duke
> 
> On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> (apologies if you receive multiple copies of this)
>> 
>> All,
>> 
>> We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:
>> 
>> http://redmine.open-bio.org/
>> 
>> All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.
>> 
>> For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:
>> 
>> 1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.
>> 
>> 2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.
>> 
>> Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
>> 
>> Let us know if you have any questions.
>> 
>> chris
>> 
>> Christopher Fields
>> IGB Postdoctoral Fellow
>> Genomics of Neural & Behavioral Plasticity
>> University of Illinois Urbana-Champaign
>> Institute for Genomic Biology
>> 1206 W. Gregory Dr. , MC-195
>> Urbana, IL 61801
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> Jonathan "Duke" Leto
> jonathan at leto.net
> http://leto.net
> <obf_redmine.png>




From hlapp at drycafe.net  Wed Mar 16 23:05:15 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 16 Mar 2011 23:05:15 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
Message-ID: <1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>


On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:

> Okay, we have bioperl.org set up to use OpenID, works well:

Seems to work mostly - there seems to be some odd small problem with  
ClaimID: typing in my username leads to an OpenID error, whereas  
entering my full ClaimID OpenID works.  Not sure why that would be.

Any chance this can be enabled for BioSQL too (and accordingly account  
creation disabled there, too)?

	-hilmar

>
>
> http://www.bioperl.org/wiki/Special:OpenIDLogin
>
> I have also temporarily shut down new user account creation (new  
> users must now use OpenID); old users can still use the login, but  
> they can also tie their account to an OpenID.  Let's see if it cuts  
> down on the spam.
>
> chris
>
> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>
>> Any update on the OpenID extension?
>>
>> 	-hilmar
>>
>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>
>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit 
>>> ):
>>>
>>> "Unfortunately, reCAPTCHA might be a victim of its own success -  
>>> as of 2011, some spammers appear to have figured out a way to  
>>> bypass it, either through character recognition or by using  
>>> humans. For that reason, it is not necessarily recommended."
>>>
>>> I agree about the barrier to entry issue, but unfortunately with  
>>> the wiki we're facing a reality check re: spam attacks.  We can  
>>> probably set up a new group for users that allows account  
>>> approval, though, which might alleviate the process somewhat.
>>>
>>> chris
>>>
>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>
>>>> Hi Chris,
>>>>
>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>> account, you have the ability to approve other people's  
>>>> accounts.  The
>>>> hope being to distribute the load.  I'm not thrilled about it  
>>>> though:
>>>> I want the barrier to entry to be as low as possible.  We already  
>>>> make
>>>> it so that you have to have an account to edit, passing a  
>>>> recaptcha on
>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu 
>>>> > wrote:
>>>>> All,
>>>>>
>>>>> We have been getting inundated on the wiki with spam lately.  In  
>>>>> order to get on top of this, I'm thinking about having the wiki  
>>>>> set up so wiki admins approve new user accounts, using the  
>>>>> ConfirmAccount plugin:
>>>>>
>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>
>>>>> I wanted to get everyone's opinion on this prior to enforcing  
>>>>> it.  The queue is pretty configurable, and one can set this to  
>>>>> auto-delete old requests.
>>>>>
>>>>> Any thoughts?
>>>>>
>>>>> chris
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>
>>>>
>>>>
>>>> -- 
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at  
>>>> scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                      
>>>> 216-392-3087
>>>> Ontario Institute for Cancer Research
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>> ===========================================================
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From cjfields at illinois.edu  Wed Mar 16 23:08:11 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 22:08:11 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
Message-ID: <E0AD66F8-13FE-4940-A0F5-2E4CC0C02755@illinois.edu>

I can work on that.  Peter, need this for biopython?

chris

On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:

> 
> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
> 
>> Okay, we have bioperl.org set up to use OpenID, works well:
> 
> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works.  Not sure why that would be.
> 
> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
> 
> 	-hilmar
> 
>> 
>> 
>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>> 
>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.
>> 
>> chris
>> 
>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>> 
>>> Any update on the OpenID extension?
>>> 
>>> 	-hilmar
>>> 
>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>> 
>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>> 
>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>> 
>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>> 
>>>> chris
>>>> 
>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>> 
>>>>> Hi Chris,
>>>>> 
>>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>> account, you have the ability to approve other people's accounts.  The
>>>>> hope being to distribute the load.  I'm not thrilled about it though:
>>>>> I want the barrier to entry to be as low as possible.  We already make
>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>> 
>>>>> Scott
>>>>> 
>>>>> 
>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>> All,
>>>>>> 
>>>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>> 
>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>> 
>>>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>> 
>>>>>> Any thoughts?
>>>>>> 
>>>>>> chris
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> -- 
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>> ===========================================================
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 




From cjfields at illinois.edu  Wed Mar 16 23:59:17 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 22:59:17 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
Message-ID: <B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>

Done, for BioSQL.  Let me know about Biopython and the others.

-c 

On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:

> 
> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
> 
>> Okay, we have bioperl.org set up to use OpenID, works well:
> 
> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works.  Not sure why that would be.
> 
> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
> 
> 	-hilmar
> 
>> 
>> 
>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>> 
>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.
>> 
>> chris
>> 
>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>> 
>>> Any update on the OpenID extension?
>>> 
>>> 	-hilmar
>>> 
>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>> 
>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>> 
>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>> 
>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>> 
>>>> chris
>>>> 
>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>> 
>>>>> Hi Chris,
>>>>> 
>>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>> account, you have the ability to approve other people's accounts.  The
>>>>> hope being to distribute the load.  I'm not thrilled about it though:
>>>>> I want the barrier to entry to be as low as possible.  We already make
>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>> 
>>>>> Scott
>>>>> 
>>>>> 
>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>> All,
>>>>>> 
>>>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>> 
>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>> 
>>>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>> 
>>>>>> Any thoughts?
>>>>>> 
>>>>>> chris
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> -- 
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>> ===========================================================
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 




From hlapp at drycafe.net  Thu Mar 17 00:07:45 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Thu, 17 Mar 2011 00:07:45 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
Message-ID: <6747C6EA-27BC-43C1-89B4-0F3AEF18BFA4@drycafe.net>


On Mar 16, 2011, at 11:59 PM, Chris Fields wrote:

> Done, for BioSQL.  Let me know about Biopython and the others.

Great, works! -hilmar


-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From p.j.a.cock at googlemail.com  Thu Mar 17 04:27:22 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 17 Mar 2011 08:27:22 +0000
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
Message-ID: <AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>

Yes please - thanks Chris!

Peter

On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu> wrote:
> Done, for BioSQL. ?Let me know about Biopython and the others.
>
> -c
>
> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>
>>
>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>
>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>
>> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works. ?Not sure why that would be.
>>
>> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
>>
>> ? ? ? -hilmar
>>
>>>
>>>
>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>
>>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID. ?Let's see if it cuts down on the spam.
>>>
>>> chris
>>>
>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>
>>>> Any update on the OpenID extension?
>>>>
>>>> ? ? -hilmar
>>>>
>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>
>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>>>
>>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>>>
>>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks. ?We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>>>
>>>>> chris
>>>>>
>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>
>>>>>> Hi Chris,
>>>>>>
>>>>>> The GMOD wiki has been getting hit similarly. ?I've been thinking
>>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>>> account, you have the ability to approve other people's accounts. ?The
>>>>>> hope being to distribute the load. ?I'm not thrilled about it though:
>>>>>> I want the barrier to entry to be as low as possible. ?We already make
>>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>>> the way. ?Apparently that barrier is already a little too low :-/
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>>> All,
>>>>>>>
>>>>>>> We have been getting inundated on the wiki with spam lately. ?In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>>>
>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>
>>>>>>> I wanted to get everyone's opinion on this prior to enforcing it. ?The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>>>
>>>>>>> Any thoughts?
>>>>>>>
>>>>>>> chris
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> ------------------------------------------------------------------------
>>>>>> Scott Cain, Ph. D.



From David.Messina at sbc.su.se  Thu Mar 17 04:51:21 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 17 Mar 2011 09:51:21 +0100
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <F380825D-8F8B-4766-99C3-36FDD8E9C99D@illinois.edu>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
	<AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
	<F380825D-8F8B-4766-99C3-36FDD8E9C99D@illinois.edu>
Message-ID: <AANLkTik8oYG1yJ7HdV119K08NsbqpDTUpDAtKUPSKUMF@mail.gmail.com>

Works for me now ? I was able to reset the password and log in.

Thanks, Chris!

Dave




On Wed, Mar 16, 2011 at 23:50, Chris Fields <cjfields at illinois.edu> wrote:

> I reset the plugins and reloaded the database.  Does that help?  I tested
> it out again using a test user (using the 'Lost password' link) and it
> seemed to work.
>
> If not, I can manually reset and send the password to you.
>
> chris
>
> On Mar 16, 2011, at 3:48 PM, Jonathan Duke Leto wrote:
>
> > Howdy,
> >
> > Thanks for working on this Chris!
> >
> > I am not sure the password reset works properly.
> >
> > Attached is a screenshot of it giving odd errors.
> >
> > This was on Firefox 3.6.
> >
> > Duke
> >
> > On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu>
> wrote:
> >> (apologies if you receive multiple copies of this)
> >>
> >> All,
> >>
> >> We are currently about 95% done with a transition over to our new
> Redmine tracking system, to the point where we feel comfortable in going
> ahead with opening it to developers:
> >>
> >> http://redmine.open-bio.org/
> >>
> >> All edits to bugzilla reports on our old system (
> http://bugzilla.open-bio.org/) are now disabled and the system is now
> read-only.  Any new bugs and comments to old ones should be reported on the
> new Redmine server.
> >>
> >> For current Bugzilla users, we have migrated login IDs to Redmine (this
> is normally an email address), but we have reset user passwords for security
> reasons.  There are two ways to access your account:
> >>
> >> 1) When logging in (http://redmine.open-bio.org/login), click on the
> 'Lost password' link.  You will be prompted for your email address (this
> should be the same as your bugzilla login).  An new email will be sent out
> containing directions for resetting your password and logging in.
> >>
> >> 2) It is possible the above may be automatically detected as spam.  If
> the above doesn't work or the reset email isn't received within a day,
> contact support at helpdesk.open-bio.org to receive your new password.
> >>
> >> Also, note that Redmine has a different syntax for those who want to add
> links to their reports; see
> http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
> >>
> >> Let us know if you have any questions.
> >>
> >> chris
> >>
> >> Christopher Fields
> >> IGB Postdoctoral Fellow
> >> Genomics of Neural & Behavioral Plasticity
> >> University of Illinois Urbana-Champaign
> >> Institute for Genomic Biology
> >> 1206 W. Gregory Dr. , MC-195
> >> Urbana, IL 61801
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> >
> >
> > --
> > Jonathan "Duke" Leto
> > jonathan at leto.net
> > http://leto.net
> > <obf_redmine.png>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From cjfields at illinois.edu  Thu Mar 17 07:36:05 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Mar 2011 06:36:05 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <AANLkTik8oYG1yJ7HdV119K08NsbqpDTUpDAtKUPSKUMF@mail.gmail.com>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
	<AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
	<F380825D-8F8B-4766-99C3-36FDD8E9C99D@illinois.edu>
	<AANLkTik8oYG1yJ7HdV119K08NsbqpDTUpDAtKUPSKUMF@mail.gmail.com>
Message-ID: <B8AB68C4-0DD8-408E-8C49-D33339E6C6ED@illinois.edu>

I did a little database cleansing; the email notification settings were screwy (why the warnings popped up).

chris

On Mar 17, 2011, at 3:51 AM, Dave Messina wrote:

> Works for me now ? I was able to reset the password and log in.
> 
> Thanks, Chris!
> 
> Dave
> 
> 
> 
> 
> On Wed, Mar 16, 2011 at 23:50, Chris Fields <cjfields at illinois.edu> wrote:
> I reset the plugins and reloaded the database.  Does that help?  I tested it out again using a test user (using the 'Lost password' link) and it seemed to work.
> 
> If not, I can manually reset and send the password to you.
> 
> chris
> 
> On Mar 16, 2011, at 3:48 PM, Jonathan Duke Leto wrote:
> 
> > Howdy,
> >
> > Thanks for working on this Chris!
> >
> > I am not sure the password reset works properly.
> >
> > Attached is a screenshot of it giving odd errors.
> >
> > This was on Firefox 3.6.
> >
> > Duke
> >
> > On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
> >> (apologies if you receive multiple copies of this)
> >>
> >> All,
> >>
> >> We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:
> >>
> >> http://redmine.open-bio.org/
> >>
> >> All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.
> >>
> >> For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:
> >>
> >> 1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.
> >>
> >> 2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.
> >>
> >> Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
> >>
> >> Let us know if you have any questions.
> >>
> >> chris
> >>
> >> Christopher Fields
> >> IGB Postdoctoral Fellow
> >> Genomics of Neural & Behavioral Plasticity
> >> University of Illinois Urbana-Champaign
> >> Institute for Genomic Biology
> >> 1206 W. Gregory Dr. , MC-195
> >> Urbana, IL 61801
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> >
> >
> > --
> > Jonathan "Duke" Leto
> > jonathan at leto.net
> > http://leto.net
> > <obf_redmine.png>
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From cjfields at illinois.edu  Thu Mar 17 12:16:19 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Mar 2011 11:16:19 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
	<AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
Message-ID: <B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>

Peter, 

It's set up for biopython.  Will make an announcement on open-bio-l and post something on the blog when I catch my breath (redmine and this in one week is a little tiring!).

Will also ping biojava and the other wiki groups about switching over.

chris

On Mar 17, 2011, at 3:27 AM, Peter Cock wrote:

> Yes please - thanks Chris!
> 
> Peter
> 
> On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu> wrote:
>> Done, for BioSQL.  Let me know about Biopython and the others.
>> 
>> -c
>> 
>> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>> 
>>> 
>>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>> 
>>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>> 
>>> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works.  Not sure why that would be.
>>> 
>>> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
>>> 
>>>       -hilmar
>>> 
>>>> 
>>>> 
>>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>> 
>>>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.
>>>> 
>>>> chris
>>>> 
>>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>> 
>>>>> Any update on the OpenID extension?
>>>>> 
>>>>>     -hilmar
>>>>> 
>>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>> 
>>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>>>> 
>>>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>>>> 
>>>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>>>> 
>>>>>> chris
>>>>>> 
>>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>> 
>>>>>>> Hi Chris,
>>>>>>> 
>>>>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>>>> account, you have the ability to approve other people's accounts.  The
>>>>>>> hope being to distribute the load.  I'm not thrilled about it though:
>>>>>>> I want the barrier to entry to be as low as possible.  We already make
>>>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>>>> 
>>>>>>> Scott
>>>>>>> 
>>>>>>> 
>>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>>>> All,
>>>>>>>> 
>>>>>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>>>> 
>>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>> 
>>>>>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>>>> 
>>>>>>>> Any thoughts?
>>>>>>>> 
>>>>>>>> chris
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> --
>>>>>>> ------------------------------------------------------------------------
>>>>>>> Scott Cain, Ph. D.




From adam at retchless.us  Thu Mar 17 12:32:37 2011
From: adam at retchless.us (Adam Retchless)
Date: Thu, 17 Mar 2011 12:32:37 -0400
Subject: [Bioperl-l] Wiki login with OpenId
Message-ID: <4D8237A5.4050706@retchless.us>

Greetings all,

First: A "thank you" to everyone who has developed BioPerl and the 
BioPerl Wiki -- I'm new to BioPerl, but have already benefited from its 
ability to simplify tasks that would otherwise be very tedious.

Anyway, I noticed some outdated information on the Wiki, and wanted to 
change it, but had a little trouble figuring out how to do so. 
Basically, it wasn't clear that the way to create an account was to 
click on the "Login with OpenId" button. As someone who doesn't use 
OpenID, I immediately went to the traditional "Login" page, but got 
stumped there. It did not occur to me that the OpenID page would be any 
different. Only after looking at the recent discussion on the mailing 
list did I figure out what I needed to do.

In the interest of eliminating any obstacle to participation, I think it 
would be helpful for the Wiki itself to clearly indicate how to create a 
new account. Either by changing the wording of the "login with OpenID 
link", or placing a message on the traditional "Log In" page telling 
people what they need to do to make an account.

Thanks, and I look forward to participating here.

-Adam

-- 

Adam Retchless
Center for Genomic Sciences
Allegheny-Singer Research Institute



From cjfields at illinois.edu  Thu Mar 17 13:13:14 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Mar 2011 12:13:14 -0500
Subject: [Bioperl-l] Wiki login with OpenId
In-Reply-To: <4D8237A5.4050706@retchless.us>
References: <4D8237A5.4050706@retchless.us>
Message-ID: <62E050E8-E567-4117-B14C-1F613CC81016@illinois.edu>

Adam, 

We're in the process of doing so; the addition of OpenID logins is a few days old.  I'm actually writing a blog post right now on the problems we've had and the use of OpenID, and will add a few things to the wiki pages so the login is clearer (including adding text to the normal login page).

chris

On Mar 17, 2011, at 11:32 AM, Adam Retchless wrote:

> Greetings all,
> 
> First: A "thank you" to everyone who has developed BioPerl and the BioPerl Wiki -- I'm new to BioPerl, but have already benefited from its ability to simplify tasks that would otherwise be very tedious.
> 
> Anyway, I noticed some outdated information on the Wiki, and wanted to change it, but had a little trouble figuring out how to do so. Basically, it wasn't clear that the way to create an account was to click on the "Login with OpenId" button. As someone who doesn't use OpenID, I immediately went to the traditional "Login" page, but got stumped there. It did not occur to me that the OpenID page would be any different. Only after looking at the recent discussion on the mailing list did I figure out what I needed to do.
> 
> In the interest of eliminating any obstacle to participation, I think it would be helpful for the Wiki itself to clearly indicate how to create a new account. Either by changing the wording of the "login with OpenID link", or placing a message on the traditional "Log In" page telling people what they need to do to make an account.
> 
> Thanks, and I look forward to participating here.
> 
> -Adam
> 
> -- 
> 
> Adam Retchless
> Center for Genomic Sciences
> Allegheny-Singer Research Institute
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hlapp at drycafe.net  Thu Mar 17 15:38:01 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Thu, 17 Mar 2011 15:38:01 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
	<AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
	<B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>
Message-ID: <A95A687E-25DD-4325-983D-BE9A5F45FA23@drycafe.net>

Just a thought towards the future - OpenIDs are so easy to obtain that  
the way it is right now (any OpenID will do) is built on the premise  
that it's not used widely enough (yet!) to make it worth the spammers'  
time.  Same story as with reCaptcha, probably. So once OpenID is used  
widely, we'll probably have to restrict the OpenID providers that we  
permit.

	-hilmar

On Mar 17, 2011, at 12:16 PM, Chris Fields wrote:

> Peter,
>
> It's set up for biopython.  Will make an announcement on open-bio-l  
> and post something on the blog when I catch my breath (redmine and  
> this in one week is a little tiring!).
>
> Will also ping biojava and the other wiki groups about switching over.
>
> chris
>
> On Mar 17, 2011, at 3:27 AM, Peter Cock wrote:
>
>> Yes please - thanks Chris!
>>
>> Peter
>>
>> On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu>  
>> wrote:
>>> Done, for BioSQL.  Let me know about Biopython and the others.
>>>
>>> -c
>>>
>>> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>>>
>>>>
>>>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>>>
>>>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>>>
>>>> Seems to work mostly - there seems to be some odd small problem  
>>>> with ClaimID: typing in my username leads to an OpenID error,  
>>>> whereas entering my full ClaimID OpenID works.  Not sure why that  
>>>> would be.
>>>>
>>>> Any chance this can be enabled for BioSQL too (and accordingly  
>>>> account creation disabled there, too)?
>>>>
>>>>      -hilmar
>>>>
>>>>>
>>>>>
>>>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>>>
>>>>> I have also temporarily shut down new user account creation (new  
>>>>> users must now use OpenID); old users can still use the login,  
>>>>> but they can also tie their account to an OpenID.  Let's see if  
>>>>> it cuts down on the spam.
>>>>>
>>>>> chris
>>>>>
>>>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>>>
>>>>>> Any update on the OpenID extension?
>>>>>>
>>>>>>    -hilmar
>>>>>>
>>>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>>>
>>>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit 
>>>>>>> ):
>>>>>>>
>>>>>>> "Unfortunately, reCAPTCHA might be a victim of its own success  
>>>>>>> - as of 2011, some spammers appear to have figured out a way  
>>>>>>> to bypass it, either through character recognition or by using  
>>>>>>> humans. For that reason, it is not necessarily recommended."
>>>>>>>
>>>>>>> I agree about the barrier to entry issue, but unfortunately  
>>>>>>> with the wiki we're facing a reality check re: spam attacks.   
>>>>>>> We can probably set up a new group for users that allows  
>>>>>>> account approval, though, which might alleviate the process  
>>>>>>> somewhat.
>>>>>>>
>>>>>>> chris
>>>>>>>
>>>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>>>
>>>>>>>> Hi Chris,
>>>>>>>>
>>>>>>>> The GMOD wiki has been getting hit similarly.  I've been  
>>>>>>>> thinking
>>>>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>>>>> account, you have the ability to approve other people's  
>>>>>>>> accounts.  The
>>>>>>>> hope being to distribute the load.  I'm not thrilled about it  
>>>>>>>> though:
>>>>>>>> I want the barrier to entry to be as low as possible.  We  
>>>>>>>> already make
>>>>>>>> it so that you have to have an account to edit, passing a  
>>>>>>>> recaptcha on
>>>>>>>> the way.  Apparently that barrier is already a little too  
>>>>>>>> low :-/
>>>>>>>>
>>>>>>>> Scott
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu 
>>>>>>>> > wrote:
>>>>>>>>> All,
>>>>>>>>>
>>>>>>>>> We have been getting inundated on the wiki with spam  
>>>>>>>>> lately.  In order to get on top of this, I'm thinking about  
>>>>>>>>> having the wiki set up so wiki admins approve new user  
>>>>>>>>> accounts, using the ConfirmAccount plugin:
>>>>>>>>>
>>>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>>>
>>>>>>>>> I wanted to get everyone's opinion on this prior to  
>>>>>>>>> enforcing it.  The queue is pretty configurable, and one can  
>>>>>>>>> set this to auto-delete old requests.
>>>>>>>>>
>>>>>>>>> Any thoughts?
>>>>>>>>>
>>>>>>>>> chris
>>>>>>>>> _______________________________________________
>>>>>>>>> Bioperl-l mailing list
>>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> Scott Cain, Ph. D.
>

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From cjfields at illinois.edu  Thu Mar 17 15:40:47 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Mar 2011 14:40:47 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <A95A687E-25DD-4325-983D-BE9A5F45FA23@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
	<AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
	<B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>
	<A95A687E-25DD-4325-983D-BE9A5F45FA23@drycafe.net>
Message-ID: <2E6327AD-4CD3-45CE-A105-66FA3A474294@illinois.edu>

That's easy enough to do with the OpenID plugin settings:

$wgOpenIDConsumerAllow
an array of regular expressions that match OpenIDs you want to allow to log in. For example, "@^(http://)?wikitravel.org/@" will allow OpenIDs from the Wikitravel domain.
$wgOpenIDConsumerDeny
an array of regular expressions that match OpenIDs you want to deny access to. This is mostly useful for servers that are known to be bad. Example: "#^(http://)?example.com/#".

chris

On Mar 17, 2011, at 2:38 PM, Hilmar Lapp wrote:

> Just a thought towards the future - OpenIDs are so easy to obtain that the way it is right now (any OpenID will do) is built on the premise that it's not used widely enough (yet!) to make it worth the spammers' time.  Same story as with reCaptcha, probably. So once OpenID is used widely, we'll probably have to restrict the OpenID providers that we permit.
> 
> 	-hilmar
> 
> On Mar 17, 2011, at 12:16 PM, Chris Fields wrote:
> 
>> Peter,
>> 
>> It's set up for biopython.  Will make an announcement on open-bio-l and post something on the blog when I catch my breath (redmine and this in one week is a little tiring!).
>> 
>> Will also ping biojava and the other wiki groups about switching over.
>> 
>> chris
>> 
>> On Mar 17, 2011, at 3:27 AM, Peter Cock wrote:
>> 
>>> Yes please - thanks Chris!
>>> 
>>> Peter
>>> 
>>> On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu> wrote:
>>>> Done, for BioSQL.  Let me know about Biopython and the others.
>>>> 
>>>> -c
>>>> 
>>>> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>>>> 
>>>>> 
>>>>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>>>> 
>>>>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>>>> 
>>>>> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works.  Not sure why that would be.
>>>>> 
>>>>> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
>>>>> 
>>>>>     -hilmar
>>>>> 
>>>>>> 
>>>>>> 
>>>>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>>>> 
>>>>>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.
>>>>>> 
>>>>>> chris
>>>>>> 
>>>>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>>>> 
>>>>>>> Any update on the OpenID extension?
>>>>>>> 
>>>>>>>   -hilmar
>>>>>>> 
>>>>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>>>> 
>>>>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>>>>>> 
>>>>>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>>>>>> 
>>>>>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>>>>>> 
>>>>>>>> chris
>>>>>>>> 
>>>>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>>>> 
>>>>>>>>> Hi Chris,
>>>>>>>>> 
>>>>>>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>>>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>>>>>> account, you have the ability to approve other people's accounts.  The
>>>>>>>>> hope being to distribute the load.  I'm not thrilled about it though:
>>>>>>>>> I want the barrier to entry to be as low as possible.  We already make
>>>>>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>>>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>>>>>> 
>>>>>>>>> Scott
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>>>>>> All,
>>>>>>>>>> 
>>>>>>>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>>>>>> 
>>>>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>>>> 
>>>>>>>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>>>>>> 
>>>>>>>>>> Any thoughts?
>>>>>>>>>> 
>>>>>>>>>> chris
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Bioperl-l mailing list
>>>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> --
>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>> Scott Cain, Ph. D.
>> 
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 




From hlapp at drycafe.net  Thu Mar 17 16:01:42 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Thu, 17 Mar 2011 16:01:42 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <2E6327AD-4CD3-45CE-A105-66FA3A474294@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
	<AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
	<B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>
	<A95A687E-25DD-4325-983D-BE9A5F45FA23@drycafe.net>
	<2E6327AD-4CD3-45CE-A105-66FA3A474294@illinois.edu>
Message-ID: <14304AC6-1AAA-44C3-A169-F0111BA59AC2@drycafe.net>

Indeed. And I guess we can add "bad" providers incrementally as we  
spam from them trickle in. I can imagine that at some point there'll  
also be a blacklist of spam OpenID providers.

	-hilmar

On Mar 17, 2011, at 3:40 PM, Chris Fields wrote:

> That's easy enough to do with the OpenID plugin settings:
>
> $wgOpenIDConsumerAllow
> an array of regular expressions that match OpenIDs you want to allow  
> to log in. For example, "@^(http://)?wikitravel.org/@" will allow  
> OpenIDs from the Wikitravel domain.
> $wgOpenIDConsumerDeny
> an array of regular expressions that match OpenIDs you want to deny  
> access to. This is mostly useful for servers that are known to be  
> bad. Example: "#^(http://)?example.com/#".
>
> chris
>
> On Mar 17, 2011, at 2:38 PM, Hilmar Lapp wrote:
>
>> Just a thought towards the future - OpenIDs are so easy to obtain  
>> that the way it is right now (any OpenID will do) is built on the  
>> premise that it's not used widely enough (yet!) to make it worth  
>> the spammers' time.  Same story as with reCaptcha, probably. So  
>> once OpenID is used widely, we'll probably have to restrict the  
>> OpenID providers that we permit.
>>
>> 	-hilmar
>>
>> On Mar 17, 2011, at 12:16 PM, Chris Fields wrote:
>>
>>> Peter,
>>>
>>> It's set up for biopython.  Will make an announcement on open-bio- 
>>> l and post something on the blog when I catch my breath (redmine  
>>> and this in one week is a little tiring!).
>>>
>>> Will also ping biojava and the other wiki groups about switching  
>>> over.
>>>
>>> chris
>>>
>>> On Mar 17, 2011, at 3:27 AM, Peter Cock wrote:
>>>
>>>> Yes please - thanks Chris!
>>>>
>>>> Peter
>>>>
>>>> On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu>  
>>>> wrote:
>>>>> Done, for BioSQL.  Let me know about Biopython and the others.
>>>>>
>>>>> -c
>>>>>
>>>>> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>>>>>
>>>>>>
>>>>>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>>>>>
>>>>>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>>>>>
>>>>>> Seems to work mostly - there seems to be some odd small problem  
>>>>>> with ClaimID: typing in my username leads to an OpenID error,  
>>>>>> whereas entering my full ClaimID OpenID works.  Not sure why  
>>>>>> that would be.
>>>>>>
>>>>>> Any chance this can be enabled for BioSQL too (and accordingly  
>>>>>> account creation disabled there, too)?
>>>>>>
>>>>>>    -hilmar
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>>>>>
>>>>>>> I have also temporarily shut down new user account creation  
>>>>>>> (new users must now use OpenID); old users can still use the  
>>>>>>> login, but they can also tie their account to an OpenID.   
>>>>>>> Let's see if it cuts down on the spam.
>>>>>>>
>>>>>>> chris
>>>>>>>
>>>>>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>>>>>
>>>>>>>> Any update on the OpenID extension?
>>>>>>>>
>>>>>>>>  -hilmar
>>>>>>>>
>>>>>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>>>>>
>>>>>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit 
>>>>>>>>> ):
>>>>>>>>>
>>>>>>>>> "Unfortunately, reCAPTCHA might be a victim of its own  
>>>>>>>>> success - as of 2011, some spammers appear to have figured  
>>>>>>>>> out a way to bypass it, either through character recognition  
>>>>>>>>> or by using humans. For that reason, it is not necessarily  
>>>>>>>>> recommended."
>>>>>>>>>
>>>>>>>>> I agree about the barrier to entry issue, but unfortunately  
>>>>>>>>> with the wiki we're facing a reality check re: spam  
>>>>>>>>> attacks.  We can probably set up a new group for users that  
>>>>>>>>> allows account approval, though, which might alleviate the  
>>>>>>>>> process somewhat.
>>>>>>>>>
>>>>>>>>> chris
>>>>>>>>>
>>>>>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>>>>>
>>>>>>>>>> Hi Chris,
>>>>>>>>>>
>>>>>>>>>> The GMOD wiki has been getting hit similarly.  I've been  
>>>>>>>>>> thinking
>>>>>>>>>> about the "vampire" model that EcoliWiki uses: once you  
>>>>>>>>>> have an
>>>>>>>>>> account, you have the ability to approve other people's  
>>>>>>>>>> accounts.  The
>>>>>>>>>> hope being to distribute the load.  I'm not thrilled about  
>>>>>>>>>> it though:
>>>>>>>>>> I want the barrier to entry to be as low as possible.  We  
>>>>>>>>>> already make
>>>>>>>>>> it so that you have to have an account to edit, passing a  
>>>>>>>>>> recaptcha on
>>>>>>>>>> the way.  Apparently that barrier is already a little too  
>>>>>>>>>> low :-/
>>>>>>>>>>
>>>>>>>>>> Scott
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu 
>>>>>>>>>> > wrote:
>>>>>>>>>>> All,
>>>>>>>>>>>
>>>>>>>>>>> We have been getting inundated on the wiki with spam  
>>>>>>>>>>> lately.  In order to get on top of this, I'm thinking  
>>>>>>>>>>> about having the wiki set up so wiki admins approve new  
>>>>>>>>>>> user accounts, using the ConfirmAccount plugin:
>>>>>>>>>>>
>>>>>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>>>>>
>>>>>>>>>>> I wanted to get everyone's opinion on this prior to  
>>>>>>>>>>> enforcing it.  The queue is pretty configurable, and one  
>>>>>>>>>>> can set this to auto-delete old requests.
>>>>>>>>>>>
>>>>>>>>>>> Any thoughts?
>>>>>>>>>>>
>>>>>>>>>>> chris
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Bioperl-l mailing list
>>>>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>> Scott Cain, Ph. D.
>>>
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>> ===========================================================
>>
>>
>>
>>
>

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From tzhu at mail.bnu.edu.cn  Fri Mar 18 00:33:32 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Fri, 18 Mar 2011 12:33:32 +0800
Subject: [Bioperl-l] What's wrong with the script about module
 Bio::SeqFeature::Gene::GeneStructure
Message-ID: <1300422812.12949.5.camel@ubuntu>

I wrote my script like this,

#!/usr/bin/perl -w
use Bio::SeqIO;
my $catch_seq = Bio::SeqIO -> new(-file => 'test.gbk',-format=>
'genbank');
while( my $seq_obj = $catch_seq -> next_seq)
{
	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
get_SeqFeatures;
	for my $mRNA_feature (@all_mRNA_features)
	{
			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
		{
			@exons=$mRNA_feature->exons;
			$exon_number = scalar(@exons);
			print "$exon_number\n";
		}
	}
}

I hope to count exon number in every mRNA. But it print nothing(You can
arbitrarily get a genbank file to test it). What's wrong?


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)




From hrh at fmi.ch  Fri Mar 18 05:17:30 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Fri, 18 Mar 2011 10:17:30 +0100
Subject: [Bioperl-l] What's wrong with the script about module
	Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300422812.12949.5.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu>
Message-ID: <4D83232A.9050502@fmi.ch>

Hi Tao

I don't fully understand your script, but I do see a major problem:

why do you select for "primary_tag eq 'mRNA'" first?


this simple loop will probably do what you want:

while( my $seq_obj = $catch_seq -> next_seq) {

	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
$seq_obj ->get_SeqFeatures;
	$exon_number = scalar(@all_exon_features);
	print "$exon_number\n";
}


Alternatively, I recommend to read the HOWTO page:

http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

which has a nice example to print out all 'primary_tag' (ie the 'feature 
keys' in a GenBank formated file)

I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
definition:
http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html


Regards, Hans



On 03/18/2011 05:33 AM, Tao Zhu wrote:
> I wrote my script like this,
>
> #!/usr/bin/perl -w
> use Bio::SeqIO;
> my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
> 'genbank');
> while( my $seq_obj = $catch_seq ->  next_seq)
> {
> 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
> get_SeqFeatures;
> 	for my $mRNA_feature (@all_mRNA_features)
> 	{
> 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
> 		{
> 			@exons=$mRNA_feature->exons;
> 			$exon_number = scalar(@exons);
> 			print "$exon_number\n";
> 		}
> 	}
> }
>
> I hope to count exon number in every mRNA. But it print nothing(You can
> arbitrarily get a genbank file to test it). What's wrong?
>
>


From tzhu at mail.bnu.edu.cn  Fri Mar 18 07:32:00 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Fri, 18 Mar 2011 19:32:00 +0800
Subject: [Bioperl-l] What's wrong with the script about module
 Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <4D83232A.9050502@fmi.ch>
References: <1300422812.12949.5.camel@ubuntu>  <4D83232A.9050502@fmi.ch>
Message-ID: <1300447920.16670.2.camel@ubuntu>

Of course that's OK. But what I really want to know is how to use module
Bio::SeqFeature::Gene::GeneStructure. 

? 2011-03-18?? 10:17 +0100?Hans-Rudolf Hotz???
> Hi Tao
> 
> I don't fully understand your script, but I do see a major problem:
> 
> why do you select for "primary_tag eq 'mRNA'" first?
> 
> 
> this simple loop will probably do what you want:
> 
> while( my $seq_obj = $catch_seq -> next_seq) {
> 
> 	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
> $seq_obj ->get_SeqFeatures;
> 	$exon_number = scalar(@all_exon_features);
> 	print "$exon_number\n";
> }
> 
> 
> Alternatively, I recommend to read the HOWTO page:
> 
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> 
> which has a nice example to print out all 'primary_tag' (ie the 'feature 
> keys' in a GenBank formated file)
> 
> I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
> definition:
> http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
> 
> 
> Regards, Hans
> 
> 
> 
> On 03/18/2011 05:33 AM, Tao Zhu wrote:
> > I wrote my script like this,
> >
> > #!/usr/bin/perl -w
> > use Bio::SeqIO;
> > my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
> > 'genbank');
> > while( my $seq_obj = $catch_seq ->  next_seq)
> > {
> > 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
> > get_SeqFeatures;
> > 	for my $mRNA_feature (@all_mRNA_features)
> > 	{
> > 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
> > 		{
> > 			@exons=$mRNA_feature->exons;
> > 			$exon_number = scalar(@exons);
> > 			print "$exon_number\n";
> > 		}
> > 	}
> > }
> >
> > I hope to count exon number in every mRNA. But it print nothing(You can
> > arbitrarily get a genbank file to test it). What's wrong?
> >
> >

-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)




From cjfields at illinois.edu  Fri Mar 18 09:04:34 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 18 Mar 2011 08:04:34 -0500
Subject: [Bioperl-l] What's wrong with the script about module
	Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300447920.16670.2.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu> <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
Message-ID: <2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>

The SeqFeatures derived from a GenBank file are simple Bio::SeqFeature::Generic instances.  I don't think there is a straightforward way to have the parser return Bio::SeqFeature::Gene::GeneStructure instances.

chris

On Mar 18, 2011, at 6:32 AM, Tao Zhu wrote:

> Of course that's OK. But what I really want to know is how to use module
> Bio::SeqFeature::Gene::GeneStructure. 
> 
> ? 2011-03-18?? 10:17 +0100?Hans-Rudolf Hotz???
>> Hi Tao
>> 
>> I don't fully understand your script, but I do see a major problem:
>> 
>> why do you select for "primary_tag eq 'mRNA'" first?
>> 
>> 
>> this simple loop will probably do what you want:
>> 
>> while( my $seq_obj = $catch_seq -> next_seq) {
>> 
>> 	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
>> $seq_obj ->get_SeqFeatures;
>> 	$exon_number = scalar(@all_exon_features);
>> 	print "$exon_number\n";
>> }
>> 
>> 
>> Alternatively, I recommend to read the HOWTO page:
>> 
>> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
>> 
>> which has a nice example to print out all 'primary_tag' (ie the 'feature 
>> keys' in a GenBank formated file)
>> 
>> I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
>> definition:
>> http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
>> 
>> 
>> Regards, Hans
>> 
>> 
>> 
>> On 03/18/2011 05:33 AM, Tao Zhu wrote:
>>> I wrote my script like this,
>>> 
>>> #!/usr/bin/perl -w
>>> use Bio::SeqIO;
>>> my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
>>> 'genbank');
>>> while( my $seq_obj = $catch_seq ->  next_seq)
>>> {
>>> 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
>>> get_SeqFeatures;
>>> 	for my $mRNA_feature (@all_mRNA_features)
>>> 	{
>>> 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
>>> 		{
>>> 			@exons=$mRNA_feature->exons;
>>> 			$exon_number = scalar(@exons);
>>> 			print "$exon_number\n";
>>> 		}
>>> 	}
>>> }
>>> 
>>> I hope to count exon number in every mRNA. But it print nothing(You can
>>> arbitrarily get a genbank file to test it). What's wrong?
>>> 
>>> 
> 
> -- 
> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> 100875, China
> Email: tzhu at mail.bnu.edu.cn
> Website: http://bnuzt.org (mainly written in Chinese)
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From ross at cuhk.edu.hk  Fri Mar 18 09:22:40 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Fri, 18 Mar 2011 21:22:40 +0800
Subject: [Bioperl-l]  failure in unsubscription
In-Reply-To: <1300447920.16670.2.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu> <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
Message-ID: <018101cbe56f$8ec755f0$ac5601d0$@edu.hk>

unable to unsubscribe bioperl mailing list, anybody can help? the web link, after clicking "unsubscribe", there is no confirmation email sent to my email account and I keep receiving emails from bioperl mailing list.




From tzhu at mail.bnu.edu.cn  Fri Mar 18 09:57:21 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Fri, 18 Mar 2011 21:57:21 +0800
Subject: [Bioperl-l] What's wrong with the script about module
 Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
References: <1300422812.12949.5.camel@ubuntu>  <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
	<2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
Message-ID: <1300456641.18688.4.camel@ubuntu>

Yes. But in the document
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
Bio::SeqFeature::Generic. I wonder how to do such inheritance.

? 2011-03-18?? 08:04 -0500?Chris Fields???
> The SeqFeatures derived from a GenBank file are simple Bio::SeqFeature::Generic instances.  I don't think there is a straightforward way to have the parser return Bio::SeqFeature::Gene::GeneStructure instances.
> 
> chris
> 
> On Mar 18, 2011, at 6:32 AM, Tao Zhu wrote:
> 
> > Of course that's OK. But what I really want to know is how to use module
> > Bio::SeqFeature::Gene::GeneStructure. 
> > 
> > ? 2011-03-18?? 10:17 +0100?Hans-Rudolf Hotz???
> >> Hi Tao
> >> 
> >> I don't fully understand your script, but I do see a major problem:
> >> 
> >> why do you select for "primary_tag eq 'mRNA'" first?
> >> 
> >> 
> >> this simple loop will probably do what you want:
> >> 
> >> while( my $seq_obj = $catch_seq -> next_seq) {
> >> 
> >> 	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
> >> $seq_obj ->get_SeqFeatures;
> >> 	$exon_number = scalar(@all_exon_features);
> >> 	print "$exon_number\n";
> >> }
> >> 
> >> 
> >> Alternatively, I recommend to read the HOWTO page:
> >> 
> >> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> >> 
> >> which has a nice example to print out all 'primary_tag' (ie the 'feature 
> >> keys' in a GenBank formated file)
> >> 
> >> I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
> >> definition:
> >> http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
> >> 
> >> 
> >> Regards, Hans
> >> 
> >> 
> >> 
> >> On 03/18/2011 05:33 AM, Tao Zhu wrote:
> >>> I wrote my script like this,
> >>> 
> >>> #!/usr/bin/perl -w
> >>> use Bio::SeqIO;
> >>> my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
> >>> 'genbank');
> >>> while( my $seq_obj = $catch_seq ->  next_seq)
> >>> {
> >>> 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
> >>> get_SeqFeatures;
> >>> 	for my $mRNA_feature (@all_mRNA_features)
> >>> 	{
> >>> 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
> >>> 		{
> >>> 			@exons=$mRNA_feature->exons;
> >>> 			$exon_number = scalar(@exons);
> >>> 			print "$exon_number\n";
> >>> 		}
> >>> 	}
> >>> }
> >>> 
> >>> I hope to count exon number in every mRNA. But it print nothing(You can
> >>> arbitrarily get a genbank file to test it). What's wrong?
> >>> 
> >>> 
> > 
> > -- 
> > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> > 100875, China
> > Email: tzhu at mail.bnu.edu.cn
> > Website: http://bnuzt.org (mainly written in Chinese)
> > 
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 





From fs5 at sanger.ac.uk  Fri Mar 18 11:05:29 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Fri, 18 Mar 2011 15:05:29 +0000
Subject: [Bioperl-l] What's wrong with the script about
	module	Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300456641.18688.4.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu>  <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
	<2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
	<1300456641.18688.4.camel@ubuntu>
Message-ID: <1300460730.12411.50.camel@deskpro15336.internal.sanger.ac.uk>

maybe I'm missing the point here but I think an "mRNA" feature should
not be a Bio::SeqFeature::Gene::GeneStructure and it should not have
exons - it would not make sense biologically.

Frank


On Fri, 2011-03-18 at 21:57 +0800, Tao Zhu wrote:
> Yes. But in the document
> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
> It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
> Bio::SeqFeature::Generic. I wonder how to do such inheritance.
> 
> ? 2011-03-18?? 08:04 -0500?Chris Fields???
> > The SeqFeatures derived from a GenBank file are simple Bio::SeqFeature::Generic instances.  I don't think there is a straightforward way to have the parser return Bio::SeqFeature::Gene::GeneStructure instances.
> > 
> > chris
> > 
> > On Mar 18, 2011, at 6:32 AM, Tao Zhu wrote:
> > 
> > > Of course that's OK. But what I really want to know is how to use module
> > > Bio::SeqFeature::Gene::GeneStructure. 
> > > 
> > > ? 2011-03-18?? 10:17 +0100?Hans-Rudolf Hotz???
> > >> Hi Tao
> > >> 
> > >> I don't fully understand your script, but I do see a major problem:
> > >> 
> > >> why do you select for "primary_tag eq 'mRNA'" first?
> > >> 
> > >> 
> > >> this simple loop will probably do what you want:
> > >> 
> > >> while( my $seq_obj = $catch_seq -> next_seq) {
> > >> 
> > >> 	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
> > >> $seq_obj ->get_SeqFeatures;
> > >> 	$exon_number = scalar(@all_exon_features);
> > >> 	print "$exon_number\n";
> > >> }
> > >> 
> > >> 
> > >> Alternatively, I recommend to read the HOWTO page:
> > >> 
> > >> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> > >> 
> > >> which has a nice example to print out all 'primary_tag' (ie the 'feature 
> > >> keys' in a GenBank formated file)
> > >> 
> > >> I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
> > >> definition:
> > >> http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
> > >> 
> > >> 
> > >> Regards, Hans
> > >> 
> > >> 
> > >> 
> > >> On 03/18/2011 05:33 AM, Tao Zhu wrote:
> > >>> I wrote my script like this,
> > >>> 
> > >>> #!/usr/bin/perl -w
> > >>> use Bio::SeqIO;
> > >>> my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
> > >>> 'genbank');
> > >>> while( my $seq_obj = $catch_seq ->  next_seq)
> > >>> {
> > >>> 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
> > >>> get_SeqFeatures;
> > >>> 	for my $mRNA_feature (@all_mRNA_features)
> > >>> 	{
> > >>> 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
> > >>> 		{
> > >>> 			@exons=$mRNA_feature->exons;
> > >>> 			$exon_number = scalar(@exons);
> > >>> 			print "$exon_number\n";
> > >>> 		}
> > >>> 	}
> > >>> }
> > >>> 
> > >>> I hope to count exon number in every mRNA. But it print nothing(You can
> > >>> arbitrarily get a genbank file to test it). What's wrong?
> > >>> 
> > >>> 
> > > 
> > > -- 
> > > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> > > 100875, China
> > > Email: tzhu at mail.bnu.edu.cn
> > > Website: http://bnuzt.org (mainly written in Chinese)
> > > 
> > > 
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 



From chapmanb at 50mail.com  Fri Mar  4 07:37:28 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Fri, 4 Mar 2011 07:37:28 -0500
Subject: [Bioperl-l] Bioinformatics Open Source Conference (BOSC 2011)--Call
 for Abstracts
Message-ID: <20110304123728.GD27839@sobchak>

We invite you to submit an abstract to BOSC 2011! Please forward this
message as appropriate, and forgive multiple postings.

Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference (BOSC 2011)
An ISMB 2011 Special Interest Group (SIG)

Dates: July 15-16, 2011
Location: Vienna, Austria
Web site: http://www.open-bio.org/wiki/BOSC_2011
Email: bosc at open-bio.org
BOSC announcements mailing list:  http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:
April 18, 2011: Deadline for submitting abstracts to BOSC 2011
May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors
July 13-14, 2011: Codefest 2011 programming session (see http://www.open-bio.org/wiki/Codefest_2011 for details)
July 15-16, 2011: BOSC 2011
July 17-19, 2011: ISMB 2011

The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.

We invite you to submit abstracts for talks and posters.  Sessions include:
- Approaches to parallel processing
- Cloud-based approaches to improving software and data accessibility
- The Semantic Web in open source bioinformatics
- Data visualization
- Tools for next-generation sequencing
- Other Open Source software

In addition to the above sessions, there will be a panel discussion
about "Meeting the challenges of inter-institutional collaboration". We
are also working to arrange a joint session with one of the other ISMB
SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student Travel
Awards for BOSC 2011. Each winner will be awarded $250 to defray the
costs of travel to BOSC 2011.
 
For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee:
Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor 


From bill_zt at sina.com  Thu Mar 17 20:48:19 2011
From: bill_zt at sina.com (Tao Zhu)
Date: Fri, 18 Mar 2011 08:48:19 +0800
Subject: [Bioperl-l] Perl/BioPerl (Simon No?l)
Message-ID: <1300409299.2349.5.camel@ubuntu>

In order to learn BioPerl, you should first learn and master Perl. If
you are not majoring in Bioinformatics, learning Perl is just OK.
Otherwise you should learn both Perl and BioPerl.


> Message: 2
> Date: Wed, 16 Mar 2011 15:40:09 -0400
> From: Simon No?l <simon.noel.2 at ulaval.ca>
> Subject: [Bioperl-l]  Perl/BioPerl
> To: "bioperl-l at lists.open-bio.org" <bioperl-l at lists.open-bio.org>
> Message-ID:
>         <1C970CA8E580A84394CE5CF42FEC0046DF67A4FA81 at EXCH-MBX-E.ulaval.ca>
> Content-Type: text/plain; charset="iso-8859-1"
> 
>  Hi, 
>  
> I don't know if I am on the right mailling list for this.
>  
> My director say that I should have a class of Perl or BioPerl.  Witch
> one should be better?  Do you know where I can find such class?
> 
> 
> Simon No?l
> CdeC
> 


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)



From bio.justin100 at gmail.com  Fri Mar  4 15:24:51 2011
From: bio.justin100 at gmail.com (justin100)
Date: Fri, 4 Mar 2011 12:24:51 -0800 (PST)
Subject: [Bioperl-l] Please recommend Perl module to parse phylogentic trees
Message-ID: <2e94f0bb-0282-4d53-b205-56ff895665de@w7g2000pre.googlegroups.com>

Hi,

I am writing a script to parse phylogenetic trees. The input will be
trees in Newick format for now (maybe NEXUS in the future).

Quite a few Perl modules can parse phylogenetic trees. For Newick
format, there are Bio::TreeIO and  Bio::Phylo::Parsers. For NEXUS
format, there is Bio::NEXUS. From my understanding, it's not difficult
to convert from Newick to NEXUS or vice versa, if only for the purpose
of parsing trees.

I'd to know the advantages and disadvantages of these modules when
compared with each other. Please recommend one that you think is the
most capable parser (and hopefully has the least bugs).

Thanks.

Justin


From jonathan at leto.net  Wed Mar 16 16:48:24 2011
From: jonathan at leto.net (Jonathan "Duke" Leto)
Date: Wed, 16 Mar 2011 13:48:24 -0700
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
Message-ID: <AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>

Howdy,

Thanks for working on this Chris!

I am not sure the password reset works properly.

Attached is a screenshot of it giving odd errors.

This was on Firefox 3.6.

Duke

On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
> (apologies if you receive multiple copies of this)
>
> All,
>
> We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:
>
> http://redmine.open-bio.org/
>
> All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only. ?Any new bugs and comments to old ones should be reported on the new Redmine server.
>
> For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons. ?There are two ways to access your account:
>
> 1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link. ?You will be prompted for your email address (this should be the same as your bugzilla login). ?An new email will be sent out containing directions for resetting your password and logging in.
>
> 2) It is possible the above may be automatically detected as spam. ?If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.
>
> Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
>
> Let us know if you have any questions.
>
> chris
>
> Christopher Fields
> IGB Postdoctoral Fellow
> Genomics of Neural & Behavioral Plasticity
> University of Illinois Urbana-Champaign
> Institute for Genomic Biology
> 1206 W. Gregory Dr. , MC-195
> Urbana, IL 61801
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Jonathan "Duke" Leto
jonathan at leto.net
http://leto.net
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From rutgeraldo at gmail.com  Fri Mar 18 10:16:25 2011
From: rutgeraldo at gmail.com (Rutger Vos)
Date: Fri, 18 Mar 2011 14:16:25 +0000
Subject: [Bioperl-l] Please forward: collecting support for Japanese
	scientists
Message-ID: <AANLkTiksWdna1MLpbBWk2nDv0LAyrXdU7xV3Fs5gSHkF@mail.gmail.com>

Dear colleagues,

A web page has been launched to collect support for Japanese
(bio-)scientists: http://biohelpathon.org - please forward this
address widely.

The purpose of the web page is to establish a knowledge base of
available support for our colleagues in Japan. You are invited to
submit any tips, ideas and offers including accommodation, funding
resources, exchange schemes, lab space, server space and open
positions for visiting students and research personnel from Japan.

We will collect your suggestions and offers and will share them with
whoever is best placed to disseminate them. This initiative originates
with the attendees of the BioHackathons (the Japanese website
http://hackathon.dbcls.jp is offline due to the earthquake), but
anyone is very welcome to contribute. To get in touch, join
http://groups.google.com/group/biohelpathon.

This initiative is no alternative to first responders who are helping
out in Japan right now. The rescue operation and food and shelter
support comes first. If you can only do one thing, it should be a
donation to something like the Red Cross. This comes later.

See also:
A different initiative, with which we're in touch:
http://www.nipponsciencesupport.net/
More info on Nature blogs:
http://blogs.nature.com/news/thegreatbeyond/2011/03/helping_hand_for_scientistrefu.html

PLEASE NOTE: WE ARE NOT HANDLING MONEY. This is simply a way to
crowdsource information about available resources.

Thank you.

Rutger Vos


From spotforever at tiscali.it  Sun Mar 13 14:15:54 2011
From: spotforever at tiscali.it (marcocirilli)
Date: Sun, 13 Mar 2011 11:15:54 -0700 (PDT)
Subject: [Bioperl-l]  slit sequence with BioPerl by ID-query
Message-ID: <31138653.post@talk.nabble.com>


Hello, I have 2 fasta file with similar sequences and I want to compare them
and eliminate sequences with the same IDquery (or extract only different
ID-query). How can I do it with BioPerl? Thanks 
-- 
View this message in context: http://old.nabble.com/slit-sequence-with-BioPerl-by-ID-query-tp31138653p31138653.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From suhail.mn12 at yahoo.co.uk  Fri Mar 18 12:18:49 2011
From: suhail.mn12 at yahoo.co.uk (Suhail M)
Date: Fri, 18 Mar 2011 16:18:49 +0000 (GMT)
Subject: [Bioperl-l] RemoteBlast
Message-ID: <988359.99459.qm@web132309.mail.ird.yahoo.com>

Dear Sir or Madam,
I am using a remote blast and encounter either a too many hsp or CPU overload 
problem with my specific gene. The gene itself is not that big so I was 
wondering is there a parameter I can pass when using the submit option to 
restrict number of hsp and to avoid the cpu and too many hsp problem? (I know I 
can use repeat masking and change the e-value but I need something that does not 
require those changes)

my $prog = 'blastn';
#my $db   = 'swissprot';
my $e_val= '1e-10';

my @params = ( '-prog'       => $prog,
#       '-data'       => $db,
               '-expect'     => $e_val,
               '-readmethod' => 'SearchIO'
            );

my $factory = Bio::Tools::Run::RemoteBlast->new(@params);

$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens [ORGN]';

delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};

my $str = Bio::SeqIO->new(-file            =>'temporary.fa' , 
 '-format'         => 'fasta');

my $r = $factory->submit_blast('temporary.fa');

Thank you for your help.
Suhail


      


From shalabh.sharma7 at gmail.com  Fri Mar 18 12:41:42 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Fri, 18 Mar 2011 12:41:42 -0400
Subject: [Bioperl-l] RemoteBlast
In-Reply-To: <988359.99459.qm@web132309.mail.ird.yahoo.com>
References: <988359.99459.qm@web132309.mail.ird.yahoo.com>
Message-ID: <AANLkTikLD+A9o0Nujg9ThGbFL3HvtaAGXaihoEX5OmTE@mail.gmail.com>

Suhail,
         You can restrict the number of hits by using "-v" and "-b"
parameters.

-Shalabh


On Fri, Mar 18, 2011 at 12:18 PM, Suhail M <suhail.mn12 at yahoo.co.uk> wrote:

> Dear Sir or Madam,
> I am using a remote blast and encounter either a too many hsp or CPU
> overload
> problem with my specific gene. The gene itself is not that big so I was
> wondering is there a parameter I can pass when using the submit option to
> restrict number of hsp and to avoid the cpu and too many hsp problem? (I
> know I
> can use repeat masking and change the e-value but I need something that
> does not
> require those changes)
>
> my $prog = 'blastn';
> #my $db   = 'swissprot';
> my $e_val= '1e-10';
>
> my @params = ( '-prog'       => $prog,
> #       '-data'       => $db,
>               '-expect'     => $e_val,
>               '-readmethod' => 'SearchIO'
>            );
>
> my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
>
> $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens
> [ORGN]';
>
> delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};
>
> my $str = Bio::SeqIO->new(-file            =>'temporary.fa' ,
>  '-format'         => 'fasta');
>
> my $r = $factory->submit_blast('temporary.fa');
>
> Thank you for your help.
> Suhail
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


From rmb32 at cornell.edu  Fri Mar 18 15:24:03 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Fri, 18 Mar 2011 15:24:03 -0400
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
Message-ID: <4D83B153.6010006@cornell.edu>

Hi all,

Great news: Google announced today that the Open Bioinformatics
Foundation has been accepted as a mentoring organization for this
summer's Google Summer of Code!

GSoC is a Google-sponsored student internship program for open-source
projects, open to students from around the world (not just US
residents).   Students are paid a $5000 USD stipend to work as a
developer on an open-source project for the summer. For more on GSoC,
see GSoC 2011 FAQ at http://bit.ly/hpoz8W

Student applications are due April 8, 2011 at 19:00 UTC.  Students who
are interested in participating should look at the OBF's GSoC page at
http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
ideas, and whom to contact about applying.

For current developers on OBF projects, please consider volunteering to
be a mentor if you have not already, and contribute project ideas.  Just
list your name and project ideas on OBF wiki and on the relevant
project's GSoC wiki page.

Thanks to all who helped make OBF's application to GSoC a success, and
let's have a great, productive summer of code!

Rob Buels
OBF GSoC 2011 Administrator




From cjfields at illinois.edu  Fri Mar 18 16:06:36 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 18 Mar 2011 15:06:36 -0500
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <4D83B153.6010006@cornell.edu>
References: <4D83B153.6010006@cornell.edu>
Message-ID: <AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>

Congrats Rob!

chris

On Mar 18, 2011, at 2:24 PM, Robert Buels wrote:

> Hi all,
> 
> Great news: Google announced today that the Open Bioinformatics
> Foundation has been accepted as a mentoring organization for this
> summer's Google Summer of Code!
> 
> GSoC is a Google-sponsored student internship program for open-source
> projects, open to students from around the world (not just US
> residents).   Students are paid a $5000 USD stipend to work as a
> developer on an open-source project for the summer. For more on GSoC,
> see GSoC 2011 FAQ at http://bit.ly/hpoz8W
> 
> Student applications are due April 8, 2011 at 19:00 UTC.  Students who
> are interested in participating should look at the OBF's GSoC page at
> http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
> ideas, and whom to contact about applying.
> 
> For current developers on OBF projects, please consider volunteering to
> be a mentor if you have not already, and contribute project ideas.  Just
> list your name and project ideas on OBF wiki and on the relevant
> project's GSoC wiki page.
> 
> Thanks to all who helped make OBF's application to GSoC a success, and
> let's have a great, productive summer of code!
> 
> Rob Buels
> OBF GSoC 2011 Administrator
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From ross at cuhk.edu.hk  Fri Mar 18 19:28:51 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Sat, 19 Mar 2011 07:28:51 +0800
Subject: [Bioperl-l]  failure in unsubscription
In-Reply-To: <AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
Message-ID: <018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>

unable to unsubscribe bioperl mailing list, can anybody help? the web link,
after clicking "unsubscribe" at
http://lists.open-bio.org/mailman/options/bioperl-announce-l, there is no
confirmation email sent to my email account and I keep receiving emails from
bioperl mailing list.



From Kevin.M.Brown at asu.edu  Fri Mar 18 19:35:37 2011
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Fri, 18 Mar 2011 16:35:37 -0700
Subject: [Bioperl-l] failure in unsubscription
In-Reply-To: <018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>
References: <4D83B153.6010006@cornell.edu><AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
	<018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>
Message-ID: <1A4207F8295607498283FE9E93B775B407816AC4@EX02.asurite.ad.asu.edu>

Looks like you're unsubscribing to the wrong list. That is for the
Bioperl ANNOUNCE list. See the signature at the bottom of the emails for
the correct link to remove yourself from the Bioperl-l list.

Kevin Brown
Center for Innovations in Medicine
Biodesign Institute
Arizona State University 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Ross KK Leung
> Sent: Friday, March 18, 2011 4:29 PM
> To: 'Chris Fields'; 'Robert Buels'
> Cc: 'BioPerl List'
> Subject: [Bioperl-l] failure in unsubscription
> 
> unable to unsubscribe bioperl mailing list, can anybody help? the web
> link,
> after clicking "unsubscribe" at
> http://lists.open-bio.org/mailman/options/bioperl-announce-l, there is
> no
> confirmation email sent to my email account and I keep receiving
emails
> from
> bioperl mailing list.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From David.Messina at sbc.su.se  Fri Mar 18 19:55:08 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Sat, 19 Mar 2011 00:55:08 +0100
Subject: [Bioperl-l] failure in unsubscription
In-Reply-To: <018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
	<018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>
Message-ID: <AANLkTin6k3AfwYFxgRKLGWbL5BhqxkQr7Vv6MebhObzY@mail.gmail.com>

Looks like you accidentally found the page for the wrong email list. This is
bioperl-l, not bioperl-announce-l.

Try clicking unsubscribe on this page:
http://lists.open-bio.org/mailman/listinfo/bioperl-l



On Sat, Mar 19, 2011 at 00:28, Ross KK Leung <ross at cuhk.edu.hk> wrote:

> unable to unsubscribe bioperl mailing list, can anybody help? the web link,
> after clicking "unsubscribe" at
> http://lists.open-bio.org/mailman/options/bioperl-announce-l, there is no
> confirmation email sent to my email account and I keep receiving emails
> from
> bioperl mailing list.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From David.Messina at sbc.su.se  Fri Mar 18 19:56:12 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Sat, 19 Mar 2011 00:56:12 +0100
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
Message-ID: <AANLkTikTsPeJvs0StBPzicxM55XgfvGbjrZMrwX9mwNo@mail.gmail.com>

Hear, hear! Thanks again Rob for leading this effort. You rock!

Dave



On Fri, Mar 18, 2011 at 21:06, Chris Fields <cjfields at illinois.edu> wrote:

> Congrats Rob!
>
> chris
>
> On Mar 18, 2011, at 2:24 PM, Robert Buels wrote:
>
> > Hi all,
> >
> > Great news: Google announced today that the Open Bioinformatics
> > Foundation has been accepted as a mentoring organization for this
> > summer's Google Summer of Code!
> >
> > GSoC is a Google-sponsored student internship program for open-source
> > projects, open to students from around the world (not just US
> > residents).   Students are paid a $5000 USD stipend to work as a
> > developer on an open-source project for the summer. For more on GSoC,
> > see GSoC 2011 FAQ at http://bit.ly/hpoz8W
> >
> > Student applications are due April 8, 2011 at 19:00 UTC.  Students who
> > are interested in participating should look at the OBF's GSoC page at
> > http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
> > ideas, and whom to contact about applying.
> >
> > For current developers on OBF projects, please consider volunteering to
> > be a mentor if you have not already, and contribute project ideas.  Just
> > list your name and project ideas on OBF wiki and on the relevant
> > project's GSoC wiki page.
> >
> > Thanks to all who helped make OBF's application to GSoC a success, and
> > let's have a great, productive summer of code!
> >
> > Rob Buels
> > OBF GSoC 2011 Administrator
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From hlapp at drycafe.net  Fri Mar 18 22:04:28 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Fri, 18 Mar 2011 22:04:28 -0400
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <AANLkTikTsPeJvs0StBPzicxM55XgfvGbjrZMrwX9mwNo@mail.gmail.com>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
	<AANLkTikTsPeJvs0StBPzicxM55XgfvGbjrZMrwX9mwNo@mail.gmail.com>
Message-ID: <19636599-D2B1-49E5-B557-3E406B405523@drycafe.net>

Yes! -hilmar

On Mar 18, 2011, at 7:56 PM, Dave Messina wrote:

> Hear, hear! Thanks again Rob for leading this effort. You rock!
>
> Dave
>
>
>
> On Fri, Mar 18, 2011 at 21:06, Chris Fields <cjfields at illinois.edu>  
> wrote:
>
>> Congrats Rob!
>>
>> chris
>>
>> On Mar 18, 2011, at 2:24 PM, Robert Buels wrote:
>>
>>> Hi all,
>>>
>>> Great news: Google announced today that the Open Bioinformatics
>>> Foundation has been accepted as a mentoring organization for this
>>> summer's Google Summer of Code!
>>>
>>> GSoC is a Google-sponsored student internship program for open- 
>>> source
>>> projects, open to students from around the world (not just US
>>> residents).   Students are paid a $5000 USD stipend to work as a
>>> developer on an open-source project for the summer. For more on  
>>> GSoC,
>>> see GSoC 2011 FAQ at http://bit.ly/hpoz8W
>>>
>>> Student applications are due April 8, 2011 at 19:00 UTC.  Students  
>>> who
>>> are interested in participating should look at the OBF's GSoC page  
>>> at
>>> http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
>>> ideas, and whom to contact about applying.
>>>
>>> For current developers on OBF projects, please consider  
>>> volunteering to
>>> be a mentor if you have not already, and contribute project  
>>> ideas.  Just
>>> list your name and project ideas on OBF wiki and on the relevant
>>> project's GSoC wiki page.
>>>
>>> Thanks to all who helped make OBF's application to GSoC a success,  
>>> and
>>> let's have a great, productive summer of code!
>>>
>>> Rob Buels
>>> OBF GSoC 2011 Administrator
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From chiragmatkarbioinfo at gmail.com  Fri Mar 18 23:44:32 2011
From: chiragmatkarbioinfo at gmail.com (Chirag Matkar)
Date: Sat, 19 Mar 2011 10:44:32 +0700
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <19636599-D2B1-49E5-B557-3E406B405523@drycafe.net>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
	<AANLkTikTsPeJvs0StBPzicxM55XgfvGbjrZMrwX9mwNo@mail.gmail.com>
	<19636599-D2B1-49E5-B557-3E406B405523@drycafe.net>
Message-ID: <AANLkTin6_H-T7Eq2jxU-SM4CuMF=nBZpXoM_n6joFfmn@mail.gmail.com>

Great News

On Sat, Mar 19, 2011 at 9:04 AM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> Yes! -hilmar
>
>
> On Mar 18, 2011, at 7:56 PM, Dave Messina wrote:
>
>  Hear, hear! Thanks again Rob for leading this effort. You rock!
>>
>> Dave
>>
>>
>>
>> On Fri, Mar 18, 2011 at 21:06, Chris Fields <cjfields at illinois.edu>
>> wrote:
>>
>>  Congrats Rob!
>>>
>>> chris
>>>
>>> On Mar 18, 2011, at 2:24 PM, Robert Buels wrote:
>>>
>>>  Hi all,
>>>>
>>>> Great news: Google announced today that the Open Bioinformatics
>>>> Foundation has been accepted as a mentoring organization for this
>>>> summer's Google Summer of Code!
>>>>
>>>> GSoC is a Google-sponsored student internship program for open-source
>>>> projects, open to students from around the world (not just US
>>>> residents).   Students are paid a $5000 USD stipend to work as a
>>>> developer on an open-source project for the summer. For more on GSoC,
>>>> see GSoC 2011 FAQ at http://bit.ly/hpoz8W
>>>>
>>>> Student applications are due April 8, 2011 at 19:00 UTC.  Students who
>>>> are interested in participating should look at the OBF's GSoC page at
>>>> http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
>>>> ideas, and whom to contact about applying.
>>>>
>>>> For current developers on OBF projects, please consider volunteering to
>>>> be a mentor if you have not already, and contribute project ideas.  Just
>>>> list your name and project ideas on OBF wiki and on the relevant
>>>> project's GSoC wiki page.
>>>>
>>>> Thanks to all who helped make OBF's application to GSoC a success, and
>>>> let's have a great, productive summer of code!
>>>>
>>>> Rob Buels
>>>> OBF GSoC 2011 Administrator
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>  _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Regards,
Chirag Matkar


From tzhu at mail.bnu.edu.cn  Sat Mar 19 05:49:22 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Sat, 19 Mar 2011 17:49:22 +0800
Subject: [Bioperl-l] What's wrong with the script about module
 Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300460730.12411.50.camel@deskpro15336.internal.sanger.ac.uk>
References: <1300422812.12949.5.camel@ubuntu>  <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
	<2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
	<1300456641.18688.4.camel@ubuntu>
	<1300460730.12411.50.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <1300528162.5998.4.camel@ubuntu>

But I think an "mRNA" feature should have exons. For example:


     mRNA            complement(join(1031434..1031901,1031940..1032269,
                     1032329..1032418,1032472..1032489))
                     /locus_tag="SPCC825.05c"
                     /transcript_id="NM_001023047.1"
                     /db_xref="GI:68021105"
                     /db_xref="GeneID:2539459"

Such mRNA should have 4 exons and 3 introns, right? And I just want to
calculate the lengths of every exons and introns quickly.

Besides, in the document of module Bio::SeqFeature::Gene::GeneStructure,
it writes like these:

@exons = $gene->exons();
@introns = $gene->introns();
@utr_sites = $gene->utrs();

Then where does the object "$gene" come from? I've searched through all
the google sites but found nothing.

? 2011-03-18?? 15:05 +0000?Frank Schwach??? 
> maybe I'm missing the point here but I think an "mRNA" feature should
> not be a Bio::SeqFeature::Gene::GeneStructure and it should not have
> exons - it would not make sense biologically.
> 
> Frank
> 
> 
> On Fri, 2011-03-18 at 21:57 +0800, Tao Zhu wrote:
> > Yes. But in the document
> > http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
> > It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
> > Bio::SeqFeature::Generic. I wonder how to do such inheritance.


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)





From manju.rawat2 at gmail.com  Sat Mar 19 06:29:32 2011
From: manju.rawat2 at gmail.com (manju rawat)
Date: Sat, 19 Mar 2011 15:59:32 +0530
Subject: [Bioperl-l] bio-scf installation error
Message-ID: <AANLkTikQwcqs0YyaHvddq9yjowOpoe_YDRj4Z03zXRdv@mail.gmail.com>

Hello ,

I want to install Bio-SCF module on windows..But i am unable to do this bcs
to install bio-scf i have to install io_lib oe zlib on windows..
I download both from the described url in install file of bio-scf....i also
indtalled MinGW ..but now i dont know how to install it???
pls help to install it..

Thanks in Advance
Manju Rawat


From jason.stajich at gmail.com  Sat Mar 19 14:19:23 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 19 Mar 2011 11:19:23 -0700
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <4D83B153.6010006@cornell.edu>
References: <4D83B153.6010006@cornell.edu>
Message-ID: <6387373A-E17F-4CE2-9B19-E296A2668018@gmail.com>

Nice work Rob. Thanks for leading the effort and thanks to those who agreed to mentor. 

Sent from my iPhone-please excuse typos

--
Jason Stajich

On Mar 18, 2011, at 12:24 PM, Robert Buels <rmb32 at cornell.edu> wrote:

> Hi all,
> 
> Great news: Google announced today that the Open Bioinformatics
> Foundation has been accepted as a mentoring organization for this
> summer's Google Summer of Code!
> 
> GSoC is a Google-sponsored student internship program for open-source
> projects, open to students from around the world (not just US
> residents).   Students are paid a $5000 USD stipend to work as a
> developer on an open-source project for the summer. For more on GSoC,
> see GSoC 2011 FAQ at http://bit.ly/hpoz8W
> 
> Student applications are due April 8, 2011 at 19:00 UTC.  Students who
> are interested in participating should look at the OBF's GSoC page at
> http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
> ideas, and whom to contact about applying.
> 
> For current developers on OBF projects, please consider volunteering to
> be a mentor if you have not already, and contribute project ideas.  Just
> list your name and project ideas on OBF wiki and on the relevant
> project's GSoC wiki page.
> 
> Thanks to all who helped make OBF's application to GSoC a success, and
> let's have a great, productive summer of code!
> 
> Rob Buels
> OBF GSoC 2011 Administrator
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jason.stajich at gmail.com  Sat Mar 19 14:31:17 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 19 Mar 2011 11:31:17 -0700
Subject: [Bioperl-l] What's wrong with the script about module
	Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300528162.5998.4.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu> <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
	<2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
	<1300456641.18688.4.camel@ubuntu>
	<1300460730.12411.50.camel@deskpro15336.internal.sanger.ac.uk>
	<1300528162.5998.4.camel@ubuntu>
Message-ID: <093660B8-458E-4617-8D12-228985CA88CD@gmail.com>

You have to instantiate the gene structure and copy the exon objects into the substructure. Unless you have specific methods in the GeneStructure I would just pull out the data from the generic objects. 

See the genbank to gff script and the Unflattener for ways to more simply destruct the mRNA feature into gene->mRNA->CDS,Exons 

If you are just wanting to count Exons 
You can see example on slide 27 or so. 

http://jason.open-bio.org/Bioperl_Tutorials/ProgrammingBiology2008/ProgBiology_BioPerl_I.pdf

Sent from my iPhone-please excuse typos

--
Jason Stajich

On Mar 19, 2011, at 2:49 AM, Tao Zhu <tzhu at mail.bnu.edu.cn> wrote:

> But I think an "mRNA" feature should have exons. For example:
> 
> 
>     mRNA            complement(join(1031434..1031901,1031940..1032269,
>                     1032329..1032418,1032472..1032489))
>                     /locus_tag="SPCC825.05c"
>                     /transcript_id="NM_001023047.1"
>                     /db_xref="GI:68021105"
>                     /db_xref="GeneID:2539459"
> 
> Such mRNA should have 4 exons and 3 introns, right? And I just want to
> calculate the lengths of every exons and introns quickly.
> 
> Besides, in the document of module Bio::SeqFeature::Gene::GeneStructure,
> it writes like these:
> 
> @exons = $gene->exons();
> @introns = $gene->introns();
> @utr_sites = $gene->utrs();
> 
> Then where does the object "$gene" come from? I've searched through all
> the google sites but found nothing.
> 
> ? 2011-03-18?? 15:05 +0000?Frank Schwach??? 
>> maybe I'm missing the point here but I think an "mRNA" feature should
>> not be a Bio::SeqFeature::Gene::GeneStructure and it should not have
>> exons - it would not make sense biologically.
>> 
>> Frank
>> 
>> 
>> On Fri, 2011-03-18 at 21:57 +0800, Tao Zhu wrote:
>>> Yes. But in the document
>>> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
>>> It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
>>> Bio::SeqFeature::Generic. I wonder how to do such inheritance.
> 
> 
> -- 
> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> 100875, China
> Email: tzhu at mail.bnu.edu.cn
> Website: http://bnuzt.org (mainly written in Chinese)
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jason.stajich at gmail.com  Sat Mar 19 14:36:49 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 19 Mar 2011 11:36:49 -0700
Subject: [Bioperl-l] Please recommend Perl module to parse phylogentic
	trees
In-Reply-To: <2e94f0bb-0282-4d53-b205-56ff895665de@w7g2000pre.googlegroups.com>
References: <2e94f0bb-0282-4d53-b205-56ff895665de@w7g2000pre.googlegroups.com>
Message-ID: <447BFFD2-06E6-41E0-81BF-B03EB919316C@gmail.com>

Nexus is richer and we only parse the trees from that format. Since the format is a newick tree embedded within it relies on the same code in the newick parser. 

Knowing what you want to do would more likely lead to better answer.  As for bugs - you can search the redmine big tracker to see whether they are reported issues that are unresolved and you can examine the tests in the t directory to see what compliance is tested. 

Jason
Sent from my iPhone-please excuse typos

--
Jason Stajich

On Mar 4, 2011, at 12:24 PM, justin100 <bio.justin100 at gmail.com> wrote:

> Hi,
> 
> I am writing a script to parse phylogenetic trees. The input will be
> trees in Newick format for now (maybe NEXUS in the future).
> 
> Quite a few Perl modules can parse phylogenetic trees. For Newick
> format, there are Bio::TreeIO and  Bio::Phylo::Parsers. For NEXUS
> format, there is Bio::NEXUS. From my understanding, it's not difficult
> to convert from Newick to NEXUS or vice versa, if only for the purpose
> of parsing trees.
> 
> I'd to know the advantages and disadvantages of these modules when
> compared with each other. Please recommend one that you think is the
> most capable parser (and hopefully has the least bugs).
> 
> Thanks.
> 
> Justin
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From veer_lovepune at yahoo.co.in  Sat Mar 19 16:56:06 2011
From: veer_lovepune at yahoo.co.in (virendra patil)
Date: Sun, 20 Mar 2011 02:26:06 +0530 (IST)
Subject: [Bioperl-l] Bioperl-l Digest, Vol 95, Issue 19
In-Reply-To: <mailman.21.1300550405.26148.bioperl-l@lists.open-bio.org>
Message-ID: <790813.91588.qm@web137312.mail.in.yahoo.com>

hi can some one help me i tried to install ?bioperl many time but it show message likeCan't locate Bio/Seq.pm in @INC (@INC contains: E:/JAVA1/.metadata/.plugins/org.epic.debug E:/JAVA1/PERL EXAM D:/Perl/site/lib D:/Perl/lib .) at E:/JAVA1/PERL EXAM/PERLEXAM.pl line 2.BEGIN failed--compilation aborted at E:/JAVA1/PERL EXAM/PERLEXAM.pl line 2.?

---i try with java perl intgration my perl is working but bioperl show upper message




From ngoodman at systemsbiology.org  Tue Mar 22 09:57:50 2011
From: ngoodman at systemsbiology.org (Nathan (Nat) Goodman)
Date: Tue, 22 Mar 2011 06:57:50 -0700
Subject: [Bioperl-l] Ensembl stable_id_event table
Message-ID: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>

With apologies, this is not technically a bioperl question, but hopefully close enough.  I'm trying to map old Ensembl IDs to current ones.  Table stable_id_event on their ftp site seems to be the place to get this information, but the data in that table (for human build 61) is cyclic, meaning that old IDs are sometimes mapped to new ones which in turn are mapped back to the old one.  This seems wrong...  And, it's not a rare occurrence: 18% of IDs in the table lie on cycles, the largest of which contains more than 6000 IDs!

To see one short cycle, run this query (against human build 61).

mysql> select * from stable_id_event where 
    ->     (old_stable_id='ENSP00000399673' or new_stable_id='ENSP00000399673')
    -> and (old_stable_id='ENSP00000365536' or new_stable_id='ENSP00000365536');

The results are

+-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
| old_stable_id   | old_version | new_stable_id   | new_version | mapping_session_id | type        | score |
+-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
| ENSP00000399673 |           2 | ENSP00000365536 |           3 |                380 | translation |     1 | 
| ENSP00000399673 |           2 | ENSP00000365536 |           3 |                381 | translation |     1 | 
| ENSP00000365536 |           3 | ENSP00000399673 |           2 |                381 | translation |     1 | 
| ENSP00000399673 |           2 | ENSP00000365536 |           3 |                382 | translation |     1 | 
| ENSP00000365536 |           3 | ENSP00000399673 |           2 |                382 | translation |     1 | 
+-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+

The first and last lines reveal the cycle:

line 1) ENSP00000399673-> ENSP00000365536
line 5) ENSP00000365536-> ENSP00000399673

If anyone can shed some light, I would be most grateful.

Thanks very much,
Nat Goodman




From molecules at cpan.org  Wed Mar 23 14:44:15 2011
From: molecules at cpan.org (Christopher Bottoms)
Date: Wed, 23 Mar 2011 13:44:15 -0500
Subject: [Bioperl-l] Ensembl stable_id_event table
In-Reply-To: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>
References: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>
Message-ID: <AANLkTi=acb_oG6-PiDLeh373LkYUz9K=XDhUimv922qz@mail.gmail.com>

Hi Nat,

Have you tried contacting someone at Ensembl about it? That is the
first place I would try.

--Christopher Bottoms


On Tue, Mar 22, 2011 at 8:57 AM, Nathan (Nat) Goodman
<ngoodman at systemsbiology.org> wrote:
> With apologies, this is not technically a bioperl question, but hopefully close enough. ?I'm trying to map old Ensembl IDs to current ones. ?Table stable_id_event on their ftp site seems to be the place to get this information, but the data in that table (for human build 61) is cyclic, meaning that old IDs are sometimes mapped to new ones which in turn are mapped back to the old one. ?This seems wrong... ?And, it's not a rare occurrence: 18% of IDs in the table lie on cycles, the largest of which contains more than 6000 IDs!
>
> To see one short cycle, run this query (against human build 61).
>
> mysql> select * from stable_id_event where
> ? ?-> ? ? (old_stable_id='ENSP00000399673' or new_stable_id='ENSP00000399673')
> ? ?-> and (old_stable_id='ENSP00000365536' or new_stable_id='ENSP00000365536');
>
> The results are
>
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> | old_stable_id ? | old_version | new_stable_id ? | new_version | mapping_session_id | type ? ? ? ?| score |
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> | ENSP00000399673 | ? ? ? ? ? 2 | ENSP00000365536 | ? ? ? ? ? 3 | ? ? ? ? ? ? ? ?380 | translation | ? ? 1 |
> | ENSP00000399673 | ? ? ? ? ? 2 | ENSP00000365536 | ? ? ? ? ? 3 | ? ? ? ? ? ? ? ?381 | translation | ? ? 1 |
> | ENSP00000365536 | ? ? ? ? ? 3 | ENSP00000399673 | ? ? ? ? ? 2 | ? ? ? ? ? ? ? ?381 | translation | ? ? 1 |
> | ENSP00000399673 | ? ? ? ? ? 2 | ENSP00000365536 | ? ? ? ? ? 3 | ? ? ? ? ? ? ? ?382 | translation | ? ? 1 |
> | ENSP00000365536 | ? ? ? ? ? 3 | ENSP00000399673 | ? ? ? ? ? 2 | ? ? ? ? ? ? ? ?382 | translation | ? ? 1 |
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
>
> The first and last lines reveal the cycle:
>
> line 1) ENSP00000399673-> ENSP00000365536
> line 5) ENSP00000365536-> ENSP00000399673
>
> If anyone can shed some light, I would be most grateful.
>
> Thanks very much,
> Nat Goodman
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From cjfields at illinois.edu  Wed Mar 23 18:23:47 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 23 Mar 2011 17:23:47 -0500
Subject: [Bioperl-l] Ensembl stable_id_event table
In-Reply-To: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>
References: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>
Message-ID: <890FA151-63D4-4EAF-8141-8975911126E4@illinois.edu>

Odd, wonder what the ensembl folks have to say about it.  Have you asked them?

chris

On Mar 22, 2011, at 8:57 AM, Nathan (Nat) Goodman wrote:

> With apologies, this is not technically a bioperl question, but hopefully close enough.  I'm trying to map old Ensembl IDs to current ones.  Table stable_id_event on their ftp site seems to be the place to get this information, but the data in that table (for human build 61) is cyclic, meaning that old IDs are sometimes mapped to new ones which in turn are mapped back to the old one.  This seems wrong...  And, it's not a rare occurrence: 18% of IDs in the table lie on cycles, the largest of which contains more than 6000 IDs!
> 
> To see one short cycle, run this query (against human build 61).
> 
> mysql> select * from stable_id_event where 
>    ->     (old_stable_id='ENSP00000399673' or new_stable_id='ENSP00000399673')
>    -> and (old_stable_id='ENSP00000365536' or new_stable_id='ENSP00000365536');
> 
> The results are
> 
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> | old_stable_id   | old_version | new_stable_id   | new_version | mapping_session_id | type        | score |
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> | ENSP00000399673 |           2 | ENSP00000365536 |           3 |                380 | translation |     1 | 
> | ENSP00000399673 |           2 | ENSP00000365536 |           3 |                381 | translation |     1 | 
> | ENSP00000365536 |           3 | ENSP00000399673 |           2 |                381 | translation |     1 | 
> | ENSP00000399673 |           2 | ENSP00000365536 |           3 |                382 | translation |     1 | 
> | ENSP00000365536 |           3 | ENSP00000399673 |           2 |                382 | translation |     1 | 
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> 
> The first and last lines reveal the cycle:
> 
> line 1) ENSP00000399673-> ENSP00000365536
> line 5) ENSP00000365536-> ENSP00000399673
> 
> If anyone can shed some light, I would be most grateful.
> 
> Thanks very much,
> Nat Goodman
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From roy.chaudhuri at gmail.com  Thu Mar 24 09:47:27 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Thu, 24 Mar 2011 13:47:27 +0000
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
Message-ID: <4D8B4B6F.7010407@gmail.com>

Hi all,

I have discovered a possible bug in Bioperl, although maybe it's my 
expectations that are wrong, not the code.

I noticed that when calculating molecular weights for a bunch of protein 
sequences using Bio::Tools::SeqStats->get_mol_wt, the values I was 
getting were slightly different from the ones given by Emboss pepstats. 
This was due to my protein sequences ending with *, since they were 
derived from translating annotated genes including the stop codon. 
Surprisingly (to me, at least) Bio::Seq->length gives a value that 
counts the terminal *, so one greater than the number of amino acids. 
SeqStats->get_mol_wt calls Bio::Seq->length to determine the number of 
water molecules to subtract from the total molecular weight, so the 
reported weights for my sequence were the weight of one water molecule 
less than they should have been. I'm not sure if this is a bug in 
get_mol_wt, in Bio::Seq->length, or if it's bad practice to use protein 
sequences with a terminal asterisk (I've never had a problem doing so 
before).

Cheers,
Roy.


From adsj at novozymes.com  Thu Mar 24 11:01:25 2011
From: adsj at novozymes.com (Adam =?utf-8?Q?Sj=C3=B8gren?=)
Date: Thu, 24 Mar 2011 16:01:25 +0100
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
In-Reply-To: <4D8B4B6F.7010407@gmail.com> (Roy Chaudhuri's message of "Thu, 24
	Mar 2011 13:47:27 +0000")
References: <4D8B4B6F.7010407@gmail.com>
Message-ID: <87mxkkbm0q.fsf@topper.koldfront.dk>

On Thu, 24 Mar 2011 13:47:27 +0000, Roy wrote:

> This was due to my protein sequences ending with *, since they were
> derived from translating annotated genes including the stop codon.

If you give ->translate() the -complete=>1 option, the stop codon will
not be included in the resulting protein sequence.

 * http://bioperl.org/cgi-bin/deob_detail.cgi?method=Bio::PrimarySeqI::translate


  Best regards,

    Adam

-- 
                                                          Adam Sj?gren
                                                    adsj at novozymes.com



From roy.chaudhuri at gmail.com  Thu Mar 24 11:27:36 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Thu, 24 Mar 2011 15:27:36 +0000
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
In-Reply-To: <87mxkkbm0q.fsf@topper.koldfront.dk>
References: <4D8B4B6F.7010407@gmail.com> <87mxkkbm0q.fsf@topper.koldfront.dk>
Message-ID: <4D8B62E8.2050902@gmail.com>

On 24/03/2011 15:01, Adam Sj?gren wrote:
> If you give ->translate() the -complete=>1 option, the stop codon will
> not be included in the resulting protein sequence.

Ah, that's useful to know, thanks Adam. I still think that get_mol_wt 
should deal with such sequences without giving an incorrect weight, though.


From cjfields at illinois.edu  Thu Mar 24 11:47:29 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 24 Mar 2011 10:47:29 -0500
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
In-Reply-To: <4D8B4B6F.7010407@gmail.com>
References: <4D8B4B6F.7010407@gmail.com>
Message-ID: <2F1303AE-4678-4901-A33C-A7811FF8F309@illinois.edu>


On Mar 24, 2011, at 8:47 AM, Roy Chaudhuri wrote:

> Hi all,
> 
> I have discovered a possible bug in Bioperl, although maybe it's my expectations that are wrong, not the code.
> 
> I noticed that when calculating molecular weights for a bunch of protein sequences using Bio::Tools::SeqStats->get_mol_wt, the values I was getting were slightly different from the ones given by Emboss pepstats. This was due to my protein sequences ending with *, since they were derived from translating annotated genes including the stop codon. Surprisingly (to me, at least) Bio::Seq->length gives a value that counts the terminal *, so one greater than the number of amino acids. SeqStats->get_mol_wt calls Bio::Seq->length to determine the number of water molecules to subtract from the total molecular weight, so the reported weights for my sequence were the weight of one water molecule less than they should have been. I'm not sure if this is a bug in get_mol_wt, in Bio::Seq->length, or if it's bad practice to use protein sequences with a terminal asterisk (I've never had a problem doing so before).

The method should account for the possibility that '*' is present; should be easy enough to fix with something like:

my $len = $seq =~ tr/A-Za-z/A-Za-z/;

I'm not able to do this right away (on fam vacation), can you file this on our new bug server?

http://redmine.open-bio.org

> Cheers,
> Roy.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

chris


From roy.chaudhuri at gmail.com  Thu Mar 24 12:08:22 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Thu, 24 Mar 2011 16:08:22 +0000
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
In-Reply-To: <2F1303AE-4678-4901-A33C-A7811FF8F309@illinois.edu>
References: <4D8B4B6F.7010407@gmail.com>
	<2F1303AE-4678-4901-A33C-A7811FF8F309@illinois.edu>
Message-ID: <4D8B6C76.6090401@gmail.com>

Done:
http://redmine.open-bio.org/issues/3185

Have a good break,
Roy.

On 24/03/2011 15:47, Chris Fields wrote:
>
> On Mar 24, 2011, at 8:47 AM, Roy Chaudhuri wrote:
>
>> Hi all,
>>
>> I have discovered a possible bug in Bioperl, although maybe it's my
>> expectations that are wrong, not the code.
>>
>> I noticed that when calculating molecular weights for a bunch of
>> protein sequences using Bio::Tools::SeqStats->get_mol_wt, the
>> values I was getting were slightly different from the ones given by
>> Emboss pepstats. This was due to my protein sequences ending with
>> *, since they were derived from translating annotated genes
>> including the stop codon. Surprisingly (to me, at least)
>> Bio::Seq->length gives a value that counts the terminal *, so one
>> greater than the number of amino acids. SeqStats->get_mol_wt calls
>> Bio::Seq->length to determine the number of water molecules to
>> subtract from the total molecular weight, so the reported weights
>> for my sequence were the weight of one water molecule less than
>> they should have been. I'm not sure if this is a bug in get_mol_wt,
>> in Bio::Seq->length, or if it's bad practice to use protein
>> sequences with a terminal asterisk (I've never had a problem doing
>> so before).
>
> The method should account for the possibility that '*' is present;
> should be easy enough to fix with something like:
>
> my $len = $seq =~ tr/A-Za-z/A-Za-z/;
>
> I'm not able to do this right away (on fam vacation), can you file
> this on our new bug server?
>
> http://redmine.open-bio.org
>
>> Cheers, Roy. _______________________________________________
>> Bioperl-l mailing list Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> chris



From rachitasharma at gmail.com  Thu Mar 24 13:12:43 2011
From: rachitasharma at gmail.com (Rachita Sharma)
Date: Thu, 24 Mar 2011 11:12:43 -0600
Subject: [Bioperl-l] Genbank to gff3 format
Message-ID: <AANLkTimarbmi3XnFZ9VjT2GMHUoS6COkVGnbtawYh2a+@mail.gmail.com>

I am having trouble using the perl script bp_genbank2gff3.pl for
converting my genbank file into gff3 format. Unique IDs are not
created by the Bioperl converter so I cannot get the gff3 file
validated on the official GFF validator I want to use the final gff3
file on Gbrowse without errors. Will appreciate your suggestions.

Thanks!
Rachita


From dan.bolser at gmail.com  Fri Mar 25 07:21:57 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Fri, 25 Mar 2011 11:21:57 +0000
Subject: [Bioperl-l] from SimpleAlign to SAM/BAM
In-Reply-To: <AANLkTinEo3Ac8h5Gh-l4aqiKE0C1-iPiP96XilazQ4Hd@mail.gmail.com>
References: <AANLkTilHpBojt1AoAR6qe8YgqXrt8vp_dl64GOblTH3h@mail.gmail.com>
	<CF66A9BB040D49189BB80C9E057422AC@NewLife>
	<AANLkTinEo3Ac8h5Gh-l4aqiKE0C1-iPiP96XilazQ4Hd@mail.gmail.com>
Message-ID: <AANLkTikk4jNjG203Lw764Exdb9VBoZPVkXki8n8jVwLO@mail.gmail.com>

On 19 May 2010 17:40, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Bio::Samtools, which is separate from bioperl but compatible with it,
> provides read/write access to SAM and BAM via Heng's C library.

If I understand correctly, Bio::Samtools is a meta package that
encompasses Bio::DB::Sam and friends. However, when I look at
Bio::DB::Sam, I only see "Read SAM/BAM database files", not write, and
I don't see how to write SAM files from the docs there.

I just looked at the pod for Bio::Assembly::IO::sam (how come this
isn't documented in CPAN?), and I read:

This is a (currently) read-only IO module designed to convert
Sequence/Alignment Map (SAM) ...

I guess this is what was being discussed on in this thread (the fact
that IO doesn't yet write, but XS can be used to get it writing).

Did I understand correctly, or is there some way to write SAM from BioPerl?


Cheers,
Dan..

> Lincoln
>
> On Wed, May 19, 2010 at 9:34 AM, Mark A. Jensen <maj at fortinbras.us> wrote:
>
>> Albert-- have a look at Bio::Tools::Run::Samtools which incorporates the
>> use of Bio::Assembly::IO::sam (I think). I know there is only read
>> capability for B:A:I:sam, but Samtools may give you the appropriate wrapper
>> for doing writes (some assembly (so to speak) required...)-- cheers MAJ
>> ----- Original Message ----- From: "Albert Vilella" <avilella at gmail.com>
>>
>> To: <bioperl-l at bioperl.org>
>> Sent: Wednesday, May 19, 2010 4:36 AM
>>
>> Subject: [Bioperl-l] from SimpleAlign to SAM/BAM
>>
>>
>> ?Hi,
>>>
>>> I would like to know what would be the best way to generate a SAM/BAM file
>>> with cDNA alignments against the human reference from a bunch of
>>> Bio::SimpleAlign
>>> cDNA multiple sequence alignment objects.
>>>
>>> Considering I've got a way to map the cDNAs to chromosome coordinates,
>>> how can I generate a SAM/BAM file with ~1,000,000 entries against ~23.000
>>> human
>>> coordinates?
>>>
>>> As far as I can see, there is an Bio::Assembly::IO::sam.pm which loads
>>> assemblies.
>>> Should I be using some other tool existing not in bioperl?
>>>
>>> Cheers,
>>>
>>> Albert.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From dan.bolser at gmail.com  Sat Mar 26 20:11:27 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Sun, 27 Mar 2011 00:11:27 +0000
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
Message-ID: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>

Hi all,

I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm uses:
    if (length $source_tag) {

within the '_types_sql' function to test if $source_tag is defined
(and has a length). This obviously fails when $source_tag it isn't
defined, and I see the above error message from my script when I call
the 'features' function (as shown below).

>From tests (thanks to rbuels in #bioperl) it seems the value of $type
is simply 'fwd link intensity', so:
      ($primary_tag,$source_tag) = split ':',$type,2;

on line 1047 leaves $source_tag undefined.

Here is my proposed fix:

diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
index 00103c2..dfc70c0 100644
--- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
+++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
@@ -1057,8 +1057,8 @@ sub _types_sql {
       ($primary_tag,$source_tag) = split ':',$type,2;
     }

-    if (length $source_tag) {
-      if (length($primary_tag)) {
+    if (defined $source_tag && length $source_tag) {
+      if (defined $primary_tag && length($primary_tag)) {
         push @matches,"tl.tag=?";
         push @args,"$primary_tag:$source_tag";
       }


which seems to work. I'd write some tests, but an old bug that I can't
track down prevents me from running tests on this package
(http://bugzilla.open-bio.org/show_bug.cgi?id=2899).

Cheers,
Dan.


Here are some snippets of code to give context:

my $intensities = Bio::DB::SeqFeature::Store->
  new( -adaptor => 'DBI::mysql',
	-dsn => 'db:mysql.server.ac.uk',
	-user => 'me',
	-pass => 'secret',
       -verbose => $verbose,
     );

my @fwd_intensity = $intensities->
    features( -seqid => 'some-id', -type => 'fwd link intensity',
              -start => 10,
              -end   => 200,
    );


From hufeiyc at gmail.com  Tue Mar 22 15:14:54 2011
From: hufeiyc at gmail.com (Fei Hu)
Date: Tue, 22 Mar 2011 15:14:54 -0400
Subject: [Bioperl-l] GSoC 2011
Message-ID: <AANLkTim6o3bJ6NkBRmoUC5e76GaGzpjP5+xE+ZrWcEdc@mail.gmail.com>

Hi, All.

My name is Fei Hu from U. of South Carolina. I am currently a second-year
Ph.D student in computer science focusing on gene order and sequence(DNA &
AA) phylogeny as well as whole genome alignment. I am instreseted in joining
bioperl project of GSoC 2011. I have two ideas that would like to share.

My first idea is to extend the bioperl so that it can process and analysis
gene order data using published package such as MGR, GRAPPA and distance
estimator. This is a relatively new type of data and many great researchers
have contributed to this type of phylogeny reconstruction (Dr. Pavel Penzer,
Dr. Bernard Moret and Dr. David Sankoff).

Secondly as maximum likelihood becomes more and more popular, especially
RAxML has been widely recognized and used(over 1000 citations). I think it's
time to integrate that as well as GARLI into the Bio::Tools. I extensively
used and explored RAxML in my last publication on gene order phylogeny.

Those are just my preliminary thoughts, not even a plan and any suggestion
is greatly appreciated!!! I use perl on daily bases for data processing and
composing testing scripts, but not much OOP involved.

PS: Rest api for CIPRES is no longer available. So this following task can't
be finished right now:
Development of a
Bio::Tools::Run::RemoteBlast<http://bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast>-like
interface to CIPRES remote analyses; for more see this
thread<http://thread.gmane.org/gmane.comp.lang.perl.bio.general/16524>
.

And Thank you all.
Best

Fei

-- 
*Fei Hu
Bioinformatics Lab
3D-11 Swearingen Building
U of South Carolina
Tel: 803-397-5240*


From Dallas.Thomas at AGR.GC.CA  Wed Mar 23 13:08:12 2011
From: Dallas.Thomas at AGR.GC.CA (Thomas, Dallas)
Date: Wed, 23 Mar 2011 11:08:12 -0600
Subject: [Bioperl-l] Bio::Tools::Protparam
Message-ID: <DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>

Need help.  I am trying to use the Bio::Tools::Protparam perl module.

 

For testing purposes I have copied and pasted the example in the module,
I have set:

 

use strict;

use Bio::Tools::Protparam;

use Bio::DB::GenBank;

 

Every time I try and run the script I get the following error:

                        

                              Can't locate object method "new" via
package "Protparam" (perhaps you forgot to load "Protparam"?) at ...

 

Do you have any ideas?  Any help would be very much appreciated.

 

Sincerely

Dallas Thomas

 




From ravimbt at gmail.com  Thu Mar 24 08:33:55 2011
From: ravimbt at gmail.com (=?UTF-8?B?wrbigKLil4/guYvigKLgrofgrrDgrrXgrr/Rj86xzr3OueKXj+C5i+KAouKAosK2?=)
Date: Thu, 24 Mar 2011 18:03:55 +0530
Subject: [Bioperl-l] Bioperl installation doubt
Message-ID: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>

Hi,

Could you please help me installing bioperl-db, bioperl-run & other packages
using ppm on windows 7? Please find the attachment for the error message I
get. I would really appreciate if you help me fix this issue.

Thanks,

With regards,
Ravi.
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From abualiga at gmail.com  Sun Mar 27 09:34:05 2011
From: abualiga at gmail.com (Galeb Abu-Ali)
Date: Sun, 27 Mar 2011 06:34:05 -0700 (PDT)
Subject: [Bioperl-l] CDS complement statements from GenBank
Message-ID: <cdf62961-ac89-4274-91ed-9a233d2de15c@k10g2000prh.googlegroups.com>

Hi,

I'm trying to parse CDS complement statements from GenBank files of
bacterial genomes. I know it works for 'join' statements with
Bio::Location::SplitLocationI, but there is no spliced genes in
bacterial annotations and therefore no 'join()' statements. When I
replace 'complement' with 'join' in the bacterial GenBank file,
Bio::Location::SplitLocationI gets the coordinates. I took a look at
SplitLocationI.pm and Split.pm to see if I could replace 'join' with
'complement' to get it to work but no luck. At your convenience,
please advise.

cheers,

galeb


From drinmontana at gmail.com  Sun Mar 27 10:37:17 2011
From: drinmontana at gmail.com (Drin)
Date: Sun, 27 Mar 2011 07:37:17 -0700 (PDT)
Subject: [Bioperl-l] Various bioperl build test errors
Message-ID: <799d8933-c2de-4c88-ac2c-03bb1b32dd78@z27g2000prz.googlegroups.com>

Hello BioPerl mailing list!

So I have been successfully building BioPerl (though I thought I was
failing), but have been getting some errors during said builds. I'm
running ubuntu 9.04 and I ran 'perl Build.PL', then './Build test'
using bash. If any other information is desired, please let me know.
And here are some gists to help with some context:
perl Build.PL - https://gist.github.com/e4be0891635463b07812
./Build test - https://gist.github.com/3e9a1cba10ca0e9b087d


From cjfields at illinois.edu  Sun Mar 27 12:43:11 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 27 Mar 2011 11:43:11 -0500
Subject: [Bioperl-l] Bio::Tools::Protparam
In-Reply-To: <DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>
References: <DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>
Message-ID: <851BC032-98F0-441D-9185-5079527CDA3E@illinois.edu>

Dallas,

Can you send a script example?  Hard to judge what is going wrong w/o code.

chris
 
On Mar 23, 2011, at 12:08 PM, Thomas, Dallas wrote:

> Need help.  I am trying to use the Bio::Tools::Protparam perl module.
> 
> 
> 
> For testing purposes I have copied and pasted the example in the module,
> I have set:
> 
> 
> 
> use strict;
> 
> use Bio::Tools::Protparam;
> 
> use Bio::DB::GenBank;
> 
> 
> 
> Every time I try and run the script I get the following error:
> 
> 
> 
>                              Can't locate object method "new" via
> package "Protparam" (perhaps you forgot to load "Protparam"?) at ...
> 
> 
> 
> Do you have any ideas?  Any help would be very much appreciated.
> 
> 
> 
> Sincerely
> 
> Dallas Thomas
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From David.Messina at sbc.su.se  Sun Mar 27 13:05:05 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Sun, 27 Mar 2011 19:05:05 +0200
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
Message-ID: <AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>

Hi Ravi,

The get_sequence and write_sequence methods are in the Bio::Perl module, not
Bio::Seq. So your first line

use Bio::Seq;

should be replaced with

use Bio::Perl;


More examples in the BioPerl Tutorial here:
http://www.bioperl.org/wiki/BioPerl_Tutorial


Dve



2011/3/24 ?????????????????? <ravimbt at gmail.com>

> Hi,
>
> Could you please help me installing bioperl-db, bioperl-run & other
> packages
> using ppm on windows 7? Please find the attachment for the error message I
> get. I would really appreciate if you help me fix this issue.
>
> Thanks,
>
> With regards,
> Ravi.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From jason at bioperl.org  Sun Mar 27 13:28:04 2011
From: jason at bioperl.org (Jason Stajich)
Date: Sun, 27 Mar 2011 10:28:04 -0700
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
Message-ID: <4D8F73A4.8050408@bioperl.org>

Dan - not sure why you would need to do this as length on an undef 
should still return false (an undef).

$ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} 
print "\n"'
no
$ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"} 
print "\n"'
no

Also, having no 'source' is probably not proper GFF3.

BTW bugzilla is dead so the bug that you refer to is here
   http://redmine.open-bio.org/issues/2899
I've assigned the bug to Lincoln to help figure out what should be done 
with it.

Thanks,
jason

Dan Bolser wrote:
> Hi all,
>
> I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm uses:
>      if (length $source_tag) {
>
> within the '_types_sql' function to test if $source_tag is defined
> (and has a length). This obviously fails when $source_tag it isn't
> defined, and I see the above error message from my script when I call
> the 'features' function (as shown below).
>
> > From tests (thanks to rbuels in #bioperl) it seems the value of $type
> is simply 'fwd link intensity', so:
>        ($primary_tag,$source_tag) = split ':',$type,2;
>
> on line 1047 leaves $source_tag undefined.
>
> Here is my proposed fix:
>
> diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
> index 00103c2..dfc70c0 100644
> --- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
> +++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
> @@ -1057,8 +1057,8 @@ sub _types_sql {
>         ($primary_tag,$source_tag) = split ':',$type,2;
>       }
>
> -    if (length $source_tag) {
> -      if (length($primary_tag)) {
> +    if (defined $source_tag&&  length $source_tag) {
> +      if (defined $primary_tag&&  length($primary_tag)) {
>           push @matches,"tl.tag=?";
>           push @args,"$primary_tag:$source_tag";
>         }
>
>
> which seems to work. I'd write some tests, but an old bug that I can't
> track down prevents me from running tests on this package
> (http://bugzilla.open-bio.org/show_bug.cgi?id=2899).
>
> Cheers,
> Dan.
>
>
> Here are some snippets of code to give context:
>
> my $intensities = Bio::DB::SeqFeature::Store->
>    new( -adaptor =>  'DBI::mysql',
> 	-dsn =>  'db:mysql.server.ac.uk',
> 	-user =>  'me',
> 	-pass =>  'secret',
>         -verbose =>  $verbose,
>       );
>
> my @fwd_intensity = $intensities->
>      features( -seqid =>  'some-id', -type =>  'fwd link intensity',
>                -start =>  10,
>                -end   =>  200,
>      );
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki



From dan.bolser at gmail.com  Sun Mar 27 13:55:02 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Sun, 27 Mar 2011 18:55:02 +0100
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <4D8F73A4.8050408@bioperl.org>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
	<4D8F73A4.8050408@bioperl.org>
Message-ID: <AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>

On 27 March 2011 18:28, Jason Stajich <jason at bioperl.org> wrote:
> Dan - not sure why you would need to do this as length on an undef should
> still return false (an undef).
>
> $ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} print
> "\n"'
> no
> $ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"}
> print "\n"'
> no

Doesn't the latter spew a warning? (The output before / after my 'bug
fix' is the same, I just don't see 100s of warnings about undefined
values).


> Also, having no 'source' is probably not proper GFF3.

I'm quite sure it is, but by GFF does have a source. I'm just calling
'features' with only a feature type and not a feature type and a
source (because I only care about source). My call is pretty similar
to the example here:

http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/DB/SeqFeature/Store.pm#features

 @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');


> BTW bugzilla is dead so the bug that you refer to is here
> ?http://redmine.open-bio.org/issues/2899
> I've assigned the bug to Lincoln to help figure out what should be done with
> it.
>
> Thanks,
> jason

Cheers Jason,
Dan.


> Dan Bolser wrote:
>>
>> Hi all,
>>
>> I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm
>> uses:
>> ? ? if (length $source_tag) {
>>
>> within the '_types_sql' function to test if $source_tag is defined
>> (and has a length). This obviously fails when $source_tag it isn't
>> defined, and I see the above error message from my script when I call
>> the 'features' function (as shown below).
>>
>> > From tests (thanks to rbuels in #bioperl) it seems the value of $type
>> is simply 'fwd link intensity', so:
>> ? ? ? ($primary_tag,$source_tag) = split ':',$type,2;
>>
>> on line 1047 leaves $source_tag undefined.
>>
>> Here is my proposed fix:
>>
>> diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
>> index 00103c2..dfc70c0 100644
>> --- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>> +++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>> @@ -1057,8 +1057,8 @@ sub _types_sql {
>> ? ? ? ?($primary_tag,$source_tag) = split ':',$type,2;
>> ? ? ?}
>>
>> - ? ?if (length $source_tag) {
>> - ? ? ?if (length($primary_tag)) {
>> + ? ?if (defined $source_tag&& ?length $source_tag) {
>> + ? ? ?if (defined $primary_tag&& ?length($primary_tag)) {
>> ? ? ? ? ?push @matches,"tl.tag=?";
>> ? ? ? ? ?push @args,"$primary_tag:$source_tag";
>> ? ? ? ?}
>>
>>
>> which seems to work. I'd write some tests, but an old bug that I can't
>> track down prevents me from running tests on this package
>> (http://bugzilla.open-bio.org/show_bug.cgi?id=2899).
>>
>> Cheers,
>> Dan.
>>
>>
>> Here are some snippets of code to give context:
>>
>> my $intensities = Bio::DB::SeqFeature::Store->
>> ? new( -adaptor => ?'DBI::mysql',
>> ? ? ? ?-dsn => ?'db:mysql.server.ac.uk',
>> ? ? ? ?-user => ?'me',
>> ? ? ? ?-pass => ?'secret',
>> ? ? ? ?-verbose => ?$verbose,
>> ? ? ?);
>>
>> my @fwd_intensity = $intensities->
>> ? ? features( -seqid => ?'some-id', -type => ?'fwd link intensity',
>> ? ? ? ? ? ? ? -start => ?10,
>> ? ? ? ? ? ? ? -end ? => ?200,
>> ? ? );
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> jason at bioperl.org
> http://bioperl.org/wiki
>
>



From jason at bioperl.org  Sun Mar 27 13:59:09 2011
From: jason at bioperl.org (Jason Stajich)
Date: Sun, 27 Mar 2011 10:59:09 -0700
Subject: [Bioperl-l] CDS complement statements from GenBank
In-Reply-To: <cdf62961-ac89-4274-91ed-9a233d2de15c@k10g2000prh.googlegroups.com>
References: <cdf62961-ac89-4274-91ed-9a233d2de15c@k10g2000prh.googlegroups.com>
Message-ID: <4D8F7AED.1070705@bioperl.org>

they won't be split locations they will be Bio::Location::Simple 
locations then - I don't understand if that is causing you problems?



Galeb Abu-Ali wrote:
> Hi,
>
> I'm trying to parse CDS complement statements from GenBank files of
> bacterial genomes. I know it works for 'join' statements with
> Bio::Location::SplitLocationI, but there is no spliced genes in
> bacterial annotations and therefore no 'join()' statements. When I
> replace 'complement' with 'join' in the bacterial GenBank file,
> Bio::Location::SplitLocationI gets the coordinates. I took a look at
> SplitLocationI.pm and Split.pm to see if I could replace 'join' with
> 'complement' to get it to work but no luck. At your convenience,
> please advise.
>
> cheers,
>
> galeb
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki



From dan.bolser at gmail.com  Sun Mar 27 14:00:40 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Sun, 27 Mar 2011 19:00:40 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
Message-ID: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>

Hello,

I'm trying to get Bio::DB::BigWig installed again, this time on a different box.

I installed kent from git as described here:
http://genome.ucsc.edu/admin/git.html


I made the following changes, similar to those described previously:

git diff
diff --git a/src/inc/common.mk b/src/inc/common.mk
index c7fc557..5187901 100644
--- a/src/inc/common.mk
+++ b/src/inc/common.mk
@@ -3,7 +3,7 @@ CC=gcc
 ifeq (${COPT},)
     COPT=-O -g
 endif
-CFLAGS=
+CFLAGS=-fPIC
 HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
-DMACHTYPE_${MACHTYPE}
 HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
-I../../../../../inc

diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
index fa2292b..acb97d2 100644
--- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
+++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
@@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
     /* Parse current line. */
     wordCount = chopLine(line, row);
     if (wordCount == ArraySize(row))
-         errAbort("Too many fields (%d max is %lu) line %d of %s",
wordCount, ArraySize(row),
+         errAbort("Too many fields (%d max is %u) line %d of %s",
wordCount, ArraySize(row),
             lf->lineIx, lf->fileName);
     char *chrom = row[0];
     unsigned int start = lineFileNeedNum(lf, row, 1);


After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
-lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
correctly after typing 'make' in kent/src (should I be building it
differently?)



Now when I try to install Bio::DB::BigWig via cpan, things look like this:

cpan

cpan shell -- CPAN exploration and modules installation (v1.9600)
Enter 'h' for help.

cpan[1]> install Bio::DB::BigWig
CPAN: Storable loaded ok (v2.25)
Going to read '/homes/dbolser/.cpan/Metadata'
  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
Running install for module 'Bio::DB::BigWig'
Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
CPAN: Digest::SHA loaded ok (v5.61)
CPAN: Compress::Zlib loaded ok (v2.03)
Checksum for /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
ok
CPAN: Archive::Tar loaded ok (v1.76)
Bio-BigFile-1.05
Bio-BigFile-1.05/Changes
Bio-BigFile-1.05/LICENSE
Bio-BigFile-1.05/DISCLAIMER
Bio-BigFile-1.05/Build.PL
Bio-BigFile-1.05/typemap
Bio-BigFile-1.05/META.yml
Bio-BigFile-1.05/README
Bio-BigFile-1.05/MANIFEST
Bio-BigFile-1.05/ExampleData
Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
Bio-BigFile-1.05/ExampleData/refSeqTest.as
Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
Bio-BigFile-1.05/bin
Bio-BigFile-1.05/bin/bigWigToWig.pl
Bio-BigFile-1.05/bin/wigToBigWig.pl
Bio-BigFile-1.05/bin/index_bigwigset.pl
Bio-BigFile-1.05/lib
Bio-BigFile-1.05/lib/Bio
Bio-BigFile-1.05/lib/Bio/DB
Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
Bio-BigFile-1.05/lib/Bio/DB/BigFile
Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
Bio-BigFile-1.05/t
Bio-BigFile-1.05/t/02.bigbed.t
Bio-BigFile-1.05/t/03.bigwig_high.t
Bio-BigFile-1.05/t/04.bigbed_high.t
Bio-BigFile-1.05/t/05.bigwig_set.t
/bin/tar: Read 9216 bytes from -
Bio-BigFile-1.05/t/01.bigwig.t
Bio-BigFile-1.05/patches
Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
CPAN: File::Temp loaded ok (v0.22)
CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
CPAN: CPAN::Meta loaded ok (v2.110580)
CPAN: Module::CoreList loaded ok (v2.46)
CPAN: Time::HiRes loaded ok (v1.9717)

  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz


This module requires the compiled jkweb.a library from Jim Kent's source tree.
If you haven't already done so, please download the source from
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
contents of the "kent/src/lib" subdirectory as directed in the README. Then
enter the location of the "kent/src" subdirectory at the prompt below.
To prevent
this message from appearing in the future, set the environment
variable KENT_SRC
to point to the "kent/src" subdirectory.

Please enter the location of Kent source tree: /homes/dbolser/build/src/kent/src

Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-BigFile' version '1.05'
Building Bio-BigFile
gcc -I/homes/dbolser/build/src/kent/src/inc
-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
-DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
-c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
-Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
lib/Bio/DB/BigFile.c
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be undefined
lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be undefined
lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be undefined
lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be undefined
lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
lib/Bio/DB/BigFile.xs: In function
?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be undefined
lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
lib/Bio/DB/BigFile.xs: In function
?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be undefined
lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
-mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
/homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
  LDS/Bio-BigFile-1.05.tar.gz
  ./Build -- OK
CPAN: YAML loaded ok (v0.72)
Running Build test
t/01.bigwig.t ....... Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at t/01.bigwig.t line 28
Compilation failed in require at t/01.bigwig.t line 28.
BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
Failed 29/29 subtests
t/02.bigbed.t ....... Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at t/02.bigbed.t line 28
Compilation failed in require at t/02.bigbed.t line 28.
BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
Failed 15/15 subtests
t/03.bigwig_high.t .. Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
Compilation failed in require at t/03.bigwig_high.t line 28.
BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 32/32 subtests
t/04.bigbed_high.t .. Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
line 7.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
line 7.
Compilation failed in require at t/04.bigbed_high.t line 28.
BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 35/35 subtests
t/05.bigwig_set.t ... Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
line 177.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
line 177.
Compilation failed in require at t/05.bigwig_set.t line 19.
BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
No subtests run

Test Summary Report
-------------------
t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 29 tests but ran 0.
t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 15 tests but ran 0.
t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 32 tests but ran 0.
t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 35 tests but ran 0.
t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
0.11 csys =  1.09 CPU)
Result: FAIL
Failed 5/5 test programs. 0/0 subtests failed.
  LDS/Bio-BigFile-1.05.tar.gz
  ./Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports LDS/Bio-BigFile-1.05.tar.gz
Running Build install
  make test had returned bad status, won't install without force
Failed during this command:
 LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO

cpan[2]>






Any hints?

Cheers,
Dan.



From roy.chaudhuri at gmail.com  Sun Mar 27 14:26:55 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Sun, 27 Mar 2011 19:26:55 +0100
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>	<4D8F73A4.8050408@bioperl.org>
	<AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
Message-ID: <4D8F816F.5010809@gmail.com>

Hi Dan,

I think your problem is that you are using the outdated -w flag, which 
reports warnings from inside modules that may not have been designed 
with warnings in mind. The "use warnings" pragma is preferred. See:
http://perldoc.perl.org/perllexwarn.html#What%27s-wrong-with-*-w*-and-$^W

Cheers,
Roy.

On 27/03/2011 18:55, Dan Bolser wrote:
> On 27 March 2011 18:28, Jason Stajich<jason at bioperl.org>  wrote:
>> Dan - not sure why you would need to do this as length on an undef should
>> still return false (an undef).
>>
>> $ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} print
>> "\n"'
>> no
>> $ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"}
>> print "\n"'
>> no
>
> Doesn't the latter spew a warning? (The output before / after my 'bug
> fix' is the same, I just don't see 100s of warnings about undefined
> values).
>
>
>> Also, having no 'source' is probably not proper GFF3.
>
> I'm quite sure it is, but by GFF does have a source. I'm just calling
> 'features' with only a feature type and not a feature type and a
> source (because I only care about source). My call is pretty similar
> to the example here:
>
> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/DB/SeqFeature/Store.pm#features
>
>   @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');
>
>
>> BTW bugzilla is dead so the bug that you refer to is here
>>   http://redmine.open-bio.org/issues/2899
>> I've assigned the bug to Lincoln to help figure out what should be done with
>> it.
>>
>> Thanks,
>> jason
>
> Cheers Jason,
> Dan.
>
>
>> Dan Bolser wrote:
>>>
>>> Hi all,
>>>
>>> I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> uses:
>>>      if (length $source_tag) {
>>>
>>> within the '_types_sql' function to test if $source_tag is defined
>>> (and has a length). This obviously fails when $source_tag it isn't
>>> defined, and I see the above error message from my script when I call
>>> the 'features' function (as shown below).
>>>
>>>>  From tests (thanks to rbuels in #bioperl) it seems the value of $type
>>> is simply 'fwd link intensity', so:
>>>        ($primary_tag,$source_tag) = split ':',$type,2;
>>>
>>> on line 1047 leaves $source_tag undefined.
>>>
>>> Here is my proposed fix:
>>>
>>> diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
>>> index 00103c2..dfc70c0 100644
>>> --- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> +++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> @@ -1057,8 +1057,8 @@ sub _types_sql {
>>>         ($primary_tag,$source_tag) = split ':',$type,2;
>>>       }
>>>
>>> -    if (length $source_tag) {
>>> -      if (length($primary_tag)) {
>>> +    if (defined $source_tag&&    length $source_tag) {
>>> +      if (defined $primary_tag&&    length($primary_tag)) {
>>>           push @matches,"tl.tag=?";
>>>           push @args,"$primary_tag:$source_tag";
>>>         }
>>>
>>>
>>> which seems to work. I'd write some tests, but an old bug that I can't
>>> track down prevents me from running tests on this package
>>> (http://bugzilla.open-bio.org/show_bug.cgi?id=2899).
>>>
>>> Cheers,
>>> Dan.
>>>
>>>
>>> Here are some snippets of code to give context:
>>>
>>> my $intensities = Bio::DB::SeqFeature::Store->
>>>    new( -adaptor =>    'DBI::mysql',
>>>         -dsn =>    'db:mysql.server.ac.uk',
>>>         -user =>    'me',
>>>         -pass =>    'secret',
>>>         -verbose =>    $verbose,
>>>       );
>>>
>>> my @fwd_intensity = $intensities->
>>>      features( -seqid =>    'some-id', -type =>    'fwd link intensity',
>>>                -start =>    10,
>>>                -end   =>    200,
>>>      );
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> --
>> Jason Stajich
>> jason at bioperl.org
>> http://bioperl.org/wiki
>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Sun Mar 27 16:13:14 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 27 Mar 2011 15:13:14 -0500
Subject: [Bioperl-l] Use of uninitialized value in length at
	Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
	<4D8F73A4.8050408@bioperl.org>
	<AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
Message-ID: <4960971A-8C61-49F2-B43A-E32BAFC4C59E@illinois.edu>

On Mar 27, 2011, at 12:55 PM, Dan Bolser wrote:

> On 27 March 2011 18:28, Jason Stajich <jason at bioperl.org> wrote:
>> Dan - not sure why you would need to do this as length on an undef should
>> still return false (an undef).
>> 
>> $ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} print
>> "\n"'
>> no
>> $ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"}
>> print "\n"'
>> no
> 
> Doesn't the latter spew a warning? (The output before / after my 'bug
> fix' is the same, I just don't see 100s of warnings about undefined
> values).

Only with later versions of perl (I think perl 5.12).

>> Also, having no 'source' is probably not proper GFF3.
> 
> I'm quite sure it is, but by GFF does have a source. I'm just calling
> 'features' with only a feature type and not a feature type and a
> source (because I only care about source). My call is pretty similar
> to the example here:
> 
> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/DB/SeqFeature/Store.pm#features
> 
> @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');

I think Jason is inferring that the GFF3 is invalid from your statement below re: $source_tag not being defined, which to me means the source attribute for the feature is not defined.

Note: b/c something works with SF::Store does NOT mean the source is proper GFF3; it is quite possible to have invalid GFF3 loaded into the database w/o a hiccup.  I think the loader assumes the data loaded has already been validated; IIRC there is very little validation done on GFF3 loaded into SF::Store, particularly the 'type'.

chris

>> BTW bugzilla is dead so the bug that you refer to is here
>>  http://redmine.open-bio.org/issues/2899
>> I've assigned the bug to Lincoln to help figure out what should be done with
>> it.
>> 
>> Thanks,
>> jason
> 
> Cheers Jason,
> Dan.
> 
> 
>> Dan Bolser wrote:
>>> 
>>> Hi all,
>>> 
>>> I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> uses:
>>>     if (length $source_tag) {
>>> 
>>> within the '_types_sql' function to test if $source_tag is defined
>>> (and has a length). This obviously fails when $source_tag it isn't
>>> defined, and I see the above error message from my script when I call
>>> the 'features' function (as shown below).
>>> 
>>>> From tests (thanks to rbuels in #bioperl) it seems the value of $type
>>> is simply 'fwd link intensity', so:
>>>       ($primary_tag,$source_tag) = split ':',$type,2;
>>> 
>>> on line 1047 leaves $source_tag undefined.
>>> 
>>> Here is my proposed fix:
>>> 
>>> diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
>>> index 00103c2..dfc70c0 100644
>>> --- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> +++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> @@ -1057,8 +1057,8 @@ sub _types_sql {
>>>        ($primary_tag,$source_tag) = split ':',$type,2;
>>>      }
>>> 
>>> -    if (length $source_tag) {
>>> -      if (length($primary_tag)) {
>>> +    if (defined $source_tag&&  length $source_tag) {
>>> +      if (defined $primary_tag&&  length($primary_tag)) {
>>>          push @matches,"tl.tag=?";
>>>          push @args,"$primary_tag:$source_tag";
>>>        }
>>> 
>>> 
>>> which seems to work. I'd write some tests, but an old bug that I can't
>>> track down prevents me from running tests on this package
>>> (http://bugzilla.open-bio.org/show_bug.cgi?id=2899).
>>> 
>>> Cheers,
>>> Dan.
>>> 
>>> 
>>> Here are some snippets of code to give context:
>>> 
>>> my $intensities = Bio::DB::SeqFeature::Store->
>>>   new( -adaptor =>  'DBI::mysql',
>>>        -dsn =>  'db:mysql.server.ac.uk',
>>>        -user =>  'me',
>>>        -pass =>  'secret',
>>>        -verbose =>  $verbose,
>>>      );
>>> 
>>> my @fwd_intensity = $intensities->
>>>     features( -seqid =>  'some-id', -type =>  'fwd link intensity',
>>>               -start =>  10,
>>>               -end   =>  200,
>>>     );
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> --
>> Jason Stajich
>> jason at bioperl.org
>> http://bioperl.org/wiki
>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Sun Mar 27 16:13:56 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 27 Mar 2011 15:13:56 -0500
Subject: [Bioperl-l] Various bioperl build test errors
In-Reply-To: <799d8933-c2de-4c88-ac2c-03bb1b32dd78@z27g2000prz.googlegroups.com>
References: <799d8933-c2de-4c88-ac2c-03bb1b32dd78@z27g2000prz.googlegroups.com>
Message-ID: <FFAB293A-555E-4F4B-90C4-A50458AB2B8C@illinois.edu>

Re: the two problems:

1) The build failures are a new one, haven't seen that before.  

2) The failed tests are all related to NeXML and Bio::Phylo; it appears that Bio::Phylo is having versioning problems.  

Feel free to report these on our bug tracker:

http://redmine.open-bio.org/

chris


On Mar 27, 2011, at 9:37 AM, Drin wrote:

> Hello BioPerl mailing list!
> 
> So I have been successfully building BioPerl (though I thought I was
> failing), but have been getting some errors during said builds. I'm
> running ubuntu 9.04 and I ran 'perl Build.PL', then './Build test'
> using bash. If any other information is desired, please let me know.
> And here are some gists to help with some context:
> perl Build.PL - https://gist.github.com/e4be0891635463b07812
> ./Build test - https://gist.github.com/3e9a1cba10ca0e9b087d
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From heikki.lehvaslaiho at gmail.com  Mon Mar 28 02:11:12 2011
From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho)
Date: Mon, 28 Mar 2011 09:11:12 +0300
Subject: [Bioperl-l] Bio::Tools::Protparam
In-Reply-To: <DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>
References: <AcvpfORY7lvf7BT4TLGDgl1oKgOEwg==>
	<DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>
Message-ID: <AANLkTi=3wtG+7HO4O8vUbdrnVEu-NXofwmZfVHvRLeVH@mail.gmail.com>

The synopsis code should read:

	my $pp = Bio::Tools::Protparam->new(seq=>$seq->seq);

Fixed in the repository.

? ?? -Heikki

Heikki Lehvaslaiho - skype:heikki_lehvaslaiho http://about.me/heikki
cell: +966 545 595 849? office: +966 2 808 2429

Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
4700 King Abdullah University of Science and Technology (KAUST)
Thuwal 23955-6900, Kingdom of Saudi Arabia




On 23 March 2011 20:08, Thomas, Dallas <Dallas.Thomas at agr.gc.ca> wrote:
> Need help. ?I am trying to use the Bio::Tools::Protparam perl module.
>
>
>
> For testing purposes I have copied and pasted the example in the module,
> I have set:
>
>
>
> use strict;
>
> use Bio::Tools::Protparam;
>
> use Bio::DB::GenBank;
>
>
>
> Every time I try and run the script I get the following error:
>
>
>
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?Can't locate object method "new" via
> package "Protparam" (perhaps you forgot to load "Protparam"?) at ...
>
>
>
> Do you have any ideas? ?Any help would be very much appreciated.
>
>
>
> Sincerely
>
> Dallas Thomas
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From David.Messina at sbc.su.se  Mon Mar 28 03:33:25 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 28 Mar 2011 09:33:25 +0200
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
Message-ID: <AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>

Hi Ravi,

Please make sure to "Reply All" so that everyone on the mailing list can
follow (and add to) the discussion.

If you read the first line of the exception, you'll see it states what the
error is:
"WebDBSeqI Error ? check query sequences!"

You'd have no way of knowing this, but that ID and database combination is
not functioning anymore, so that's why in this case you're getting an error.
Please try using the example in the tutorial here:

  http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts

which has been updated to a different ID which should work.

Sorry for the confusion! So that we can prevent other people from having the
same issue, could you tell me where you got that example code?

Dave






2011/3/28 ?????????????????? <ravimbt at gmail.com>

> Hi Dave,
>
> Thanks a lot for your reply. It is really helpful. Please find the
> screenshot after making the change you pointed out. But I am getting
> "Exception: Bio::Root::Exception" error. I think I have to set the
> environment variables but I am not sure how to do that. Could you please
> guide me on this too.
>
> I can go to the "Environment Variable" Window in my pc. But I dont know
> what to enter once I click "New" on that window.
>
> Thanks in advance.
>
> With regards,
> Ravi.
>
>
> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>
>> Hi Ravi,
>>
>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>> not Bio::Seq. So your first line
>>
>> use Bio::Seq;
>>
>> should be replaced with
>>
>> use Bio::Perl;
>>
>>
>> More examples in the BioPerl Tutorial here:
>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>
>>
>> Dve
>>
>>
>>
>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>
>>> Hi,
>>>
>>> Could you please help me installing bioperl-db, bioperl-run & other
>>> packages
>>> using ppm on windows 7? Please find the attachment for the error message
>>> I
>>> get. I would really appreciate if you help me fix this issue.
>>>
>>> Thanks,
>>>
>>> With regards,
>>> Ravi.
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>



From David.Messina at sbc.su.se  Mon Mar 28 07:51:41 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 28 Mar 2011 13:51:41 +0200
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
Message-ID: <AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>

>
> Thank you very much. It is working. I got the program code from the
> following link.
>
> http://www.bioperl.org/Core/Latest/bptutorial.html


Aha, okay. You got there from Google, I guess? That is *way* out of date.

To the other core devs, in order to prevent this confusion in the future,
I'd like to delete the Core/ directory from our website since it's been
superseded at this point by other docs and is not current. I intend to put
up a ticket at Redmine, but I will wait a bit before doing so to allow time
for people to see this and comment ? please do speak up if there's good
reason to keep it.


Could you please give me the link to join this forum to see other
> discussions, which would be more helpful to me?
>

Sure, you can sign up for the mailing list here:

 <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


And the archives are also searchable:

    http://news.gmane.org/gmane.comp.lang.perl.bio.general


Please let me know if you have any suggestion for me to keep learning the
> bioperl.


I would also suggest reading the (current) tutorial and HOWTOs at
www.bioperl.org . Lots of good links on the main page there, particularly
under the Documentation heading.


Dave





> With regards,
> Ravi.
>
>
> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>
>> Hi Ravi,
>>
>> Please make sure to "Reply All" so that everyone on the mailing list can
>> follow (and add to) the discussion.
>>
>> If you read the first line of the exception, you'll see it states what the
>> error is:
>> "WebDBSeqI Error ? check query sequences!"
>>
>> You'd have no way of knowing this, but that ID and database combination is
>> not functioning anymore, so that's why in this case you're getting an error.
>> Please try using the example in the tutorial here:
>>
>>
>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>
>> which has been updated to a different ID which should work.
>>
>> Sorry for the confusion! So that we can prevent other people from having
>> the same issue, could you tell me where you got that example code?
>>
>> Dave
>>
>>
>>
>>
>>
>>
>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>
>>> Hi Dave,
>>>
>>> Thanks a lot for your reply. It is really helpful. Please find the
>>> screenshot after making the change you pointed out. But I am getting
>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>> environment variables but I am not sure how to do that. Could you please
>>> guide me on this too.
>>>
>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>> what to enter once I click "New" on that window.
>>>
>>> Thanks in advance.
>>>
>>> With regards,
>>> Ravi.
>>>
>>>
>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>
>>>> Hi Ravi,
>>>>
>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>> not Bio::Seq. So your first line
>>>>
>>>> use Bio::Seq;
>>>>
>>>> should be replaced with
>>>>
>>>> use Bio::Perl;
>>>>
>>>>
>>>> More examples in the BioPerl Tutorial here:
>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>
>>>>
>>>> Dve
>>>>
>>>>
>>>>
>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>
>>>>> Hi,
>>>>>
>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>> packages
>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>> message I
>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> With regards,
>>>>> Ravi.
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>
>>>>
>>>
>>
>



From David.Messina at sbc.su.se  Mon Mar 28 08:45:34 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 28 Mar 2011 14:45:34 +0200
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTinhqidOd7VBDT+hr6E-VNKwOobtyZ1Zn=A1uPfy@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
	<AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
	<AANLkTinhqidOd7VBDT+hr6E-VNKwOobtyZ1Zn=A1uPfy@mail.gmail.com>
Message-ID: <AANLkTikiN9J28oNWWnQ5hJSWYB_DKTPHPegj+7wZ-ELr@mail.gmail.com>

Again, please "Reply All" so that your messages go to the mailing list.

Ravi, PLEASE read the documentation on the website first and try to figure
out how to solve your problem on your own. BioPerl is a complex system and
requires some effort to learn how to use. I and everyone on this list
volunteers our time answering questions, and we are happy to do so, but you
have to meet us halfway.


Dave




2011/3/28 ?????????????????? <ravimbt at gmail.com>

> Hi Dave,
>
> Thanks for the information. I have also signed up to join the forum.
>
> I could not retrieve the sequence from other databases other than Genbank.
> Could you please do the changes on the below programme to make it working so
> that I can try in my system.
> --------------------
> use Bio::Perl;
>
> $seq_object = get_sequence('genbank',"ECORHO");
>
> write_sequence(">ael.fasta",'fasta',$seq_object);
> ------------------
>
> Thanks once again.
>
> With regards,
> Ravi.
>
>
> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>
>> Thank you very much. It is working. I got the program code from the
>>> following link.
>>>
>>> http://www.bioperl.org/Core/Latest/bptutorial.html
>>
>>
>> Aha, okay. You got there from Google, I guess? That is *way* out of date.
>>
>> To the other core devs, in order to prevent this confusion in the future,
>> I'd like to delete the Core/ directory from our website since it's been
>> superseded at this point by other docs and is not current. I intend to put
>> up a ticket at Redmine, but I will wait a bit before doing so to allow time
>> for people to see this and comment ? please do speak up if there's good
>> reason to keep it.
>>
>>
>> Could you please give me the link to join this forum to see other
>>> discussions, which would be more helpful to me?
>>>
>>
>> Sure, you can sign up for the mailing list here:
>>
>>  <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> And the archives are also searchable:
>>
>>     http://news.gmane.org/gmane.comp.lang.perl.bio.general
>>
>>
>> Please let me know if you have any suggestion for me to keep learning the
>>> bioperl.
>>
>>
>> I would also suggest reading the (current) tutorial and HOWTOs at
>> www.bioperl.org . Lots of good links on the main page there, particularly
>> under the Documentation heading.
>>
>>
>> Dave
>>
>>
>>
>>
>>
>>> With regards,
>>> Ravi.
>>>
>>>
>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>>>
>>>> Hi Ravi,
>>>>
>>>> Please make sure to "Reply All" so that everyone on the mailing list can
>>>> follow (and add to) the discussion.
>>>>
>>>> If you read the first line of the exception, you'll see it states what
>>>> the error is:
>>>> "WebDBSeqI Error ? check query sequences!"
>>>>
>>>> You'd have no way of knowing this, but that ID and database combination
>>>> is not functioning anymore, so that's why in this case you're getting an
>>>> error. Please try using the example in the tutorial here:
>>>>
>>>>
>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>>>
>>>> which has been updated to a different ID which should work.
>>>>
>>>> Sorry for the confusion! So that we can prevent other people from having
>>>> the same issue, could you tell me where you got that example code?
>>>>
>>>> Dave
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>>>
>>>>> Hi Dave,
>>>>>
>>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>>> screenshot after making the change you pointed out. But I am getting
>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>>> environment variables but I am not sure how to do that. Could you please
>>>>> guide me on this too.
>>>>>
>>>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>>>> what to enter once I click "New" on that window.
>>>>>
>>>>> Thanks in advance.
>>>>>
>>>>> With regards,
>>>>> Ravi.
>>>>>
>>>>>
>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>>>
>>>>>> Hi Ravi,
>>>>>>
>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl
>>>>>> module, not Bio::Seq. So your first line
>>>>>>
>>>>>> use Bio::Seq;
>>>>>>
>>>>>> should be replaced with
>>>>>>
>>>>>> use Bio::Perl;
>>>>>>
>>>>>>
>>>>>> More examples in the BioPerl Tutorial here:
>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>>>
>>>>>>
>>>>>> Dve
>>>>>>
>>>>>>
>>>>>>
>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>>>> packages
>>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>>> message I
>>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> With regards,
>>>>>>> Ravi.
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>



From abualiga at gmail.com  Mon Mar 28 09:19:00 2011
From: abualiga at gmail.com (Galeb Abu-Ali)
Date: Mon, 28 Mar 2011 09:19:00 -0400
Subject: [Bioperl-l] CDS complement statements from GenBank
In-Reply-To: <4D8F7AED.1070705@bioperl.org>
References: <cdf62961-ac89-4274-91ed-9a233d2de15c@k10g2000prh.googlegroups.com>
	<4D8F7AED.1070705@bioperl.org>
Message-ID: <AANLkTimpN2sRvrkn86Ges7100ssRizHr5GU7rPhDvyUS@mail.gmail.com>

I was using the wrong module, Bio::Location::Simple was what I needed.
thanks much!

galeb

On Sun, Mar 27, 2011 at 1:59 PM, Jason Stajich <jason at bioperl.org> wrote:

> they won't be split locations they will be Bio::Location::Simple locations
> then - I don't understand if that is causing you problems?
>
>
>
> Galeb Abu-Ali wrote:
>
>> Hi,
>>
>> I'm trying to parse CDS complement statements from GenBank files of
>> bacterial genomes. I know it works for 'join' statements with
>> Bio::Location::SplitLocationI, but there is no spliced genes in
>> bacterial annotations and therefore no 'join()' statements. When I
>> replace 'complement' with 'join' in the bacterial GenBank file,
>> Bio::Location::SplitLocationI gets the coordinates. I took a look at
>> SplitLocationI.pm and Split.pm to see if I could replace 'join' with
>> 'complement' to get it to work but no luck. At your convenience,
>> please advise.
>>
>> cheers,
>>
>> galeb
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> --
> Jason Stajich
> jason at bioperl.org
> http://bioperl.org/wiki
>
>


From cjfields at illinois.edu  Mon Mar 28 09:27:38 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 28 Mar 2011 08:27:38 -0500
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
	<AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
Message-ID: <6CE8AACF-0D78-4BBA-8094-CC189B0FF872@illinois.edu>

Dave,

+1 on removing old docs to prevent confusion.  Or, alternatively, +1 to syncing those to current docs (though I think decreasing the replication effort in keeping docs up-to-date is probably the best tact).

chris

On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:

>> 
>> Thank you very much. It is working. I got the program code from the
>> following link.
>> 
>> http://www.bioperl.org/Core/Latest/bptutorial.html
> 
> 
> Aha, okay. You got there from Google, I guess? That is *way* out of date.
> 
> To the other core devs, in order to prevent this confusion in the future,
> I'd like to delete the Core/ directory from our website since it's been
> superseded at this point by other docs and is not current. I intend to put
> up a ticket at Redmine, but I will wait a bit before doing so to allow time
> for people to see this and comment ? please do speak up if there's good
> reason to keep it.
> 
> 
> Could you please give me the link to join this forum to see other
>> discussions, which would be more helpful to me?
>> 
> 
> Sure, you can sign up for the mailing list here:
> 
> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> And the archives are also searchable:
> 
>    http://news.gmane.org/gmane.comp.lang.perl.bio.general
> 
> 
> Please let me know if you have any suggestion for me to keep learning the
>> bioperl.
> 
> 
> I would also suggest reading the (current) tutorial and HOWTOs at
> www.bioperl.org . Lots of good links on the main page there, particularly
> under the Documentation heading.
> 
> 
> Dave
> 
> 
> 
> 
> 
>> With regards,
>> Ravi.
>> 
>> 
>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>> 
>>> Hi Ravi,
>>> 
>>> Please make sure to "Reply All" so that everyone on the mailing list can
>>> follow (and add to) the discussion.
>>> 
>>> If you read the first line of the exception, you'll see it states what the
>>> error is:
>>> "WebDBSeqI Error ? check query sequences!"
>>> 
>>> You'd have no way of knowing this, but that ID and database combination is
>>> not functioning anymore, so that's why in this case you're getting an error.
>>> Please try using the example in the tutorial here:
>>> 
>>> 
>>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>> 
>>> which has been updated to a different ID which should work.
>>> 
>>> Sorry for the confusion! So that we can prevent other people from having
>>> the same issue, could you tell me where you got that example code?
>>> 
>>> Dave
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>> 
>>>> Hi Dave,
>>>> 
>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>> screenshot after making the change you pointed out. But I am getting
>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>> environment variables but I am not sure how to do that. Could you please
>>>> guide me on this too.
>>>> 
>>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>>> what to enter once I click "New" on that window.
>>>> 
>>>> Thanks in advance.
>>>> 
>>>> With regards,
>>>> Ravi.
>>>> 
>>>> 
>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>> 
>>>>> Hi Ravi,
>>>>> 
>>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>>> not Bio::Seq. So your first line
>>>>> 
>>>>> use Bio::Seq;
>>>>> 
>>>>> should be replaced with
>>>>> 
>>>>> use Bio::Perl;
>>>>> 
>>>>> 
>>>>> More examples in the BioPerl Tutorial here:
>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>> 
>>>>> 
>>>>> Dve
>>>>> 
>>>>> 
>>>>> 
>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>>> packages
>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>> message I
>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>> 
>>>>>> Thanks,
>>>>>> 
>>>>>> With regards,
>>>>>> Ravi.
>>>>>> 
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>> 
>>>>> 
>>>>> 
>>>> 
>>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From dan.bolser at gmail.com  Mon Mar 28 13:15:32 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 28 Mar 2011 18:15:32 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
Message-ID: <AANLkTikQgn2-YU4-4JBdLkSopFFihhJ-=2KG25P0Ugv6@mail.gmail.com>

--- Build.PL~   2011-03-14 20:27:57.000000000 +0000
+++ Build.PL    2011-03-28 18:06:45.503757000 +0100
@@ -16,7 +16,7 @@
     dist_abstract      => "Manipulate Jim Kent's BigWig and BigBed
index files for genomic features.",
     license            => 'perl',
     include_dirs       => [$jk_include],
-    extra_linker_flags => ["$jk_lib/$LibFile",'-lz'],
+    extra_linker_flags => ["$jk_lib/$LibFile",'-lz','-lssl'],

     extra_compiler_flags=>[
        # turn off warnings originating in Perl's Newx* calls

On 27 March 2011 19:00, Dan Bolser <dan.bolser at gmail.com> wrote:
> Hello,
>
> I'm trying to get Bio::DB::BigWig installed again, this time on a different box.
>
> I installed kent from git as described here:
> http://genome.ucsc.edu/admin/git.html
>
>
> I made the following changes, similar to those described previously:
>
> git diff
> diff --git a/src/inc/common.mk b/src/inc/common.mk
> index c7fc557..5187901 100644
> --- a/src/inc/common.mk
> +++ b/src/inc/common.mk
> @@ -3,7 +3,7 @@ CC=gcc
> ?ifeq (${COPT},)
> ? ? COPT=-O -g
> ?endif
> -CFLAGS=
> +CFLAGS=-fPIC
> ?HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> -DMACHTYPE_${MACHTYPE}
> ?HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> -I../../../../../inc
>
> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> index fa2292b..acb97d2 100644
> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
> ? ? /* Parse current line. */
> ? ? wordCount = chopLine(line, row);
> ? ? if (wordCount == ArraySize(row))
> - ? ? ? ? errAbort("Too many fields (%d max is %lu) line %d of %s",
> wordCount, ArraySize(row),
> + ? ? ? ? errAbort("Too many fields (%d max is %u) line %d of %s",
> wordCount, ArraySize(row),
> ? ? ? ? ? ? lf->lineIx, lf->fileName);
> ? ? char *chrom = row[0];
> ? ? unsigned int start = lineFileNeedNum(lf, row, 1);
>
>
> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> correctly after typing 'make' in kent/src (should I be building it
> differently?)
>
>
>
> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>
> cpan
>
> cpan shell -- CPAN exploration and modules installation (v1.9600)
> Enter 'h' for help.
>
> cpan[1]> install Bio::DB::BigWig
> CPAN: Storable loaded ok (v2.25)
> Going to read '/homes/dbolser/.cpan/Metadata'
> ?Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> Running install for module 'Bio::DB::BigWig'
> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> CPAN: Digest::SHA loaded ok (v5.61)
> CPAN: Compress::Zlib loaded ok (v2.03)
> Checksum for /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> ok
> CPAN: Archive::Tar loaded ok (v1.76)
> Bio-BigFile-1.05
> Bio-BigFile-1.05/Changes
> Bio-BigFile-1.05/LICENSE
> Bio-BigFile-1.05/DISCLAIMER
> Bio-BigFile-1.05/Build.PL
> Bio-BigFile-1.05/typemap
> Bio-BigFile-1.05/META.yml
> Bio-BigFile-1.05/README
> Bio-BigFile-1.05/MANIFEST
> Bio-BigFile-1.05/ExampleData
> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> Bio-BigFile-1.05/bin
> Bio-BigFile-1.05/bin/bigWigToWig.pl
> Bio-BigFile-1.05/bin/wigToBigWig.pl
> Bio-BigFile-1.05/bin/index_bigwigset.pl
> Bio-BigFile-1.05/lib
> Bio-BigFile-1.05/lib/Bio
> Bio-BigFile-1.05/lib/Bio/DB
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> Bio-BigFile-1.05/t
> Bio-BigFile-1.05/t/02.bigbed.t
> Bio-BigFile-1.05/t/03.bigwig_high.t
> Bio-BigFile-1.05/t/04.bigbed_high.t
> Bio-BigFile-1.05/t/05.bigwig_set.t
> /bin/tar: Read 9216 bytes from -
> Bio-BigFile-1.05/t/01.bigwig.t
> Bio-BigFile-1.05/patches
> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> CPAN: File::Temp loaded ok (v0.22)
> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> CPAN: CPAN::Meta loaded ok (v2.110580)
> CPAN: Module::CoreList loaded ok (v2.46)
> CPAN: Time::HiRes loaded ok (v1.9717)
>
> ?CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>
>
> This module requires the compiled jkweb.a library from Jim Kent's source tree.
> If you haven't already done so, please download the source from
> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
> contents of the "kent/src/lib" subdirectory as directed in the README. Then
> enter the location of the "kent/src" subdirectory at the prompt below.
> To prevent
> this message from appearing in the future, set the environment
> variable KENT_SRC
> to point to the "kent/src" subdirectory.
>
> Please enter the location of Kent source tree: /homes/dbolser/build/src/kent/src
>
> Created MYMETA.yml and MYMETA.json
> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> Building Bio-BigFile
> gcc -I/homes/dbolser/build/src/kent/src/inc
> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> lib/Bio/DB/BigFile.c
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be undefined
> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be undefined
> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
> ?LDS/Bio-BigFile-1.05.tar.gz
> ?./Build -- OK
> CPAN: YAML loaded ok (v0.72)
> Running Build test
> t/01.bigwig.t ....... Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at t/01.bigwig.t line 28
> Compilation failed in require at t/01.bigwig.t line 28.
> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 29/29 subtests
> t/02.bigbed.t ....... Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at t/02.bigbed.t line 28
> Compilation failed in require at t/02.bigbed.t line 28.
> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 15/15 subtests
> t/03.bigwig_high.t .. Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at t/03.bigwig_high.t line 28.
> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 32/32 subtests
> t/04.bigbed_high.t .. Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> Compilation failed in require at t/04.bigbed_high.t line 28.
> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 35/35 subtests
> t/05.bigwig_set.t ... Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> Compilation failed in require at t/05.bigwig_set.t line 19.
> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> No subtests run
>
> Test Summary Report
> -------------------
> t/01.bigwig.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: Bad plan. ?You planned 29 tests but ran 0.
> t/02.bigbed.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: Bad plan. ?You planned 15 tests but ran 0.
> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: Bad plan. ?You planned 32 tests but ran 0.
> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: Bad plan. ?You planned 35 tests but ran 0.
> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: No plan found in TAP output
> Files=5, Tests=0, ?1 wallclock secs ( 0.04 usr ?0.01 sys + ?0.93 cusr
> 0.11 csys = ?1.09 CPU)
> Result: FAIL
> Failed 5/5 test programs. 0/0 subtests failed.
> ?LDS/Bio-BigFile-1.05.tar.gz
> ?./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module, try:
> ?reports LDS/Bio-BigFile-1.05.tar.gz
> Running Build install
> ?make test had returned bad status, won't install without force
> Failed during this command:
> ?LDS/Bio-BigFile-1.05.tar.gz ? ? ? ? ? ? ? ? ?: make_test NO
>
> cpan[2]>
>
>
>
>
>
>
> Any hints?
>
> Cheers,
> Dan.
>



From dan.bolser at gmail.com  Mon Mar 28 16:08:52 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 28 Mar 2011 21:08:52 +0100
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <4960971A-8C61-49F2-B43A-E32BAFC4C59E@illinois.edu>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
	<4D8F73A4.8050408@bioperl.org>
	<AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
	<4960971A-8C61-49F2-B43A-E32BAFC4C59E@illinois.edu>
Message-ID: <AANLkTi=H4opbLx+qv8XM5+VpQNy2Fhxtbyx54iumRcE5@mail.gmail.com>

On 27 March 2011 21:13, Chris Fields <cjfields at illinois.edu> wrote:
> On Mar 27, 2011, at 12:55 PM, Dan Bolser wrote:
>
>> On 27 March 2011 18:28, Jason Stajich <jason at bioperl.org> wrote:
>>> Dan - not sure why you would need to do this as length on an undef should
>>> still return false (an undef).
>>>
>>> $ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} print
>>> "\n"'
>>> no
>>> $ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"}
>>> print "\n"'
>>> no
>>
>> Doesn't the latter spew a warning? (The output before / after my 'bug
>> fix' is the same, I just don't see 100s of warnings about undefined
>> values).
>
> Only with later versions of perl (I think perl 5.12).
>
>>> Also, having no 'source' is probably not proper GFF3.
>>
>> I'm quite sure it is, but by GFF does have a source. I'm just calling
>> 'features' with only a feature type and not a feature type and a
>> source (because I only care about source). My call is pretty similar
>> to the example here:
>>
>> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/DB/SeqFeature/Store.pm#features
>>
>> @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');
>
> I think Jason is inferring that the GFF3 is invalid from your statement below re: $source_tag not being defined, which to me means the source attribute for the feature is not defined.
>
> Note: b/c something works with SF::Store does NOT mean the source is proper GFF3; it is quite possible to have invalid GFF3 loaded into the database w/o a hiccup. ?I think the loader assumes the data loaded has already been validated; IIRC there is very little validation done on GFF3 loaded into SF::Store, particularly the 'type'.

As I said, my GFF3 does have a source. I'll try to put together a test
script, as it seems like the value should not be undef (but thanks for
the tip Roy).

I had a feeling that this relatively trivial fix was a sticking
plaster on a larger problem.


> chris
Dan



From dan.bolser at gmail.com  Mon Mar 28 16:12:19 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 28 Mar 2011 21:12:19 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTikQgn2-YU4-4JBdLkSopFFihhJ-=2KG25P0Ugv6@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTikQgn2-YU4-4JBdLkSopFFihhJ-=2KG25P0Ugv6@mail.gmail.com>
Message-ID: <AANLkTikjJpMcFWvvAt+bJoXJHHaORfecYmz053RScFjn@mail.gmail.com>

Context, this patch in the distro's Build.PL fixes the errors with the
tests, but doesn't fix the warnings.

On 28 March 2011 18:15, Dan Bolser <dan.bolser at gmail.com> wrote:
> --- Build.PL~ ? 2011-03-14 20:27:57.000000000 +0000
> +++ Build.PL ? ?2011-03-28 18:06:45.503757000 +0100
> @@ -16,7 +16,7 @@
> ? ? dist_abstract ? ? ?=> "Manipulate Jim Kent's BigWig and BigBed
> index files for genomic features.",
> ? ? license ? ? ? ? ? ?=> 'perl',
> ? ? include_dirs ? ? ? => [$jk_include],
> - ? ?extra_linker_flags => ["$jk_lib/$LibFile",'-lz'],
> + ? ?extra_linker_flags => ["$jk_lib/$LibFile",'-lz','-lssl'],
>
> ? ? extra_compiler_flags=>[
> ? ? ? ?# turn off warnings originating in Perl's Newx* calls



From cjfields at illinois.edu  Mon Mar 28 16:23:38 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 28 Mar 2011 15:23:38 -0500
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTikjJpMcFWvvAt+bJoXJHHaORfecYmz053RScFjn@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTikQgn2-YU4-4JBdLkSopFFihhJ-=2KG25P0Ugv6@mail.gmail.com>
	<AANLkTikjJpMcFWvvAt+bJoXJHHaORfecYmz053RScFjn@mail.gmail.com>
Message-ID: <91759940-6457-460D-95F5-EF7098A7412C@illinois.edu>

Dan,

Was this using the latest kent src and Bio::DB::BigWig?

chris

PS : cc'ing gbrowse, which is where these seem to get answered a bit faster, context thread here: http://lists.open-bio.org/pipermail/bioperl-l/2011-March/034738.html

On Mar 28, 2011, at 3:12 PM, Dan Bolser wrote:

> Context, this patch in the distro's Build.PL fixes the errors with the
> tests, but doesn't fix the warnings.
> 
> On 28 March 2011 18:15, Dan Bolser <dan.bolser at gmail.com> wrote:
>> --- Build.PL~   2011-03-14 20:27:57.000000000 +0000
>> +++ Build.PL    2011-03-28 18:06:45.503757000 +0100
>> @@ -16,7 +16,7 @@
>>     dist_abstract      => "Manipulate Jim Kent's BigWig and BigBed
>> index files for genomic features.",
>>     license            => 'perl',
>>     include_dirs       => [$jk_include],
>> -    extra_linker_flags => ["$jk_lib/$LibFile",'-lz'],
>> +    extra_linker_flags => ["$jk_lib/$LibFile",'-lz','-lssl'],
>> 
>>     extra_compiler_flags=>[
>>        # turn off warnings originating in Perl's Newx* calls
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From lincoln.stein at gmail.com  Mon Mar 28 17:26:20 2011
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Mon, 28 Mar 2011 17:26:20 -0400
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
Message-ID: <AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>

Hi Dan,

There are two problems that I can see. One is a series of compiler warnings
when compiling the Perl .XS interface file. These are likely nothing to
worry about, but I should fix them. What versions of Perl and gcc do you
have installed? I don't see them when I compile on my system.

The second issue is that the SSL library is not being linked in. Previously
there was no dependency on SSL, but Jim may recently have added this to the
BigWig library in order to allow it to read bigwig files from https servers.
I see that you added a -lssl to Build.PL; does this make the tests work
again?

Lincoln


On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com> wrote:

> Hello,
>
> I'm trying to get Bio::DB::BigWig installed again, this time on a different
> box.
>
> I installed kent from git as described here:
> http://genome.ucsc.edu/admin/git.html
>
>
> I made the following changes, similar to those described previously:
>
> git diff
> diff --git a/src/inc/common.mk b/src/inc/common.mk
> index c7fc557..5187901 100644
> --- a/src/inc/common.mk
> +++ b/src/inc/common.mk
> @@ -3,7 +3,7 @@ CC=gcc
>  ifeq (${COPT},)
>     COPT=-O -g
>  endif
> -CFLAGS=
> +CFLAGS=-fPIC
>  HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> -DMACHTYPE_${MACHTYPE}
>  HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> -I../../../../../inc
>
> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> index fa2292b..acb97d2 100644
> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
>     /* Parse current line. */
>     wordCount = chopLine(line, row);
>     if (wordCount == ArraySize(row))
> -         errAbort("Too many fields (%d max is %lu) line %d of %s",
> wordCount, ArraySize(row),
> +         errAbort("Too many fields (%d max is %u) line %d of %s",
> wordCount, ArraySize(row),
>             lf->lineIx, lf->fileName);
>     char *chrom = row[0];
>     unsigned int start = lineFileNeedNum(lf, row, 1);
>
>
> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> correctly after typing 'make' in kent/src (should I be building it
> differently?)
>
>
>
> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>
> cpan
>
> cpan shell -- CPAN exploration and modules installation (v1.9600)
> Enter 'h' for help.
>
> cpan[1]> install Bio::DB::BigWig
> CPAN: Storable loaded ok (v2.25)
> Going to read '/homes/dbolser/.cpan/Metadata'
>  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> Running install for module 'Bio::DB::BigWig'
> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> CPAN: Digest::SHA loaded ok (v5.61)
> CPAN: Compress::Zlib loaded ok (v2.03)
> Checksum for
> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> ok
> CPAN: Archive::Tar loaded ok (v1.76)
> Bio-BigFile-1.05
> Bio-BigFile-1.05/Changes
> Bio-BigFile-1.05/LICENSE
> Bio-BigFile-1.05/DISCLAIMER
> Bio-BigFile-1.05/Build.PL
> Bio-BigFile-1.05/typemap
> Bio-BigFile-1.05/META.yml
> Bio-BigFile-1.05/README
> Bio-BigFile-1.05/MANIFEST
> Bio-BigFile-1.05/ExampleData
> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> Bio-BigFile-1.05/bin
> Bio-BigFile-1.05/bin/bigWigToWig.pl
> Bio-BigFile-1.05/bin/wigToBigWig.pl
> Bio-BigFile-1.05/bin/index_bigwigset.pl
> Bio-BigFile-1.05/lib
> Bio-BigFile-1.05/lib/Bio
> Bio-BigFile-1.05/lib/Bio/DB
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> Bio-BigFile-1.05/t
> Bio-BigFile-1.05/t/02.bigbed.t
> Bio-BigFile-1.05/t/03.bigwig_high.t
> Bio-BigFile-1.05/t/04.bigbed_high.t
> Bio-BigFile-1.05/t/05.bigwig_set.t
> /bin/tar: Read 9216 bytes from -
> Bio-BigFile-1.05/t/01.bigwig.t
> Bio-BigFile-1.05/patches
> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> CPAN: File::Temp loaded ok (v0.22)
> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> CPAN: CPAN::Meta loaded ok (v2.110580)
> CPAN: Module::CoreList loaded ok (v2.46)
> CPAN: Time::HiRes loaded ok (v1.9717)
>
>  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>
>
> This module requires the compiled jkweb.a library from Jim Kent's source
> tree.
> If you haven't already done so, please download the source from
> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
> contents of the "kent/src/lib" subdirectory as directed in the README. Then
> enter the location of the "kent/src" subdirectory at the prompt below.
> To prevent
> this message from appearing in the future, set the environment
> variable KENT_SRC
> to point to the "kent/src" subdirectory.
>
> Please enter the location of Kent source tree:
> /homes/dbolser/build/src/kent/src
>
> Created MYMETA.yml and MYMETA.json
> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> Building Bio-BigFile
> gcc -I/homes/dbolser/build/src/kent/src/inc
> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> lib/Bio/DB/BigFile.c
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
> undefined
> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
> undefined
> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
>
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build -- OK
> CPAN: YAML loaded ok (v0.72)
> Running Build test
> t/01.bigwig.t ....... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/01.bigwig.t line 28
> Compilation failed in require at t/01.bigwig.t line 28.
> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 29/29 subtests
> t/02.bigbed.t ....... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/02.bigbed.t line 28
> Compilation failed in require at t/02.bigbed.t line 28.
> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 15/15 subtests
> t/03.bigwig_high.t .. Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at t/03.bigwig_high.t line 28.
> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 32/32 subtests
> t/04.bigbed_high.t .. Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> Compilation failed in require at t/04.bigbed_high.t line 28.
> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 35/35 subtests
> t/05.bigwig_set.t ... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> Compilation failed in require at t/05.bigwig_set.t line 19.
> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> No subtests run
>
> Test Summary Report
> -------------------
> t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 29 tests but ran 0.
> t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 32 tests but ran 0.
> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 35 tests but ran 0.
> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: No plan found in TAP output
> Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
> 0.11 csys =  1.09 CPU)
> Result: FAIL
> Failed 5/5 test programs. 0/0 subtests failed.
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module, try:
>  reports LDS/Bio-BigFile-1.05.tar.gz
> Running Build install
>  make test had returned bad status, won't install without force
> Failed during this command:
>  LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO
>
> cpan[2]>
>
>
>
>
>
>
> Any hints?
>
> Cheers,
> Dan.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>



From lincoln.stein at gmail.com  Mon Mar 28 17:26:20 2011
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Mon, 28 Mar 2011 17:26:20 -0400
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
Message-ID: <AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>

Hi Dan,

There are two problems that I can see. One is a series of compiler warnings
when compiling the Perl .XS interface file. These are likely nothing to
worry about, but I should fix them. What versions of Perl and gcc do you
have installed? I don't see them when I compile on my system.

The second issue is that the SSL library is not being linked in. Previously
there was no dependency on SSL, but Jim may recently have added this to the
BigWig library in order to allow it to read bigwig files from https servers.
I see that you added a -lssl to Build.PL; does this make the tests work
again?

Lincoln


On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com> wrote:

> Hello,
>
> I'm trying to get Bio::DB::BigWig installed again, this time on a different
> box.
>
> I installed kent from git as described here:
> http://genome.ucsc.edu/admin/git.html
>
>
> I made the following changes, similar to those described previously:
>
> git diff
> diff --git a/src/inc/common.mk b/src/inc/common.mk
> index c7fc557..5187901 100644
> --- a/src/inc/common.mk
> +++ b/src/inc/common.mk
> @@ -3,7 +3,7 @@ CC=gcc
>  ifeq (${COPT},)
>     COPT=-O -g
>  endif
> -CFLAGS=
> +CFLAGS=-fPIC
>  HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> -DMACHTYPE_${MACHTYPE}
>  HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> -I../../../../../inc
>
> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> index fa2292b..acb97d2 100644
> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
>     /* Parse current line. */
>     wordCount = chopLine(line, row);
>     if (wordCount == ArraySize(row))
> -         errAbort("Too many fields (%d max is %lu) line %d of %s",
> wordCount, ArraySize(row),
> +         errAbort("Too many fields (%d max is %u) line %d of %s",
> wordCount, ArraySize(row),
>             lf->lineIx, lf->fileName);
>     char *chrom = row[0];
>     unsigned int start = lineFileNeedNum(lf, row, 1);
>
>
> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> correctly after typing 'make' in kent/src (should I be building it
> differently?)
>
>
>
> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>
> cpan
>
> cpan shell -- CPAN exploration and modules installation (v1.9600)
> Enter 'h' for help.
>
> cpan[1]> install Bio::DB::BigWig
> CPAN: Storable loaded ok (v2.25)
> Going to read '/homes/dbolser/.cpan/Metadata'
>  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> Running install for module 'Bio::DB::BigWig'
> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> CPAN: Digest::SHA loaded ok (v5.61)
> CPAN: Compress::Zlib loaded ok (v2.03)
> Checksum for
> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> ok
> CPAN: Archive::Tar loaded ok (v1.76)
> Bio-BigFile-1.05
> Bio-BigFile-1.05/Changes
> Bio-BigFile-1.05/LICENSE
> Bio-BigFile-1.05/DISCLAIMER
> Bio-BigFile-1.05/Build.PL
> Bio-BigFile-1.05/typemap
> Bio-BigFile-1.05/META.yml
> Bio-BigFile-1.05/README
> Bio-BigFile-1.05/MANIFEST
> Bio-BigFile-1.05/ExampleData
> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> Bio-BigFile-1.05/bin
> Bio-BigFile-1.05/bin/bigWigToWig.pl
> Bio-BigFile-1.05/bin/wigToBigWig.pl
> Bio-BigFile-1.05/bin/index_bigwigset.pl
> Bio-BigFile-1.05/lib
> Bio-BigFile-1.05/lib/Bio
> Bio-BigFile-1.05/lib/Bio/DB
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> Bio-BigFile-1.05/t
> Bio-BigFile-1.05/t/02.bigbed.t
> Bio-BigFile-1.05/t/03.bigwig_high.t
> Bio-BigFile-1.05/t/04.bigbed_high.t
> Bio-BigFile-1.05/t/05.bigwig_set.t
> /bin/tar: Read 9216 bytes from -
> Bio-BigFile-1.05/t/01.bigwig.t
> Bio-BigFile-1.05/patches
> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> CPAN: File::Temp loaded ok (v0.22)
> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> CPAN: CPAN::Meta loaded ok (v2.110580)
> CPAN: Module::CoreList loaded ok (v2.46)
> CPAN: Time::HiRes loaded ok (v1.9717)
>
>  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>
>
> This module requires the compiled jkweb.a library from Jim Kent's source
> tree.
> If you haven't already done so, please download the source from
> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
> contents of the "kent/src/lib" subdirectory as directed in the README. Then
> enter the location of the "kent/src" subdirectory at the prompt below.
> To prevent
> this message from appearing in the future, set the environment
> variable KENT_SRC
> to point to the "kent/src" subdirectory.
>
> Please enter the location of Kent source tree:
> /homes/dbolser/build/src/kent/src
>
> Created MYMETA.yml and MYMETA.json
> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> Building Bio-BigFile
> gcc -I/homes/dbolser/build/src/kent/src/inc
> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> lib/Bio/DB/BigFile.c
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
> undefined
> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
> undefined
> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
>
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build -- OK
> CPAN: YAML loaded ok (v0.72)
> Running Build test
> t/01.bigwig.t ....... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/01.bigwig.t line 28
> Compilation failed in require at t/01.bigwig.t line 28.
> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 29/29 subtests
> t/02.bigbed.t ....... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/02.bigbed.t line 28
> Compilation failed in require at t/02.bigbed.t line 28.
> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 15/15 subtests
> t/03.bigwig_high.t .. Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at t/03.bigwig_high.t line 28.
> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 32/32 subtests
> t/04.bigbed_high.t .. Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> Compilation failed in require at t/04.bigbed_high.t line 28.
> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 35/35 subtests
> t/05.bigwig_set.t ... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> Compilation failed in require at t/05.bigwig_set.t line 19.
> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> No subtests run
>
> Test Summary Report
> -------------------
> t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 29 tests but ran 0.
> t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 32 tests but ran 0.
> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 35 tests but ran 0.
> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: No plan found in TAP output
> Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
> 0.11 csys =  1.09 CPU)
> Result: FAIL
> Failed 5/5 test programs. 0/0 subtests failed.
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module, try:
>  reports LDS/Bio-BigFile-1.05.tar.gz
> Running Build install
>  make test had returned bad status, won't install without force
> Failed during this command:
>  LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO
>
> cpan[2]>
>
>
>
>
>
>
> Any hints?
>
> Cheers,
> Dan.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>



From bosborne11 at verizon.net  Mon Mar 28 16:43:51 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Mon, 28 Mar 2011 16:43:51 -0400
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <6CE8AACF-0D78-4BBA-8094-CC189B0FF872@illinois.edu>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
	<AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
	<6CE8AACF-0D78-4BBA-8094-CC189B0FF872@illinois.edu>
Message-ID: <63E35F39-D70C-4D6F-A792-D2738B850567@verizon.net>

Chris,

I'll get started on dissembling bptutorial. There's certainly useful text in there but there's also duplicated or outdated material. Looks like there are 3 options for any given section:

- put it into an existing HOWTO
- make it into a new HOWTO
- delete it

BIO

On Mar 28, 2011, at 9:27 AM, Chris Fields wrote:

> Dave,
> 
> +1 on removing old docs to prevent confusion.  Or, alternatively, +1 to syncing those to current docs (though I think decreasing the replication effort in keeping docs up-to-date is probably the best tact).
> 
> chris
> 
> On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:
> 
>>> 
>>> Thank you very much. It is working. I got the program code from the
>>> following link.
>>> 
>>> http://www.bioperl.org/Core/Latest/bptutorial.html
>> 
>> 
>> Aha, okay. You got there from Google, I guess? That is *way* out of date.
>> 
>> To the other core devs, in order to prevent this confusion in the future,
>> I'd like to delete the Core/ directory from our website since it's been
>> superseded at this point by other docs and is not current. I intend to put
>> up a ticket at Redmine, but I will wait a bit before doing so to allow time
>> for people to see this and comment ? please do speak up if there's good
>> reason to keep it.
>> 
>> 
>> Could you please give me the link to join this forum to see other
>>> discussions, which would be more helpful to me?
>>> 
>> 
>> Sure, you can sign up for the mailing list here:
>> 
>> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> And the archives are also searchable:
>> 
>>   http://news.gmane.org/gmane.comp.lang.perl.bio.general
>> 
>> 
>> Please let me know if you have any suggestion for me to keep learning the
>>> bioperl.
>> 
>> 
>> I would also suggest reading the (current) tutorial and HOWTOs at
>> www.bioperl.org . Lots of good links on the main page there, particularly
>> under the Documentation heading.
>> 
>> 
>> Dave
>> 
>> 
>> 
>> 
>> 
>>> With regards,
>>> Ravi.
>>> 
>>> 
>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>>> 
>>>> Hi Ravi,
>>>> 
>>>> Please make sure to "Reply All" so that everyone on the mailing list can
>>>> follow (and add to) the discussion.
>>>> 
>>>> If you read the first line of the exception, you'll see it states what the
>>>> error is:
>>>> "WebDBSeqI Error ? check query sequences!"
>>>> 
>>>> You'd have no way of knowing this, but that ID and database combination is
>>>> not functioning anymore, so that's why in this case you're getting an error.
>>>> Please try using the example in the tutorial here:
>>>> 
>>>> 
>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>>> 
>>>> which has been updated to a different ID which should work.
>>>> 
>>>> Sorry for the confusion! So that we can prevent other people from having
>>>> the same issue, could you tell me where you got that example code?
>>>> 
>>>> Dave
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>>> 
>>>>> Hi Dave,
>>>>> 
>>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>>> screenshot after making the change you pointed out. But I am getting
>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>>> environment variables but I am not sure how to do that. Could you please
>>>>> guide me on this too.
>>>>> 
>>>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>>>> what to enter once I click "New" on that window.
>>>>> 
>>>>> Thanks in advance.
>>>>> 
>>>>> With regards,
>>>>> Ravi.
>>>>> 
>>>>> 
>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>>> 
>>>>>> Hi Ravi,
>>>>>> 
>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>>>> not Bio::Seq. So your first line
>>>>>> 
>>>>>> use Bio::Seq;
>>>>>> 
>>>>>> should be replaced with
>>>>>> 
>>>>>> use Bio::Perl;
>>>>>> 
>>>>>> 
>>>>>> More examples in the BioPerl Tutorial here:
>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>>> 
>>>>>> 
>>>>>> Dve
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>>> 
>>>>>>> Hi,
>>>>>>> 
>>>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>>>> packages
>>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>>> message I
>>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>>> 
>>>>>>> Thanks,
>>>>>>> 
>>>>>>> With regards,
>>>>>>> Ravi.
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Mon Mar 28 18:40:39 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 28 Mar 2011 17:40:39 -0500
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <63E35F39-D70C-4D6F-A792-D2738B850567@verizon.net>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
	<AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
	<6CE8AACF-0D78-4BBA-8094-CC189B0FF872@illinois.edu>
	<63E35F39-D70C-4D6F-A792-D2738B850567@verizon.net>
Message-ID: <1569920B-D132-487F-BBC6-9A81A430E6E0@illinois.edu>

Brian,

I think this was started:

http://www.bioperl.org/wiki/Bptutorial.pl

It certainly could be cleaned up, organized, and updated (that and the FAQ).  Makes sense to have it as a HOWTO or maybe split it into several HOWTOs.  Maybe even combine it with the beginner's HOWTO into various sections?

chris

On Mar 28, 2011, at 3:43 PM, Brian Osborne wrote:

> Chris,
> 
> I'll get started on dissembling bptutorial. There's certainly useful text in there but there's also duplicated or outdated material. Looks like there are 3 options for any given section:
> 
> - put it into an existing HOWTO
> - make it into a new HOWTO
> - delete it
> 
> BIO
> 
> On Mar 28, 2011, at 9:27 AM, Chris Fields wrote:
> 
>> Dave,
>> 
>> +1 on removing old docs to prevent confusion.  Or, alternatively, +1 to syncing those to current docs (though I think decreasing the replication effort in keeping docs up-to-date is probably the best tact).
>> 
>> chris
>> 
>> On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:
>> 
>>>> 
>>>> Thank you very much. It is working. I got the program code from the
>>>> following link.
>>>> 
>>>> http://www.bioperl.org/Core/Latest/bptutorial.html
>>> 
>>> 
>>> Aha, okay. You got there from Google, I guess? That is *way* out of date.
>>> 
>>> To the other core devs, in order to prevent this confusion in the future,
>>> I'd like to delete the Core/ directory from our website since it's been
>>> superseded at this point by other docs and is not current. I intend to put
>>> up a ticket at Redmine, but I will wait a bit before doing so to allow time
>>> for people to see this and comment ? please do speak up if there's good
>>> reason to keep it.
>>> 
>>> 
>>> Could you please give me the link to join this forum to see other
>>>> discussions, which would be more helpful to me?
>>>> 
>>> 
>>> Sure, you can sign up for the mailing list here:
>>> 
>>> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>>> And the archives are also searchable:
>>> 
>>>  http://news.gmane.org/gmane.comp.lang.perl.bio.general
>>> 
>>> 
>>> Please let me know if you have any suggestion for me to keep learning the
>>>> bioperl.
>>> 
>>> 
>>> I would also suggest reading the (current) tutorial and HOWTOs at
>>> www.bioperl.org . Lots of good links on the main page there, particularly
>>> under the Documentation heading.
>>> 
>>> 
>>> Dave
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> With regards,
>>>> Ravi.
>>>> 
>>>> 
>>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>>>> 
>>>>> Hi Ravi,
>>>>> 
>>>>> Please make sure to "Reply All" so that everyone on the mailing list can
>>>>> follow (and add to) the discussion.
>>>>> 
>>>>> If you read the first line of the exception, you'll see it states what the
>>>>> error is:
>>>>> "WebDBSeqI Error ? check query sequences!"
>>>>> 
>>>>> You'd have no way of knowing this, but that ID and database combination is
>>>>> not functioning anymore, so that's why in this case you're getting an error.
>>>>> Please try using the example in the tutorial here:
>>>>> 
>>>>> 
>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>>>> 
>>>>> which has been updated to a different ID which should work.
>>>>> 
>>>>> Sorry for the confusion! So that we can prevent other people from having
>>>>> the same issue, could you tell me where you got that example code?
>>>>> 
>>>>> Dave
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>>>> 
>>>>>> Hi Dave,
>>>>>> 
>>>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>>>> screenshot after making the change you pointed out. But I am getting
>>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>>>> environment variables but I am not sure how to do that. Could you please
>>>>>> guide me on this too.
>>>>>> 
>>>>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>>>>> what to enter once I click "New" on that window.
>>>>>> 
>>>>>> Thanks in advance.
>>>>>> 
>>>>>> With regards,
>>>>>> Ravi.
>>>>>> 
>>>>>> 
>>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>>>> 
>>>>>>> Hi Ravi,
>>>>>>> 
>>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>>>>> not Bio::Seq. So your first line
>>>>>>> 
>>>>>>> use Bio::Seq;
>>>>>>> 
>>>>>>> should be replaced with
>>>>>>> 
>>>>>>> use Bio::Perl;
>>>>>>> 
>>>>>>> 
>>>>>>> More examples in the BioPerl Tutorial here:
>>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>>>> 
>>>>>>> 
>>>>>>> Dve
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>>>> 
>>>>>>>> Hi,
>>>>>>>> 
>>>>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>>>>> packages
>>>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>>>> message I
>>>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>>>> 
>>>>>>>> Thanks,
>>>>>>>> 
>>>>>>>> With regards,
>>>>>>>> Ravi.
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
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>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
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>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From dan.kortschak at adelaide.edu.au  Mon Mar 28 21:12:55 2011
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Tue, 29 Mar 2011 11:42:55 +1030
Subject: [Bioperl-l] GuessSeqFormat GFF vs VCF
Message-ID: <1301361175.4727.17.camel@sueno>

Hi All,

I'm going through the BEDTools wrapper to bring it up to date. A number
BEDTools executables now accept GFF and VCF as well as BED format input
files.

Part of the WrapperBase::CommandExts give acceptable input formats, so
I'm adding to GuessSeqFormat guessers for GFF and VCF, which from the
point of view of a stateless guesser, are indistinguishable unless (and
I don't like this idea), GFF is additionally defined as not VCF and VCF
is additionally defined as not VCF (these can be identified from the
##gff-version and ##fileformat=VCF lines).

Can people provide their thoughts on this?

cheers
Dan



From dan.bolser at gmail.com  Tue Mar 29 04:57:29 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 29 Mar 2011 09:57:29 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
Message-ID: <AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>

On 28 March 2011 22:26, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Hi Dan,
> There are two problems that I can see. One is a series of compiler warnings
> when compiling the Perl .XS interface file. These are likely nothing to
> worry about, but I should fix them. What versions of Perl and gcc do you
> have installed? I don't see them when I compile on my system.

gcc --version # gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
perl --version # v5.8.8 built for i386-linux-thread-multi

uname -a # Linux cricket 2.6.18-194.32.1.el5PAE #1 SMP Wed Jan 5
18:43:13 EST 2011 i686 i686 i386 GNU/Linux



I got kent from git and built it with the following commands:

cd kent/src/lib/
echo $MACHTYPE # i686-redhat-linux-gnu
export MACHTYPE=i686
make
cd ../
export KENT_SRC=`pwd`

# NOTE, both $MACHTYPE and $KENT_SRC should be defined here
cpan -i Bio::DB::BigWig # FAILS AS DESCRIBED

cd /tmp
wget http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
tar zxfv Bio-BigFile-1.05.tar.gz
cd Bio-BigFile-1.05
# PATCH  Build.PL AS DESCRIBED (add -lssl after -lz)
perl Build.PL
./Build # SEE WARNINGS AS BEFORE
./Build test # Files=5, Tests=135, Result: PASS
./Build install


Note, above I didn't patch kent to include -fPIC as suggested
previously. I don't see any noticeable difference if I do on this
arch.

It would be good if the instructions above could make it into the
Bio::DB::BigWig README, as a few people have expressed confusion about
the exact steps (the README in kent is a bit confusing, and mostly
unnecessary for the purposes of building Bio::DB::BigWig).


> The second issue is that the SSL library is not being linked in. Previously
> there was no dependency on SSL, but Jim may recently have added this to the
> BigWig library in order to allow it to read bigwig files from https servers.
> I see that you added a -lssl to Build.PL; does this make the tests work
> again?

Yup, when I add -lssl to Build.PL (as per the previous diff), the
tests pass, but I still see the warnings.

I'm sure I saw the warnings disappear when I was playing with
different versions of Bio::DB::BigWig, but now they occur without
fail... if you pardon the pun.

I have a seeking suspicion that it's related to my perl 'build kit'...
However, since I'm not sure what module versions to report, and since
you promised to fix these issues anyway, I won't dig into it.


Thanks for help, and thanks for the support on
irc://irc.freenode.net/#bioperl, without which I would have probably
give up!

Cheers,
Dan.

> Lincoln
>
> On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com> wrote:
>>
>> Hello,
>>
>> I'm trying to get Bio::DB::BigWig installed again, this time on a
>> different box.
>>
>> I installed kent from git as described here:
>> http://genome.ucsc.edu/admin/git.html
>>
>>
>> I made the following changes, similar to those described previously:
>>
>> git diff
>> diff --git a/src/inc/common.mk b/src/inc/common.mk
>> index c7fc557..5187901 100644
>> --- a/src/inc/common.mk
>> +++ b/src/inc/common.mk
>> @@ -3,7 +3,7 @@ CC=gcc
>> ?ifeq (${COPT},)
>> ? ? COPT=-O -g
>> ?endif
>> -CFLAGS=
>> +CFLAGS=-fPIC
>> ?HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
>> -DMACHTYPE_${MACHTYPE}
>> ?HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
>> -I../../../../../inc
>>
>> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> index fa2292b..acb97d2 100644
>> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
>> ? ? /* Parse current line. */
>> ? ? wordCount = chopLine(line, row);
>> ? ? if (wordCount == ArraySize(row))
>> - ? ? ? ? errAbort("Too many fields (%d max is %lu) line %d of %s",
>> wordCount, ArraySize(row),
>> + ? ? ? ? errAbort("Too many fields (%d max is %u) line %d of %s",
>> wordCount, ArraySize(row),
>> ? ? ? ? ? ? lf->lineIx, lf->fileName);
>> ? ? char *chrom = row[0];
>> ? ? unsigned int start = lineFileNeedNum(lf, row, 1);
>>
>>
>> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
>> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
>> correctly after typing 'make' in kent/src (should I be building it
>> differently?)
>>
>>
>>
>> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>>
>> cpan
>>
>> cpan shell -- CPAN exploration and modules installation (v1.9600)
>> Enter 'h' for help.
>>
>> cpan[1]> install Bio::DB::BigWig
>> CPAN: Storable loaded ok (v2.25)
>> Going to read '/homes/dbolser/.cpan/Metadata'
>> ?Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
>> Running install for module 'Bio::DB::BigWig'
>> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
>> CPAN: Digest::SHA loaded ok (v5.61)
>> CPAN: Compress::Zlib loaded ok (v2.03)
>> Checksum for
>> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
>> ok
>> CPAN: Archive::Tar loaded ok (v1.76)
>> Bio-BigFile-1.05
>> Bio-BigFile-1.05/Changes
>> Bio-BigFile-1.05/LICENSE
>> Bio-BigFile-1.05/DISCLAIMER
>> Bio-BigFile-1.05/Build.PL
>> Bio-BigFile-1.05/typemap
>> Bio-BigFile-1.05/META.yml
>> Bio-BigFile-1.05/README
>> Bio-BigFile-1.05/MANIFEST
>> Bio-BigFile-1.05/ExampleData
>> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
>> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
>> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
>> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
>> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
>> Bio-BigFile-1.05/ExampleData/refSeqTest.as
>> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
>> Bio-BigFile-1.05/bin
>> Bio-BigFile-1.05/bin/bigWigToWig.pl
>> Bio-BigFile-1.05/bin/wigToBigWig.pl
>> Bio-BigFile-1.05/bin/index_bigwigset.pl
>> Bio-BigFile-1.05/lib
>> Bio-BigFile-1.05/lib/Bio
>> Bio-BigFile-1.05/lib/Bio/DB
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
>> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
>> Bio-BigFile-1.05/t
>> Bio-BigFile-1.05/t/02.bigbed.t
>> Bio-BigFile-1.05/t/03.bigwig_high.t
>> Bio-BigFile-1.05/t/04.bigbed_high.t
>> Bio-BigFile-1.05/t/05.bigwig_set.t
>> /bin/tar: Read 9216 bytes from -
>> Bio-BigFile-1.05/t/01.bigwig.t
>> Bio-BigFile-1.05/patches
>> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
>> CPAN: File::Temp loaded ok (v0.22)
>> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
>> CPAN: CPAN::Meta loaded ok (v2.110580)
>> CPAN: Module::CoreList loaded ok (v2.46)
>> CPAN: Time::HiRes loaded ok (v1.9717)
>>
>> ?CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>>
>>
>> This module requires the compiled jkweb.a library from Jim Kent's source
>> tree.
>> If you haven't already done so, please download the source from
>> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
>> contents of the "kent/src/lib" subdirectory as directed in the README.
>> Then
>> enter the location of the "kent/src" subdirectory at the prompt below.
>> To prevent
>> this message from appearing in the future, set the environment
>> variable KENT_SRC
>> to point to the "kent/src" subdirectory.
>>
>> Please enter the location of Kent source tree:
>> /homes/dbolser/build/src/kent/src
>>
>> Created MYMETA.yml and MYMETA.json
>> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
>> Building Bio-BigFile
>> gcc -I/homes/dbolser/build/src/kent/src/inc
>> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
>> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
>> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
>> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
>> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
>> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
>> lib/Bio/DB/BigFile.c
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
>> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
>> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
>> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
>> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
>> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
>> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
>> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
>> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
>> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
>>
>> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
>> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
>> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
>> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
>> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
>> ?LDS/Bio-BigFile-1.05.tar.gz
>> ?./Build -- OK
>> CPAN: YAML loaded ok (v0.72)
>> Running Build test
>> t/01.bigwig.t ....... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at t/01.bigwig.t line 28
>> Compilation failed in require at t/01.bigwig.t line 28.
>> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
>> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 29/29 subtests
>> t/02.bigbed.t ....... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at t/02.bigbed.t line 28
>> Compilation failed in require at t/02.bigbed.t line 28.
>> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
>> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 15/15 subtests
>> t/03.bigwig_high.t .. Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at t/03.bigwig_high.t line 28.
>> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
>> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 32/32 subtests
>> t/04.bigbed_high.t .. Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
>> line 7.
>> Compilation failed in require at t/04.bigbed_high.t line 28.
>> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
>> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 35/35 subtests
>> t/05.bigwig_set.t ... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
>> line 177.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
>> line 177.
>> Compilation failed in require at t/05.bigwig_set.t line 19.
>> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
>> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
>> No subtests run
>>
>> Test Summary Report
>> -------------------
>> t/01.bigwig.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 29 tests but ran 0.
>> t/02.bigbed.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 15 tests but ran 0.
>> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 32 tests but ran 0.
>> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 35 tests but ran 0.
>> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: No plan found in TAP output
>> Files=5, Tests=0, ?1 wallclock secs ( 0.04 usr ?0.01 sys + ?0.93 cusr
>> 0.11 csys = ?1.09 CPU)
>> Result: FAIL
>> Failed 5/5 test programs. 0/0 subtests failed.
>> ?LDS/Bio-BigFile-1.05.tar.gz
>> ?./Build test -- NOT OK
>> //hint// to see the cpan-testers results for installing this module, try:
>> ?reports LDS/Bio-BigFile-1.05.tar.gz
>> Running Build install
>> ?make test had returned bad status, won't install without force
>> Failed during this command:
>> ?LDS/Bio-BigFile-1.05.tar.gz ? ? ? ? ? ? ? ? ?: make_test NO
>>
>> cpan[2]>
>>
>>
>>
>>
>>
>>
>> Any hints?
>>
>> Cheers,
>> Dan.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
>



From dan.bolser at gmail.com  Tue Mar 29 04:57:29 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 29 Mar 2011 09:57:29 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
Message-ID: <AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>

On 28 March 2011 22:26, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Hi Dan,
> There are two problems that I can see. One is a series of compiler warnings
> when compiling the Perl .XS interface file. These are likely nothing to
> worry about, but I should fix them. What versions of Perl and gcc do you
> have installed? I don't see them when I compile on my system.

gcc --version # gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
perl --version # v5.8.8 built for i386-linux-thread-multi

uname -a # Linux cricket 2.6.18-194.32.1.el5PAE #1 SMP Wed Jan 5
18:43:13 EST 2011 i686 i686 i386 GNU/Linux



I got kent from git and built it with the following commands:

cd kent/src/lib/
echo $MACHTYPE # i686-redhat-linux-gnu
export MACHTYPE=i686
make
cd ../
export KENT_SRC=`pwd`

# NOTE, both $MACHTYPE and $KENT_SRC should be defined here
cpan -i Bio::DB::BigWig # FAILS AS DESCRIBED

cd /tmp
wget http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
tar zxfv Bio-BigFile-1.05.tar.gz
cd Bio-BigFile-1.05
# PATCH  Build.PL AS DESCRIBED (add -lssl after -lz)
perl Build.PL
./Build # SEE WARNINGS AS BEFORE
./Build test # Files=5, Tests=135, Result: PASS
./Build install


Note, above I didn't patch kent to include -fPIC as suggested
previously. I don't see any noticeable difference if I do on this
arch.

It would be good if the instructions above could make it into the
Bio::DB::BigWig README, as a few people have expressed confusion about
the exact steps (the README in kent is a bit confusing, and mostly
unnecessary for the purposes of building Bio::DB::BigWig).


> The second issue is that the SSL library is not being linked in. Previously
> there was no dependency on SSL, but Jim may recently have added this to the
> BigWig library in order to allow it to read bigwig files from https servers.
> I see that you added a -lssl to Build.PL; does this make the tests work
> again?

Yup, when I add -lssl to Build.PL (as per the previous diff), the
tests pass, but I still see the warnings.

I'm sure I saw the warnings disappear when I was playing with
different versions of Bio::DB::BigWig, but now they occur without
fail... if you pardon the pun.

I have a seeking suspicion that it's related to my perl 'build kit'...
However, since I'm not sure what module versions to report, and since
you promised to fix these issues anyway, I won't dig into it.


Thanks for help, and thanks for the support on
irc://irc.freenode.net/#bioperl, without which I would have probably
give up!

Cheers,
Dan.

> Lincoln
>
> On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com> wrote:
>>
>> Hello,
>>
>> I'm trying to get Bio::DB::BigWig installed again, this time on a
>> different box.
>>
>> I installed kent from git as described here:
>> http://genome.ucsc.edu/admin/git.html
>>
>>
>> I made the following changes, similar to those described previously:
>>
>> git diff
>> diff --git a/src/inc/common.mk b/src/inc/common.mk
>> index c7fc557..5187901 100644
>> --- a/src/inc/common.mk
>> +++ b/src/inc/common.mk
>> @@ -3,7 +3,7 @@ CC=gcc
>> ?ifeq (${COPT},)
>> ? ? COPT=-O -g
>> ?endif
>> -CFLAGS=
>> +CFLAGS=-fPIC
>> ?HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
>> -DMACHTYPE_${MACHTYPE}
>> ?HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
>> -I../../../../../inc
>>
>> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> index fa2292b..acb97d2 100644
>> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
>> ? ? /* Parse current line. */
>> ? ? wordCount = chopLine(line, row);
>> ? ? if (wordCount == ArraySize(row))
>> - ? ? ? ? errAbort("Too many fields (%d max is %lu) line %d of %s",
>> wordCount, ArraySize(row),
>> + ? ? ? ? errAbort("Too many fields (%d max is %u) line %d of %s",
>> wordCount, ArraySize(row),
>> ? ? ? ? ? ? lf->lineIx, lf->fileName);
>> ? ? char *chrom = row[0];
>> ? ? unsigned int start = lineFileNeedNum(lf, row, 1);
>>
>>
>> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
>> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
>> correctly after typing 'make' in kent/src (should I be building it
>> differently?)
>>
>>
>>
>> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>>
>> cpan
>>
>> cpan shell -- CPAN exploration and modules installation (v1.9600)
>> Enter 'h' for help.
>>
>> cpan[1]> install Bio::DB::BigWig
>> CPAN: Storable loaded ok (v2.25)
>> Going to read '/homes/dbolser/.cpan/Metadata'
>> ?Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
>> Running install for module 'Bio::DB::BigWig'
>> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
>> CPAN: Digest::SHA loaded ok (v5.61)
>> CPAN: Compress::Zlib loaded ok (v2.03)
>> Checksum for
>> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
>> ok
>> CPAN: Archive::Tar loaded ok (v1.76)
>> Bio-BigFile-1.05
>> Bio-BigFile-1.05/Changes
>> Bio-BigFile-1.05/LICENSE
>> Bio-BigFile-1.05/DISCLAIMER
>> Bio-BigFile-1.05/Build.PL
>> Bio-BigFile-1.05/typemap
>> Bio-BigFile-1.05/META.yml
>> Bio-BigFile-1.05/README
>> Bio-BigFile-1.05/MANIFEST
>> Bio-BigFile-1.05/ExampleData
>> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
>> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
>> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
>> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
>> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
>> Bio-BigFile-1.05/ExampleData/refSeqTest.as
>> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
>> Bio-BigFile-1.05/bin
>> Bio-BigFile-1.05/bin/bigWigToWig.pl
>> Bio-BigFile-1.05/bin/wigToBigWig.pl
>> Bio-BigFile-1.05/bin/index_bigwigset.pl
>> Bio-BigFile-1.05/lib
>> Bio-BigFile-1.05/lib/Bio
>> Bio-BigFile-1.05/lib/Bio/DB
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
>> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
>> Bio-BigFile-1.05/t
>> Bio-BigFile-1.05/t/02.bigbed.t
>> Bio-BigFile-1.05/t/03.bigwig_high.t
>> Bio-BigFile-1.05/t/04.bigbed_high.t
>> Bio-BigFile-1.05/t/05.bigwig_set.t
>> /bin/tar: Read 9216 bytes from -
>> Bio-BigFile-1.05/t/01.bigwig.t
>> Bio-BigFile-1.05/patches
>> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
>> CPAN: File::Temp loaded ok (v0.22)
>> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
>> CPAN: CPAN::Meta loaded ok (v2.110580)
>> CPAN: Module::CoreList loaded ok (v2.46)
>> CPAN: Time::HiRes loaded ok (v1.9717)
>>
>> ?CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>>
>>
>> This module requires the compiled jkweb.a library from Jim Kent's source
>> tree.
>> If you haven't already done so, please download the source from
>> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
>> contents of the "kent/src/lib" subdirectory as directed in the README.
>> Then
>> enter the location of the "kent/src" subdirectory at the prompt below.
>> To prevent
>> this message from appearing in the future, set the environment
>> variable KENT_SRC
>> to point to the "kent/src" subdirectory.
>>
>> Please enter the location of Kent source tree:
>> /homes/dbolser/build/src/kent/src
>>
>> Created MYMETA.yml and MYMETA.json
>> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
>> Building Bio-BigFile
>> gcc -I/homes/dbolser/build/src/kent/src/inc
>> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
>> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
>> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
>> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
>> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
>> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
>> lib/Bio/DB/BigFile.c
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
>> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
>> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
>> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
>> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
>> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
>> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
>> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
>> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
>> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
>>
>> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
>> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
>> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
>> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
>> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
>> ?LDS/Bio-BigFile-1.05.tar.gz
>> ?./Build -- OK
>> CPAN: YAML loaded ok (v0.72)
>> Running Build test
>> t/01.bigwig.t ....... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at t/01.bigwig.t line 28
>> Compilation failed in require at t/01.bigwig.t line 28.
>> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
>> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 29/29 subtests
>> t/02.bigbed.t ....... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at t/02.bigbed.t line 28
>> Compilation failed in require at t/02.bigbed.t line 28.
>> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
>> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 15/15 subtests
>> t/03.bigwig_high.t .. Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at t/03.bigwig_high.t line 28.
>> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
>> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 32/32 subtests
>> t/04.bigbed_high.t .. Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
>> line 7.
>> Compilation failed in require at t/04.bigbed_high.t line 28.
>> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
>> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 35/35 subtests
>> t/05.bigwig_set.t ... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
>> line 177.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
>> line 177.
>> Compilation failed in require at t/05.bigwig_set.t line 19.
>> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
>> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
>> No subtests run
>>
>> Test Summary Report
>> -------------------
>> t/01.bigwig.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 29 tests but ran 0.
>> t/02.bigbed.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 15 tests but ran 0.
>> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 32 tests but ran 0.
>> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 35 tests but ran 0.
>> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: No plan found in TAP output
>> Files=5, Tests=0, ?1 wallclock secs ( 0.04 usr ?0.01 sys + ?0.93 cusr
>> 0.11 csys = ?1.09 CPU)
>> Result: FAIL
>> Failed 5/5 test programs. 0/0 subtests failed.
>> ?LDS/Bio-BigFile-1.05.tar.gz
>> ?./Build test -- NOT OK
>> //hint// to see the cpan-testers results for installing this module, try:
>> ?reports LDS/Bio-BigFile-1.05.tar.gz
>> Running Build install
>> ?make test had returned bad status, won't install without force
>> Failed during this command:
>> ?LDS/Bio-BigFile-1.05.tar.gz ? ? ? ? ? ? ? ? ?: make_test NO
>>
>> cpan[2]>
>>
>>
>>
>>
>>
>>
>> Any hints?
>>
>> Cheers,
>> Dan.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
>



From David.Messina at sbc.su.se  Tue Mar 29 05:11:26 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 29 Mar 2011 11:11:26 +0200
Subject: [Bioperl-l] GSoC 2011
In-Reply-To: <AANLkTim6o3bJ6NkBRmoUC5e76GaGzpjP5+xE+ZrWcEdc@mail.gmail.com>
References: <AANLkTim6o3bJ6NkBRmoUC5e76GaGzpjP5+xE+ZrWcEdc@mail.gmail.com>
Message-ID: <AANLkTi=OW4OYGwB1AWRe4TXZTXyLuENxZakArcVoAjHF@mail.gmail.com>

Hi Fei,

Glad to hear you're interested in working on BioPerl!

Just to throw in my two cents, I think it would be great to have a RAxML
wrapper in BioPerl. Although actually any of the projects you mentioned
sound like they're about the right size for a summer project.

I'm not directly involved with GSoC, so I think if you haven't already you
should take a look at our GsOC page here

    http://news.open-bio.org/news/2011/03/obf-gsoc-2011/

and get in touch with Rob Buels, our coordinator (rmb32 at cornell.edu)



Best,
Dave





On Tue, Mar 22, 2011 at 20:14, Fei Hu <hufeiyc at gmail.com> wrote:

> Hi, All.
>
> My name is Fei Hu from U. of South Carolina. I am currently a second-year
> Ph.D student in computer science focusing on gene order and sequence(DNA &
> AA) phylogeny as well as whole genome alignment. I am instreseted in
> joining
> bioperl project of GSoC 2011. I have two ideas that would like to share.
>
> My first idea is to extend the bioperl so that it can process and analysis
> gene order data using published package such as MGR, GRAPPA and distance
> estimator. This is a relatively new type of data and many great researchers
> have contributed to this type of phylogeny reconstruction (Dr. Pavel
> Penzer,
> Dr. Bernard Moret and Dr. David Sankoff).
>
> Secondly as maximum likelihood becomes more and more popular, especially
> RAxML has been widely recognized and used(over 1000 citations). I think
> it's
> time to integrate that as well as GARLI into the Bio::Tools. I extensively
> used and explored RAxML in my last publication on gene order phylogeny.
>
> Those are just my preliminary thoughts, not even a plan and any suggestion
> is greatly appreciated!!! I use perl on daily bases for data processing and
> composing testing scripts, but not much OOP involved.
>
> PS: Rest api for CIPRES is no longer available. So this following task
> can't
> be finished right now:
> Development of a
> Bio::Tools::Run::RemoteBlast<
> http://bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast>-like
> interface to CIPRES remote analyses; for more see this
> thread<http://thread.gmane.org/gmane.comp.lang.perl.bio.general/16524>
> .
>
> And Thank you all.
> Best
>
> Fei
>
> --
> *Fei Hu
> Bioinformatics Lab
> 3D-11 Swearingen Building
> U of South Carolina
> Tel: 803-397-5240*
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From tzhu at mail.bnu.edu.cn  Tue Mar 29 06:33:59 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Tue, 29 Mar 2011 18:33:59 +0800
Subject: [Bioperl-l] How to use module Bio::SeqFeature::Gene::GeneStructure?
Message-ID: <1301394839.6397.1.camel@ubuntu>

I've referred the ducument
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
It says, @transcripts = $gene->transcripts(); @exons = $gene->exons();
The object $gene should mean a Bio::SeqFeature::Gene::GeneStructure
object. But how could I get such object? I hope to see a good example.
Thank you! 


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)




From lincoln.stein at gmail.com  Tue Mar 29 09:59:22 2011
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Tue, 29 Mar 2011 09:59:22 -0400
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
	<AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>
Message-ID: <AANLkTi=Jrw3adAgigbAeG_-KT4VqLBsPBE08x_NQyOHD@mail.gmail.com>

I'll release a new version with a fixed Build.PL and README today.

Lincoln

On Tue, Mar 29, 2011 at 4:57 AM, Dan Bolser <dan.bolser at gmail.com> wrote:

> On 28 March 2011 22:26, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> > Hi Dan,
> > There are two problems that I can see. One is a series of compiler
> warnings
> > when compiling the Perl .XS interface file. These are likely nothing to
> > worry about, but I should fix them. What versions of Perl and gcc do you
> > have installed? I don't see them when I compile on my system.
>
> gcc --version # gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
> perl --version # v5.8.8 built for i386-linux-thread-multi
>
> uname -a # Linux cricket 2.6.18-194.32.1.el5PAE #1 SMP Wed Jan 5
> 18:43:13 EST 2011 i686 i686 i386 GNU/Linux
>
>
>
> I got kent from git and built it with the following commands:
>
> cd kent/src/lib/
> echo $MACHTYPE # i686-redhat-linux-gnu
> export MACHTYPE=i686
> make
> cd ../
> export KENT_SRC=`pwd`
>
> # NOTE, both $MACHTYPE and $KENT_SRC should be defined here
> cpan -i Bio::DB::BigWig # FAILS AS DESCRIBED
>
> cd /tmp
> wget
> http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> tar zxfv Bio-BigFile-1.05.tar.gz
> cd Bio-BigFile-1.05
> # PATCH  Build.PL AS DESCRIBED (add -lssl after -lz)
> perl Build.PL
> ./Build # SEE WARNINGS AS BEFORE
> ./Build test # Files=5, Tests=135, Result: PASS
> ./Build install
>
>
> Note, above I didn't patch kent to include -fPIC as suggested
> previously. I don't see any noticeable difference if I do on this
> arch.
>
> It would be good if the instructions above could make it into the
> Bio::DB::BigWig README, as a few people have expressed confusion about
> the exact steps (the README in kent is a bit confusing, and mostly
> unnecessary for the purposes of building Bio::DB::BigWig).
>
>
> > The second issue is that the SSL library is not being linked in.
> Previously
> > there was no dependency on SSL, but Jim may recently have added this to
> the
> > BigWig library in order to allow it to read bigwig files from https
> servers.
> > I see that you added a -lssl to Build.PL; does this make the tests work
> > again?
>
> Yup, when I add -lssl to Build.PL (as per the previous diff), the
> tests pass, but I still see the warnings.
>
> I'm sure I saw the warnings disappear when I was playing with
> different versions of Bio::DB::BigWig, but now they occur without
> fail... if you pardon the pun.
>
> I have a seeking suspicion that it's related to my perl 'build kit'...
> However, since I'm not sure what module versions to report, and since
> you promised to fix these issues anyway, I won't dig into it.
>
>
> Thanks for help, and thanks for the support on
> irc://irc.freenode.net/#bioperl, without which I would have probably
> give up!
>
> Cheers,
> Dan.
>
> > Lincoln
> >
> > On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com>
> wrote:
> >>
> >> Hello,
> >>
> >> I'm trying to get Bio::DB::BigWig installed again, this time on a
> >> different box.
> >>
> >> I installed kent from git as described here:
> >> http://genome.ucsc.edu/admin/git.html
> >>
> >>
> >> I made the following changes, similar to those described previously:
> >>
> >> git diff
> >> diff --git a/src/inc/common.mk b/src/inc/common.mk
> >> index c7fc557..5187901 100644
> >> --- a/src/inc/common.mk
> >> +++ b/src/inc/common.mk
> >> @@ -3,7 +3,7 @@ CC=gcc
> >>  ifeq (${COPT},)
> >>     COPT=-O -g
> >>  endif
> >> -CFLAGS=
> >> +CFLAGS=-fPIC
> >>  HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> >> -DMACHTYPE_${MACHTYPE}
> >>  HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> >> -I../../../../../inc
> >>
> >> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> index fa2292b..acb97d2 100644
> >> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
> >>     /* Parse current line. */
> >>     wordCount = chopLine(line, row);
> >>     if (wordCount == ArraySize(row))
> >> -         errAbort("Too many fields (%d max is %lu) line %d of %s",
> >> wordCount, ArraySize(row),
> >> +         errAbort("Too many fields (%d max is %u) line %d of %s",
> >> wordCount, ArraySize(row),
> >>             lf->lineIx, lf->fileName);
> >>     char *chrom = row[0];
> >>     unsigned int start = lineFileNeedNum(lf, row, 1);
> >>
> >>
> >> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> >> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> >> correctly after typing 'make' in kent/src (should I be building it
> >> differently?)
> >>
> >>
> >>
> >> Now when I try to install Bio::DB::BigWig via cpan, things look like
> this:
> >>
> >> cpan
> >>
> >> cpan shell -- CPAN exploration and modules installation (v1.9600)
> >> Enter 'h' for help.
> >>
> >> cpan[1]> install Bio::DB::BigWig
> >> CPAN: Storable loaded ok (v2.25)
> >> Going to read '/homes/dbolser/.cpan/Metadata'
> >>  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> >> Running install for module 'Bio::DB::BigWig'
> >> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >> CPAN: Digest::SHA loaded ok (v5.61)
> >> CPAN: Compress::Zlib loaded ok (v2.03)
> >> Checksum for
> >> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >> ok
> >> CPAN: Archive::Tar loaded ok (v1.76)
> >> Bio-BigFile-1.05
> >> Bio-BigFile-1.05/Changes
> >> Bio-BigFile-1.05/LICENSE
> >> Bio-BigFile-1.05/DISCLAIMER
> >> Bio-BigFile-1.05/Build.PL
> >> Bio-BigFile-1.05/typemap
> >> Bio-BigFile-1.05/META.yml
> >> Bio-BigFile-1.05/README
> >> Bio-BigFile-1.05/MANIFEST
> >> Bio-BigFile-1.05/ExampleData
> >> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> >> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> >> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> >> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> >> Bio-BigFile-1.05/bin
> >> Bio-BigFile-1.05/bin/bigWigToWig.pl
> >> Bio-BigFile-1.05/bin/wigToBigWig.pl
> >> Bio-BigFile-1.05/bin/index_bigwigset.pl
> >> Bio-BigFile-1.05/lib
> >> Bio-BigFile-1.05/lib/Bio
> >> Bio-BigFile-1.05/lib/Bio/DB
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> >> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> >> Bio-BigFile-1.05/t
> >> Bio-BigFile-1.05/t/02.bigbed.t
> >> Bio-BigFile-1.05/t/03.bigwig_high.t
> >> Bio-BigFile-1.05/t/04.bigbed_high.t
> >> Bio-BigFile-1.05/t/05.bigwig_set.t
> >> /bin/tar: Read 9216 bytes from -
> >> Bio-BigFile-1.05/t/01.bigwig.t
> >> Bio-BigFile-1.05/patches
> >> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> >> CPAN: File::Temp loaded ok (v0.22)
> >> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> >> CPAN: CPAN::Meta loaded ok (v2.110580)
> >> CPAN: Module::CoreList loaded ok (v2.46)
> >> CPAN: Time::HiRes loaded ok (v1.9717)
> >>
> >>  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >>
> >>
> >> This module requires the compiled jkweb.a library from Jim Kent's source
> >> tree.
> >> If you haven't already done so, please download the source from
> >> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build
> the
> >> contents of the "kent/src/lib" subdirectory as directed in the README.
> >> Then
> >> enter the location of the "kent/src" subdirectory at the prompt below.
> >> To prevent
> >> this message from appearing in the future, set the environment
> >> variable KENT_SRC
> >> to point to the "kent/src" subdirectory.
> >>
> >> Please enter the location of Kent source tree:
> >> /homes/dbolser/build/src/kent/src
> >>
> >> Created MYMETA.yml and MYMETA.json
> >> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> >> Building Bio-BigFile
> >> gcc -I/homes/dbolser/build/src/kent/src/inc
> >> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> >> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> >> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> >> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> >> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> >> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> >> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> >> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> >> lib/Bio/DB/BigFile.c
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> >> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> >> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> >> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> >> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> >> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> >> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> >> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> >> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> >> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
> >>
> >>
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> >> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> >> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> >> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> >> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> >> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
> >>  LDS/Bio-BigFile-1.05.tar.gz
> >>  ./Build -- OK
> >> CPAN: YAML loaded ok (v0.72)
> >> Running Build test
> >> t/01.bigwig.t ....... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at t/01.bigwig.t line 28
> >> Compilation failed in require at t/01.bigwig.t line 28.
> >> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> >> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 29/29 subtests
> >> t/02.bigbed.t ....... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at t/02.bigbed.t line 28
> >> Compilation failed in require at t/02.bigbed.t line 28.
> >> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> >> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 15/15 subtests
> >> t/03.bigwig_high.t .. Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at t/03.bigwig_high.t line 28.
> >> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> >> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 32/32 subtests
> >> t/04.bigbed_high.t .. Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> >> line 7.
> >> Compilation failed in require at t/04.bigbed_high.t line 28.
> >> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> >> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 35/35 subtests
> >> t/05.bigwig_set.t ... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> >> line 177.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> >> line 177.
> >> Compilation failed in require at t/05.bigwig_set.t line 19.
> >> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> >> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> >> No subtests run
> >>
> >> Test Summary Report
> >> -------------------
> >> t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 29 tests but ran 0.
> >> t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> >> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 32 tests but ran 0.
> >> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 35 tests but ran 0.
> >> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: No plan found in TAP output
> >> Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
> >> 0.11 csys =  1.09 CPU)
> >> Result: FAIL
> >> Failed 5/5 test programs. 0/0 subtests failed.
> >>  LDS/Bio-BigFile-1.05.tar.gz
> >>  ./Build test -- NOT OK
> >> //hint// to see the cpan-testers results for installing this module,
> try:
> >>  reports LDS/Bio-BigFile-1.05.tar.gz
> >> Running Build install
> >>  make test had returned bad status, won't install without force
> >> Failed during this command:
> >>  LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO
> >>
> >> cpan[2]>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Any hints?
> >>
> >> Cheers,
> >> Dan.
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
> > --
> > Lincoln D. Stein
> > Director, Informatics and Biocomputing Platform
> > Ontario Institute for Cancer Research
> > 101 College St., Suite 800
> > Toronto, ON, Canada M5G0A3
> > 416 673-8514
> > Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> >
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>



From lincoln.stein at gmail.com  Tue Mar 29 09:59:22 2011
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Tue, 29 Mar 2011 09:59:22 -0400
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
	<AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>
Message-ID: <AANLkTi=Jrw3adAgigbAeG_-KT4VqLBsPBE08x_NQyOHD@mail.gmail.com>

I'll release a new version with a fixed Build.PL and README today.

Lincoln

On Tue, Mar 29, 2011 at 4:57 AM, Dan Bolser <dan.bolser at gmail.com> wrote:

> On 28 March 2011 22:26, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> > Hi Dan,
> > There are two problems that I can see. One is a series of compiler
> warnings
> > when compiling the Perl .XS interface file. These are likely nothing to
> > worry about, but I should fix them. What versions of Perl and gcc do you
> > have installed? I don't see them when I compile on my system.
>
> gcc --version # gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
> perl --version # v5.8.8 built for i386-linux-thread-multi
>
> uname -a # Linux cricket 2.6.18-194.32.1.el5PAE #1 SMP Wed Jan 5
> 18:43:13 EST 2011 i686 i686 i386 GNU/Linux
>
>
>
> I got kent from git and built it with the following commands:
>
> cd kent/src/lib/
> echo $MACHTYPE # i686-redhat-linux-gnu
> export MACHTYPE=i686
> make
> cd ../
> export KENT_SRC=`pwd`
>
> # NOTE, both $MACHTYPE and $KENT_SRC should be defined here
> cpan -i Bio::DB::BigWig # FAILS AS DESCRIBED
>
> cd /tmp
> wget
> http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> tar zxfv Bio-BigFile-1.05.tar.gz
> cd Bio-BigFile-1.05
> # PATCH  Build.PL AS DESCRIBED (add -lssl after -lz)
> perl Build.PL
> ./Build # SEE WARNINGS AS BEFORE
> ./Build test # Files=5, Tests=135, Result: PASS
> ./Build install
>
>
> Note, above I didn't patch kent to include -fPIC as suggested
> previously. I don't see any noticeable difference if I do on this
> arch.
>
> It would be good if the instructions above could make it into the
> Bio::DB::BigWig README, as a few people have expressed confusion about
> the exact steps (the README in kent is a bit confusing, and mostly
> unnecessary for the purposes of building Bio::DB::BigWig).
>
>
> > The second issue is that the SSL library is not being linked in.
> Previously
> > there was no dependency on SSL, but Jim may recently have added this to
> the
> > BigWig library in order to allow it to read bigwig files from https
> servers.
> > I see that you added a -lssl to Build.PL; does this make the tests work
> > again?
>
> Yup, when I add -lssl to Build.PL (as per the previous diff), the
> tests pass, but I still see the warnings.
>
> I'm sure I saw the warnings disappear when I was playing with
> different versions of Bio::DB::BigWig, but now they occur without
> fail... if you pardon the pun.
>
> I have a seeking suspicion that it's related to my perl 'build kit'...
> However, since I'm not sure what module versions to report, and since
> you promised to fix these issues anyway, I won't dig into it.
>
>
> Thanks for help, and thanks for the support on
> irc://irc.freenode.net/#bioperl, without which I would have probably
> give up!
>
> Cheers,
> Dan.
>
> > Lincoln
> >
> > On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com>
> wrote:
> >>
> >> Hello,
> >>
> >> I'm trying to get Bio::DB::BigWig installed again, this time on a
> >> different box.
> >>
> >> I installed kent from git as described here:
> >> http://genome.ucsc.edu/admin/git.html
> >>
> >>
> >> I made the following changes, similar to those described previously:
> >>
> >> git diff
> >> diff --git a/src/inc/common.mk b/src/inc/common.mk
> >> index c7fc557..5187901 100644
> >> --- a/src/inc/common.mk
> >> +++ b/src/inc/common.mk
> >> @@ -3,7 +3,7 @@ CC=gcc
> >>  ifeq (${COPT},)
> >>     COPT=-O -g
> >>  endif
> >> -CFLAGS=
> >> +CFLAGS=-fPIC
> >>  HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> >> -DMACHTYPE_${MACHTYPE}
> >>  HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> >> -I../../../../../inc
> >>
> >> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> index fa2292b..acb97d2 100644
> >> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
> >>     /* Parse current line. */
> >>     wordCount = chopLine(line, row);
> >>     if (wordCount == ArraySize(row))
> >> -         errAbort("Too many fields (%d max is %lu) line %d of %s",
> >> wordCount, ArraySize(row),
> >> +         errAbort("Too many fields (%d max is %u) line %d of %s",
> >> wordCount, ArraySize(row),
> >>             lf->lineIx, lf->fileName);
> >>     char *chrom = row[0];
> >>     unsigned int start = lineFileNeedNum(lf, row, 1);
> >>
> >>
> >> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> >> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> >> correctly after typing 'make' in kent/src (should I be building it
> >> differently?)
> >>
> >>
> >>
> >> Now when I try to install Bio::DB::BigWig via cpan, things look like
> this:
> >>
> >> cpan
> >>
> >> cpan shell -- CPAN exploration and modules installation (v1.9600)
> >> Enter 'h' for help.
> >>
> >> cpan[1]> install Bio::DB::BigWig
> >> CPAN: Storable loaded ok (v2.25)
> >> Going to read '/homes/dbolser/.cpan/Metadata'
> >>  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> >> Running install for module 'Bio::DB::BigWig'
> >> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >> CPAN: Digest::SHA loaded ok (v5.61)
> >> CPAN: Compress::Zlib loaded ok (v2.03)
> >> Checksum for
> >> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >> ok
> >> CPAN: Archive::Tar loaded ok (v1.76)
> >> Bio-BigFile-1.05
> >> Bio-BigFile-1.05/Changes
> >> Bio-BigFile-1.05/LICENSE
> >> Bio-BigFile-1.05/DISCLAIMER
> >> Bio-BigFile-1.05/Build.PL
> >> Bio-BigFile-1.05/typemap
> >> Bio-BigFile-1.05/META.yml
> >> Bio-BigFile-1.05/README
> >> Bio-BigFile-1.05/MANIFEST
> >> Bio-BigFile-1.05/ExampleData
> >> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> >> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> >> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> >> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> >> Bio-BigFile-1.05/bin
> >> Bio-BigFile-1.05/bin/bigWigToWig.pl
> >> Bio-BigFile-1.05/bin/wigToBigWig.pl
> >> Bio-BigFile-1.05/bin/index_bigwigset.pl
> >> Bio-BigFile-1.05/lib
> >> Bio-BigFile-1.05/lib/Bio
> >> Bio-BigFile-1.05/lib/Bio/DB
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> >> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> >> Bio-BigFile-1.05/t
> >> Bio-BigFile-1.05/t/02.bigbed.t
> >> Bio-BigFile-1.05/t/03.bigwig_high.t
> >> Bio-BigFile-1.05/t/04.bigbed_high.t
> >> Bio-BigFile-1.05/t/05.bigwig_set.t
> >> /bin/tar: Read 9216 bytes from -
> >> Bio-BigFile-1.05/t/01.bigwig.t
> >> Bio-BigFile-1.05/patches
> >> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> >> CPAN: File::Temp loaded ok (v0.22)
> >> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> >> CPAN: CPAN::Meta loaded ok (v2.110580)
> >> CPAN: Module::CoreList loaded ok (v2.46)
> >> CPAN: Time::HiRes loaded ok (v1.9717)
> >>
> >>  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >>
> >>
> >> This module requires the compiled jkweb.a library from Jim Kent's source
> >> tree.
> >> If you haven't already done so, please download the source from
> >> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build
> the
> >> contents of the "kent/src/lib" subdirectory as directed in the README.
> >> Then
> >> enter the location of the "kent/src" subdirectory at the prompt below.
> >> To prevent
> >> this message from appearing in the future, set the environment
> >> variable KENT_SRC
> >> to point to the "kent/src" subdirectory.
> >>
> >> Please enter the location of Kent source tree:
> >> /homes/dbolser/build/src/kent/src
> >>
> >> Created MYMETA.yml and MYMETA.json
> >> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> >> Building Bio-BigFile
> >> gcc -I/homes/dbolser/build/src/kent/src/inc
> >> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> >> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> >> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> >> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> >> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> >> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> >> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> >> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> >> lib/Bio/DB/BigFile.c
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> >> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> >> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> >> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> >> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> >> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> >> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> >> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> >> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> >> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
> >>
> >>
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> >> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> >> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> >> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> >> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> >> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
> >>  LDS/Bio-BigFile-1.05.tar.gz
> >>  ./Build -- OK
> >> CPAN: YAML loaded ok (v0.72)
> >> Running Build test
> >> t/01.bigwig.t ....... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at t/01.bigwig.t line 28
> >> Compilation failed in require at t/01.bigwig.t line 28.
> >> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> >> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 29/29 subtests
> >> t/02.bigbed.t ....... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at t/02.bigbed.t line 28
> >> Compilation failed in require at t/02.bigbed.t line 28.
> >> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> >> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 15/15 subtests
> >> t/03.bigwig_high.t .. Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at t/03.bigwig_high.t line 28.
> >> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> >> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 32/32 subtests
> >> t/04.bigbed_high.t .. Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> >> line 7.
> >> Compilation failed in require at t/04.bigbed_high.t line 28.
> >> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> >> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 35/35 subtests
> >> t/05.bigwig_set.t ... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> >> line 177.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> >> line 177.
> >> Compilation failed in require at t/05.bigwig_set.t line 19.
> >> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> >> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> >> No subtests run
> >>
> >> Test Summary Report
> >> -------------------
> >> t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 29 tests but ran 0.
> >> t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> >> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 32 tests but ran 0.
> >> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 35 tests but ran 0.
> >> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: No plan found in TAP output
> >> Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
> >> 0.11 csys =  1.09 CPU)
> >> Result: FAIL
> >> Failed 5/5 test programs. 0/0 subtests failed.
> >>  LDS/Bio-BigFile-1.05.tar.gz
> >>  ./Build test -- NOT OK
> >> //hint// to see the cpan-testers results for installing this module,
> try:
> >>  reports LDS/Bio-BigFile-1.05.tar.gz
> >> Running Build install
> >>  make test had returned bad status, won't install without force
> >> Failed during this command:
> >>  LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO
> >>
> >> cpan[2]>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Any hints?
> >>
> >> Cheers,
> >> Dan.
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
> > --
> > Lincoln D. Stein
> > Director, Informatics and Biocomputing Platform
> > Ontario Institute for Cancer Research
> > 101 College St., Suite 800
> > Toronto, ON, Canada M5G0A3
> > 416 673-8514
> > Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> >
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>



From ravimbt at gmail.com  Mon Mar 28 05:56:58 2011
From: ravimbt at gmail.com (=?UTF-8?B?wrbigKLil4/guYvigKLgrofgrrDgrrXgrr/Rj86xzr3OueKXj+C5i+KAouKAosK2?=)
Date: Mon, 28 Mar 2011 15:26:58 +0530
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
Message-ID: <AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>

Hi Dave,

Thank you very much. It is working. I got the program code from the
following link.

http://www.bioperl.org/Core/Latest/bptutorial.html

I spent so much time on browsing, downloading and installing programs and
packages. But, it seems like the code error is the reason it dint work.
Thanks Dave.

Could you please give me the link to join this forum to see other
discussions, which would be more helpful to me? Please let me know if you
have any suggestion for me to keep learning the bioperl.

With regards,
Ravi.

2011/3/28 Dave Messina <David.Messina at sbc.su.se>

> Hi Ravi,
>
> Please make sure to "Reply All" so that everyone on the mailing list can
> follow (and add to) the discussion.
>
> If you read the first line of the exception, you'll see it states what the
> error is:
> "WebDBSeqI Error ? check query sequences!"
>
> You'd have no way of knowing this, but that ID and database combination is
> not functioning anymore, so that's why in this case you're getting an error.
> Please try using the example in the tutorial here:
>
>
> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>
> which has been updated to a different ID which should work.
>
> Sorry for the confusion! So that we can prevent other people from having
> the same issue, could you tell me where you got that example code?
>
> Dave
>
>
>
>
>
>
> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>
>> Hi Dave,
>>
>> Thanks a lot for your reply. It is really helpful. Please find the
>> screenshot after making the change you pointed out. But I am getting
>> "Exception: Bio::Root::Exception" error. I think I have to set the
>> environment variables but I am not sure how to do that. Could you please
>> guide me on this too.
>>
>> I can go to the "Environment Variable" Window in my pc. But I dont know
>> what to enter once I click "New" on that window.
>>
>> Thanks in advance.
>>
>> With regards,
>> Ravi.
>>
>>
>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>
>>> Hi Ravi,
>>>
>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>> not Bio::Seq. So your first line
>>>
>>> use Bio::Seq;
>>>
>>> should be replaced with
>>>
>>> use Bio::Perl;
>>>
>>>
>>> More examples in the BioPerl Tutorial here:
>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>
>>>
>>> Dve
>>>
>>>
>>>
>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>
>>>> Hi,
>>>>
>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>> packages
>>>> using ppm on windows 7? Please find the attachment for the error message
>>>> I
>>>> get. I would really appreciate if you help me fix this issue.
>>>>
>>>> Thanks,
>>>>
>>>> With regards,
>>>> Ravi.
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>>
>>
>



From rmb32 at cornell.edu  Tue Mar 29 17:20:41 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Tue, 29 Mar 2011 14:20:41 -0700
Subject: [Bioperl-l] Announcing OBF Summer of Code - please forward!
Message-ID: <4D924D29.3020707@cornell.edu>

Hi all,

Here's an advertising-ready announcement for OBF's Summer of Code, 
thanks to Christian Zmasek and Hilmar Lapp for their excellent writing.

Student applications are due April 8!  Please spread it widely, we need 
to reach lots of students with it!

Rob Buels
OBF GSoC 2011 Admin


============================================================

*** Please disseminate widely at your local institutions ***
*** including posting to message and job boards, so that ***
*** we reach as many students as possible.               ***

============================================================


OPEN BIOINFORMATICS FOUNDATION SUMMER OF CODE 2011

Applications due 19:00 UTC, April 8, 2010.
http://www.open-bio.org/wiki/Google_Summer_of_Code

The Open Bioinformatics Foundation Summer of Code program provides a 
unique opportunity for undergraduate, masters, and PhD students to 
obtain hands-on experience writing and extending open-source software 
for bioinformatics under the mentorship of experienced developers from 
around the world. The program is the participation of the Open 
Bioinformatics Foundation (OBF) as a mentoring organization in the 
Google Summer of Code(tm) (http://code.google.com/soc/).

Students successfully completing the 3 month program receive a $5,000 
USD stipend, and may work entirely from their home or home institution. 
  Participation is open to students from any country in the world except 
countries subject to US trade restrictions.  Each student will have at 
least one dedicated mentor to show them the ropes and help them complete 
their project.

The Open Bioinformatics Foundation is particularly seeking students 
interested in both bioinformatics (computational biology) and software 
development. Some initial project ideas are listed on the website. These 
range from Galaxy phylogenetics pipeline development in Biopython to 
lightweight sequence objects and lazy parsing in BioPerl, a DAS Server 
for large files on local filesystems, and mapping Java libraries to 
Perl/Ruby/Python using Biolib+SWIG+JNI.  All project ideas are flexible 
and many can be adjusted in scope to match the skills of the student. We 
also welcome and encourage students proposing their own project ideas; 
historically some of the most successful Summer of Code projects are 
ones proposed by the students themselves.

TO APPLY: Apply online at the Google Summer of Code website 
(http://socghop.appspot.com/), where you will also find GSoC program 
rules and eligibility requirements. The 12-day application period for 
students runs from Monday, March 28 through Friday, April 8th, 2011.

INQUIRIES:

We strongly encourage all interested students to get in touch with us 
with their ideas as early on as possible.  See the OBF GSoC page for 
contact details.

2011 OBF Summer of Code:
http://www.open-bio.org/wiki/Google_Summer_of_Code

Google Summer of Code FAQ:
http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs





From cjfields at illinois.edu  Wed Mar 30 09:58:00 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 30 Mar 2011 08:58:00 -0500
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
Message-ID: <9EDCB97E-3256-476C-AA40-EDE27BF96033@illinois.edu>

Ravi,

You can sign up for the email list here:

http://lists.open-bio.org/mailman/listinfo/bioperl-l

Once you are signed up, you should be able to post questions.

chris

On Mar 28, 2011, at 4:56 AM, ?????????????????? wrote:

> Hi Dave,
> 
> Thank you very much. It is working. I got the program code from the
> following link.
> 
> http://www.bioperl.org/Core/Latest/bptutorial.html
> 
> I spent so much time on browsing, downloading and installing programs and
> packages. But, it seems like the code error is the reason it dint work.
> Thanks Dave.
> 
> Could you please give me the link to join this forum to see other
> discussions, which would be more helpful to me? Please let me know if you
> have any suggestion for me to keep learning the bioperl.
> 
> With regards,
> Ravi.
> 
> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
> 
>> Hi Ravi,
>> 
>> Please make sure to "Reply All" so that everyone on the mailing list can
>> follow (and add to) the discussion.
>> 
>> If you read the first line of the exception, you'll see it states what the
>> error is:
>> "WebDBSeqI Error ? check query sequences!"
>> 
>> You'd have no way of knowing this, but that ID and database combination is
>> not functioning anymore, so that's why in this case you're getting an error.
>> Please try using the example in the tutorial here:
>> 
>> 
>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>> 
>> which has been updated to a different ID which should work.
>> 
>> Sorry for the confusion! So that we can prevent other people from having
>> the same issue, could you tell me where you got that example code?
>> 
>> Dave
>> 
>> 
>> 
>> 
>> 
>> 
>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>> 
>>> Hi Dave,
>>> 
>>> Thanks a lot for your reply. It is really helpful. Please find the
>>> screenshot after making the change you pointed out. But I am getting
>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>> environment variables but I am not sure how to do that. Could you please
>>> guide me on this too.
>>> 
>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>> what to enter once I click "New" on that window.
>>> 
>>> Thanks in advance.
>>> 
>>> With regards,
>>> Ravi.
>>> 
>>> 
>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>> 
>>>> Hi Ravi,
>>>> 
>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>> not Bio::Seq. So your first line
>>>> 
>>>> use Bio::Seq;
>>>> 
>>>> should be replaced with
>>>> 
>>>> use Bio::Perl;
>>>> 
>>>> 
>>>> More examples in the BioPerl Tutorial here:
>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>> 
>>>> 
>>>> Dve
>>>> 
>>>> 
>>>> 
>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>> 
>>>>> Hi,
>>>>> 
>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>> packages
>>>>> using ppm on windows 7? Please find the attachment for the error message
>>>>> I
>>>>> get. I would really appreciate if you help me fix this issue.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> With regards,
>>>>> Ravi.
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> 
>>>> 
>>>> 
>>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From dvadell at clustering.com.ar  Wed Mar 30 10:51:38 2011
From: dvadell at clustering.com.ar (Diego M. Vadell)
Date: Wed, 30 Mar 2011 11:51:38 -0300
Subject: [Bioperl-l] Newbie alert: Aligning and printing first position
Message-ID: <201103301151.38752.dvadell@clustering.com.ar>

Hi list,

    I have an alignment ( done with Bio::Tools::Run::Alignment::Clustalw ) 
that I can see ( printing $aln->match_line() along with the sequences ):

        ********* .:                                   (match_line)
.......TDDSFDTDVSSS.........[...].............   ($seq1)
SDKIIHLTDDSFDTDVLKADGA[...]EFLDANLA   ($seq2)

    It looks right ( that "[...]" is mine, it's larger ). Now I want to get 
the position of the match ( the first "T" ), which should be "7". I thought I 
needed to use something like:

my $seq = $aln->get_seq_by_pos(1);
my $loc = $seq->location_from_column(1);
say $loc;

And $loc would be 7, but it's undef. If I try to iterate from 1 to 10, I start 
getting Bio::Location::Simple objects at the 8th place. So, should I loop 
untill I location_from_column() gives me an object? Is it another way of 
finding the position of the match?

As you can see, I'm just starting with bioinformatics. Any pointer will be 
appreciated.

Thanks in advance,
 -- Diego 


From joshearl1 at hotmail.com  Wed Mar 30 11:23:21 2011
From: joshearl1 at hotmail.com (Josh Earl)
Date: Wed, 30 Mar 2011 11:23:21 -0400
Subject: [Bioperl-l] Difficulty downloading biosql schema
Message-ID: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>


Hello all,

I'm trying to download the schema for biosql, however, when I run the command:
svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql-schema

(as per the instructions @ https://github.com/biosql/biosql/blob/master/INSTALL)
I either get no response, or it times out.  I've tried this a couple of times, the last time was a few weeks ago.  Anyone know what's going on?

Here's an example error:
svn: Can't connect to host 'code.open-bio.org': Connection timed out

thanks,
~josh

Center for Genomic Sciences
(412)-359-8341

 		 	   		  


From hlapp at drycafe.net  Wed Mar 30 11:52:22 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 30 Mar 2011 11:52:22 -0400
Subject: [Bioperl-l] Difficulty downloading biosql schema
In-Reply-To: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
References: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
Message-ID: <4C1B95A9-0480-4B9B-91E2-1D35BCB568B4@drycafe.net>

(moving this to BioSQL list)
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From cjfields at illinois.edu  Wed Mar 30 11:54:00 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 30 Mar 2011 10:54:00 -0500
Subject: [Bioperl-l] Difficulty downloading biosql schema
In-Reply-To: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
References: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
Message-ID: <87CBA000-B964-40DA-BF35-BC229CF24BB6@illinois.edu>

BioSQL moved to github a while back:

https://github.com/biosql/biosql

(this might be better asked on the biosql-l list, which I've cc'd)

chris

On Mar 30, 2011, at 10:23 AM, Josh Earl wrote:

> 
> Hello all,
> 
> I'm trying to download the schema for biosql, however, when I run the command:
> svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql-schema
> 
> (as per the instructions @ https://github.com/biosql/biosql/blob/master/INSTALL)
> I either get no response, or it times out.  I've tried this a couple of times, the last time was a few weeks ago.  Anyone know what's going on?
> 
> Here's an example error:
> svn: Can't connect to host 'code.open-bio.org': Connection timed out
> 
> thanks,
> ~josh
> 
> Center for Genomic Sciences
> (412)-359-8341
> 
> 		 	   		  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From p.j.a.cock at googlemail.com  Wed Mar 30 11:55:49 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 30 Mar 2011 16:55:49 +0100
Subject: [Bioperl-l] Difficulty downloading biosql schema
In-Reply-To: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
References: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
Message-ID: <AANLkTi=v80WkLtJxiDu1MBLoyKD0RTR5eBhmb4NF5zO7@mail.gmail.com>

On Wed, Mar 30, 2011 at 4:23 PM, Josh Earl <joshearl1 at hotmail.com> wrote:
>
> Hello all,
>
> I'm trying to download the schema for biosql, however, when I run the command:
> svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql-schema
>
> (as per the instructions @ https://github.com/biosql/biosql/blob/master/INSTALL)
> I either get no response, or it times out. ?I've tried this a couple of times, the last
> time was a few weeks ago. ?Anyone know what's going on?
>
> Here's an example error:
> svn: Can't connect to host 'code.open-bio.org': Connection timed out
>
> thanks,
> ~josh

Hi Josh

First the code.open-bio.org has been having trouble and is being rebuilt.
Even if it did work, it would give you an out of date copy prior to the move
from SVN to git.

Secondly, the instructions you pointed to are out of date, we'll have to
fix that. Just use git:

git clone git://github.com/biosql/biosql.git

Thanks for the heads up!

Peter

P.S. There is a dedicated BioSQL mailing list.



From roy.chaudhuri at gmail.com  Wed Mar 30 11:43:35 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Wed, 30 Mar 2011 16:43:35 +0100
Subject: [Bioperl-l] Newbie alert: Aligning and printing first position
In-Reply-To: <201103301151.38752.dvadell@clustering.com.ar>
References: <201103301151.38752.dvadell@clustering.com.ar>
Message-ID: <4D934FA7.2080206@gmail.com>

Hi Diego,

Column refers to the position in the alignment, not the individual 
sequence. location_from_column therefore gives the position in the 
individual sequence that corresponds to the requested column (you get 
undef since there is a gap in the first column of the alignment for 
seq1). If I understand correctly, you want the reverse, the position in 
the alignment that corresponds to the first position in your sequence. 
For that you need the opposite function, column_from_residue_number:

my $loc=$seq->column_from_residue_number(1);

$loc will now contain 8 (not 7), since position 1 of your sequence is in 
column 8 of the alignment.

Hope this helps,
Roy.

On 30/03/2011 15:51, Diego M. Vadell wrote:
> Hi list,
>
>      I have an alignment ( done with Bio::Tools::Run::Alignment::Clustalw )
> that I can see ( printing $aln->match_line() along with the sequences ):
>
>          ********* .:                                   (match_line)
> .......TDDSFDTDVSSS.........[...].............   ($seq1)
> SDKIIHLTDDSFDTDVLKADGA[...]EFLDANLA   ($seq2)
>
>      It looks right ( that "[...]" is mine, it's larger ). Now I want to get
> the position of the match ( the first "T" ), which should be "7". I thought I
> needed to use something like:
>
> my $seq = $aln->get_seq_by_pos(1);
> my $loc = $seq->location_from_column(1);
> say $loc;
>
> And $loc would be 7, but it's undef. If I try to iterate from 1 to 10, I start
> getting Bio::Location::Simple objects at the 8th place. So, should I loop
> untill I location_from_column() gives me an object? Is it another way of
> finding the position of the match?
>
> As you can see, I'm just starting with bioinformatics. Any pointer will be
> appreciated.
>
> Thanks in advance,
>   -- Diego
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From zheboyang at gmail.com  Thu Mar 31 08:28:53 2011
From: zheboyang at gmail.com (boyang zhe)
Date: Thu, 31 Mar 2011 14:28:53 +0200
Subject: [Bioperl-l] blast best hit
Message-ID: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>

Hi,

I just want to parse the blast results ,and get the best hit.

One way is to parse the results as usual, then get the first hit and exit
the loop.

I checked the bioperl document, and find that there is a method
best_hit_only in Bio::SearchIO::blast.pm.
But it only return 1/0. So my question is how to use this method to get the
best hit.

Thank you very much!

Boyang


From dvadell at clustering.com.ar  Thu Mar 31 08:59:46 2011
From: dvadell at clustering.com.ar (Diego M. Vadell)
Date: Thu, 31 Mar 2011 09:59:46 -0300
Subject: [Bioperl-l] Newbie alert: Aligning and printing first position
In-Reply-To: <4D934FA7.2080206@gmail.com>
References: <201103301151.38752.dvadell@clustering.com.ar>
	<4D934FA7.2080206@gmail.com>
Message-ID: <201103311000.36567.dvadell@clustering.com.ar>

Hi Roy,

  Thanks!! I can't beleive I didn't see that method in the documentation. 
Thank you very much. It worked perfectly.

Cheers,
 -- Diego

On Wednesday, March 30, 2011 12:43:35 pm Roy Chaudhuri wrote:
> Hi Diego,
> 
> Column refers to the position in the alignment, not the individual
> sequence. location_from_column therefore gives the position in the
> individual sequence that corresponds to the requested column (you get
> undef since there is a gap in the first column of the alignment for
> seq1). If I understand correctly, you want the reverse, the position in
> the alignment that corresponds to the first position in your sequence.
> For that you need the opposite function, column_from_residue_number:
> 
> my $loc=$seq->column_from_residue_number(1);
> 
> $loc will now contain 8 (not 7), since position 1 of your sequence is in
> column 8 of the alignment.
> 
> Hope this helps,
> Roy.
> 
> On 30/03/2011 15:51, Diego M. Vadell wrote:
> > Hi list,
> > 
> >      I have an alignment ( done with Bio::Tools::Run::Alignment::Clustalw
> >      )
> > 
> > that I can see ( printing $aln->match_line() along with the sequences ):
> >          ********* .:                                   (match_line)
> > 
> > .......TDDSFDTDVSSS.........[...].............   ($seq1)
> > SDKIIHLTDDSFDTDVLKADGA[...]EFLDANLA   ($seq2)
> > 
> >      It looks right ( that "[...]" is mine, it's larger ). Now I want to
> >      get
> > 
> > the position of the match ( the first "T" ), which should be "7". I
> > thought I needed to use something like:
> > 
> > my $seq = $aln->get_seq_by_pos(1);
> > my $loc = $seq->location_from_column(1);
> > say $loc;
> > 
> > And $loc would be 7, but it's undef. If I try to iterate from 1 to 10, I
> > start getting Bio::Location::Simple objects at the 8th place. So, should
> > I loop untill I location_from_column() gives me an object? Is it another
> > way of finding the position of the match?
> > 
> > As you can see, I'm just starting with bioinformatics. Any pointer will
> > be appreciated.
> > 
> > Thanks in advance,
> > 
> >   -- Diego
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l


From bosborne11 at verizon.net  Thu Mar 31 09:04:22 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Thu, 31 Mar 2011 09:04:22 -0400
Subject: [Bioperl-l] blast best hit
In-Reply-To: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
References: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
Message-ID: <A29F9EB5-BEC6-4DF3-924F-F8F98F96C6F1@verizon.net>

Boyang,

You can sort the hits, by any criterion you want:

my @hits = $result->hits;
@hits = sort { $a-> bits <=> $b->bits } @hits;

BIO

On Mar 31, 2011, at 8:28 AM, boyang zhe wrote:

> Hi,
> 
> I just want to parse the blast results ,and get the best hit.
> 
> One way is to parse the results as usual, then get the first hit and exit
> the loop.
> 
> I checked the bioperl document, and find that there is a method
> best_hit_only in Bio::SearchIO::blast.pm.
> But it only return 1/0. So my question is how to use this method to get the
> best hit.
> 
> Thank you very much!
> 
> Boyang
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jordi.durban at gmail.com  Thu Mar 31 10:23:54 2011
From: jordi.durban at gmail.com (Jordi Durban)
Date: Thu, 31 Mar 2011 16:23:54 +0200
Subject: [Bioperl-l] blast best hit
In-Reply-To: <A29F9EB5-BEC6-4DF3-924F-F8F98F96C6F1@verizon.net>
References: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
	<A29F9EB5-BEC6-4DF3-924F-F8F98F96C6F1@verizon.net>
Message-ID: <AANLkTimiAanHL89eJ3uKgnGXKbcbJh+jBmw6MRs1VC1t@mail.gmail.com>

Hi,
I did a pair of scripts to parse a blastxml report. I'd like know your
opinion.
First I obtained a file with tab separated results (whatever you want) from
the blast results according to some Bioperl modules as SearchIO. That is:
hit_name    query_name    e-value    score
hit_name    query-name   e-value     score
.
.

Then, I parse that file as an array where:
foreach my $line ($array[0]){ ###### best hit
        next if $seen {$line}++; ##### non-repeated lines
        push @unique , $line[1]; ### best hit outcome in a new array
       }

I hope this helps and I look forward some opinions.






2011/3/31 Brian Osborne <bosborne11 at verizon.net>

> Boyang,
>
> You can sort the hits, by any criterion you want:
>
> my @hits = $result->hits;
> @hits = sort { $a-> bits <=> $b->bits } @hits;
>
> BIO
>
> On Mar 31, 2011, at 8:28 AM, boyang zhe wrote:
>
> > Hi,
> >
> > I just want to parse the blast results ,and get the best hit.
> >
> > One way is to parse the results as usual, then get the first hit and exit
> > the loop.
> >
> > I checked the bioperl document, and find that there is a method
> > best_hit_only in Bio::SearchIO::blast.pm.
> > But it only return 1/0. So my question is how to use this method to get
> the
> > best hit.
> >
> > Thank you very much!
> >
> > Boyang
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Jordi


From fs5 at sanger.ac.uk  Thu Mar 31 10:23:33 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 31 Mar 2011 15:23:33 +0100
Subject: [Bioperl-l] blast best hit
In-Reply-To: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
References: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
Message-ID: <1301581413.12411.188.camel@deskpro15336.internal.sanger.ac.uk>

Yes, best_hit_only is a boolean that can be set to true if you only want
one hit to be returned from the stream of hits (the best hit). I have
never actualyl used this one but you shoud be able to set it in the
constructor as in:
my $blast = Bio::SearchIO->new( ...., -best_hit_only => 1 )



Frank

On Thu, 2011-03-31 at 14:28 +0200, boyang zhe wrote:
> Hi,
> 
> I just want to parse the blast results ,and get the best hit.
> 
> One way is to parse the results as usual, then get the first hit and exit
> the loop.
> 
> I checked the bioperl document, and find that there is a method
> best_hit_only in Bio::SearchIO::blast.pm.
> But it only return 1/0. So my question is how to use this method to get the
> best hit.
> 
> Thank you very much!
> 
> Boyang
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From fs5 at sanger.ac.uk  Thu Mar 31 11:06:41 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 31 Mar 2011 16:06:41 +0100
Subject: [Bioperl-l] blast best hit
In-Reply-To: <AANLkTimXj+D8VQO_Mb4vpgfadXqFfgD1dHQL+fwCMsX5@mail.gmail.com>
References: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
	<1301581413.12411.188.camel@deskpro15336.internal.sanger.ac.uk>
	<AANLkTimXj+D8VQO_Mb4vpgfadXqFfgD1dHQL+fwCMsX5@mail.gmail.com>
Message-ID: <1301584001.12411.202.camel@deskpro15336.internal.sanger.ac.uk>

Hi Boyang,

With best_hit_only set to "true" (as you have done now) you should be
able to use the usual way of parsing the BLAST report with 

while (my $result = $blast_io->next_result) {
  my $hit = $result->next_hit;
  ... (do something with the hit)
}

Because there should be only one hit now. 'best_hit_only' is a flag, an
indicator that tells the parser to limit the output to the best hit. It
does not itself return any hits.

Even if you used the 

while (my $hit=$result->next_hit){..

inner loop (as in the BioPerl HOWTOs) you should now only ever get one
hit retunred from that loop, which is the best hit for the result. I
haven't tried this but it should work.

Personally, I'd not use this option and rather sort or filter the hits
because tomorrow you might want to find out what the next best hit
actually was and how close the e-values and bits were or something like
that. 

Hope this helps,

Frank


On Thu, 2011-03-31 at 16:43 +0200, boyang zhe wrote:
> I try this at the constructor
> 
> my $blast_io = Bio::SearchIO->new(-file => 'test', -format => 'blast',
> -best_hit_only => 1);
> 
> What I need to do in the following steps? It seems that setting
> best_hit_only or not does not change the way of blast parser working.
> 
> In my opinion, if we can use it as a similar way following, it will be
> much better.
> 
> my $blast_io = Bio::SearchIO->new(-file => 'test', -format => 'blast',
> -best_hit_only => 1);
> 
> while (my $blast_result = $blast_io->next_result()) {
>       my $best_hit = $blast_result->best_hit_only();  # just assume it
> working here; in fact, it does not work
>       my $best_hit_name = $best_hit->name();
>       ...................................
> }
> 
> thank you !
> 
> On Thu, Mar 31, 2011 at 4:23 PM, Frank Schwach <fs5 at sanger.ac.uk>
> wrote:
>         Yes, best_hit_only is a boolean that can be set to true if you
>         only want
>         one hit to be returned from the stream of hits (the best hit).
>         I have
>         never actualyl used this one but you shoud be able to set it
>         in the
>         constructor as in:
>         my $blast = Bio::SearchIO->new( ...., -best_hit_only => 1 )
>         
>         
>         
>         Frank
>         
>         
>         On Thu, 2011-03-31 at 14:28 +0200, boyang zhe wrote:
>         > Hi,
>         >
>         > I just want to parse the blast results ,and get the best
>         hit.
>         >
>         > One way is to parse the results as usual, then get the first
>         hit and exit
>         > the loop.
>         >
>         > I checked the bioperl document, and find that there is a
>         method
>         > best_hit_only in Bio::SearchIO::blast.pm.
>         > But it only return 1/0. So my question is how to use this
>         method to get the
>         > best hit.
>         >
>         > Thank you very much!
>         >
>         > Boyang
>         
>         
>         > _______________________________________________
>         > Bioperl-l mailing list
>         > Bioperl-l at lists.open-bio.org
>         > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>         
>         
>         
>         
>         --
>          The Wellcome Trust Sanger Institute is operated by Genome
>         Research
>          Limited, a charity registered in England with number 1021457
>         and a
>          company registered in England with number 2742969, whose
>         registered
>          office is 215 Euston Road, London, NW1 2BE.
> 



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From suy at big.ac.cn  Thu Mar 31 03:24:55 2011
From: suy at big.ac.cn (suy)
Date: Thu, 31 Mar 2011 15:24:55 +0800
Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
Message-ID: <201103311524549534382@big.ac.cn>

I want to use Bio::Tools::HMM, but I can not find it in bioperl 1.6.1. Could anyone tell me how to do it ? 

2011-03-31 



suy 


From cjfields at illinois.edu  Thu Mar 31 13:01:13 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 31 Mar 2011 12:01:13 -0500
Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
In-Reply-To: <201103311524549534382@big.ac.cn>
References: <201103311524549534382@big.ac.cn>
Message-ID: <93E13DE0-5888-4B5C-AC9D-F68623D0D891@illinois.edu>

It's now in it's own distribution, along with the related C code.  See:

https://github.com/bioperl/Bio-Tools-HMM

It hasn't been released to CPAN yet, and (IIRC) it may be failing some tests.

chris

On Mar 31, 2011, at 2:24 AM, suy wrote:

> I want to use Bio::Tools::HMM, but I can not find it in bioperl 1.6.1. Could anyone tell me how to do it ? 
> 
> 2011-03-31 
> 
> 
> 
> suy 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From David.Messina at sbc.su.se  Thu Mar 31 13:07:54 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 31 Mar 2011 19:07:54 +0200
Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
In-Reply-To: <201103311524549534382@big.ac.cn>
References: <201103311524549534382@big.ac.cn>
Message-ID: <AANLkTin2qe1V=2swW1qd8O=s8eQTi5p1LDHc-=sViKPT@mail.gmail.com>

It's distributed separately from BioPerl now. You can get it here:

https://github.com/bioperl/Bio-Tools-HMM


Dave



On Thu, Mar 31, 2011 at 09:24, suy <suy at big.ac.cn> wrote:

> I want to use Bio::Tools::HMM, but I can not find it in bioperl 1.6.1.
> Could anyone tell me how to do it ?
>
> 2011-03-31
>
>
>
> suy
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From Kevin.M.Brown at asu.edu  Thu Mar 31 14:22:06 2011
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Thu, 31 Mar 2011 11:22:06 -0700
Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
In-Reply-To: <201103311524549534382@big.ac.cn>
References: <201103311524549534382@big.ac.cn>
Message-ID: <1A4207F8295607498283FE9E93B775B40781779B@EX02.asurite.ad.asu.edu>

https://github.com/bioperl/Bio-Tools-HMM

"moved Bio::Tools::HMM and Bio::Ext::HMM into their own distro, got them
compiling cleanly. tests not passing yet
svn path=/Bio-Tools-HMM/trunk/; revision=15966"

Kevin Brown
Center for Innovations in Medicine
Biodesign Institute
Arizona State University 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of suy
> Sent: Thursday, March 31, 2011 12:25 AM
> To: bioperl-l
> Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
> 
> I want to use Bio::Tools::HMM, but I can not find it in bioperl 1.6.1.
> Could anyone tell me how to do it ?
> 
> 2011-03-31
> 
> 
> 
> suy
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From David.Messina at sbc.su.se  Thu Mar 31 15:43:14 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 31 Mar 2011 21:43:14 +0200
Subject: [Bioperl-l] Old docs cleanup (was Re: Bioperl installation doubt)
Message-ID: <AANLkTikzx+iP6ws0CpwEEA2USiLwYVHTHjZU8KO+3vMo@mail.gmail.com>

Hi,

Just to clarify:

Brian, is it okay with you if I go ahead and remove the Core/ directory from
the website? (and okay with everyone else, too, for that matter? I haven't
heard any nays so far.)


Dave



On Tue, Mar 29, 2011 at 00:40, Chris Fields <cjfields at illinois.edu> wrote:

> Brian,
>
> I think this was started:
>
> http://www.bioperl.org/wiki/Bptutorial.pl
>
> It certainly could be cleaned up, organized, and updated (that and the
> FAQ).  Makes sense to have it as a HOWTO or maybe split it into several
> HOWTOs.  Maybe even combine it with the beginner's HOWTO into various
> sections?
>
> chris
>
> On Mar 28, 2011, at 3:43 PM, Brian Osborne wrote:
>
> > Chris,
> >
> > I'll get started on dissembling bptutorial. There's certainly useful text
> in there but there's also duplicated or outdated material. Looks like there
> are 3 options for any given section:
> >
> > - put it into an existing HOWTO
> > - make it into a new HOWTO
> > - delete it
> >
> > BIO
> >
> > On Mar 28, 2011, at 9:27 AM, Chris Fields wrote:
> >
> >> Dave,
> >>
> >> +1 on removing old docs to prevent confusion.  Or, alternatively, +1 to
> syncing those to current docs (though I think decreasing the replication
> effort in keeping docs up-to-date is probably the best tact).
> >>
> >> chris
> >>
> >> On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:
> >>
> >>>>
> >>>> Thank you very much. It is working. I got the program code from the
> >>>> following link.
> >>>>
> >>>> http://www.bioperl.org/Core/Latest/bptutorial.html
> >>>
> >>>
> >>> Aha, okay. You got there from Google, I guess? That is *way* out of
> date.
> >>>
> >>> To the other core devs, in order to prevent this confusion in the
> future,
> >>> I'd like to delete the Core/ directory from our website since it's been
> >>> superseded at this point by other docs and is not current. I intend to
> put
> >>> up a ticket at Redmine, but I will wait a bit before doing so to allow
> time
> >>> for people to see this and comment ? please do speak up if there's good
> >>> reason to keep it.
> >>>
> >>>
> >>> Could you please give me the link to join this forum to see other
> >>>> discussions, which would be more helpful to me?
> >>>>
> >>>
> >>> Sure, you can sign up for the mailing list here:
> >>>
> >>> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
> >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>>
> >>> And the archives are also searchable:
> >>>
> >>>  http://news.gmane.org/gmane.comp.lang.perl.bio.general
> >>>
> >>>
> >>> Please let me know if you have any suggestion for me to keep learning
> the
> >>>> bioperl.
> >>>
> >>>
> >>> I would also suggest reading the (current) tutorial and HOWTOs at
> >>> www.bioperl.org . Lots of good links on the main page there,
> particularly
> >>> under the Documentation heading.
> >>>
> >>>
> >>> Dave
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>> With regards,
> >>>> Ravi.
> >>>>
> >>>>
> >>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
> >>>>
> >>>>> Hi Ravi,
> >>>>>
> >>>>> Please make sure to "Reply All" so that everyone on the mailing list
> can
> >>>>> follow (and add to) the discussion.
> >>>>>
> >>>>> If you read the first line of the exception, you'll see it states
> what the
> >>>>> error is:
> >>>>> "WebDBSeqI Error ? check query sequences!"
> >>>>>
> >>>>> You'd have no way of knowing this, but that ID and database
> combination is
> >>>>> not functioning anymore, so that's why in this case you're getting an
> error.
> >>>>> Please try using the example in the tutorial here:
> >>>>>
> >>>>>
> >>>>>
> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
> >>>>>
> >>>>> which has been updated to a different ID which should work.
> >>>>>
> >>>>> Sorry for the confusion! So that we can prevent other people from
> having
> >>>>> the same issue, could you tell me where you got that example code?
> >>>>>
> >>>>> Dave
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
> >>>>>
> >>>>>> Hi Dave,
> >>>>>>
> >>>>>> Thanks a lot for your reply. It is really helpful. Please find the
> >>>>>> screenshot after making the change you pointed out. But I am getting
> >>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
> >>>>>> environment variables but I am not sure how to do that. Could you
> please
> >>>>>> guide me on this too.
> >>>>>>
> >>>>>> I can go to the "Environment Variable" Window in my pc. But I dont
> know
> >>>>>> what to enter once I click "New" on that window.
> >>>>>>
> >>>>>> Thanks in advance.
> >>>>>>
> >>>>>> With regards,
> >>>>>> Ravi.
> >>>>>>
> >>>>>>
> >>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
> >>>>>>
> >>>>>>> Hi Ravi,
> >>>>>>>
> >>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl
> module,
> >>>>>>> not Bio::Seq. So your first line
> >>>>>>>
> >>>>>>> use Bio::Seq;
> >>>>>>>
> >>>>>>> should be replaced with
> >>>>>>>
> >>>>>>> use Bio::Perl;
> >>>>>>>
> >>>>>>>
> >>>>>>> More examples in the BioPerl Tutorial here:
> >>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
> >>>>>>>
> >>>>>>>
> >>>>>>> Dve
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
> >>>>>>>
> >>>>>>>> Hi,
> >>>>>>>>
> >>>>>>>> Could you please help me installing bioperl-db, bioperl-run &
> other
> >>>>>>>> packages
> >>>>>>>> using ppm on windows 7? Please find the attachment for the error
> >>>>>>>> message I
> >>>>>>>> get. I would really appreciate if you help me fix this issue.
> >>>>>>>>
> >>>>>>>> Thanks,
> >>>>>>>>
> >>>>>>>> With regards,
> >>>>>>>> Ravi.
> >>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> Bioperl-l mailing list
> >>>>>>>> Bioperl-l at lists.open-bio.org
> >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>



From cjfields at illinois.edu  Thu Mar 31 15:49:08 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 31 Mar 2011 14:49:08 -0500
Subject: [Bioperl-l] Old docs cleanup (was Re: Bioperl installation
	doubt)
In-Reply-To: <AANLkTikzx+iP6ws0CpwEEA2USiLwYVHTHjZU8KO+3vMo@mail.gmail.com>
References: <AANLkTikzx+iP6ws0CpwEEA2USiLwYVHTHjZU8KO+3vMo@mail.gmail.com>
Message-ID: <1D3D2910-F1F9-40A1-9A39-656D3DF17847@illinois.edu>

+1 from me.  Go ahead.  Old misleading documentation is bad to have around.

chris

On Mar 31, 2011, at 2:43 PM, Dave Messina wrote:

> Hi,
> 
> Just to clarify:
> 
> Brian, is it okay with you if I go ahead and remove the Core/ directory from
> the website? (and okay with everyone else, too, for that matter? I haven't
> heard any nays so far.)
> 
> 
> Dave
> 
> 
> 
> On Tue, Mar 29, 2011 at 00:40, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Brian,
>> 
>> I think this was started:
>> 
>> http://www.bioperl.org/wiki/Bptutorial.pl
>> 
>> It certainly could be cleaned up, organized, and updated (that and the
>> FAQ).  Makes sense to have it as a HOWTO or maybe split it into several
>> HOWTOs.  Maybe even combine it with the beginner's HOWTO into various
>> sections?
>> 
>> chris
>> 
>> On Mar 28, 2011, at 3:43 PM, Brian Osborne wrote:
>> 
>>> Chris,
>>> 
>>> I'll get started on dissembling bptutorial. There's certainly useful text
>> in there but there's also duplicated or outdated material. Looks like there
>> are 3 options for any given section:
>>> 
>>> - put it into an existing HOWTO
>>> - make it into a new HOWTO
>>> - delete it
>>> 
>>> BIO
>>> 
>>> On Mar 28, 2011, at 9:27 AM, Chris Fields wrote:
>>> 
>>>> Dave,
>>>> 
>>>> +1 on removing old docs to prevent confusion.  Or, alternatively, +1 to
>> syncing those to current docs (though I think decreasing the replication
>> effort in keeping docs up-to-date is probably the best tact).
>>>> 
>>>> chris
>>>> 
>>>> On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:
>>>> 
>>>>>> 
>>>>>> Thank you very much. It is working. I got the program code from the
>>>>>> following link.
>>>>>> 
>>>>>> http://www.bioperl.org/Core/Latest/bptutorial.html
>>>>> 
>>>>> 
>>>>> Aha, okay. You got there from Google, I guess? That is *way* out of
>> date.
>>>>> 
>>>>> To the other core devs, in order to prevent this confusion in the
>> future,
>>>>> I'd like to delete the Core/ directory from our website since it's been
>>>>> superseded at this point by other docs and is not current. I intend to
>> put
>>>>> up a ticket at Redmine, but I will wait a bit before doing so to allow
>> time
>>>>> for people to see this and comment ? please do speak up if there's good
>>>>> reason to keep it.
>>>>> 
>>>>> 
>>>>> Could you please give me the link to join this forum to see other
>>>>>> discussions, which would be more helpful to me?
>>>>>> 
>>>>> 
>>>>> Sure, you can sign up for the mailing list here:
>>>>> 
>>>>> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> 
>>>>> 
>>>>> And the archives are also searchable:
>>>>> 
>>>>> http://news.gmane.org/gmane.comp.lang.perl.bio.general
>>>>> 
>>>>> 
>>>>> Please let me know if you have any suggestion for me to keep learning
>> the
>>>>>> bioperl.
>>>>> 
>>>>> 
>>>>> I would also suggest reading the (current) tutorial and HOWTOs at
>>>>> www.bioperl.org . Lots of good links on the main page there,
>> particularly
>>>>> under the Documentation heading.
>>>>> 
>>>>> 
>>>>> Dave
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> With regards,
>>>>>> Ravi.
>>>>>> 
>>>>>> 
>>>>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>>>>>> 
>>>>>>> Hi Ravi,
>>>>>>> 
>>>>>>> Please make sure to "Reply All" so that everyone on the mailing list
>> can
>>>>>>> follow (and add to) the discussion.
>>>>>>> 
>>>>>>> If you read the first line of the exception, you'll see it states
>> what the
>>>>>>> error is:
>>>>>>> "WebDBSeqI Error ? check query sequences!"
>>>>>>> 
>>>>>>> You'd have no way of knowing this, but that ID and database
>> combination is
>>>>>>> not functioning anymore, so that's why in this case you're getting an
>> error.
>>>>>>> Please try using the example in the tutorial here:
>>>>>>> 
>>>>>>> 
>>>>>>> 
>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>>>>>> 
>>>>>>> which has been updated to a different ID which should work.
>>>>>>> 
>>>>>>> Sorry for the confusion! So that we can prevent other people from
>> having
>>>>>>> the same issue, could you tell me where you got that example code?
>>>>>>> 
>>>>>>> Dave
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>>>>>> 
>>>>>>>> Hi Dave,
>>>>>>>> 
>>>>>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>>>>>> screenshot after making the change you pointed out. But I am getting
>>>>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>>>>>> environment variables but I am not sure how to do that. Could you
>> please
>>>>>>>> guide me on this too.
>>>>>>>> 
>>>>>>>> I can go to the "Environment Variable" Window in my pc. But I dont
>> know
>>>>>>>> what to enter once I click "New" on that window.
>>>>>>>> 
>>>>>>>> Thanks in advance.
>>>>>>>> 
>>>>>>>> With regards,
>>>>>>>> Ravi.
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>>>>>> 
>>>>>>>>> Hi Ravi,
>>>>>>>>> 
>>>>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl
>> module,
>>>>>>>>> not Bio::Seq. So your first line
>>>>>>>>> 
>>>>>>>>> use Bio::Seq;
>>>>>>>>> 
>>>>>>>>> should be replaced with
>>>>>>>>> 
>>>>>>>>> use Bio::Perl;
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> More examples in the BioPerl Tutorial here:
>>>>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> Dve
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>>>>>> 
>>>>>>>>>> Hi,
>>>>>>>>>> 
>>>>>>>>>> Could you please help me installing bioperl-db, bioperl-run &
>> other
>>>>>>>>>> packages
>>>>>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>>>>>> message I
>>>>>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>>>>>> 
>>>>>>>>>> Thanks,
>>>>>>>>>> 
>>>>>>>>>> With regards,
>>>>>>>>>> Ravi.
>>>>>>>>>> 
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Bioperl-l mailing list
>>>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From rmb32 at cornell.edu  Thu Mar 31 17:58:52 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 31 Mar 2011 14:58:52 -0700
Subject: [Bioperl-l] Reminder: GSoC proposals due in 1 week
Message-ID: <4D94F91C.1080005@cornell.edu>

Hi all,

Just a reminder, Google Summer of Code student applications are due April 8!

If you're a student planning to apply to GSoC with OBF, it's very much 
in your best interest to write your proposal *early*, like now, and get 
it into the hands of the developers and mentors on your subproject 
(BioPerl/Ruby/Python/etc) so that they can give you some feedback on it.

The final proposals must, of course, still be submitted to Google 
through the GSoC web application, as described on the main GSoC site 
(http://www.google-melange.com/gsoc/homepage/google/gsoc2011).

Rob Buels
OBF GSoC 2011 Administrator




From rmb32 at cornell.edu  Thu Mar 31 18:04:49 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 31 Mar 2011 15:04:49 -0700
Subject: [Bioperl-l] GSoC call for mentors
Message-ID: <4D94FA81.5090701@cornell.edu>

Hi all,

For current developers on OBF projects:

If you would not mind being a mentor to a Summer of Code student this 
summer, please make sure you sign up as an OBF mentor in the GSoC web 
app.  There's a link under "mentors: apply now!" midway down the page at 
http://www.google-melange.com/.  If you didn't do last year's summer of 
code, it would be a good idea to drop me an email introducing yourself, 
as well, or I won't know whether to approve your request. :-)

Being signed up as an OBF GSoC mentor will give you access to the 
student proposals, as they come in, and the ability to comment on them 
and assign scores to the ones you think show the most promise.

If you sign up as a mentor, please also add yourself to the two OBF GSoC 
mailing lists: OBF-GSoC and OBF-GSoC-mentors

OBF-GSoC list: http://lists.open-bio.org/mailman/listinfo/gsoc
OBF mentors:   http://lists.open-bio.org/mailman/listinfo/gsoc-mentors


Thanks in advance!

Rob

---
Robert Buels
OBF GSoC 2011 Administrator



From zuz17 at psu.edu  Thu Mar 31 18:18:59 2011
From: zuz17 at psu.edu (Zhenguo Zhang)
Date: Thu, 31 Mar 2011 18:18:59 -0400
Subject: [Bioperl-l] FW: How to specify color for each feature in a track?
In-Reply-To: 1301604855l.1593384l.0l@psu.edu
References: <1301604855l.1593384l.0l@psu.edu>
Message-ID: <1301609939l.901330l.0l@psu.edu>

Dear Dr. Stein,

Sorry for interruption. I found the problems, I used
$f->get_tag_values('color'); to return the tag value, it is not correct. The
list context should be provided. It is my mistake. Thanks.

Best wishes!

Zhenguo

---------------- Forwarded Message ----------------
From: "Zhenguo Zhang" <zuz17 at psu.edu>
Date: Thu, Mar 31, 2011 04:54 PM
Subject: How to specify color for each feature in a track?
To: lstein at cshl.edu, bioperl-l at lists.open-bio.org

Dear Dr. Stein,

I am using your excellent module Bio::Graphics for
programming to show protein domains. I want to put all the domains for a
sequence into one track, and give each domain (one feature here) one designated
color. The following is the cold to add_track:


 75        
$panel->add_track($seq,
 78                 -glyph    =>  'segments',
 81                 -bgcolor  => sub {
 82                     my $f = shift;
 87                     return $f->get_tag_values('color');
 88                 },
 89                 -fgcolor  => 'black',
 90                 -font2color => 'red',
 91                 -key      => "$seq",
 92                 -label    => 1,
 93                 -bump     => +1,
 94                 -height   => 8,
 95                 -description => 1,
 96 #               -part_label_merge => 1
 97                 );

Here $seq is an array reference, each element being one domain feature. I
specify the -bgcolor based on the tag 'color'  defined when domain feature was
constructed. However, it does not work. All the domains in all sequences show
the same color. Based on the document, the -glyph can be changed by calling
back the anonymous functions (I have not tried this). The color might be
changed in a similar way. Thank you in advance!

Best regards!

Zhenguo

**************************************************************
Zhenguo Zhang
Postdoctoral Scholar
Institute of Molecular Evolutionary Genetics
Penn State University
312 Mueller Lab
University Park, PA 16802
Tel: 814-865-2796
Homepage: <http://www.personal.psu.edu/zuz17/>
Lab page:  <http://homes.bio.psu.edu/people/Faculty/Nei/>




**************************************************************
Zhenguo Zhang
Postdoctoral Scholar
Institute of Molecular Evolutionary Genetics
Penn State University
312 Mueller Lab
University Park, PA 16802
Tel: 814-865-2796
Homepage: <http://www.personal.psu.edu/zuz17/>
Lab page:  <http://homes.bio.psu.edu/people/Faculty/Nei/>





From scott at scottcain.net  Thu Mar 31 19:13:06 2011
From: scott at scottcain.net (Scott Cain)
Date: Thu, 31 Mar 2011 19:13:06 -0400
Subject: [Bioperl-l] git help
Message-ID: <AANLkTin9BRdaSY_p-5rKSCFvpUr+rfCSZ8hjVTgyhxC5@mail.gmail.com>

Hi all,

I just want to know if it is safe for me to commit.  Here is what git
said to me:

scott-cains-macbook-pro:bioperl-live cain$ git commit
# On branch master
# Your branch is behind 'origin/master' by 47 commits, and can be
fast-forwarded.
#
# Changed but not updated:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#	modified:   Bio/DB/GFF.pm
#	modified:   Bio/FeatureIO/gff.pm
#	modified:   scripts/Bio-DB-GFF/bulk_load_gff.PLS
#	modified:   scripts/Bio-DB-GFF/fast_load_gff.PLS
#	modified:   t/SeqFeature/FeatureIO.t
#	modified:   t/data/knownGene.gff3
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#	scripts/Bio-DB-GFF/genbank2gff3.diff
no changes added to commit (use "git add" and/or "git commit -a")
----------------------

so should I do a git commit -a?

Also, when I try a git pull, this is what it tells me:

scott-cains-macbook-pro:bioperl-live cain$ git pull
Updating 1c2cf24..d5de022
error: Your local changes to 'Bio/FeatureIO/gff.pm' would be
overwritten by merge.  Aborting.
Please, commit your changes or stash them before you can merge.

Thanks,
Scott



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From dan.kortschak at adelaide.edu.au  Thu Mar 31 19:24:25 2011
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Fri, 01 Apr 2011 09:54:25 +1030
Subject: [Bioperl-l] BEDTools.pm update
Message-ID: <1301613865.3334.35.camel@sueno>

Hi All,

I have completed a revision of the BEDTools module that makes use of the
v2.10.1 BEDTools additions, including the ability to read GFF and VCF
file formats.

Because of the interactions between CommandExts/Config and the way
BEDTools executables can receive input files, I have had to change the
parameter names for a number of the filespecs from -bed* to -bvg* (for
BED/GFF/VCF). The alternative, though possible was much more involved
for little gain in my view.

This change will break BEDTools.pm-using scripts that use the -bed[12]?
filespecs (except for those wrapping genomeCoverageBed which cannot read
bgv and so which see no change).

I just wanted to get an idea if this is going to be a significant
problem for people before I push the changes to bioperl-run.

cheers
Dan



From scott at scottcain.net  Thu Mar 31 20:19:33 2011
From: scott at scottcain.net (Scott Cain)
Date: Thu, 31 Mar 2011 20:19:33 -0400
Subject: [Bioperl-l] git help
In-Reply-To: <AANLkTin9BRdaSY_p-5rKSCFvpUr+rfCSZ8hjVTgyhxC5@mail.gmail.com>
References: <AANLkTin9BRdaSY_p-5rKSCFvpUr+rfCSZ8hjVTgyhxC5@mail.gmail.com>
Message-ID: <AANLkTimaOpkH1+S3Yn-14uLj+OVy5T=PBH3KGPi6gjnN@mail.gmail.com>

I just went a head and:

  git commit -a
  git pull --rebase
  git push

as suggested by rbuels.  That appeared to work.

Scott


On Thu, Mar 31, 2011 at 7:13 PM, Scott Cain <scott at scottcain.net> wrote:
> Hi all,
>
> I just want to know if it is safe for me to commit. ?Here is what git
> said to me:
>
> scott-cains-macbook-pro:bioperl-live cain$ git commit
> # On branch master
> # Your branch is behind 'origin/master' by 47 commits, and can be
> fast-forwarded.
> #
> # Changed but not updated:
> # ? (use "git add <file>..." to update what will be committed)
> # ? (use "git checkout -- <file>..." to discard changes in working directory)
> #
> # ? ? ? modified: ? Bio/DB/GFF.pm
> # ? ? ? modified: ? Bio/FeatureIO/gff.pm
> # ? ? ? modified: ? scripts/Bio-DB-GFF/bulk_load_gff.PLS
> # ? ? ? modified: ? scripts/Bio-DB-GFF/fast_load_gff.PLS
> # ? ? ? modified: ? t/SeqFeature/FeatureIO.t
> # ? ? ? modified: ? t/data/knownGene.gff3
> #
> # Untracked files:
> # ? (use "git add <file>..." to include in what will be committed)
> #
> # ? ? ? scripts/Bio-DB-GFF/genbank2gff3.diff
> no changes added to commit (use "git add" and/or "git commit -a")
> ----------------------
>
> so should I do a git commit -a?
>
> Also, when I try a git pull, this is what it tells me:
>
> scott-cains-macbook-pro:bioperl-live cain$ git pull
> Updating 1c2cf24..d5de022
> error: Your local changes to 'Bio/FeatureIO/gff.pm' would be
> overwritten by merge. ?Aborting.
> Please, commit your changes or stash them before you can merge.
>
> Thanks,
> Scott
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
> Ontario Institute for Cancer Research
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From cjfields at illinois.edu  Thu Mar 31 20:43:33 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 31 Mar 2011 19:43:33 -0500
Subject: [Bioperl-l] BEDTools.pm update
In-Reply-To: <1301613865.3334.35.camel@sueno>
References: <1301613865.3334.35.camel@sueno>
Message-ID: <557CDC9D-E16D-4DF2-A27A-1DFD7092A926@illinois.edu>

I would say push away, I don't think this will be a problem. 

chris

On Mar 31, 2011, at 6:24 PM, Dan Kortschak wrote:

> Hi All,
> 
> I have completed a revision of the BEDTools module that makes use of the
> v2.10.1 BEDTools additions, including the ability to read GFF and VCF
> file formats.
> 
> Because of the interactions between CommandExts/Config and the way
> BEDTools executables can receive input files, I have had to change the
> parameter names for a number of the filespecs from -bed* to -bvg* (for
> BED/GFF/VCF). The alternative, though possible was much more involved
> for little gain in my view.
> 
> This change will break BEDTools.pm-using scripts that use the -bed[12]?
> filespecs (except for those wrapping genomeCoverageBed which cannot read
> bgv and so which see no change).
> 
> I just wanted to get an idea if this is going to be a significant
> problem for people before I push the changes to bioperl-run.
> 
> cheers
> Dan
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Thu Mar 31 20:44:38 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 31 Mar 2011 19:44:38 -0500
Subject: [Bioperl-l] git help
In-Reply-To: <AANLkTimaOpkH1+S3Yn-14uLj+OVy5T=PBH3KGPi6gjnN@mail.gmail.com>
References: <AANLkTin9BRdaSY_p-5rKSCFvpUr+rfCSZ8hjVTgyhxC5@mail.gmail.com>
	<AANLkTimaOpkH1+S3Yn-14uLj+OVy5T=PBH3KGPi6gjnN@mail.gmail.com>
Message-ID: <27E55B19-4795-4F41-88DC-824CC9A9C3C4@illinois.edu>

Yep, that's generally the way to do it, though you sometimes have to be careful with the '--rebase' if there are changes in the same code (I think git will catch this if it occurs).

chris

On Mar 31, 2011, at 7:19 PM, Scott Cain wrote:

> I just went a head and:
> 
>  git commit -a
>  git pull --rebase
>  git push
> 
> as suggested by rbuels.  That appeared to work.
> 
> Scott
> 
> 
> On Thu, Mar 31, 2011 at 7:13 PM, Scott Cain <scott at scottcain.net> wrote:
>> Hi all,
>> 
>> I just want to know if it is safe for me to commit.  Here is what git
>> said to me:
>> 
>> scott-cains-macbook-pro:bioperl-live cain$ git commit
>> # On branch master
>> # Your branch is behind 'origin/master' by 47 commits, and can be
>> fast-forwarded.
>> #
>> # Changed but not updated:
>> #   (use "git add <file>..." to update what will be committed)
>> #   (use "git checkout -- <file>..." to discard changes in working directory)
>> #
>> #       modified:   Bio/DB/GFF.pm
>> #       modified:   Bio/FeatureIO/gff.pm
>> #       modified:   scripts/Bio-DB-GFF/bulk_load_gff.PLS
>> #       modified:   scripts/Bio-DB-GFF/fast_load_gff.PLS
>> #       modified:   t/SeqFeature/FeatureIO.t
>> #       modified:   t/data/knownGene.gff3
>> #
>> # Untracked files:
>> #   (use "git add <file>..." to include in what will be committed)
>> #
>> #       scripts/Bio-DB-GFF/genbank2gff3.diff
>> no changes added to commit (use "git add" and/or "git commit -a")
>> ----------------------
>> 
>> so should I do a git commit -a?
>> 
>> Also, when I try a git pull, this is what it tells me:
>> 
>> scott-cains-macbook-pro:bioperl-live cain$ git pull
>> Updating 1c2cf24..d5de022
>> error: Your local changes to 'Bio/FeatureIO/gff.pm' would be
>> overwritten by merge.  Aborting.
>> Please, commit your changes or stash them before you can merge.
>> 
>> Thanks,
>> Scott
>> 
>> 
>> 
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Thu Mar 31 20:47:49 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 31 Mar 2011 19:47:49 -0500
Subject: [Bioperl-l] git help
In-Reply-To: <AANLkTimaOpkH1+S3Yn-14uLj+OVy5T=PBH3KGPi6gjnN@mail.gmail.com>
References: <AANLkTin9BRdaSY_p-5rKSCFvpUr+rfCSZ8hjVTgyhxC5@mail.gmail.com>
	<AANLkTimaOpkH1+S3Yn-14uLj+OVy5T=PBH3KGPi6gjnN@mail.gmail.com>
Message-ID: <9E536349-3EA4-43FC-B4C9-665BC81D68F8@illinois.edu>

Also, forgot to mention but we've moved FeatureIO out to it's own repo to reorganize it somewhat, so I'll likely migrate your changes over there.  We're eschewing Bio::SeqFeature::Annotated for simpler features and a few other bits that should allow for more flexibility in the future.  

chris

On Mar 31, 2011, at 7:19 PM, Scott Cain wrote:

> I just went a head and:
> 
>  git commit -a
>  git pull --rebase
>  git push
> 
> as suggested by rbuels.  That appeared to work.
> 
> Scott
> 
> 
> On Thu, Mar 31, 2011 at 7:13 PM, Scott Cain <scott at scottcain.net> wrote:
>> Hi all,
>> 
>> I just want to know if it is safe for me to commit.  Here is what git
>> said to me:
>> 
>> scott-cains-macbook-pro:bioperl-live cain$ git commit
>> # On branch master
>> # Your branch is behind 'origin/master' by 47 commits, and can be
>> fast-forwarded.
>> #
>> # Changed but not updated:
>> #   (use "git add <file>..." to update what will be committed)
>> #   (use "git checkout -- <file>..." to discard changes in working directory)
>> #
>> #       modified:   Bio/DB/GFF.pm
>> #       modified:   Bio/FeatureIO/gff.pm
>> #       modified:   scripts/Bio-DB-GFF/bulk_load_gff.PLS
>> #       modified:   scripts/Bio-DB-GFF/fast_load_gff.PLS
>> #       modified:   t/SeqFeature/FeatureIO.t
>> #       modified:   t/data/knownGene.gff3
>> #
>> # Untracked files:
>> #   (use "git add <file>..." to include in what will be committed)
>> #
>> #       scripts/Bio-DB-GFF/genbank2gff3.diff
>> no changes added to commit (use "git add" and/or "git commit -a")
>> ----------------------
>> 
>> so should I do a git commit -a?
>> 
>> Also, when I try a git pull, this is what it tells me:
>> 
>> scott-cains-macbook-pro:bioperl-live cain$ git pull
>> Updating 1c2cf24..d5de022
>> error: Your local changes to 'Bio/FeatureIO/gff.pm' would be
>> overwritten by merge.  Aborting.
>> Please, commit your changes or stash them before you can merge.
>> 
>> Thanks,
>> Scott
>> 
>> 
>> 
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From armendarez77 at hotmail.com  Thu Mar 31 20:45:11 2011
From: armendarez77 at hotmail.com (Veronica A.)
Date: Thu, 31 Mar 2011 17:45:11 -0700
Subject: [Bioperl-l] StandAloneBlastPlus Question
Message-ID: <BLU156-w251B5A50D1CFF47EE8CA4ED2BE0@phx.gbl>





Hello,

I'm trying to create a Perl script using StandAloneBlastPlus that can either create a new database or update it with new FASTA sequences.  However, I can only find information on the creation of a new database.  I've checked the information on doc.bioperl.org but a lot of the Methods don't have descriptions yet.


Is it possible to use StandAloneBlastPlus or is there another/a better way?

Thank you,

Veronica




 		 	   		  


From zuz17 at psu.edu  Thu Mar 31 16:54:15 2011
From: zuz17 at psu.edu (Zhenguo Zhang)
Date: Thu, 31 Mar 2011 16:54:15 -0400
Subject: [Bioperl-l] How to specify color for each feature in a track?
Message-ID: <1301604855l.1593384l.0l@psu.edu>

Dear Dr. Stein,

I am using your excellent module Bio::Graphics for programming to show protein
domains. I want to put all the domains for a sequence into one track, and give
each domain (one feature here) one designated color. The following is the cold
to add_track: 

 75         $panel->add_track($seq,
 78                 -glyph    =>  'segments',
 81                 -bgcolor  => sub {
 82                     my $f = shift;
 87                     return $f->get_tag_values('color');
 88                 },
 89                 -fgcolor  => 'black',
 90                 -font2color => 'red',
 91                 -key      => "$seq",
 92                 -label    => 1,
 93                 -bump     => +1,
 94                 -height   => 8,
 95                 -description => 1,
 96 #               -part_label_merge => 1
 97                 );

Here $seq is an array reference, each element being one domain feature. I
specify the -bgcolor based on the tag 'color'  defined when domain feature was
constructed. However, it does not work. All the domains in all sequences show
the same color. Based on the document, the -glyph can be changed by calling
back the anonymous functions (I have not tried this). The color might be
changed in a similar way. Thank you in advance!

Best regards!

Zhenguo

**************************************************************
Zhenguo Zhang
Postdoctoral Scholar
Institute of Molecular Evolutionary Genetics
Penn State University
312 Mueller Lab
University Park, PA 16802
Tel: 814-865-2796
Homepage: <http://www.personal.psu.edu/zuz17/>
Lab page:  <http://homes.bio.psu.edu/people/Faculty/Nei/>





From David.Messina at sbc.su.se  Tue Mar  1 14:02:59 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 1 Mar 2011 15:02:59 +0100
Subject: [Bioperl-l] Plans for the next release (and beyond)
In-Reply-To: <11F5BA8C-D4F4-419B-870B-D4B5180F4D7D@illinois.edu>
References: <11F5BA8C-D4F4-419B-870B-D4B5180F4D7D@illinois.edu>
Message-ID: <AANLkTinSR+RwUrvTeyund+CoxDzgEEqrGP0F2RW0_666@mail.gmail.com>

Hi Chris and everyone,

The plans sound great.

My only concern would be on point 3, moving some of the wiki docs into the
distros.

- In what format would the docs be in the distros?

Would it be POD? There is rich markup (URLs, code blocks, syntax coloring,
font sizes, etc) available on the wiki that I'd hate to lose.


- Are there discordant versions now?

I agree that we shouldn't maintain separate versions of these, but I thought
the tutorial had been moved completely to the wiki a while ago, and AFAIK,
the HOWTOs are only present on the wiki. I admit, though, I haven't looked
into this extensively.


- Tying the docs to the version of the code they came with

This could be beneficial if we expect people to have a (good) reason to be
using different (read: OLD) versions of the code. But in practice we're
pretty much always going to recommend people use the latest version, right?
In which case having the docs on the wiki (in sync with the latest, greatest
version) would be fairly practical.

Even if there is a good case for supporting older versions of the code and
docs, I don't know that that's enough of an asset to outweigh the downsides
such as loss of rich formatting and having to have some POD->wiki bridge and
keep it in sync.


I raise all the above mostly to ask for more information on that part of the
plan ? I suspect you've considered most of my concerns already, so I'm quite
open to seeing a different point of view on this.


Dave








3) I would like to work on moving the HOWTO's and other relevant
> documentation (Tutorial) back into the distributions, maybe in a particular
> namespace (Bio::Manual or similar).  The reason is simple: maintaining
> possibly discordant versions of documentation is unsustainable.  We could
> possibly set up a way of converting POD->wiki for on-line documentation, but
> I would like the documentation be tied to the version of the code it comes
> with, and the only easy way to do so is to package them all together.
>



From awitney at sgul.ac.uk  Tue Mar  1 17:08:12 2011
From: awitney at sgul.ac.uk (Adam Witney)
Date: Tue, 1 Mar 2011 17:08:12 +0000
Subject: [Bioperl-l] building NGS pipeline
In-Reply-To: <0FF71A5D-F5F6-4AAD-9501-4F4911DB40D8@illinois.edu>
References: <86D567CE-1735-4D85-B40F-B67823749FB7@sgul.ac.uk>
	<AANLkTi=eU0f=GuHE=zLfLoc5LhaiHBG_A2mjmMybQeNH@mail.gmail.com>
	<0FF71A5D-F5F6-4AAD-9501-4F4911DB40D8@illinois.edu>
Message-ID: <066A6A2B-05F7-4523-8A22-A91209953BB7@sgul.ac.uk>


On 28 Feb 2011, at 15:03, Chris Fields wrote:

> On Feb 28, 2011, at 6:04 AM, Sean Davis wrote:
> 
>> On Mon, Feb 28, 2011 at 6:06 AM, Adam Witney <awitney at sgul.ac.uk> wrote:
>> 
>>> Hi,
>>> 
>>> I'm trying to put together a set of steps to runs some analysis on NGS data
>>> we have. I have found modules that wrap alignment software such as
>>> bowtie/bwa/maq, but are there any packages to calculate RPKM's etc? what are
>>> people using for this?
>>> 
>>> 
>> scripture, cufflinks/cuffdiff, bioconductor (GenomicFeatures package, for
>> example), ERANGE (wold lab), and several others.  I don't know of perl
>> wrappers for these, but they are all command-line applications, generally
>> speaking.
>> 
>> This is an interesting site to follow for RNA-seq analysis and applications:
>> 
>> http://rna-seqblog.com/
>> 
>> Sean
> 
> BioPerl does have wrappers and interfaces for some packages, particularly Lincoln's Bio::DB::Sam (samtools package) and wrappers for bowtie, tophat, and bwa.  Locally, for comparative gene expression analyses we use bioconductor (many packages to choose from) as well as the command-line tools Sean mentions.
> 
> chris 

Thanks Sean, Chris,

the bowtie/tophat/cufflinks set of tools seem to work well. I have also come across myrna also but I am still getting that setup.

Thanks again

adam




From cjfields at illinois.edu  Tue Mar  1 17:37:29 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 1 Mar 2011 11:37:29 -0600
Subject: [Bioperl-l] Plans for the next release (and beyond)
In-Reply-To: <AANLkTinSR+RwUrvTeyund+CoxDzgEEqrGP0F2RW0_666@mail.gmail.com>
References: <11F5BA8C-D4F4-419B-870B-D4B5180F4D7D@illinois.edu>
	<AANLkTinSR+RwUrvTeyund+CoxDzgEEqrGP0F2RW0_666@mail.gmail.com>
Message-ID: <90D9611F-0DFA-43A6-A3C4-65948DF3F071@illinois.edu>

On Mar 1, 2011, at 8:02 AM, Dave Messina wrote:

> Hi Chris and everyone,
> 
> The plans sound great.
> 
> My only concern would be on point 3, moving some of the wiki docs into the distros.
> 
> - In what format would the docs be in the distros?
> 
> Would it be POD? There is rich markup (URLs, code blocks, syntax coloring, font sizes, etc) available on the wiki that I'd hate to lose.

It would very likely be POD, though I believe there are POD extensions for adding additional markup in CPAN.  We wouldn't necessarily lose the wiki HOWTOs, but they would be only editable via changes to the official docs in github.  My thought is to have wiki pages tied to the latest version in github via POD->wiki, with additional markup added in for syntax highlighting, etc.  Lots of CPAN modules that could help with this, but it needs further investigation.  Might need a HOWTO unto itself :)

One other point: inclusion of docs may also allow easier implementation of inline testing, where synopsis or HOWTO code can be directly tested from POD when specific directives allow for it.  I believe Dist::Zilla has plugins for this, and of course there is Test::Inline:

http://search.cpan.org/dist/Test-Inline/lib/Test/Inline.pm

This pushes the developers a bit to make sure code examples actually pass tests.  In particular I have thought about using this with the eutils cookbook, just to catch any changes on NCBI's end, but then realized it's broadly applicable to other areas as well.  

> - Are there discordant versions now?
> 
> I agree that we shouldn't maintain separate versions of these, but I thought the tutorial had been moved completely to the wiki a while ago, and AFAIK, the HOWTOs are only present on the wiki. I admit, though, I haven't looked into this extensively.

The original intent on moving docs to the wiki was somewhat correct: we wanted dynamic documentation that could be marked up for easier reading, better annotation, etc.  Wiki markup and templates has proved more useful than simple POD (HOWTO for Bio::Graphics, for example).  

However, at least to me there seems to be a fundamental disconnect between the code being developed in one repository (github) and the documentation being maintained elsewhere (wiki).  In many cases, once docs are placed on the wiki they seem to be largely forgotten by the devs once they have reached 'completeness'.  Our focus tends to be the code itself, not the documentation.  I'm basically looking for ways to resolve that and have documentation evolve along with the code, if possible making it testable.

Lastly, access to critical documentation is now reliant on access to the wiki, which may not always be possible.  We've had several wiki outages over the years and have recently talked about (off-list) migrating some resource away from open bio servers, wikis being one due to maintenance overhead and spam.  We'll always have a centralized website of some sort, I just want to make sure that one has means to access good documentation all the time.  Installing it with the code seems the best way currently, but I'm open to suggestions.

> - Tying the docs to the version of the code they came with
> 
> This could be beneficial if we expect people to have a (good) reason to be using different (read: OLD) versions of the code. But in practice we're pretty much always going to recommend people use the latest version, right? In which case having the docs on the wiki (in sync with the latest, greatest version) would be fairly practical.

Right, I agree, and I believe the wikis should only contain a very specific version of the docs, probably either the latest CPAN release or master.  However, I'm thinking of cases where users might not be able to get the latest/greatest, perhaps b/c they are constrained in using a specific version: with Ensembl (v. 1.2.3) or via sysadmin restrictions. 

If we consistently point to the official documentation as being on the wiki, we're not tying it to any specific version (unless it's explicitly stated), only what should work with the current version.    The only history is via the edits on the wiki page, which is not associated with anything, just the edits made.  

We should be able to demonstrate via tests that code and examples released with a specific version of BioPerl, including those in the HOWTOs and the tutorial, should work with that version of the software; anything else is a documentation error or a bug.  We can't do that currently.

> Even if there is a good case for supporting older versions of the code and docs, I don't know that that's enough of an asset to outweigh the downsides such as loss of rich formatting and having to have some POD->wiki bridge and keep it in sync.

The actual process of including documentation with the code works as the archival process itself (v 1.7 docs go with v 1.7 code, v 2 with v2 code, etc).  And I think there are ways around the lack of rich formatting with POD, just need to look into it more.

> I raise all the above mostly to ask for more information on that part of the plan ? I suspect you've considered most of my concerns already, so I'm quite open to seeing a different point of view on this.
> 
> 
> Dave

I've thought about it (as you can probably tell) but I think thought is needed about how to approach it.  It might require testing things out a bit first.

chris




From moitrayee at mbu.iisc.ernet.in  Tue Mar  1 11:22:54 2011
From: moitrayee at mbu.iisc.ernet.in (moitrayee at mbu.iisc.ernet.in)
Date: Tue, 1 Mar 2011 16:52:54 +0530 (IST)
Subject: [Bioperl-l] clustering trees obtained from phylip neighbor
Message-ID: <57675.10.128.10.17.1298978574.squirrel@mbu.iisc.ernet.in>

Dear BioPerl Users/Developers,

I have obtained a tree using a very large number of nodes
(1000 nodes) using the neighbor joining in PHYLIP. A small
test output looks like the following:

  +------------------------------------------------Bovine
--6
  !    +-------------------------------------------Mouse
  +----5
       !                        +------------------Gibbon
       +------------------------4
                                !    +-------------Orang
                                +----3
                                     !   +---------Gorilla
                                     +---2
                                         ! +-------Chimp
                                         +-1
                                           +-------Human

The outtree in Newick format is:

(Bovine:0.81551,(Mouse:0.73556,(Gibbon:0.31044,(Orang:0.24003,
(Gorilla:0.16418,(Chimp:0.13460,Human:0.13460):0.02958):0.07586):0.07040):0.42512):0.07995);


I am trying to obtain the cluster at different fork level of this tree.

The fork level goes as an user input. I looked into the link

http://www.bioperl.org/wiki/HOWTO:Trees#Related_Modules

But the Node connectivity methods described there does not apply
to the tree I have pasted above.

Any help / suggestions would be thankfully appreciated.

Thanks a lot in advance and looking forward to hear from you.

Sincere Regards,
Moitrayee Bhattacharyya
Molecular Biophysics Unit,
Indian Institute of Science
Bangalore-560012
India



-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.



From lskatz at gmail.com  Wed Mar  2 14:32:24 2011
From: lskatz at gmail.com (Lee Katz)
Date: Wed, 2 Mar 2011 09:32:24 -0500
Subject: [Bioperl-l] GuessSeqFormat
Message-ID: <AANLkTi=Aa=a-gs4shAM3yxk7w=h5MVqPy0VKKhLYoDah@mail.gmail.com>

Hi,
I noticed that even though there is a GuessSeqFormat module, SeqIO and
probably other modules first rely on the extension of a filename rather than
the content.  Could the behavior be altered so that it first checks the
content of the file, and if it turns up nothing then check the file
extension?


From daniel.standage at gmail.com  Wed Mar  2 16:01:12 2011
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 2 Mar 2011 10:01:12 -0600
Subject: [Bioperl-l] BioPerl POD
Message-ID: <AANLkTi=tfUzD78O-mA0tq84sFrtsCnaN4ZYD7Y0T+xnk@mail.gmail.com>

BioPerl,

I've been writing Perl (and BioPerl) for several years now, but I have
little to know experience using POD. I've added some POD to a module I wrote
and now I am trying to create an HTML page from it. I was able to do so with
*pod2html*, but the output is...underwhelming. The docs at
http://doc.bioperl.org aren't the essence of beauty themselves, but they do
have a bit of color and really nice features (like links to the code, etc).

Which tool(s) was/were used to generate the BioPerl HTML docs?

--
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University


From cjfields at illinois.edu  Wed Mar  2 16:26:58 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 2 Mar 2011 10:26:58 -0600
Subject: [Bioperl-l] GuessSeqFormat
In-Reply-To: <AANLkTi=Aa=a-gs4shAM3yxk7w=h5MVqPy0VKKhLYoDah@mail.gmail.com>
References: <AANLkTi=Aa=a-gs4shAM3yxk7w=h5MVqPy0VKKhLYoDah@mail.gmail.com>
Message-ID: <4F41B8DA-93D6-4442-95DC-D0EA24322351@illinois.edu>

On Mar 2, 2011, at 8:32 AM, Lee Katz wrote:

> Hi,
> I noticed that even though there is a GuessSeqFormat module, SeqIO and
> probably other modules first rely on the extension of a filename rather than
> the content.  Could the behavior be altered so that it first checks the
> content of the file, and if it turns up nothing then check the file
> extension?

The current behavior is the most common use case; stipulating the format with the file extension is pretty common and a surer way to get the correct format beyond explicitly setting it.  

If you want the opposite you can manually run the file through GuessSeqFormat and then (using the guess) use SeqIO with the guessed format, but I'm curious as to why you would want this behavior.  If it's for validation, I would highly recommend NOT using that module for validation purposes...

chris




From cjfields at illinois.edu  Wed Mar  2 16:40:22 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 2 Mar 2011 10:40:22 -0600
Subject: [Bioperl-l] BioPerl POD
In-Reply-To: <AANLkTi=tfUzD78O-mA0tq84sFrtsCnaN4ZYD7Y0T+xnk@mail.gmail.com>
References: <AANLkTi=tfUzD78O-mA0tq84sFrtsCnaN4ZYD7Y0T+xnk@mail.gmail.com>
Message-ID: <26289423-6B39-418C-B16B-1CECA73B5983@illinois.edu>

pdoc, I believe, is used for the doc.bioperl.org site:

http://pdoc.sourceforge.net/

Most POD->HTML converters are simple for a reason, sites generally use CSS to deal with formatting.  You could get around that with a few tools that embed the formatting with the HTML elements (see below link for examples), but I highly suggest using CSS if possible.  

Here's a stackoverflow article on the search.cpan.org HTML output:

http://stackoverflow.com/questions/4996684/modern-pod-to-html-converter-to-produce-results-like-search-cpan-org

Also, ActiveState has another one that generates their custom HTML (pretty nice), it comes with their perl dist I think.

chris

On Mar 2, 2011, at 10:01 AM, Daniel Standage wrote:

> BioPerl,
> 
> I've been writing Perl (and BioPerl) for several years now, but I have
> little to know experience using POD. I've added some POD to a module I wrote
> and now I am trying to create an HTML page from it. I was able to do so with
> *pod2html*, but the output is...underwhelming. The docs at
> http://doc.bioperl.org aren't the essence of beauty themselves, but they do
> have a bit of color and really nice features (like links to the code, etc).
> 
> Which tool(s) was/were used to generate the BioPerl HTML docs?
> 
> --
> Daniel S. Standage
> Graduate Research Assistant
> Bioinformatics and Computational Biology Program
> Iowa State University
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From lskatz at gmail.com  Wed Mar  2 16:53:52 2011
From: lskatz at gmail.com (Lee Katz)
Date: Wed, 2 Mar 2011 11:53:52 -0500
Subject: [Bioperl-l] GuessSeqFormat
In-Reply-To: <4F41B8DA-93D6-4442-95DC-D0EA24322351@illinois.edu>
References: <AANLkTi=Aa=a-gs4shAM3yxk7w=h5MVqPy0VKKhLYoDah@mail.gmail.com>
	<4F41B8DA-93D6-4442-95DC-D0EA24322351@illinois.edu>
Message-ID: <AANLkTimNeG4+n21mAVQfN3PS10snVStD6WTwAqT1EMhm@mail.gmail.com>

>
> The current behavior is the most common use case; stipulating the format
> with the file extension is pretty common and a surer way to get the correct
> format beyond explicitly setting it.
>
> If you want the opposite you can manually run the file through
> GuessSeqFormat and then (using the guess) use SeqIO with the guessed format,
> but I'm curious as to why you would want this behavior.  If it's for
> validation, I would highly recommend NOT using that module for validation
> purposes...
>
> chris
>


I understand your reasoning that checking a file extension is almost like a
user setting for providing the correct format.  Also I understand that I can
use the guessing module to discover the format on my own if I should choose
to do so.

However for your curiosity I'll try to explain why I would want this.
 Occasionally I get an error that I gave the wrong format for an input file.
 This could be quickly remedied by BioPerl figuring out the format by the
contents of the file rather than the extension.

Although now that I think about it--perhaps it is not a very fast method for
discovering the format and that it only looks at the first numbers of lines
before making a decision.  This would make it error-prone and slow I
suppose.


From daniel.standage at gmail.com  Wed Mar  2 16:55:46 2011
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 2 Mar 2011 10:55:46 -0600
Subject: [Bioperl-l] BioPerl POD
In-Reply-To: <26289423-6B39-418C-B16B-1CECA73B5983@illinois.edu>
References: <AANLkTi=tfUzD78O-mA0tq84sFrtsCnaN4ZYD7Y0T+xnk@mail.gmail.com>
	<26289423-6B39-418C-B16B-1CECA73B5983@illinois.edu>
Message-ID: <AANLkTikyhzULFY9foc5rOQ4yxMEpwS-4=RxFSBjfSioD@mail.gmail.com>

Great! Thanks!

--
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University



On Wed, Mar 2, 2011 at 10:40 AM, Chris Fields <cjfields at illinois.edu> wrote:

> pdoc, I believe, is used for the doc.bioperl.org site:
>
> http://pdoc.sourceforge.net/
>
> Most POD->HTML converters are simple for a reason, sites generally use CSS
> to deal with formatting.  You could get around that with a few tools that
> embed the formatting with the HTML elements (see below link for examples),
> but I highly suggest using CSS if possible.
>
> Here's a stackoverflow article on the search.cpan.org HTML output:
>
>
> http://stackoverflow.com/questions/4996684/modern-pod-to-html-converter-to-produce-results-like-search-cpan-org
>
> Also, ActiveState has another one that generates their custom HTML (pretty
> nice), it comes with their perl dist I think.
>
> chris
>
> On Mar 2, 2011, at 10:01 AM, Daniel Standage wrote:
>
> > BioPerl,
> >
> > I've been writing Perl (and BioPerl) for several years now, but I have
> > little to know experience using POD. I've added some POD to a module I
> wrote
> > and now I am trying to create an HTML page from it. I was able to do so
> with
> > *pod2html*, but the output is...underwhelming. The docs at
> > http://doc.bioperl.org aren't the essence of beauty themselves, but they
> do
> > have a bit of color and really nice features (like links to the code,
> etc).
> >
> > Which tool(s) was/were used to generate the BioPerl HTML docs?
> >
> > --
> > Daniel S. Standage
> > Graduate Research Assistant
> > Bioinformatics and Computational Biology Program
> > Iowa State University
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From roy.chaudhuri at gmail.com  Wed Mar  2 18:06:48 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Wed, 02 Mar 2011 18:06:48 +0000
Subject: [Bioperl-l] clustering trees obtained from phylip neighbor
In-Reply-To: <57675.10.128.10.17.1298978574.squirrel@mbu.iisc.ernet.in>
References: <57675.10.128.10.17.1298978574.squirrel@mbu.iisc.ernet.in>
Message-ID: <4D6E8738.7010103@gmail.com>

Hi Moitrayee,

I know a fair amount about phylogenetics, but I have no idea what you 
mean by the "fork level" of a tree. Perhaps you could use your example 
tree to explain what input you want the user to specify, and what output 
you want to produce?

Roy.

On 01/03/2011 11:22, moitrayee at mbu.iisc.ernet.in wrote:
> Dear BioPerl Users/Developers,
>
> I have obtained a tree using a very large number of nodes
> (1000 nodes) using the neighbor joining in PHYLIP. A small
> test output looks like the following:
>
>    +------------------------------------------------Bovine
> --6
>    !    +-------------------------------------------Mouse
>    +----5
>         !                        +------------------Gibbon
>         +------------------------4
>                                  !    +-------------Orang
>                                  +----3
>                                       !   +---------Gorilla
>                                       +---2
>                                           ! +-------Chimp
>                                           +-1
>                                             +-------Human
>
> The outtree in Newick format is:
>
> (Bovine:0.81551,(Mouse:0.73556,(Gibbon:0.31044,(Orang:0.24003,
> (Gorilla:0.16418,(Chimp:0.13460,Human:0.13460):0.02958):0.07586):0.07040):0.42512):0.07995);
>
>
> I am trying to obtain the cluster at different fork level of this tree.
>
> The fork level goes as an user input. I looked into the link
>
> http://www.bioperl.org/wiki/HOWTO:Trees#Related_Modules
>
> But the Node connectivity methods described there does not apply
> to the tree I have pasted above.
>
> Any help / suggestions would be thankfully appreciated.
>
> Thanks a lot in advance and looking forward to hear from you.
>
> Sincere Regards,
> Moitrayee Bhattacharyya
> Molecular Biophysics Unit,
> Indian Institute of Science
> Bangalore-560012
> India
>
>
>



From David.Messina at sbc.su.se  Thu Mar  3 15:52:44 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 3 Mar 2011 16:52:44 +0100
Subject: [Bioperl-l] Plans for the next release (and beyond)
In-Reply-To: <90D9611F-0DFA-43A6-A3C4-65948DF3F071@illinois.edu>
References: <11F5BA8C-D4F4-419B-870B-D4B5180F4D7D@illinois.edu>
	<AANLkTinSR+RwUrvTeyund+CoxDzgEEqrGP0F2RW0_666@mail.gmail.com>
	<90D9611F-0DFA-43A6-A3C4-65948DF3F071@illinois.edu>
Message-ID: <AANLkTikiWXv9yhVDYiPcAZ9D_12=d5TrKWcCMvsir0P4@mail.gmail.com>

Thanks, Chris.


> [re inline testing]
>


> This pushes the developers a bit to make sure code examples actually pass
> tests.  In particular I have thought about using this with the eutils
> cookbook, just to catch any changes on NCBI's end, but then realized it's
> broadly applicable to other areas as well.


This is a great idea, and goes well with the docs being version controlled
(your point below) along with the code itself.



> However, at least to me there seems to be a fundamental disconnect between
> the code being developed in one repository (github) and the documentation
> being maintained elsewhere (wiki).  In many cases, once docs are placed on
> the wiki they seem to be largely forgotten by the devs once they have
> reached 'completeness'.  Our focus tends to be the code itself, not the
> documentation.  I'm basically looking for ways to resolve that and have
> documentation evolve along with the code, if possible making it testable.
>

Yes, I can't argue. This has been a problem.



>   We should be able to demonstrate via tests that code and examples
> released with a specific version of BioPerl, including those in the HOWTOs
> and the tutorial, should work with that version of the software; anything
> else is a documentation error or a bug.  We can't do that currently.


That would be great.

In the end I'd have to say correct, up-to-date, and testable documentation
is the most important thing. Hopefully, we can find a way to keep the
readability/usability high ? which I think pretty much requires richer
formatting ? at the same time. Certainly worth trying in any case!


Dave



From p.j.a.cock at googlemail.com  Thu Mar  3 20:35:29 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 3 Mar 2011 20:35:29 +0000
Subject: [Bioperl-l] Fwd: [Bosc] Bioinformatics Open Source Conference (BOSC
 2011)--Call for Abstracts
In-Reply-To: <3922D2BE-5A99-4CDE-91AB-B311C42E10CE@lbl.gov>
References: <3922D2BE-5A99-4CDE-91AB-B311C42E10CE@lbl.gov>
Message-ID: <AANLkTinwgazvb5WPV-tiS41tO8wVkQ65NT0m75TPUVVw@mail.gmail.com>

Dear all,

I hope some of you will consider coming to BOSC 2011 in Vienna, and
maybe even submitting a talk or poster abstract.

Thank you,

Peter
(Biopython)


---------- Forwarded message ----------
From: Nomi Harris <nlharris at lbl.gov>
Date: Thu, Mar 3, 2011 at 7:37 PM
Subject: [Bosc] Bioinformatics Open Source Conference (BOSC
2011)--Call for Abstracts
To: bosc-announce at lists.open-bio.org, members at open-bio.org, GMOD
Announcements List <gmod-announce at lists.sourceforge.net>, GMOD
Developers List <gmod-devel at lists.sourceforge.net>
Cc: Nomi Harris <nlharris at lbl.gov>


We invite you to submit an abstract to BOSC 2011! ?Please forward this
message as appropriate, and forgive multiple postings.

Call for Abstracts for the 12th Annual Bioinformatics Open Source
Conference (BOSC 2011)
An ISMB 2011 Special Interest Group (SIG)

Dates: July 15-16, 2011
Location: Vienna, Austria
Web site: http://www.open-bio.org/wiki/BOSC_2011
Email: bosc at open-bio.org
BOSC announcements mailing list:
http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:
April 18, 2011: Deadline for submitting abstracts to BOSC 2011
May 9, 2011: Notifications of accepted abstracts emailed to
corresponding authors
July 13-14, 2011: Codefest 2011 programming session (see
http://www.open-bio.org/wiki/Codefest_2011 for details)
July 15-16, 2011: BOSC 2011
July 17-19, 2011: ISMB 2011

The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.

We invite you to submit abstracts for talks and posters. ?Sessions include:
- Approaches to parallel processing
- Cloud-based approaches to improving software and data accessibility
- The Semantic Web in open source bioinformatics
- Data visualization
- Tools for next-generation sequencing
- Other Open Source software

In addition to the above sessions, there will be a panel discussion
about "Meeting the challenges of inter-institutional collaboration".
We are also working to arrange a joint session with one of the other
ISMB SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student
Travel Awards for BOSC 2011. Each winner will be awarded $250 to
defray the costs of travel to BOSC 2011.

For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee:
Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock,
Erwin Frise, Darin London, Ron Taylor


_______________________________________________
BOSC mailing list
BOSC at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bosc



From sac at bioperl.org  Thu Mar  3 21:45:27 2011
From: sac at bioperl.org (Steve Chervitz)
Date: Thu, 3 Mar 2011 13:45:27 -0800
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
Message-ID: <AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>

Good catch, Elia. Looks like an legitimate edge case. Your fix looks
reasonable to me, but I haven't tried running it through the regression
tests to see if it breaks anything else.

Would be good to get this fix into the upcoming release.

Cheers,
Steve


On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:

> Hi Steve and Rob,
>
> it's been sometime since I last plunged my head into the code, but today we
> nailed a bug in Bio::Restriction::Analysis.
>
> Basically if a sequence has a restriction site which is exactly at the
> start of the sequence, it fails to produce any sites. The  culprits is this
> line (536 of Analysis.pm)
>
> unless ($cut_positions[0]) {
>
> where if the position is zero, it will fail to execute the rest of the
> code, so I changed it to:
>
> unless (defined($cut_positions[0])) {
>
> Also, for similar reasons a bit further down this line:
>
> my $start=1; my $stop; my %seq; my %stop;
>
> needs to change to:
> my $start=0; my $stop; my %seq; my %stop;
>
> I didn't commit the changes because I wanted to check if it makes sense,
> etc.
>
> The bug seems reproducible also in older, stable versions of bioperl, such
> as 1.4 and 1.6...
>
> best
>
> Elia
>
>
>
> ---
> Scientific Director - Bioinformatics, UCL Genomics
> Senior Lecturer, Bioinformatics
>
> UCL Cancer Institute
> Paul O' Gorman Building
> University College London
> 72, Huntley Street
> WC1E 6BT
> London
> UK
>
> Institute of Cell and Molecular Science
> Barts and The London School of Medicine and Dentistry
> 4 Newark Street
> Whitechapel
> London
> E1 2AT
>
> Office (UCL): +44 207 679 6493
> Fax: +44 0207 6796817
> Office (ICMS): +44 0207 8822374
>
> Mobile: +44 787 6478912
>
>
>
>
-- 
Steve Chervitz, Ph.D.
Omicia Inc. |  Senior Computational Biologist
2200 Powell Street, Ste 525, Emeryville CA 94608
T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com

Omicia.com: Unlocking Individualized Medicine.


From cjfields at illinois.edu  Thu Mar  3 22:42:41 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 3 Mar 2011 16:42:41 -0600
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
Message-ID: <E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>

Elia, Steve,

Any tests we can add for this?  I ran tests with the changes below and had several failing ones, but when only implementing the first fix ('unless (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate issue (string-based positions are 0-based, bioperl coords are 1-based).

chris

On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:

> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
> reasonable to me, but I haven't tried running it through the regression
> tests to see if it breaks anything else.
> 
> Would be good to get this fix into the upcoming release.
> 
> Cheers,
> Steve
> 
> 
> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
> 
>> Hi Steve and Rob,
>> 
>> it's been sometime since I last plunged my head into the code, but today we
>> nailed a bug in Bio::Restriction::Analysis.
>> 
>> Basically if a sequence has a restriction site which is exactly at the
>> start of the sequence, it fails to produce any sites. The  culprits is this
>> line (536 of Analysis.pm)
>> 
>> unless ($cut_positions[0]) {
>> 
>> where if the position is zero, it will fail to execute the rest of the
>> code, so I changed it to:
>> 
>> unless (defined($cut_positions[0])) {
>> 
>> Also, for similar reasons a bit further down this line:
>> 
>> my $start=1; my $stop; my %seq; my %stop;
>> 
>> needs to change to:
>> my $start=0; my $stop; my %seq; my %stop;
>> 
>> I didn't commit the changes because I wanted to check if it makes sense,
>> etc.
>> 
>> The bug seems reproducible also in older, stable versions of bioperl, such
>> as 1.4 and 1.6...
>> 
>> best
>> 
>> Elia
>> 
>> 
>> 
>> ---
>> Scientific Director - Bioinformatics, UCL Genomics
>> Senior Lecturer, Bioinformatics
>> 
>> UCL Cancer Institute
>> Paul O' Gorman Building
>> University College London
>> 72, Huntley Street
>> WC1E 6BT
>> London
>> UK
>> 
>> Institute of Cell and Molecular Science
>> Barts and The London School of Medicine and Dentistry
>> 4 Newark Street
>> Whitechapel
>> London
>> E1 2AT
>> 
>> Office (UCL): +44 207 679 6493
>> Fax: +44 0207 6796817
>> Office (ICMS): +44 0207 8822374
>> 
>> Mobile: +44 787 6478912
>> 
>> 
>> 
>> 
> -- 
> Steve Chervitz, Ph.D.
> Omicia Inc. |  Senior Computational Biologist
> 2200 Powell Street, Ste 525, Emeryville CA 94608
> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
> 
> Omicia.com: Unlocking Individualized Medicine.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Thu Mar  3 22:57:57 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 3 Mar 2011 16:57:57 -0600
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
	<E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
Message-ID: <CADBF252-9F51-4C7C-8062-C98B0E8E3B13@illinois.edu>

Forgot to add the summary, just for completeness. lots of errors like this that are halting tests:

------------- EXCEPTION -------------
MSG: Bad start parameter (0). Start must be positive.
STACK Bio::PrimarySeq::subseq /Users/cjfields/bioperl/bioperl-live/blib/lib/Bio/PrimarySeq.pm:400
STACK Bio::Restriction::Analysis::fragment_maps Bio/Restriction/Analysis.pm:556
STACK toplevel t/Restriction/Analysis-refac.t:143
-------------------------------------

Test Summary Report
-------------------
t/Restriction/Analysis-refac.t (Wstat: 65280 Tests: 26 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 91 tests but ran 26.
t/Restriction/Analysis.t      (Wstat: 65280 Tests: 118 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 177 tests but ran 118.
t/Restriction/Gel.t           (Wstat: 65280 Tests: 3 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 9 tests but ran 3.
Files=4, Tests=165, 29 wallclock secs ( 0.05 usr  0.03 sys +  3.44 cusr  0.21 csys =  3.73 CPU)
Result: FAIL
Failed 3/4 test programs. 0/165 subtests failed.

-c

On Mar 3, 2011, at 4:42 PM, Chris Fields wrote:

> Elia, Steve,
> 
> Any tests we can add for this?  I ran tests with the changes below and had several failing ones, but when only implementing the first fix ('unless (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate issue (string-based positions are 0-based, bioperl coords are 1-based).
> 
> chris
> 
> On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:
> 
>> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
>> reasonable to me, but I haven't tried running it through the regression
>> tests to see if it breaks anything else.
>> 
>> Would be good to get this fix into the upcoming release.
>> 
>> Cheers,
>> Steve
>> 
>> 
>> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
>> 
>>> Hi Steve and Rob,
>>> 
>>> it's been sometime since I last plunged my head into the code, but today we
>>> nailed a bug in Bio::Restriction::Analysis.
>>> 
>>> Basically if a sequence has a restriction site which is exactly at the
>>> start of the sequence, it fails to produce any sites. The  culprits is this
>>> line (536 of Analysis.pm)
>>> 
>>> unless ($cut_positions[0]) {
>>> 
>>> where if the position is zero, it will fail to execute the rest of the
>>> code, so I changed it to:
>>> 
>>> unless (defined($cut_positions[0])) {
>>> 
>>> Also, for similar reasons a bit further down this line:
>>> 
>>> my $start=1; my $stop; my %seq; my %stop;
>>> 
>>> needs to change to:
>>> my $start=0; my $stop; my %seq; my %stop;
>>> 
>>> I didn't commit the changes because I wanted to check if it makes sense,
>>> etc.
>>> 
>>> The bug seems reproducible also in older, stable versions of bioperl, such
>>> as 1.4 and 1.6...
>>> 
>>> best
>>> 
>>> Elia
>>> 
>>> 
>>> 
>>> ---
>>> Scientific Director - Bioinformatics, UCL Genomics
>>> Senior Lecturer, Bioinformatics
>>> 
>>> UCL Cancer Institute
>>> Paul O' Gorman Building
>>> University College London
>>> 72, Huntley Street
>>> WC1E 6BT
>>> London
>>> UK
>>> 
>>> Institute of Cell and Molecular Science
>>> Barts and The London School of Medicine and Dentistry
>>> 4 Newark Street
>>> Whitechapel
>>> London
>>> E1 2AT
>>> 
>>> Office (UCL): +44 207 679 6493
>>> Fax: +44 0207 6796817
>>> Office (ICMS): +44 0207 8822374
>>> 
>>> Mobile: +44 787 6478912
>>> 
>>> 
>>> 
>>> 
>> -- 
>> Steve Chervitz, Ph.D.
>> Omicia Inc. |  Senior Computational Biologist
>> 2200 Powell Street, Ste 525, Emeryville CA 94608
>> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
>> 
>> Omicia.com: Unlocking Individualized Medicine.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From sac at bioperl.org  Thu Mar  3 23:07:52 2011
From: sac at bioperl.org (Steve Chervitz)
Date: Thu, 3 Mar 2011 15:07:52 -0800
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <CADBF252-9F51-4C7C-8062-C98B0E8E3B13@illinois.edu>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
	<E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
	<CADBF252-9F51-4C7C-8062-C98B0E8E3B13@illinois.edu>
Message-ID: <AANLkTik7CGWADGzJvenQt7kbmOoMGij4u6Q5U9NOP_rd@mail.gmail.com>

Chris: Thanks or checking. I'm not sure about this.

Elia: Can you send an example sequence + enzyme name that causes the issue
you found?

Steve

On Thu, Mar 3, 2011 at 2:57 PM, Chris Fields <cjfields at illinois.edu> wrote:

> Forgot to add the summary, just for completeness. lots of errors like this
> that are halting tests:
>
> ------------- EXCEPTION -------------
> MSG: Bad start parameter (0). Start must be positive.
> STACK Bio::PrimarySeq::subseq
> /Users/cjfields/bioperl/bioperl-live/blib/lib/Bio/PrimarySeq.pm:400
> STACK Bio::Restriction::Analysis::fragment_maps
> Bio/Restriction/Analysis.pm:556
> STACK toplevel t/Restriction/Analysis-refac.t:143
> -------------------------------------
>
> Test Summary Report
> -------------------
> t/Restriction/Analysis-refac.t (Wstat: 65280 Tests: 26 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 91 tests but ran 26.
> t/Restriction/Analysis.t      (Wstat: 65280 Tests: 118 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 177 tests but ran 118.
> t/Restriction/Gel.t           (Wstat: 65280 Tests: 3 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 9 tests but ran 3.
> Files=4, Tests=165, 29 wallclock secs ( 0.05 usr  0.03 sys +  3.44 cusr
>  0.21 csys =  3.73 CPU)
> Result: FAIL
> Failed 3/4 test programs. 0/165 subtests failed.
>
> -c
>
> On Mar 3, 2011, at 4:42 PM, Chris Fields wrote:
>
> > Elia, Steve,
> >
> > Any tests we can add for this?  I ran tests with the changes below and
> had several failing ones, but when only implementing the first fix ('unless
> (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate
> issue (string-based positions are 0-based, bioperl coords are 1-based).
> >
> > chris
> >
> > On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:
> >
> >> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
> >> reasonable to me, but I haven't tried running it through the regression
> >> tests to see if it breaks anything else.
> >>
> >> Would be good to get this fix into the upcoming release.
> >>
> >> Cheers,
> >> Steve
> >>
> >>
> >> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
> >>
> >>> Hi Steve and Rob,
> >>>
> >>> it's been sometime since I last plunged my head into the code, but
> today we
> >>> nailed a bug in Bio::Restriction::Analysis.
> >>>
> >>> Basically if a sequence has a restriction site which is exactly at the
> >>> start of the sequence, it fails to produce any sites. The  culprits is
> this
> >>> line (536 of Analysis.pm)
> >>>
> >>> unless ($cut_positions[0]) {
> >>>
> >>> where if the position is zero, it will fail to execute the rest of the
> >>> code, so I changed it to:
> >>>
> >>> unless (defined($cut_positions[0])) {
> >>>
> >>> Also, for similar reasons a bit further down this line:
> >>>
> >>> my $start=1; my $stop; my %seq; my %stop;
> >>>
> >>> needs to change to:
> >>> my $start=0; my $stop; my %seq; my %stop;
> >>>
> >>> I didn't commit the changes because I wanted to check if it makes
> sense,
> >>> etc.
> >>>
> >>> The bug seems reproducible also in older, stable versions of bioperl,
> such
> >>> as 1.4 and 1.6...
> >>>
> >>> best
> >>>
> >>> Elia
> >>>
> >>>
> >>>
> >>> ---
> >>> Scientific Director - Bioinformatics, UCL Genomics
> >>> Senior Lecturer, Bioinformatics
> >>>
> >>> UCL Cancer Institute
> >>> Paul O' Gorman Building
> >>> University College London
> >>> 72, Huntley Street
> >>> WC1E 6BT
> >>> London
> >>> UK
> >>>
> >>> Institute of Cell and Molecular Science
> >>> Barts and The London School of Medicine and Dentistry
> >>> 4 Newark Street
> >>> Whitechapel
> >>> London
> >>> E1 2AT
> >>>
> >>> Office (UCL): +44 207 679 6493
> >>> Fax: +44 0207 6796817
> >>> Office (ICMS): +44 0207 8822374
> >>>
> >>> Mobile: +44 787 6478912
> >>>
> >>>
> >>>
> >>>
> >> --
> >> Steve Chervitz, Ph.D.
> >> Omicia Inc. |  Senior Computational Biologist
> >> 2200 Powell Street, Ste 525, Emeryville CA 94608
> >> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
> >>
> >> Omicia.com: Unlocking Individualized Medicine.
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From hartzell at alerce.com  Thu Mar  3 23:04:34 2011
From: hartzell at alerce.com (George Hartzell)
Date: Thu, 3 Mar 2011 15:04:34 -0800
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
Message-ID: <19824.7810.437300.584113@gargle.gargle.HOWL>


Hi all,

I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
seems to have it.  The only tarballs that end up in Chris' directory
are these:

/Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
/Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
/Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz

It is listed in the 02packages.details.txt.gz file that is mirrored.

Thoughts, suggestions?

Thanks,

g.


From cjfields at illinois.edu  Fri Mar  4 02:24:05 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 3 Mar 2011 20:24:05 -0600
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <19824.7810.437300.584113@gargle.gargle.HOWL>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
Message-ID: <5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>

On Mar 3, 2011, at 5:04 PM, George Hartzell wrote:

> Hi all,
> 
> I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
> does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
> seems to have it.  The only tarballs that end up in Chris' directory
> are these:
> 
> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
> 
> It is listed in the 02packages.details.txt.gz file that is mirrored.
> 
> Thoughts, suggestions?
> 
> Thanks,
> 
> g.

That's odd; could it be the repo you created the mirror from?

This is my PAUSE account:

 BioPerl-1.6.0.meta                                   78518  Sun, 25 Jan 2009 05:19:20 GMT
 BioPerl-1.6.0.readme                                 12174  Sun, 25 Jan 2009 05:19:41 GMT
 BioPerl-1.6.0.tar.gz                               6813396  Sun, 25 Jan 2009 17:14:12 GMT
 BioPerl-1.6.1.meta                                   82231  Tue, 29 Sep 2009 16:33:52 GMT
 BioPerl-1.6.1.readme                                 12174  Tue, 29 Sep 2009 16:33:49 GMT
 BioPerl-1.6.1.tar.gz                               10462526  Tue, 29 Sep 2009 16:43:11 GMT
 BioPerl-DB-1.6.0_001.tar.gz                         494106  Wed, 30 Sep 2009 20:49:59 GMT
 BioPerl-Network-1.6.0_001.tar.gz                   2198338  Wed, 30 Sep 2009 20:50:18 GMT
 BioPerl-Run-1.6.1_001.tar.gz                       4289239  Wed, 30 Sep 2009 21:07:38 GMT
 BioPerl-db-1.6.0.meta                                 7728  Tue, 24 Feb 2009 02:58:05 GMT
 BioPerl-db-1.6.0.readme                               7066  Tue, 24 Feb 2009 02:58:05 GMT
 BioPerl-db-1.6.0.tar.gz                             392773  Tue, 24 Feb 2009 15:33:05 GMT
 BioPerl-network-1.6.0.meta                            1268  Tue, 24 Feb 2009 03:00:26 GMT
 BioPerl-network-1.6.0.readme                          3669  Tue, 24 Feb 2009 03:00:28 GMT
 BioPerl-network-1.6.0.tar.gz                       1410782  Tue, 24 Feb 2009 15:33:16 GMT
 BioPerl-run-1.6.0.meta                               10289  Tue, 24 Feb 2009 02:59:26 GMT
 BioPerl-run-1.6.0.readme                               576  Tue, 24 Feb 2009 02:59:26 GMT
 BioPerl-run-1.6.0.tar.gz                           4082430  Tue, 24 Feb 2009 15:34:43 GMT
 BioPerl-run-1.6.1.meta                               10289  Wed, 25 Feb 2009 16:07:06 GMT
 BioPerl-run-1.6.1.readme                               576  Wed, 25 Feb 2009 16:07:06 GMT
 BioPerl-run-1.6.1.tar.gz                           4082463  Wed, 25 Feb 2009 16:14:37 GMT
 CHECKSUMS                                             5035  Sun, 03 Oct 2010 19:21:56 GMT

chris


From hartzell at alerce.com  Fri Mar  4 05:50:49 2011
From: hartzell at alerce.com (George Hartzell)
Date: Thu, 3 Mar 2011 21:50:49 -0800
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
	<5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
Message-ID: <19824.32185.570232.624286@gargle.gargle.HOWL>

Chris Fields writes:
 > On Mar 3, 2011, at 5:04 PM, George Hartzell wrote:
 > 
 > > Hi all,
 > > 
 > > I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
 > > does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
 > > seems to have it.  The only tarballs that end up in Chris' directory
 > > are these:
 > > 
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
 > > 
 > > It is listed in the 02packages.details.txt.gz file that is mirrored.
 > > 
 > > Thoughts, suggestions?
 > > 
 > > Thanks,
 > > 
 > > g.
 > 
 > That's odd; could it be the repo you created the mirror from?
 > 
 > This is my PAUSE account:
 > 
 >  BioPerl-1.6.0.meta                                   78518  Sun, 25 Jan 2009 05:19:20 GMT
 >  BioPerl-1.6.0.readme                                 12174  Sun, 25 Jan 2009 05:19:41 GMT
 >  BioPerl-1.6.0.tar.gz                               6813396  Sun, 25 Jan 2009 17:14:12 GMT
 >  BioPerl-1.6.1.meta                                   82231  Tue, 29 Sep 2009 16:33:52 GMT
 >  BioPerl-1.6.1.readme                                 12174  Tue, 29 Sep 2009 16:33:49 GMT
 >  BioPerl-1.6.1.tar.gz                               10462526  Tue, 29 Sep 2009 16:43:11 GMT
 >  BioPerl-DB-1.6.0_001.tar.gz                         494106  Wed, 30 Sep 2009 20:49:59 GMT
 >  BioPerl-Network-1.6.0_001.tar.gz                   2198338  Wed, 30 Sep 2009 20:50:18 GMT
 >  BioPerl-Run-1.6.1_001.tar.gz                       4289239  Wed, 30 Sep 2009 21:07:38 GMT
 >  BioPerl-db-1.6.0.meta                                 7728  Tue, 24 Feb 2009 02:58:05 GMT
 >  BioPerl-db-1.6.0.readme                               7066  Tue, 24 Feb 2009 02:58:05 GMT
 >  BioPerl-db-1.6.0.tar.gz                             392773  Tue, 24 Feb 2009 15:33:05 GMT
 >  BioPerl-network-1.6.0.meta                            1268  Tue, 24 Feb 2009 03:00:26 GMT
 >  BioPerl-network-1.6.0.readme                          3669  Tue, 24 Feb 2009 03:00:28 GMT
 >  BioPerl-network-1.6.0.tar.gz                       1410782  Tue, 24 Feb 2009 15:33:16 GMT
 >  BioPerl-run-1.6.0.meta                               10289  Tue, 24 Feb 2009 02:59:26 GMT
 >  BioPerl-run-1.6.0.readme                               576  Tue, 24 Feb 2009 02:59:26 GMT
 >  BioPerl-run-1.6.0.tar.gz                           4082430  Tue, 24 Feb 2009 15:34:43 GMT
 >  BioPerl-run-1.6.1.meta                               10289  Wed, 25 Feb 2009 16:07:06 GMT
 >  BioPerl-run-1.6.1.readme                               576  Wed, 25 Feb 2009 16:07:06 GMT
 >  BioPerl-run-1.6.1.tar.gz                           4082463  Wed, 25 Feb 2009 16:14:37 GMT
 >  CHECKSUMS                                             5035  Sun, 03 Oct 2010 19:21:56 GMT
 > 
 > chris
 > 
 > 

I've tried a couple of them, a couple of times.  Wouldn't surprise me
if it's something on my end.  I'll peek under the minicpan kilt over
the weekend and see if I can see what's going on.

g.


From e.stupka at ucl.ac.uk  Fri Mar  4 09:30:17 2011
From: e.stupka at ucl.ac.uk (Elia Stupka)
Date: Fri, 4 Mar 2011 09:30:17 +0000
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
	<E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
Message-ID: <535DCA0E-A74D-483B-96FB-544387EF08C3@ucl.ac.uk>

Ignore the second fix, the first one is the useful and correct one. The 2nd one was an oversight.

Elia


---
Scientific Director - Bioinformatics, UCL Genomics
Senior Lecturer, Bioinformatics

UCL Cancer Institute
Paul O' Gorman Building
University College London
Gower Street
WC1E 6BT
London
UK

Institute of Cell and Molecular Science
Barts and The London School of Medicine and Dentistry
4 Newark Street
Whitechapel
London
E1 2AT

Office (UCL): +44 207 679 6493
Fax: +44 0207 6796817 
Office (ICMS): +44 0207 8822374

On 3 Mar 2011, at 22:42, Chris Fields <cjfields at illinois.edu> wrote:

> Elia, Steve,
> 
> Any tests we can add for this?  I ran tests with the changes below and had several failing ones, but when only implementing the first fix ('unless (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate issue (string-based positions are 0-based, bioperl coords are 1-based).
> 
> chris
> 
> On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:
> 
>> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
>> reasonable to me, but I haven't tried running it through the regression
>> tests to see if it breaks anything else.
>> 
>> Would be good to get this fix into the upcoming release.
>> 
>> Cheers,
>> Steve
>> 
>> 
>> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
>> 
>>> Hi Steve and Rob,
>>> 
>>> it's been sometime since I last plunged my head into the code, but today we
>>> nailed a bug in Bio::Restriction::Analysis.
>>> 
>>> Basically if a sequence has a restriction site which is exactly at the
>>> start of the sequence, it fails to produce any sites. The  culprits is this
>>> line (536 of Analysis.pm)
>>> 
>>> unless ($cut_positions[0]) {
>>> 
>>> where if the position is zero, it will fail to execute the rest of the
>>> code, so I changed it to:
>>> 
>>> unless (defined($cut_positions[0])) {
>>> 
>>> Also, for similar reasons a bit further down this line:
>>> 
>>> my $start=1; my $stop; my %seq; my %stop;
>>> 
>>> needs to change to:
>>> my $start=0; my $stop; my %seq; my %stop;
>>> 
>>> I didn't commit the changes because I wanted to check if it makes sense,
>>> etc.
>>> 
>>> The bug seems reproducible also in older, stable versions of bioperl, such
>>> as 1.4 and 1.6...
>>> 
>>> best
>>> 
>>> Elia
>>> 
>>> 
>>> 
>>> ---
>>> Scientific Director - Bioinformatics, UCL Genomics
>>> Senior Lecturer, Bioinformatics
>>> 
>>> UCL Cancer Institute
>>> Paul O' Gorman Building
>>> University College London
>>> 72, Huntley Street
>>> WC1E 6BT
>>> London
>>> UK
>>> 
>>> Institute of Cell and Molecular Science
>>> Barts and The London School of Medicine and Dentistry
>>> 4 Newark Street
>>> Whitechapel
>>> London
>>> E1 2AT
>>> 
>>> Office (UCL): +44 207 679 6493
>>> Fax: +44 0207 6796817
>>> Office (ICMS): +44 0207 8822374
>>> 
>>> Mobile: +44 787 6478912
>>> 
>>> 
>>> 
>>> 
>> -- 
>> Steve Chervitz, Ph.D.
>> Omicia Inc. |  Senior Computational Biologist
>> 2200 Powell Street, Ste 525, Emeryville CA 94608
>> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
>> 
>> Omicia.com: Unlocking Individualized Medicine.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From cjfields at illinois.edu  Fri Mar  4 16:09:42 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 4 Mar 2011 10:09:42 -0600
Subject: [Bioperl-l] Bug in Bio::Restriction::Analysis
In-Reply-To: <535DCA0E-A74D-483B-96FB-544387EF08C3@ucl.ac.uk>
References: <17687E9E-0A35-48D6-83B2-8B143DC33202@ucl.ac.uk>
	<AANLkTi=rmBxUYFwUQSsOTZboXrS=rzUOhe4CQNcOznt2@mail.gmail.com>
	<E1B4F9B8-A9B2-4421-B139-051A905E3245@illinois.edu>
	<535DCA0E-A74D-483B-96FB-544387EF08C3@ucl.ac.uk>
Message-ID: <243A2900-C5D3-4772-AC88-69A3ABF238E6@illinois.edu>

Committed to github, should be in the next release.  I'll see if I can add a simple test for this.

chris


On Mar 4, 2011, at 3:30 AM, Elia Stupka wrote:

> Ignore the second fix, the first one is the useful and correct one. The 2nd one was an oversight.
> 
> Elia
> 
> 
> ---
> Scientific Director - Bioinformatics, UCL Genomics
> Senior Lecturer, Bioinformatics
> 
> UCL Cancer Institute
> Paul O' Gorman Building
> University College London
> Gower Street
> WC1E 6BT
> London
> UK
> 
> Institute of Cell and Molecular Science
> Barts and The London School of Medicine and Dentistry
> 4 Newark Street
> Whitechapel
> London
> E1 2AT
> 
> Office (UCL): +44 207 679 6493
> Fax: +44 0207 6796817 
> Office (ICMS): +44 0207 8822374
> 
> On 3 Mar 2011, at 22:42, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Elia, Steve,
>> 
>> Any tests we can add for this?  I ran tests with the changes below and had several failing ones, but when only implementing the first fix ('unless (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate issue (string-based positions are 0-based, bioperl coords are 1-based).
>> 
>> chris
>> 
>> On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:
>> 
>>> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
>>> reasonable to me, but I haven't tried running it through the regression
>>> tests to see if it breaks anything else.
>>> 
>>> Would be good to get this fix into the upcoming release.
>>> 
>>> Cheers,
>>> Steve
>>> 
>>> 
>>> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
>>> 
>>>> Hi Steve and Rob,
>>>> 
>>>> it's been sometime since I last plunged my head into the code, but today we
>>>> nailed a bug in Bio::Restriction::Analysis.
>>>> 
>>>> Basically if a sequence has a restriction site which is exactly at the
>>>> start of the sequence, it fails to produce any sites. The  culprits is this
>>>> line (536 of Analysis.pm)
>>>> 
>>>> unless ($cut_positions[0]) {
>>>> 
>>>> where if the position is zero, it will fail to execute the rest of the
>>>> code, so I changed it to:
>>>> 
>>>> unless (defined($cut_positions[0])) {
>>>> 
>>>> Also, for similar reasons a bit further down this line:
>>>> 
>>>> my $start=1; my $stop; my %seq; my %stop;
>>>> 
>>>> needs to change to:
>>>> my $start=0; my $stop; my %seq; my %stop;
>>>> 
>>>> I didn't commit the changes because I wanted to check if it makes sense,
>>>> etc.
>>>> 
>>>> The bug seems reproducible also in older, stable versions of bioperl, such
>>>> as 1.4 and 1.6...
>>>> 
>>>> best
>>>> 
>>>> Elia
>>>> 
>>>> 
>>>> 
>>>> ---
>>>> Scientific Director - Bioinformatics, UCL Genomics
>>>> Senior Lecturer, Bioinformatics
>>>> 
>>>> UCL Cancer Institute
>>>> Paul O' Gorman Building
>>>> University College London
>>>> 72, Huntley Street
>>>> WC1E 6BT
>>>> London
>>>> UK
>>>> 
>>>> Institute of Cell and Molecular Science
>>>> Barts and The London School of Medicine and Dentistry
>>>> 4 Newark Street
>>>> Whitechapel
>>>> London
>>>> E1 2AT
>>>> 
>>>> Office (UCL): +44 207 679 6493
>>>> Fax: +44 0207 6796817
>>>> Office (ICMS): +44 0207 8822374
>>>> 
>>>> Mobile: +44 787 6478912
>>>> 
>>>> 
>>>> 
>>>> 
>>> -- 
>>> Steve Chervitz, Ph.D.
>>> Omicia Inc. |  Senior Computational Biologist
>>> 2200 Powell Street, Ste 525, Emeryville CA 94608
>>> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
>>> 
>>> Omicia.com: Unlocking Individualized Medicine.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 




From hartzell at alerce.com  Fri Mar  4 18:16:03 2011
From: hartzell at alerce.com (George Hartzell)
Date: Fri, 4 Mar 2011 10:16:03 -0800
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
	<5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
Message-ID: <19825.11363.446731.724414@gargle.gargle.HOWL>

Chris Fields writes:
 > On Mar 3, 2011, at 5:04 PM, George Hartzell wrote:
 > 
 > > Hi all,
 > > 
 > > I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
 > > does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
 > > seems to have it.  The only tarballs that end up in Chris' directory
 > > are these:
 > > 
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
 > > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
 > > 
 > > It is listed in the 02packages.details.txt.gz file that is mirrored.
 > > 
 > > Thoughts, suggestions?
 > > 
 > > Thanks,
 > > 
 > > g.
 > 
 > That's odd; could it be the repo you created the mirror from?
 > 
 > This is my PAUSE account:
 > 
 >  BioPerl-1.6.0.meta                                   78518  Sun, 25 Jan 2009 05:19:20 GMT
 >  BioPerl-1.6.0.readme                                 12174  Sun, 25 Jan 2009 05:19:41 GMT
 >  BioPerl-1.6.0.tar.gz                               6813396  Sun, 25 Jan 2009 17:14:12 GMT
 >  BioPerl-1.6.1.meta                                   82231  Tue, 29 Sep 2009 16:33:52 GMT
 >  BioPerl-1.6.1.readme                                 12174  Tue, 29 Sep 2009 16:33:49 GMT
 >  BioPerl-1.6.1.tar.gz                               10462526  Tue, 29 Sep 2009 16:43:11 GMT
 >  BioPerl-DB-1.6.0_001.tar.gz                         494106  Wed, 30 Sep 2009 20:49:59 GMT
 >  BioPerl-Network-1.6.0_001.tar.gz                   2198338  Wed, 30 Sep 2009 20:50:18 GMT
 >  BioPerl-Run-1.6.1_001.tar.gz                       4289239  Wed, 30 Sep 2009 21:07:38 GMT
 >  BioPerl-db-1.6.0.meta                                 7728  Tue, 24 Feb 2009 02:58:05 GMT
 >  BioPerl-db-1.6.0.readme                               7066  Tue, 24 Feb 2009 02:58:05 GMT
 >  BioPerl-db-1.6.0.tar.gz                             392773  Tue, 24 Feb 2009 15:33:05 GMT
 >  BioPerl-network-1.6.0.meta                            1268  Tue, 24 Feb 2009 03:00:26 GMT
 >  BioPerl-network-1.6.0.readme                          3669  Tue, 24 Feb 2009 03:00:28 GMT
 >  BioPerl-network-1.6.0.tar.gz                       1410782  Tue, 24 Feb 2009 15:33:16 GMT
 >  BioPerl-run-1.6.0.meta                               10289  Tue, 24 Feb 2009 02:59:26 GMT
 >  BioPerl-run-1.6.0.readme                               576  Tue, 24 Feb 2009 02:59:26 GMT
 >  BioPerl-run-1.6.0.tar.gz                           4082430  Tue, 24 Feb 2009 15:34:43 GMT
 >  BioPerl-run-1.6.1.meta                               10289  Wed, 25 Feb 2009 16:07:06 GMT
 >  BioPerl-run-1.6.1.readme                               576  Wed, 25 Feb 2009 16:07:06 GMT
 >  BioPerl-run-1.6.1.tar.gz                           4082463  Wed, 25 Feb 2009 16:14:37 GMT
 >  CHECKSUMS                                             5035  Sun, 03 Oct 2010 19:21:56 GMT
 > 
 > chris
 > 
 > 

Ok, apparently we've earned a reputation, and it has preceeded us....
Here's the code that Ricardo uses to filter the list of things to mirror:

  sub _filter_module {
    my $self = shift;
    my $args = shift;
  
    if ($self->{skip_perl}) {
      return 1 if $args->{path} =~ m{/(?:emb|syb|bio)?perl-\d}i;
      return 1 if $args->{path} =~ m{/(?:parrot|ponie)-\d}i;
      return 1 if $args->{path} =~ m{/(?:kurila)-\d}i;
      return 1 if $args->{path} =~ m{/\bperl-?5\.004}i;
      return 1 if $args->{path} =~ m{/\bperl_mlb\.zip}i;
    }
  
    return 1 if $self->__do_filter($self->{path_filters},   $args->{path});
    return 1 if $self->__do_filter($self->{module_filters}, $args->{module});
    return 0;
  }

I'll ask him why he's filtering bioperl out and we can see if we can
fix it.  I'm hoping that it's just an over-eager cut-n-paste of stuff
that he thinks of as the "perl" source (which is why it's within the
skip_perl test) and not that we've done something egregious.

g.


From cjfields at illinois.edu  Fri Mar  4 18:24:05 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 4 Mar 2011 12:24:05 -0600
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <19825.11363.446731.724414@gargle.gargle.HOWL>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
	<5934A676-EAD8-47C9-8317-E467ED28E8B7@illinois.edu>
	<19825.11363.446731.724414@gargle.gargle.HOWL>
Message-ID: <F8DFAE16-FE59-4EDF-80D0-4FE60620FFF8@illinois.edu>

On Mar 4, 2011, at 12:16 PM, George Hartzell wrote:

> Chris Fields writes:
>> On Mar 3, 2011, at 5:04 PM, George Hartzell wrote:
>> 
>>> Hi all,
>>> 
>>> I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
>>> does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
>>> seems to have it.  The only tarballs that end up in Chris' directory
>>> are these:
>>> 
>>> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
>>> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
>>> /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
>>> 
>>> It is listed in the 02packages.details.txt.gz file that is mirrored.
>>> 
>>> Thoughts, suggestions?
>>> 
>>> Thanks,
>>> 
>>> g.
>> 
>> That's odd; could it be the repo you created the mirror from?
>> 
>> This is my PAUSE account:
>> 
>> BioPerl-1.6.0.meta                                   78518  Sun, 25 Jan 2009 05:19:20 GMT
>> BioPerl-1.6.0.readme                                 12174  Sun, 25 Jan 2009 05:19:41 GMT
>> BioPerl-1.6.0.tar.gz                               6813396  Sun, 25 Jan 2009 17:14:12 GMT
>> BioPerl-1.6.1.meta                                   82231  Tue, 29 Sep 2009 16:33:52 GMT
>> BioPerl-1.6.1.readme                                 12174  Tue, 29 Sep 2009 16:33:49 GMT
>> BioPerl-1.6.1.tar.gz                               10462526  Tue, 29 Sep 2009 16:43:11 GMT
>> BioPerl-DB-1.6.0_001.tar.gz                         494106  Wed, 30 Sep 2009 20:49:59 GMT
>> BioPerl-Network-1.6.0_001.tar.gz                   2198338  Wed, 30 Sep 2009 20:50:18 GMT
>> BioPerl-Run-1.6.1_001.tar.gz                       4289239  Wed, 30 Sep 2009 21:07:38 GMT
>> BioPerl-db-1.6.0.meta                                 7728  Tue, 24 Feb 2009 02:58:05 GMT
>> BioPerl-db-1.6.0.readme                               7066  Tue, 24 Feb 2009 02:58:05 GMT
>> BioPerl-db-1.6.0.tar.gz                             392773  Tue, 24 Feb 2009 15:33:05 GMT
>> BioPerl-network-1.6.0.meta                            1268  Tue, 24 Feb 2009 03:00:26 GMT
>> BioPerl-network-1.6.0.readme                          3669  Tue, 24 Feb 2009 03:00:28 GMT
>> BioPerl-network-1.6.0.tar.gz                       1410782  Tue, 24 Feb 2009 15:33:16 GMT
>> BioPerl-run-1.6.0.meta                               10289  Tue, 24 Feb 2009 02:59:26 GMT
>> BioPerl-run-1.6.0.readme                               576  Tue, 24 Feb 2009 02:59:26 GMT
>> BioPerl-run-1.6.0.tar.gz                           4082430  Tue, 24 Feb 2009 15:34:43 GMT
>> BioPerl-run-1.6.1.meta                               10289  Wed, 25 Feb 2009 16:07:06 GMT
>> BioPerl-run-1.6.1.readme                               576  Wed, 25 Feb 2009 16:07:06 GMT
>> BioPerl-run-1.6.1.tar.gz                           4082463  Wed, 25 Feb 2009 16:14:37 GMT
>> CHECKSUMS                                             5035  Sun, 03 Oct 2010 19:21:56 GMT
>> 
>> chris
>> 
>> 
> 
> Ok, apparently we've earned a reputation, and it has preceeded us....
> Here's the code that Ricardo uses to filter the list of things to mirror:
> 
>  sub _filter_module {
>    my $self = shift;
>    my $args = shift;
> 
>    if ($self->{skip_perl}) {
>      return 1 if $args->{path} =~ m{/(?:emb|syb|bio)?perl-\d}i;
>      return 1 if $args->{path} =~ m{/(?:parrot|ponie)-\d}i;
>      return 1 if $args->{path} =~ m{/(?:kurila)-\d}i;
>      return 1 if $args->{path} =~ m{/\bperl-?5\.004}i;
>      return 1 if $args->{path} =~ m{/\bperl_mlb\.zip}i;
>    }
> 
>    return 1 if $self->__do_filter($self->{path_filters},   $args->{path});
>    return 1 if $self->__do_filter($self->{module_filters}, $args->{module});
>    return 0;
>  }
> 
> I'll ask him why he's filtering bioperl out and we can see if we can
> fix it.  I'm hoping that it's just an over-eager cut-n-paste of stuff
> that he thinks of as the "perl" source (which is why it's within the
> skip_perl test) and not that we've done something egregious.
> 
> g.

Could be the size of the distribution was considered egregious (we're at 10 MB compressed I think).  Most of the other dists that appear to be filtered are fairly large as well.  That's nothing really these days; would be interested to hear what Ricardo says.

chris




From hlapp at drycafe.net  Fri Mar  4 23:26:25 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Fri, 4 Mar 2011 18:26:25 -0500
Subject: [Bioperl-l] Informatics job opportunity at NESCent
Message-ID: <1878F27F-000D-4C80-B9EA-A83F7887828F@drycafe.net>

(Apologies if you receive multiple copies, and also if you are not  
interested in job opportunities.  In my defense, quite a few people on  
Bio* lists might qualify for (let alone enjoy) the position. And if  
you know someone who might be interested please forward.)

===================================================
User Interface Design and Web Application Developer
===================================================

The National Evolutionary Synthesis Center (NESCent) seeks a creative  
and enthusiastic individual to design user interfaces and web  
applications for scientific applications. The incumbent will work as  
part of a small informatics team in close collaboration with domain  
scientists.

NESCent is an NSF-funded center dedicated to cross-disciplinary  
research in evolutionary science. Our informatics team works closely  
with visiting and resident scientists to support their custom software  
and database development needs. All NESCent software products are open- 
source, and the Center has a number of initiatives to actively promote  
collaborative development of community software resources  
(informatics.nescent.org). Above all, we are enthusiastic about our  
work, about the mission of the Center, and about the contribution of  
informatics to that mission.

Job description: The incumbent will design and develop user interfaces  
and web applications for databases and other software tools for  
sponsored scientists and staff. The job responsibilities include all  
stages of the software development process, including requirements  
gathering, design, implementation, release packaging and  
documentation, as part of a small team (typically 2-3 individuals)  
following project management best practices. We expect the incumbent  
to present their work at conferences and contribute to publications  
with scientific collaborators; interact regularly with visiting and  
resident scientists, other members of the informatics team and Center  
staff; and generally serve as an expert resource for Center personnel.  
The position provides opportunities for professional development. Most  
informatics staff work at our Durham NC offices, located adjacent to  
Duke University, but we do support a wide range of technologies for  
virtual communication with off-site staff and collaborators.

Required Qualifications:
* Demonstrated success collaborating with clients on custom software  
solutions
* Experience with various stages of the software development cycle
* Expertise in development and testing of user interface designs
* Excellent communication skills, both virtual and face-to-face
* A four-year college degree in Computer Science, Bioinformatics or a  
related field

Preferred Qualifications:
* M.S. or Ph.D. in Computer Science, Bioinformatics or related field  
along with demonstrated interest in science, particularly biology
* Expertise in rapid application development and respective  
programming technologies and languages (e.g., modern scripting  
languages and web-application frameworks such as Python/Django, Ruby/ 
Ruby-on-Rails, and Perl/Catalyst), fluency in Java programming, and  
prior experience in relational database programming (PostgreSQL or  
MySQL)
* Expertise in dynamic and interactive web technologies (JavaScript,  
CGI), web service (SOAP, REST, XML, JSON) and semantic web technologies
* Experience with open-source, and collaborative, software  
development, software usability design and assessment
* Expertise in graphic design, data visualization and/or scientific  
data integration

How to apply: Please send cover letter, resume and contact information  
for three references to Dr. Karen Cranston, Training Coordinator and  
Bioinformatics Project Manager (karen.cranston at nescent.org). Review of  
applications will begin March 21, 2011. Informal inquires or requests  
for additional information may be directed to Dr. Cranston by email or  
phone (+1-919-613-2275).

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From hartzell at alerce.com  Sat Mar  5 21:18:50 2011
From: hartzell at alerce.com (George Hartzell)
Date: Sat, 5 Mar 2011 13:18:50 -0800
Subject: [Bioperl-l] minicpan (CPAN::Mini) doesn't mirror BioPerl-1.6.1
In-Reply-To: <19824.7810.437300.584113@gargle.gargle.HOWL>
References: <19824.7810.437300.584113@gargle.gargle.HOWL>
Message-ID: <19826.43194.173739.594355@gargle.gargle.HOWL>

George Hartzell writes:
 > 
 > Hi all,
 > 
 > I'm using minicpan (from CPAN::Mini) to keep a cpan mirror.  My mirror
 > does not contain BioPerl-1.6.1.tar.gz even though search.cpan.org
 > seems to have it.  The only tarballs that end up in Chris' directory
 > are these:
 > 
 > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz
 > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-network-1.6.0.tar.gz
 > /Users/hartzell/tmp/minicpan//authors/id/C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
 > 
 > It is listed in the 02packages.details.txt.gz file that is mirrored.
 > 

Here's the conclusion, for the list and posterity.

CPAN::Mini is excluding the BioPerl modules, as well as the perl
source distributions, because they're "too big".

You can get minicpan to mirror all this stuff by adding

 perl: 1

to your .minicpan, which causes the app to set its internal skip_perl
flag to 0, which in turn causes it to mirror the big stuff.

I'm running a few experiments to figure out how much add'l space gets
used if one allows bioperl without all of the other perl source
releases.  Maybe I can convince Ricard to do something less heavy
handed for us.

g.


From hlapp at drycafe.net  Sun Mar  6 02:58:04 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 5 Mar 2011 21:58:04 -0500
Subject: [Bioperl-l] Job opening for GMOD User Support Specialist
Message-ID: <814155D1-1CD5-4E66-B726-2CF7E33EF3CE@drycafe.net>

(Apologies if you receive multiple copies, and also if you are not  
interested in job opportunities. If you know someone who might be  
interested please forward.)

============================
GMOD User Support Specialist
============================

Are you fascinated by genomics and bioinformatics? Are you passionate  
about collaborative open-source software? Do you enjoy teaching and  
working with scientists?  If so, then this position is for you.

The Generic Model Organism Database project (GMOD) is a collection of  
open source software tools for creating and managing biological, and  
particularly genomic, databases.  GMOD has a large, highly  
distributed, and dynamic community of software users and developers.   
The University of North Carolina at Chapel Hill has an opening for a  
GMOD user support specialist, to be based at the US National  
Evolutionary Synthesis Center (NESCent, www.nescent.org) in Durham,  
North Carolina, while serving the international community of GMOD users.

Job Description:

The GMOD user support specialist will maintain online documentation;  
respond to mailing list help requests; present tutorials; organize  
short courses, conference sessions and other community building  
activities; survey user needs, and recruit members of the community to  
assist with these functions.   The incumbent will collaborate closely  
with the GMOD Coordinator (Scott Cain, The Ontario Institute for  
Cancer Research) and other distributed personnel.  See http://gmod.org/wiki/GMOD_Help_Desk 
  for more background on the activities of the user support  
specialist.  The salary range is $68,906 to $82,687, depending on  
qualifications, and the incumbent will receive a comprehensive  
benefits package as an SPA employee within the UNC system.

Qualifications:

Required qualifications include: excellent written and verbal  
communication skills; team orientation with strong interpersonal  
skills. Preferred qualifications include: an MS or PhD in biology,  
computer science or related field; three or more years of experience  
with web programming and relational database management systems; three  
or more years of experience with genome database administration or  
curation, preferably in a GMOD environment; at least one year of  
experience with web content management, ideally using MediaWiki;  
freedom to travel 5-15 weeks/yr.

To Apply:

Please provide a cover letter and CV, including contact information  
for three references, to Hilmar Lapp, Assistant Director of  
Informatics, NESCent, at hlapp at nescent.org, and submit materials  
through http://bit.ly/h9l74r.  Inquiries may be addressed to H. Lapp  
by email or by phone at 919.668.5288.

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From eigenrosen at gmail.com  Sun Mar  6 23:34:09 2011
From: eigenrosen at gmail.com (Michael Rosen)
Date: Sun, 6 Mar 2011 15:34:09 -0800
Subject: [Bioperl-l] bioperl-ext installation
Message-ID: <AANLkTinuaavEU4RwxZu=bmFpUVxpYBAisOv9wgKmQ9+9@mail.gmail.com>

Hi all,
Sorry in advance for a most likely trivial question: I did the standard
make/make test/make install of the bioperl-ext packages with no problems (I
can post the full output if useful). But when I try to run a simple program
that has no trouble on a different machine w bioperl-ext I get:

"The C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has
not been installed.
 Please install the bioperl-ext package"

Any ideas what might be happening? I don't know if the problem was with
installation (but I got "all tests successful during make test") or if I may
need to add the installed packages to some path variable? I'm relatively new
to both bioperl and perl generally so not sure where to start

Thanks


From rmb32 at cornell.edu  Mon Mar  7 16:26:28 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Mon, 07 Mar 2011 11:26:28 -0500
Subject: [Bioperl-l] call for project ideas - Google Summer of Code
Message-ID: <4D750734.4020002@cornell.edu>

Hi all,

Google's Summer of Code is coming round again, very soon now (mentoring 
organization applications are due this week).  We need to update our 
project ideas for prospective Summer of Code interns.  The rest of the 
page also needs updates, changing dates and such.

There's a page on the BioPerl wiki, please have a look and add your 
ideas for intern projects.

For more on Google Summer of Code, what it is and how it works, see 
their FAQ at 
http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2011/faqs

One of the summer intern ideas I have on the page so far is to help with 
the tough grunt work of breaking BioPerl into smaller, more easily 
managed distributions.  I'm sure you all can think of plenty more!

Here's the page: http://www.bioperl.org/wiki/Google_Summer_of_Code

Please have a look, add your project ideas, and delete ones that have 
already been done or are no longer relevant.

Rob



From tzhu at mail.bnu.edu.cn  Tue Mar  8 06:45:11 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Tue, 08 Mar 2011 14:45:11 +0800
Subject: [Bioperl-l] locate introns in a protein sequence
Message-ID: <1299566711.5243.11.camel@ubuntu>

Hello, everyone. For example, I have a GTF file annotating like this,

Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 start_codon 25009
25011 . + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 stop_codon 26003
26005 . + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 24828
25172 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25009 25172 .
+ 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 25245
25364 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25245 25364 .
+ 1 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 25414
26178 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25414 26002 .
+ 1 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";

Obviously this transcript "SPOG_00008T0" has two introns.

Also I have a corresponding protein sequence file like this( in fasta
format),

>SPOG_00008T0 | SPOG_00008 | Schizosaccharomyces cryophilus OY26 exosome
subunit Rrp45 (292 aa)
MSKSLEPSANNKGFIVNALKKELRLDGRSLTDFRDLKIEFGEDYGQVDISLGSTRVMARI
SAEITKPYSDRPFDGIFAITTELTPLASPAFETGRVSEQEVIISRLIEQAIRRSNALDTE
SLCIISGQKCWSVRASVHFINHDGNLVDAACIAVITGLCHFRRPEITVLGDEVTVHSIEE
RVPVPLSVLHTPICVTFSFFEDGSLSAIDASLEEEELRTGSMTVTLNKNREICQIFKAGG
VTIEASSVVACAHTAFQKTTSIISEIQRALDEDLSKKETQFFGGSAENQRS*

I hope to precisely locate these two introns into the protein
sequence(find their location among the amino acids). Please recommend a
relatively convenient method. Thank you!



-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)



From jason at bioperl.org  Tue Mar  8 07:42:54 2011
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 07 Mar 2011 23:42:54 -0800
Subject: [Bioperl-l] locate introns in a protein sequence
In-Reply-To: <1299566711.5243.11.camel@ubuntu>
References: <1299566711.5243.11.camel@ubuntu>
Message-ID: <4D75DDFE.9090602@bioperl.org>

I think there are several ways to do this, the easiest is to walk 
through each exon, and count up the codons, and print out the 
translation of the codons so far when you get to the end of an exon, 
keeping the overhang for the next exon.

That's basically what I do here in terms of counting, though I'm mapping 
introns into an alignment not a single peptide (though undocumented so 
it is a bit impenetrable)
  https://github.com/hyphaltip/thesis/blob/master/src/intron/map_introns_aln.pl

Use Bio::DB::SeqFeature::Store will make this much easier.  You will 
want to convert this Broad GTF to GFF3 with this script
https://github.com/hyphaltip/genome-scripts/blob/master/data_format/gtf2gff3_3level.pl

Then load the annotation along with a scaffold GFF3 (like one from this 
script run on your FASTA genome file
  https://github.com/hyphaltip/genome-scripts/blob/master/gbrowse_tools/fasta_to_gbrowse_scaffold.pl
  - just watch out -- the Broad is capitalizing the contig name 
(Supercontig_3.1) while the FASTA file will have it uncapped and 
truncated name (supercont_3.1) so you need to fix that in either of the 
files so it is consistent - a perl one liner will work here;
perl -i -p -e 's/^>supercont3\./>Supercontig_3./' GENOME.fasta

and load this in and you'll then be able to use the Bio::DB::SeqFeature 
to get all genes, walk through them a CDS for each gene, one a time, and 
then just keep count of the frame you are in and the exon length and 
you'll know where the introns go in the protein.

for my $gene ( $dbh->features(-type => 
"gene:S_cryophilus_OY26_V3_CALLGENES_FINAL_2
") ) {
  for my $mRNA ( $gene->get_SeqFeatures('mRNA') ) {
   for my $CDS ( $mRNA->get_SeqFeatures('CDS') ) {
    my $length = $CDS->length;
    # do some stuff to keep count or whatever you need to figure out 
where you are to put the intron
   }
  }
}

you can also see this code which converts folders of GFF3 + genomes into 
coding seqs, translated peps, etc.
  https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/gff3_to_cdspep.pl

It all depends on what you want to report from this type of query.

Tao Zhu wrote:
> Hello, everyone. For example, I have a GTF file annotating like this,
>
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 start_codon 25009
> 25011 . + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 stop_codon 26003
> 26005 . + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 24828
> 25172 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25009 25172 .
> + 0 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 25245
> 25364 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25245 25364 .
> + 1 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 exon 25414
> 26178 . + . gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
> Supercontig_3.3 S_cryophilus_OY26_V3_CALLGENES_FINAL_2 CDS 25414 26002 .
> + 1 gene_id "SPOG_00008"; transcript_id "SPOG_00008T0";
>
> Obviously this transcript "SPOG_00008T0" has two introns.
>
> Also I have a corresponding protein sequence file like this( in fasta
> format),
>
>> SPOG_00008T0 | SPOG_00008 | Schizosaccharomyces cryophilus OY26 exosome
> subunit Rrp45 (292 aa)
> MSKSLEPSANNKGFIVNALKKELRLDGRSLTDFRDLKIEFGEDYGQVDISLGSTRVMARI
> SAEITKPYSDRPFDGIFAITTELTPLASPAFETGRVSEQEVIISRLIEQAIRRSNALDTE
> SLCIISGQKCWSVRASVHFINHDGNLVDAACIAVITGLCHFRRPEITVLGDEVTVHSIEE
> RVPVPLSVLHTPICVTFSFFEDGSLSAIDASLEEEELRTGSMTVTLNKNREICQIFKAGG
> VTIEASSVVACAHTAFQKTTSIISEIQRALDEDLSKKETQFFGGSAENQRS*
>
> I hope to precisely locate these two introns into the protein
> sequence(find their location among the amino acids). Please recommend a
> relatively convenient method. Thank you!
>
>
>

-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki



From bio.justin100 at gmail.com  Tue Mar  8 22:31:42 2011
From: bio.justin100 at gmail.com (Justin Li)
Date: Tue, 8 Mar 2011 17:31:42 -0500
Subject: [Bioperl-l] Bio::Phylo vs Bio:TreeIO; interface to Fitch
Message-ID: <AANLkTik+HwSQNN3WCkaqQRPz3xqheaa0khmzdD5nndJa@mail.gmail.com>

Hi,

Both Bio::Phylo and Bio:TreeIO seem to be able to parse phylogenetic trees.

Could anyone having experience with both of them please comment on their
capability/robustness/ease of use?

Where can I find the documentation for
"Bio::Tools::Run::PiseApplication::fitch"?

Thanks,

Justin


From abhishek.vit at gmail.com  Tue Mar  8 22:42:03 2011
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Tue, 8 Mar 2011 14:42:03 -0800
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
	Sequences (reads)
Message-ID: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>

Hi All

I have results from different megablast of short reads(DNA sequences)
and after extracting the tophit for each read I want to bin them by
their lineage creating a tree.

For example.

If blast query hits the reference ->
gi|196110604|gb|CP001103.1|__Alteromonas_macleodii_'Deep_ecotype',_complete_genome

I want to get the lineage for this specie.

Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Alteromonas;Alteromona

The final goal is to do the above mapping as efficiently as possible.
Any pointers will be appreciated.


Thanks!
-Abhi


From miguel.pignatelli at uv.es  Wed Mar  9 09:20:47 2011
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Wed, 09 Mar 2011 09:20:47 +0000
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
Message-ID: <4D77466F.4040604@uv.es>

Hi Abhishek,

For a non bioperl related solution, take a look at Bio::LITE::Taxonomy.
It has been design to deal with great number of sequences (it is fast 
and efficient).

You may also find interesting the Blast2lca tool,

https://github.com/emepyc/Blast2lca

It currently works with the best hits for each query (calculates the 
lower common ancestor), but if you want to use only the best hit, please 
drop me a line.

Please, let me know if you need further help with any of these,

Cheers,

M;



On 08/03/11 22:42, Abhishek Pratap wrote:
> Hi All
>
> I have results from different megablast of short reads(DNA sequences)
> and after extracting the tophit for each read I want to bin them by
> their lineage creating a tree.
>
> For example.
>
> If blast query hits the reference ->
> gi|196110604|gb|CP001103.1|__Alteromonas_macleodii_'Deep_ecotype',_complete_genome
>
> I want to get the lineage for this specie.
>
> Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Alteromonas;Alteromona
>
> The final goal is to do the above mapping as efficiently as possible.
> Any pointers will be appreciated.
>
>
> Thanks!
> -Abhi
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From shalabh.sharma7 at gmail.com  Wed Mar  9 17:34:57 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 9 Mar 2011 12:34:57 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <4D77466F.4040604@uv.es>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
Message-ID: <AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>

Hey Abhishek:
                    The other way to deal with this that you can download
the gi_taxaid file from ncbi.
Convert all your GI's to taxaid and use Bio::DB:Taxanomy.
http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Taxon.html

I think there are lot of other options too, if you are interested you can
search for the thread which i started long time back.

Hope this helps.

-Shalabh Sharma
-----------------------------------------------
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636

On Wed, Mar 9, 2011 at 4:20 AM, Miguel Pignatelli
<miguel.pignatelli at uv.es>wrote:

> Hi Abhishek,
>
> For a non bioperl related solution, take a look at Bio::LITE::Taxonomy.
> It has been design to deal with great number of sequences (it is fast and
> efficient).
>
> You may also find interesting the Blast2lca tool,
>
> https://github.com/emepyc/Blast2lca
>
> It currently works with the best hits for each query (calculates the lower
> common ancestor), but if you want to use only the best hit, please drop me a
> line.
>
> Please, let me know if you need further help with any of these,
>
> Cheers,
>
> M;
>
>
>
>
> On 08/03/11 22:42, Abhishek Pratap wrote:
>
>> Hi All
>>
>> I have results from different megablast of short reads(DNA sequences)
>> and after extracting the tophit for each read I want to bin them by
>> their lineage creating a tree.
>>
>> For example.
>>
>> If blast query hits the reference ->
>>
>> gi|196110604|gb|CP001103.1|__Alteromonas_macleodii_'Deep_ecotype',_complete_genome
>>
>> I want to get the lineage for this specie.
>>
>>
>> Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Alteromonas;Alteromona
>>
>> The final goal is to do the above mapping as efficiently as possible.
>> Any pointers will be appreciated.
>>
>>
>> Thanks!
>> -Abhi
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From abhishek.vit at gmail.com  Thu Mar 10 03:25:58 2011
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Wed, 9 Mar 2011 19:25:58 -0800
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
Message-ID: <AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>

Thanks guys. I could not try either method today but will get back to
you if I face problem.

Best,
-Abhi

On Wed, Mar 9, 2011 at 9:34 AM, shalabh sharma
<shalabh.sharma7 at gmail.com> wrote:
> Hey Abhishek:
> ?? ? ? ? ? ? ? ? ? ?The other way to deal with this that you can download
> the gi_taxaid file from ncbi.
> Convert all your GI's to taxaid and use Bio::DB:Taxanomy.
> http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy
> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Taxon.html
> I think there are lot of other options too, if you are interested you can
> search for the thread which i started long time back.
> Hope this helps.
> -Shalabh Sharma
> -----------------------------------------------
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
>
> On Wed, Mar 9, 2011 at 4:20 AM, Miguel Pignatelli <miguel.pignatelli at uv.es>
> wrote:
>>
>> Hi Abhishek,
>>
>> For a non bioperl related solution, take a look at Bio::LITE::Taxonomy.
>> It has been design to deal with great number of sequences (it is fast and
>> efficient).
>>
>> You may also find interesting the Blast2lca tool,
>>
>> https://github.com/emepyc/Blast2lca
>>
>> It currently works with the best hits for each query (calculates the lower
>> common ancestor), but if you want to use only the best hit, please drop me a
>> line.
>>
>> Please, let me know if you need further help with any of these,
>>
>> Cheers,
>>
>> M;
>>
>>
>>
>> On 08/03/11 22:42, Abhishek Pratap wrote:
>>>
>>> Hi All
>>>
>>> I have results from different megablast of short reads(DNA sequences)
>>> and after extracting the tophit for each read I want to bin them by
>>> their lineage creating a tree.
>>>
>>> For example.
>>>
>>> If blast query hits the reference ->
>>>
>>> gi|196110604|gb|CP001103.1|__Alteromonas_macleodii_'Deep_ecotype',_complete_genome
>>>
>>> I want to get the lineage for this specie.
>>>
>>>
>>> Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Alteromonas;Alteromona
>>>
>>> The final goal is to do the above mapping as efficiently as possible.
>>> Any pointers will be appreciated.
>>>
>>>
>>> Thanks!
>>> -Abhi
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>



From ian.mcdowell at gmail.com  Thu Mar 10 17:11:50 2011
From: ian.mcdowell at gmail.com (Ian Mc Dowell)
Date: Thu, 10 Mar 2011 12:11:50 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
	<AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
Message-ID: <AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>

Hi all,

I would like to take local blast hit sequences, i.e. hsp_hseq, and extract
the full sequences of those hits from the original fasta file and put them
in a fasta file of all hits that I can use later.

This should be a widely performed task but I can't find any scripts that
directly address this issue.  I have not acquired the skills to make my own
scripts for this task.

Thanks so much if you have anything that can help me out,

Ian McDowell
Aquatic Pathology
University of Rhode Island


From ian.mcdowell at gmail.com  Thu Mar 10 17:13:01 2011
From: ian.mcdowell at gmail.com (Ian Mc Dowell)
Date: Thu, 10 Mar 2011 12:13:01 -0500
Subject: [Bioperl-l] Local blast hit (hsp_hseq) extracted from fasta file
Message-ID: <AANLkTinF-Ai-AvTPG6ET9xWW0NaeMQugYJpumm4g-7NH@mail.gmail.com>

Hi all,

I would like to take local blast hit sequences, i.e. hsp_hseq in blast xml
format, and extract the full sequences of those hits from the original fasta
file and put them in a fasta file of all hits that I can use later.

This should be a widely performed task but I can't find any scripts that
directly address this issue.  I have not acquired the skills to make my own
scripts for this task.

Thanks so much if you have anything that can help me out,

Ian McDowell
Aquatic Pathology
University of Rhode Island


From rmb32 at cornell.edu  Thu Mar 10 17:22:51 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 10 Mar 2011 12:22:51 -0500
Subject: [Bioperl-l] update Google Summer of Code project ideas
Message-ID: <4D7908EB.6050003@cornell.edu>

Hi all,

Please make sure the BioPerl information is up to date for 2011 on both 
the OBF and BioPerl wikis.  The current page looks pretty good, just be 
aware that Google will be looking at it in the next few days to evaluate 
whether OBF will be accepted again this year to GSoC.

OBF wiki page: http://www.open-bio.org/wiki/Google_Summer_of_Code
BioPerl wiki: http://bioperl.org/wiki/Google_Summer_of_Code

Rob

----
Robert Buels
(prospective) 2011 OBF GSoC Organization Admin


From shalabh.sharma7 at gmail.com  Thu Mar 10 17:24:04 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Thu, 10 Mar 2011 12:24:04 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
	<AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
	<AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>
Message-ID: <AANLkTik9jt9Pkrgng4zv4nRhDmK0_bRpnbGJe+i9Dark@mail.gmail.com>

Hey Ian,
            I am not sure if i understood your problem completely.
But if you have ids of blast hits you can use 'fastacmd' to fetch sequences
from the database you used for blast.

-Shalabh Sharma
-----------------------------------------
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636

On Thu, Mar 10, 2011 at 12:11 PM, Ian Mc Dowell <ian.mcdowell at gmail.com>wrote:

> Hi all,
>
> I would like to take local blast hit sequences, i.e. hsp_hseq, and extract
> the full sequences of those hits from the original fasta file and put them
> in a fasta file of all hits that I can use later.
>
> This should be a widely performed task but I can't find any scripts that
> directly address this issue.  I have not acquired the skills to make my own
> scripts for this task.
>
> Thanks so much if you have anything that can help me out,
>
> Ian McDowell
> Aquatic Pathology
> University of Rhode Island
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From ian.mcdowell at gmail.com  Thu Mar 10 17:31:29 2011
From: ian.mcdowell at gmail.com (Ian Mc Dowell)
Date: Thu, 10 Mar 2011 12:31:29 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTik9jt9Pkrgng4zv4nRhDmK0_bRpnbGJe+i9Dark@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
	<AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
	<AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>
	<AANLkTik9jt9Pkrgng4zv4nRhDmK0_bRpnbGJe+i9Dark@mail.gmail.com>
Message-ID: <AANLkTi=-12y0LWzV2gRgriE=z3=d_-OKwDRe2wSWkmwr@mail.gmail.com>

I have a deeply sequenced transcriptome so when I look for a gene of
interest in my short reads (108bp) I get thousands of hits, at very low E
values.  And I want to do this for many sequences of interest. That's why I
want a script to automate the process of grabbing the accession numbers from
the blast xml output, then searching in the fasta file which is equivalent
to my local database and pulling those relevant reads.

On Thu, Mar 10, 2011 at 12:24 PM, shalabh sharma
<shalabh.sharma7 at gmail.com>wrote:

> Hey Ian,
>             I am not sure if i understood your problem completely.
> But if you have ids of blast hits you can use 'fastacmd' to fetch sequences
> from the database you used for blast.
>
> -Shalabh Sharma
> -----------------------------------------
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
>
> On Thu, Mar 10, 2011 at 12:11 PM, Ian Mc Dowell <ian.mcdowell at gmail.com>wrote:
>
>> Hi all,
>>
>> I would like to take local blast hit sequences, i.e. hsp_hseq, and extract
>> the full sequences of those hits from the original fasta file and put them
>> in a fasta file of all hits that I can use later.
>>
>> This should be a widely performed task but I can't find any scripts that
>> directly address this issue.  I have not acquired the skills to make my
>> own
>> scripts for this task.
>>
>> Thanks so much if you have anything that can help me out,
>>
>> Ian McDowell
>> Aquatic Pathology
>> University of Rhode Island
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>


From hrh at fmi.ch  Thu Mar 10 17:37:07 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Thu, 10 Mar 2011 18:37:07 +0100
Subject: [Bioperl-l] Local blast hit (hsp_hseq) extracted from fasta file
In-Reply-To: <AANLkTinF-Ai-AvTPG6ET9xWW0NaeMQugYJpumm4g-7NH@mail.gmail.com>
References: <AANLkTinF-Ai-AvTPG6ET9xWW0NaeMQugYJpumm4g-7NH@mail.gmail.com>
Message-ID: <4D790C43.5080801@fmi.ch>



On 03/10/2011 06:13 PM, Ian Mc Dowell wrote:
> Hi all,
>
> I would like to take local blast hit sequences, i.e. hsp_hseq in blast xml
> format, and extract the full sequences of those hits from the original fasta
> file and put them in a fasta file of all hits that I can use later.
>
> This should be a widely performed task but I can't find any scripts that
> directly address this issue.  I have not acquired the skills to make my own
> scripts for this task.


Hi Ian

It is not a Bioperl solution, but a simple one:

Assuming, you are using the NCBI blast+ tools, make sure you create the 
BLAST indices with the "-parse_seqids" option. This will allow you to 
extract individual sequences (in fasta format) from the BLAST database 
with the command 'blastdbcmd' by providing a comma-delimited search 
string of sequence identifiers. Fore more details see:

http://tinyurl.com/5sq2ehg


Regards, Hans


> Thanks so much if you have anything that can help me out,
>
> Ian McDowell
> Aquatic Pathology
> University of Rhode Island
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From shalabh.sharma7 at gmail.com  Thu Mar 10 17:42:51 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Thu, 10 Mar 2011 12:42:51 -0500
Subject: [Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA
 Sequences (reads)
In-Reply-To: <AANLkTi=-12y0LWzV2gRgriE=z3=d_-OKwDRe2wSWkmwr@mail.gmail.com>
References: <AANLkTimoP5tLmvKv5waKYLTcHwuzNQsyd9i_vsa5RmCh@mail.gmail.com>
	<4D77466F.4040604@uv.es>
	<AANLkTikbtdbfNVRb=2=d3W0BBmbAWe=Bt1yznuWJMmj-@mail.gmail.com>
	<AANLkTinHboCYEZfhyVHxu9BOhpLAGMdgcyV68ojDQVhE@mail.gmail.com>
	<AANLkTinQe=wwqqjuqcdVw9-hh2YW1W29wnB3yfg5rOyi@mail.gmail.com>
	<AANLkTik9jt9Pkrgng4zv4nRhDmK0_bRpnbGJe+i9Dark@mail.gmail.com>
	<AANLkTi=-12y0LWzV2gRgriE=z3=d_-OKwDRe2wSWkmwr@mail.gmail.com>
Message-ID: <AANLkTin13Uhj8ZgQ1-+c0SjXbRBvU8VHdGhUXyqea1FV@mail.gmail.com>

Hey Ian,
             Writing that kind of script would not take that much time. But
i am not very much familiar with xml format.
But still you can do without writing a complicated script.

once you get the output you can get all the ids (use grep or simple perl
script to parse ids).
Then use that list of ids to fetch sequences from your database by using
"fastacmd" .

-Shalabh


On Thu, Mar 10, 2011 at 12:31 PM, Ian Mc Dowell <ian.mcdowell at gmail.com>wrote:

> I have a deeply sequenced transcriptome so when I look for a gene of
> interest in my short reads (108bp) I get thousands of hits, at very low E
> values.  And I want to do this for many sequences of interest. That's why I
> want a script to automate the process of grabbing the accession numbers from
> the blast xml output, then searching in the fasta file which is equivalent
> to my local database and pulling those relevant reads.
>
> On Thu, Mar 10, 2011 at 12:24 PM, shalabh sharma <
> shalabh.sharma7 at gmail.com> wrote:
>
>> Hey Ian,
>>             I am not sure if i understood your problem completely.
>> But if you have ids of blast hits you can use 'fastacmd' to fetch
>> sequences from the database you used for blast.
>>
>> -Shalabh Sharma
>> -----------------------------------------
>> Shalabh Sharma
>> Scientific Computing Professional Associate (Bioinformatics Specialist)
>> Department of Marine Sciences
>> University of Georgia
>> Athens, GA 30602-3636
>>
>> On Thu, Mar 10, 2011 at 12:11 PM, Ian Mc Dowell <ian.mcdowell at gmail.com>wrote:
>>
>>> Hi all,
>>>
>>> I would like to take local blast hit sequences, i.e. hsp_hseq, and
>>> extract
>>> the full sequences of those hits from the original fasta file and put
>>> them
>>> in a fasta file of all hits that I can use later.
>>>
>>> This should be a widely performed task but I can't find any scripts that
>>> directly address this issue.  I have not acquired the skills to make my
>>> own
>>> scripts for this task.
>>>
>>> Thanks so much if you have anything that can help me out,
>>>
>>> Ian McDowell
>>> Aquatic Pathology
>>> University of Rhode Island
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


From cjfields at illinois.edu  Mon Mar 14 17:44:44 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 12:44:44 -0500
Subject: [Bioperl-l] bioperl wiki spam
Message-ID: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>

All,

We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:

http://www.mediawiki.org/wiki/Extension:ConfirmAccount

I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.  

Any thoughts?

chris


From cjfields at illinois.edu  Mon Mar 14 17:51:51 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 12:51:51 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Google Summer of Code
Message-ID: <42CCFB33-B9FC-41C2-987D-BF969F5111EC@illinois.edu>

All,

As Rob Buels previously mentioned, the Open Bioinformatics Foundation has again applied for the Google Summer of Code (GSoC).  BioPerl has been involved with GSoC over the last several years, most recently when Jun Yin refactored the alignment subsystem, code that will be incorporated into BioPerl after the 1.6.2 release:

http://www.bioperl.org/wiki/Google_Summer_of_Code#2010

We have several ideas for projects for the upcoming GSoC 2011 on the wiki, but we are open to just about anything BioPerl-related.  We are also looking for more potential mentors!  If you have ideas or would like to be a mentor, free to submit to the web page, discuss it on this list, or join us on IRC (#obf-soc on freenode).

chris

Christopher Fields
IGB Postdoctoral Fellow
Genomics of Neural & Behavioral Plasticity
University of Illinois Urbana-Champaign
Institute for Genomic Biology
1206 W. Gregory Dr. , MC-195
Urbana, IL 61801




From scott at scottcain.net  Mon Mar 14 18:12:55 2011
From: scott at scottcain.net (Scott Cain)
Date: Mon, 14 Mar 2011 14:12:55 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
Message-ID: <AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>

Hi Chris,

The GMOD wiki has been getting hit similarly.  I've been thinking
about the "vampire" model that EcoliWiki uses: once you have an
account, you have the ability to approve other people's accounts.  The
hope being to distribute the load.  I'm not thrilled about it though:
I want the barrier to entry to be as low as possible.  We already make
it so that you have to have an account to edit, passing a recaptcha on
the way.  Apparently that barrier is already a little too low :-/

Scott


On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
> All,
>
> We have been getting inundated on the wiki with spam lately. ?In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>
> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>
> I wanted to get everyone's opinion on this prior to enforcing it. ?The queue is pretty configurable, and one can set this to auto-delete old requests.
>
> Any thoughts?
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From cjfields at illinois.edu  Mon Mar 14 18:25:05 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 13:25:05 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
Message-ID: <5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>

On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):

"Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."

I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.

chris

On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:

> Hi Chris,
> 
> The GMOD wiki has been getting hit similarly.  I've been thinking
> about the "vampire" model that EcoliWiki uses: once you have an
> account, you have the ability to approve other people's accounts.  The
> hope being to distribute the load.  I'm not thrilled about it though:
> I want the barrier to entry to be as low as possible.  We already make
> it so that you have to have an account to edit, passing a recaptcha on
> the way.  Apparently that barrier is already a little too low :-/
> 
> Scott
> 
> 
> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> All,
>> 
>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>> 
>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>> 
>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>> 
>> Any thoughts?
>> 
>> chris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research




From David.Messina at sbc.su.se  Mon Mar 14 18:25:10 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 14 Mar 2011 19:25:10 +0100
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
Message-ID: <5650D7D3-11ED-4ABF-89E8-BE9175848196@sbc.su.se>

> Any thoughts?

Do it.



From hlapp at drycafe.net  Mon Mar 14 18:48:55 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Mon, 14 Mar 2011 14:48:55 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
Message-ID: <6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>

Any update on the OpenID extension?

	-hilmar

On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:

> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit 
> ):
>
> "Unfortunately, reCAPTCHA might be a victim of its own success - as  
> of 2011, some spammers appear to have figured out a way to bypass  
> it, either through character recognition or by using humans. For  
> that reason, it is not necessarily recommended."
>
> I agree about the barrier to entry issue, but unfortunately with the  
> wiki we're facing a reality check re: spam attacks.  We can probably  
> set up a new group for users that allows account approval, though,  
> which might alleviate the process somewhat.
>
> chris
>
> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>
>> Hi Chris,
>>
>> The GMOD wiki has been getting hit similarly.  I've been thinking
>> about the "vampire" model that EcoliWiki uses: once you have an
>> account, you have the ability to approve other people's accounts.   
>> The
>> hope being to distribute the load.  I'm not thrilled about it though:
>> I want the barrier to entry to be as low as possible.  We already  
>> make
>> it so that you have to have an account to edit, passing a recaptcha  
>> on
>> the way.  Apparently that barrier is already a little too low :-/
>>
>> Scott
>>
>>
>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields  
>> <cjfields at illinois.edu> wrote:
>>> All,
>>>
>>> We have been getting inundated on the wiki with spam lately.  In  
>>> order to get on top of this, I'm thinking about having the wiki  
>>> set up so wiki admins approve new user accounts, using the  
>>> ConfirmAccount plugin:
>>>
>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>
>>> I wanted to get everyone's opinion on this prior to enforcing it.   
>>> The queue is pretty configurable, and one can set this to auto- 
>>> delete old requests.
>>>
>>> Any thoughts?
>>>
>>> chris
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>>
>> -- 
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at  
>> scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From cjfields at illinois.edu  Mon Mar 14 18:55:31 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 13:55:31 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
Message-ID: <2EB73F6E-AAD3-46BD-BB57-AAB3AA1063F7@illinois.edu>

We can test that one out first.  Maybe that will help.

chris

On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:

> Any update on the OpenID extension?
> 
> 	-hilmar
> 
> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
> 
>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>> 
>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>> 
>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>> 
>> chris
>> 
>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>> 
>>> Hi Chris,
>>> 
>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>> about the "vampire" model that EcoliWiki uses: once you have an
>>> account, you have the ability to approve other people's accounts.  The
>>> hope being to distribute the load.  I'm not thrilled about it though:
>>> I want the barrier to entry to be as low as possible.  We already make
>>> it so that you have to have an account to edit, passing a recaptcha on
>>> the way.  Apparently that barrier is already a little too low :-/
>>> 
>>> Scott
>>> 
>>> 
>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>> All,
>>>> 
>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>> 
>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>> 
>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>> 
>>>> Any thoughts?
>>>> 
>>>> chris
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hartzell at alerce.com  Tue Mar 15 00:37:36 2011
From: hartzell at alerce.com (George Hartzell)
Date: Mon, 14 Mar 2011 17:37:36 -0700
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <5650D7D3-11ED-4ABF-89E8-BE9175848196@sbc.su.se>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<5650D7D3-11ED-4ABF-89E8-BE9175848196@sbc.su.se>
Message-ID: <19838.46288.715397.413627@gargle.gargle.HOWL>

Dave Messina writes:
 > > Any thoughts?
 > 
 > Do it.

Do it^2.  You have better things to do than waste time on spammers.

It's nice to not have the bar too high for new folks, but in this age
of spam I think people understand.

g.


From cjfields at illinois.edu  Tue Mar 15 03:01:45 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 22:01:45 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
Message-ID: <84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>

Okay, we have bioperl.org set up to use OpenID, works well:  

http://www.bioperl.org/wiki/Special:OpenIDLogin

I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.

chris

On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:

> Any update on the OpenID extension?
> 
> 	-hilmar
> 
> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
> 
>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>> 
>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>> 
>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>> 
>> chris
>> 
>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>> 
>>> Hi Chris,
>>> 
>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>> about the "vampire" model that EcoliWiki uses: once you have an
>>> account, you have the ability to approve other people's accounts.  The
>>> hope being to distribute the load.  I'm not thrilled about it though:
>>> I want the barrier to entry to be as low as possible.  We already make
>>> it so that you have to have an account to edit, passing a recaptcha on
>>> the way.  Apparently that barrier is already a little too low :-/
>>> 
>>> Scott
>>> 
>>> 
>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>> All,
>>>> 
>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>> 
>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>> 
>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>> 
>>>> Any thoughts?
>>>> 
>>>> chris
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Tue Mar 15 03:12:16 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 14 Mar 2011 22:12:16 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <19838.46288.715397.413627@gargle.gargle.HOWL>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<5650D7D3-11ED-4ABF-89E8-BE9175848196@sbc.su.se>
	<19838.46288.715397.413627@gargle.gargle.HOWL>
Message-ID: <D49A790C-E30D-4587-B9B6-0D5E99B84D97@illinois.edu>

On Mar 14, 2011, at 7:37 PM, George Hartzell wrote:

> Dave Messina writes:
>>> Any thoughts?
>> 
>> Do it.
> 
> Do it^2.  You have better things to do than waste time on spammers.
> 
> It's nice to not have the bar too high for new folks, but in this age
> of spam I think people understand.
> 
> g.

I've disabled new account creation unless OpenID is used; apparently this has worked elsewhere to cut down on spam.  All old accounts are still active, but I think new users will be prompted to tie an OpenID to the account.  

Anyway, if that doesn't work we'll go to the next step (account verification).

chris




From ross at cuhk.edu.hk  Tue Mar 15 05:54:35 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Tue, 15 Mar 2011 13:54:35 +0800
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
Message-ID: <004001cbe2d5$76598200$630c8600$@edu.hk>

$gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
'Fasta');            
$allseqobj = $gb->get_Stream_by_acc("A3ZI37");        
                l
print "HEELO";                                           
while ($seqobj = $allseqobj->next_seq) {             
                        #$seqobj = $allseqobj->next_seq;

                        $seq=$seqobj->seq;

                        }

                    print "222   HEELO";



I find that the 1st HEELO can be printed while the 2nd one can't. Google
does not return checking success/failure or null/exist of the Seq Object. As
the 1st HEELO can be executed, so no throw/exception occurs for the
get_Stream_by_acc. So what can I do? The real case is not hard-coding this
A3ZI37 but reading a file that may contain a lot of these "illegitimate"
accession numbers.



From David.Messina at sbc.su.se  Tue Mar 15 09:02:05 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 15 Mar 2011 10:02:05 +0100
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <004001cbe2d5$76598200$630c8600$@edu.hk>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
Message-ID: <AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>

Hi Ross,

Your code is incomplete and you didn't provide the output from running it,
so it's not easy to figure out where you're going wrong.

Try copying the example code directly from here


http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html

and making sure that works first before modifying it.


More documentation and examples here:
http://www.bioperl.org/wiki/HOWTO:Beginners
http://www.bioperl.org/wiki/Bioperl_scripts


Dave




On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:

> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
> 'Fasta');
> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>                l
> print "HEELO";
> while ($seqobj = $allseqobj->next_seq) {
>                        #$seqobj = $allseqobj->next_seq;
>
>                        $seq=$seqobj->seq;
>
>                        }
>
>                    print "222   HEELO";
>
>
>
> I find that the 1st HEELO can be printed while the 2nd one can't. Google
> does not return checking success/failure or null/exist of the Seq Object.
> As
> the 1st HEELO can be executed, so no throw/exception occurs for the
> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
> accession numbers.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From ross at cuhk.edu.hk  Tue Mar 15 14:16:56 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Tue, 15 Mar 2011 22:16:56 +0800
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
Message-ID: <005301cbe31b$a3bee550$eb3caff0$@edu.hk>

While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...

 

 

#!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   

use Bio::DB::GenBank;

 

$gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');


$allseqobj = $gb->get_Stream_by_acc("A3ZI37");


 print "HEELO";

while ($seqobj = $allseqobj->next_seq) {
                       #$seqobj = $allseqobj->next_seq;
                       $seq=$seqobj->seq;
}
print "222   HEELO";




 

 

From: Dave Messina [mailto:David.Messina at sbc.su.se] 
Sent: 2011?3?15? 17:02
To: Ross KK Leung
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] how to prevent forced exit?

 

Hi Ross,

 

Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.

 

Try copying the example code directly from here

 

    http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html

 

and making sure that works first before modifying it.

 

 

More documentation and examples here:

http://www.bioperl.org/wiki/HOWTO:Beginners

http://www.bioperl.org/wiki/Bioperl_scripts

 

 

Dave

 

 

 

On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:

$gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
'Fasta');
$allseqobj = $gb->get_Stream_by_acc("A3ZI37");
               l
print "HEELO";
while ($seqobj = $allseqobj->next_seq) {
                       #$seqobj = $allseqobj->next_seq;

                       $seq=$seqobj->seq;

                       }

                   print "222   HEELO";



I find that the 1st HEELO can be printed while the 2nd one can't. Google
does not return checking success/failure or null/exist of the Seq Object. As
the 1st HEELO can be executed, so no throw/exception occurs for the
get_Stream_by_acc. So what can I do? The real case is not hard-coding this
A3ZI37 but reading a file that may contain a lot of these "illegitimate"
accession numbers.

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

 




From cjfields at illinois.edu  Tue Mar 15 14:44:23 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 15 Mar 2011 09:44:23 -0500
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <005301cbe31b$a3bee550$eb3caff0$@edu.hk>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
Message-ID: <DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>

Ross,

Hope you're exaggerating, you really shouldn't use this service for retrieving 1 million records as you'll likely find your IP banned by NCBI; they are starting to enforce stricter web-based access to their  server now.  Bio::DB::GenBank uses a GET HTTP request using URI-based parameters which effectively limits the length of the query to around 200-300 IDs per request, so you would have to split single one large request many.  Thousands of repeated requests, even with a timeout, may flag your IP as 'spam'.  You can use something like Bio::DB::EUtilities to grab larger groups of seqs (~1000 IDs) b/c the latest EUtilities uses POST requests vs GET for a large number of IDs, but you are still effectively limited by the number of requests.

Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?

chris

On Mar 15, 2011, at 9:16 AM, Ross KK Leung wrote:

> While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...
> 
> 
> 
> 
> 
> #!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   
> 
> use Bio::DB::GenBank;
> 
> 
> 
> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');
> 
> 
> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
> 
> 
> print "HEELO";
> 
> while ($seqobj = $allseqobj->next_seq) {
>                       #$seqobj = $allseqobj->next_seq;
>                       $seq=$seqobj->seq;
> }
> print "222   HEELO";
> 
> 
> 
> 
> 
> 
> 
> 
> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
> Sent: 2011?3?15? 17:02
> To: Ross KK Leung
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] how to prevent forced exit?
> 
> 
> 
> Hi Ross,
> 
> 
> 
> Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.
> 
> 
> 
> Try copying the example code directly from here
> 
> 
> 
>    http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html
> 
> 
> 
> and making sure that works first before modifying it.
> 
> 
> 
> 
> 
> More documentation and examples here:
> 
> http://www.bioperl.org/wiki/HOWTO:Beginners
> 
> http://www.bioperl.org/wiki/Bioperl_scripts
> 
> 
> 
> 
> 
> Dave
> 
> 
> 
> 
> 
> 
> 
> On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:
> 
> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
> 'Fasta');
> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>               l
> print "HEELO";
> while ($seqobj = $allseqobj->next_seq) {
>                       #$seqobj = $allseqobj->next_seq;
> 
>                       $seq=$seqobj->seq;
> 
>                       }
> 
>                   print "222   HEELO";
> 
> 
> 
> I find that the 1st HEELO can be printed while the 2nd one can't. Google
> does not return checking success/failure or null/exist of the Seq Object. As
> the 1st HEELO can be executed, so no throw/exception occurs for the
> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
> accession numbers.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From dvadell at clustering.com.ar  Tue Mar 15 14:59:20 2011
From: dvadell at clustering.com.ar (Diego M. Vadell)
Date: Tue, 15 Mar 2011 11:59:20 -0300
Subject: [Bioperl-l] advice about bioperl-ext -- defunct?
Message-ID: <38be317a0815ba7276d56e5a6c93d116@webmail.clustering.com.ar>

Hi,

 I have just downloaded bioperl-ext from github, and it says "XS-based
BioPerl extensions to C libraries (defunct) ? [Read more ->
https://github.com/bioperl/bioperl-ext#readme]" . I read the readme but it
looks alive ( i.e. no mention of an ending of the project ). 

 I installed it ( adding "-fPIC" in the 3 Makefile.PLs ) and I'm about to
start using it. But, does is it still maintained? Is it still in use?
Recommended for a new project? I don't mind fixing compilation errors, but
maybe there is a new package that superseded it. Maybe I'm downloading it
from the wrong place.

 Regards,
 -- Diego





From jimhu at tamu.edu  Tue Mar 15 15:25:36 2011
From: jimhu at tamu.edu (Jim Hu)
Date: Tue, 15 Mar 2011 10:25:36 -0500
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
	<DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
Message-ID: <9CD1455E-88B4-4E2A-B3BC-398C10D5AAA9@tamu.edu>

Hi Chris,

A version of this admonition should be on every wiki HOWTO that involves retrieving records from external sources, and in the docs for the relevant modules.  Speaking as someone who has used BioPerl intermittently for years, and who has Sysiphus-like relationship with the learning curve, I think the docs could use more discussion of when to use particular modules in addition to the details of how to use them provided in the perldocs. I realize this is hard, given the perl "more than one way to do it" world view, but that's my $0.02.

Since BioPerl.org is a wiki, I suppose I should do that admonition edit myself... especially since I already know the wiki markup to transclude the same text into multiple pages.

Jim

Sent from my iPad

On Mar 15, 2011, at 9:44 AM, Chris Fields <cjfields at illinois.edu> wrote:

> Ross,
> 
> Hope you're exaggerating, you really shouldn't use this service for retrieving 1 million records as you'll likely find your IP banned by NCBI; they are starting to enforce stricter web-based access to their  server now.  Bio::DB::GenBank uses a GET HTTP request using URI-based parameters which effectively limits the length of the query to around 200-300 IDs per request, so you would have to split single one large request many.  Thousands of repeated requests, even with a timeout, may flag your IP as 'spam'.  You can use something like Bio::DB::EUtilities to grab larger groups of seqs (~1000 IDs) b/c the latest EUtilities uses POST requests vs GET for a large number of IDs, but you are still effectively limited by the number of requests.
> 
> Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?
> 
> chris
> 
> On Mar 15, 2011, at 9:16 AM, Ross KK Leung wrote:
> 
>> While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...
>> 
>> 
>> 
>> 
>> 
>> #!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   
>> 
>> use Bio::DB::GenBank;
>> 
>> 
>> 
>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');
>> 
>> 
>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>> 
>> 
>> print "HEELO";
>> 
>> while ($seqobj = $allseqobj->next_seq) {
>>                      #$seqobj = $allseqobj->next_seq;
>>                      $seq=$seqobj->seq;
>> }
>> print "222   HEELO";
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
>> Sent: 2011?3?15? 17:02
>> To: Ross KK Leung
>> Cc: bioperl-l at lists.open-bio.org
>> Subject: Re: [Bioperl-l] how to prevent forced exit?
>> 
>> 
>> 
>> Hi Ross,
>> 
>> 
>> 
>> Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.
>> 
>> 
>> 
>> Try copying the example code directly from here
>> 
>> 
>> 
>>   http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html
>> 
>> 
>> 
>> and making sure that works first before modifying it.
>> 
>> 
>> 
>> 
>> 
>> More documentation and examples here:
>> 
>> http://www.bioperl.org/wiki/HOWTO:Beginners
>> 
>> http://www.bioperl.org/wiki/Bioperl_scripts
>> 
>> 
>> 
>> 
>> 
>> Dave
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:
>> 
>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
>> 'Fasta');
>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>              l
>> print "HEELO";
>> while ($seqobj = $allseqobj->next_seq) {
>>                      #$seqobj = $allseqobj->next_seq;
>> 
>>                      $seq=$seqobj->seq;
>> 
>>                      }
>> 
>>                  print "222   HEELO";
>> 
>> 
>> 
>> I find that the 1st HEELO can be printed while the 2nd one can't. Google
>> does not return checking success/failure or null/exist of the Seq Object. As
>> the 1st HEELO can be executed, so no throw/exception occurs for the
>> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
>> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
>> accession numbers.
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Tue Mar 15 15:45:20 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 15 Mar 2011 10:45:20 -0500
Subject: [Bioperl-l] advice about bioperl-ext -- defunct?
In-Reply-To: <38be317a0815ba7276d56e5a6c93d116@webmail.clustering.com.ar>
References: <38be317a0815ba7276d56e5a6c93d116@webmail.clustering.com.ar>
Message-ID: <3892F905-2D1F-43CF-8968-055C9F902504@illinois.edu>

On Mar 15, 2011, at 9:59 AM, Diego M. Vadell wrote:

> Hi,
> 
> I have just downloaded bioperl-ext from github, and it says "XS-based
> BioPerl extensions to C libraries (defunct) ? [Read more ->
> https://github.com/bioperl/bioperl-ext#readme]" . I read the readme but it
> looks alive ( i.e. no mention of an ending of the project ). 
> 
> I installed it ( adding "-fPIC" in the 3 Makefile.PLs ) and I'm about to
> start using it. But, does is it still maintained? Is it still in use?

Re: being maintained: No, except Bio::Tools::HMM (https://github.com/bioperl/Bio-Tools-HMM)

Re: in use: somewhat.  I think some still use Bio::SeqIO::staden::read and Bio::Ext::Align, but they haven't actively maintained in quite some time.

> Recommended for a new project? I don't mind fixing compilation errors, but
> maybe there is a new package that superseded it. Maybe I'm downloading it
> from the wrong place.
> 
> Regards,
> -- Diego

The code still works in some cases but is somewhat bit-rotted (I recall getting very inconsistent results from Bio::SearchUtils, not sure why).  

We (Bio* projects) are starting to consolidate around using BioLib for consistent bindings to C/C++ libraries, though that project is undergoing some changes:

http://biolib.open-bio.org/wiki/Main_Page

Pjotr Prins is the lead on that, worth talking to.  The next big step is to interface with EMBOSS libraries, which is very promising.

chris


From cjfields at illinois.edu  Tue Mar 15 15:54:38 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 15 Mar 2011 10:54:38 -0500
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <9CD1455E-88B4-4E2A-B3BC-398C10D5AAA9@tamu.edu>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
	<DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
	<9CD1455E-88B4-4E2A-B3BC-398C10D5AAA9@tamu.edu>
Message-ID: <3E73745F-A687-4229-B71E-5C56B2D1FBAE@illinois.edu>

Jim,

It's worth noting in something more prominent, like the tutorial, FAQ, and appropriate HOWTO's.  We've long considered whether it would be worth setting up a cookbook-like section that includes simple workflows, that would also be appropriate for something like this.

Also, I do think this is mentioned in the POD for several modules, but worth adding a prominent section on it if it's not present.  In Bio::DB::GenBank:

  WARNING: Please do NOT spam the Entrez web server with multiple requests.  NCBI offers Batch Entrez for this purpose.

That could be placed somewhere that is a bit more helpful.

chris


On Mar 15, 2011, at 10:25 AM, Jim Hu wrote:

> Hi Chris,
> 
> A version of this admonition should be on every wiki HOWTO that involves retrieving records from external sources, and in the docs for the relevant modules.  Speaking as someone who has used BioPerl intermittently for years, and who has Sysiphus-like relationship with the learning curve, I think the docs could use more discussion of when to use particular modules in addition to the details of how to use them provided in the perldocs. I realize this is hard, given the perl "more than one way to do it" world view, but that's my $0.02.
> 
> Since BioPerl.org is a wiki, I suppose I should do that admonition edit myself... especially since I already know the wiki markup to transclude the same text into multiple pages.
> 
> Jim
> 
> Sent from my iPad
> 
> On Mar 15, 2011, at 9:44 AM, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Ross,
>> 
>> Hope you're exaggerating, you really shouldn't use this service for retrieving 1 million records as you'll likely find your IP banned by NCBI; they are starting to enforce stricter web-based access to their  server now.  Bio::DB::GenBank uses a GET HTTP request using URI-based parameters which effectively limits the length of the query to around 200-300 IDs per request, so you would have to split single one large request many.  Thousands of repeated requests, even with a timeout, may flag your IP as 'spam'.  You can use something like Bio::DB::EUtilities to grab larger groups of seqs (~1000 IDs) b/c the latest EUtilities uses POST requests vs GET for a large number of IDs, but you are still effectively limited by the number of requests.
>> 
>> Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?
>> 
>> chris
>> 
>> On Mar 15, 2011, at 9:16 AM, Ross KK Leung wrote:
>> 
>>> While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...
>>> 
>>> 
>>> 
>>> 
>>> 
>>> #!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   
>>> 
>>> use Bio::DB::GenBank;
>>> 
>>> 
>>> 
>>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');
>>> 
>>> 
>>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>> 
>>> 
>>> print "HEELO";
>>> 
>>> while ($seqobj = $allseqobj->next_seq) {
>>>                     #$seqobj = $allseqobj->next_seq;
>>>                     $seq=$seqobj->seq;
>>> }
>>> print "222   HEELO";
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
>>> Sent: 2011?3?15? 17:02
>>> To: Ross KK Leung
>>> Cc: bioperl-l at lists.open-bio.org
>>> Subject: Re: [Bioperl-l] how to prevent forced exit?
>>> 
>>> 
>>> 
>>> Hi Ross,
>>> 
>>> 
>>> 
>>> Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.
>>> 
>>> 
>>> 
>>> Try copying the example code directly from here
>>> 
>>> 
>>> 
>>>  http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html
>>> 
>>> 
>>> 
>>> and making sure that works first before modifying it.
>>> 
>>> 
>>> 
>>> 
>>> 
>>> More documentation and examples here:
>>> 
>>> http://www.bioperl.org/wiki/HOWTO:Beginners
>>> 
>>> http://www.bioperl.org/wiki/Bioperl_scripts
>>> 
>>> 
>>> 
>>> 
>>> 
>>> Dave
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:
>>> 
>>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
>>> 'Fasta');
>>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>>             l
>>> print "HEELO";
>>> while ($seqobj = $allseqobj->next_seq) {
>>>                     #$seqobj = $allseqobj->next_seq;
>>> 
>>>                     $seq=$seqobj->seq;
>>> 
>>>                     }
>>> 
>>>                 print "222   HEELO";
>>> 
>>> 
>>> 
>>> I find that the 1st HEELO can be printed while the 2nd one can't. Google
>>> does not return checking success/failure or null/exist of the Seq Object. As
>>> the 1st HEELO can be executed, so no throw/exception occurs for the
>>> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
>>> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
>>> accession numbers.
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From dvadell at clustering.com.ar  Tue Mar 15 16:01:22 2011
From: dvadell at clustering.com.ar (Diego M. Vadell)
Date: Tue, 15 Mar 2011 13:01:22 -0300
Subject: [Bioperl-l] advice about bioperl-ext -- defunct?
In-Reply-To: <3892F905-2D1F-43CF-8968-055C9F902504@illinois.edu>
Message-ID: <218950b508a0e4a8ad07227974989e5f@webmail.clustering.com.ar>

Hi Chris,

 Thank you! I will align with bioperl-run then, and keep an eye on biolib.

Cheers,
 -- Diego


 
----------------original message-----------------
From: "Chris Fields" cjfields at illinois.edu
To: "Diego M. Vadell" dvadell at clustering.com.ar
CC: bioperl-l at lists.open-bio.org
Date: Tue, 15 Mar 2011 10:45:20 -0500
-------------------------------------------------
 
 
> On Mar 15, 2011, at 9:59 AM, Diego M. Vadell wrote:
> 
>> Hi,
>> 
>> I have just downloaded bioperl-ext from github, and it says "XS-based
>> BioPerl extensions to C libraries (defunct) ? [Read more ->
>> https://github.com/bioperl/bioperl-ext#readme]" . I read the readme but 
>> it
>> looks alive ( i.e. no mention of an ending of the project ). 
>> 
>> I installed it ( adding "-fPIC" in the 3 Makefile.PLs ) and I'm about to
>> start using it. But, does is it still maintained? Is it still in use?
> 
> Re: being maintained: No, except Bio::Tools::HMM 
> (https://github.com/bioperl/Bio-Tools-HMM)
> 
> Re: in use: somewhat. I think some still use Bio::SeqIO::staden::read and 
> Bio::Ext::Align, but they haven't actively maintained in quite some time.
> 
>> Recommended for a new project? I don't mind fixing compilation errors,
but
>> maybe there is a new package that superseded it. Maybe I'm downloading it
>> from the wrong place.
>> 
>> Regards,
>> -- Diego
> 
> The code still works in some cases but is somewhat bit-rotted (I recall
getting 
> very inconsistent results from Bio::SearchUtils, not sure why). 
> 
> We (Bio* projects) are starting to consolidate around using BioLib for 
> consistent bindings to C/C++ libraries, though that project is undergoing
some 
> changes:
> 
> http://biolib.open-bio.org/wiki/Main_Page
> 
> Pjotr Prins is the lead on that, worth talking to. The next big step is to
interface 
> with EMBOSS libraries, which is very promising.
> 
> chris
> 





From ross at cuhk.edu.hk  Wed Mar 16 00:55:42 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Wed, 16 Mar 2011 08:55:42 +0800
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
	<DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
Message-ID: <007201cbe374$dffa5eb0$9fef1c10$@edu.hk>

-----Original Message-----
From: Chris Fields [mailto:cjfields at illinois.edu] 
Sent: 2011?3?15? 22:44
To: Ross KK Leung
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] how to prevent forced exit?

Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?

chris


Dear Chris,

Thanks for your suggestion. The problem we encounter is that we don't know what database/genbank files we have to retrieve in order to accomplish the job. It seems that the nr database does not include all the records, and we don't know whether we have to concatenate all the genbank files into a very big one so to parse one by one. Any advice?

Gratefully, Ross




From jimhu at tamu.edu  Wed Mar 16 06:22:23 2011
From: jimhu at tamu.edu (Jim Hu)
Date: Wed, 16 Mar 2011 01:22:23 -0500
Subject: [Bioperl-l] how to prevent forced exit?
In-Reply-To: <3E73745F-A687-4229-B71E-5C56B2D1FBAE@illinois.edu>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
	<004001cbe2d5$76598200$630c8600$@edu.hk>
	<AANLkTinEieznrkSBAbFL-GfOaGJ9Cyg5e=hOz8u5ijKm@mail.gmail.com>
	<005301cbe31b$a3bee550$eb3caff0$@edu.hk>
	<DA562595-05C2-448B-97CC-0055F95335A8@illinois.edu>
	<9CD1455E-88B4-4E2A-B3BC-398C10D5AAA9@tamu.edu>
	<3E73745F-A687-4229-B71E-5C56B2D1FBAE@illinois.edu>
Message-ID: <D714889D-D73C-4E45-87E3-FE921BFEBA48@tamu.edu>

I put a snippet at the end of:

	http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database

The snippet is on an independent page, and is included via 

	{{:Remote_database_admonition}}
 
which allows people to put it into other pages, and to edit it and have the changes update on all the pages where it's included.  So if someone wants to reword it, make it red text, put it in a box div or whatever, it just has to be done once.  Or, since it's a wiki,  others can just kill it altogether. ;)

Jim

On Mar 15, 2011, at 10:54 AM, Chris Fields wrote:

> Jim,
> 
> It's worth noting in something more prominent, like the tutorial, FAQ, and appropriate HOWTO's.  We've long considered whether it would be worth setting up a cookbook-like section that includes simple workflows, that would also be appropriate for something like this.
> 
> Also, I do think this is mentioned in the POD for several modules, but worth adding a prominent section on it if it's not present.  In Bio::DB::GenBank:
> 
>  WARNING: Please do NOT spam the Entrez web server with multiple requests.  NCBI offers Batch Entrez for this purpose.
> 
> That could be placed somewhere that is a bit more helpful.
> 
> chris
> 
> 
> On Mar 15, 2011, at 10:25 AM, Jim Hu wrote:
> 
>> Hi Chris,
>> 
>> A version of this admonition should be on every wiki HOWTO that involves retrieving records from external sources, and in the docs for the relevant modules.  Speaking as someone who has used BioPerl intermittently for years, and who has Sysiphus-like relationship with the learning curve, I think the docs could use more discussion of when to use particular modules in addition to the details of how to use them provided in the perldocs. I realize this is hard, given the perl "more than one way to do it" world view, but that's my $0.02.
>> 
>> Since BioPerl.org is a wiki, I suppose I should do that admonition edit myself... especially since I already know the wiki markup to transclude the same text into multiple pages.
>> 
>> Jim
>> 
>> Sent from my iPad
>> 
>> On Mar 15, 2011, at 9:44 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> 
>>> Ross,
>>> 
>>> Hope you're exaggerating, you really shouldn't use this service for retrieving 1 million records as you'll likely find your IP banned by NCBI; they are starting to enforce stricter web-based access to their  server now.  Bio::DB::GenBank uses a GET HTTP request using URI-based parameters which effectively limits the length of the query to around 200-300 IDs per request, so you would have to split single one large request many.  Thousands of repeated requests, even with a timeout, may flag your IP as 'spam'.  You can use something like Bio::DB::EUtilities to grab larger groups of seqs (~1000 IDs) b/c the latest EUtilities uses POST requests vs GET for a large number of IDs, but you are still effectively limited by the number of requests.
>>> 
>>> Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?
>>> 
>>> chris
>>> 
>>> On Mar 15, 2011, at 9:16 AM, Ross KK Leung wrote:
>>> 
>>>> While the complete code is as follows, the real problem is that the get_Stream_by_acc cannot be used repeatedly, such that when I'm feeding a list of accession numbers (e.g. 1 million records) to the perl script, the program will exit with code 255 (likely equivalent to -1). I wonder anybody had encountered this similar problem and has solved it accordingly...
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> #!/usr/bin/perl                                                                                                                 use warnings;                                                                                                                                                                                                                                                   
>>>> 
>>>> use Bio::DB::GenBank;
>>>> 
>>>> 
>>>> 
>>>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>'Fasta');
>>>> 
>>>> 
>>>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>>> 
>>>> 
>>>> print "HEELO";
>>>> 
>>>> while ($seqobj = $allseqobj->next_seq) {
>>>>                    #$seqobj = $allseqobj->next_seq;
>>>>                    $seq=$seqobj->seq;
>>>> }
>>>> print "222   HEELO";
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
>>>> Sent: 2011?3?15? 17:02
>>>> To: Ross KK Leung
>>>> Cc: bioperl-l at lists.open-bio.org
>>>> Subject: Re: [Bioperl-l] how to prevent forced exit?
>>>> 
>>>> 
>>>> 
>>>> Hi Ross,
>>>> 
>>>> 
>>>> 
>>>> Your code is incomplete and you didn't provide the output from running it, so it's not easy to figure out where you're going wrong.
>>>> 
>>>> 
>>>> 
>>>> Try copying the example code directly from here
>>>> 
>>>> 
>>>> 
>>>> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html
>>>> 
>>>> 
>>>> 
>>>> and making sure that works first before modifying it.
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> More documentation and examples here:
>>>> 
>>>> http://www.bioperl.org/wiki/HOWTO:Beginners
>>>> 
>>>> http://www.bioperl.org/wiki/Bioperl_scripts
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> Dave
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On Tue, Mar 15, 2011 at 06:54, Ross KK Leung <ross at cuhk.edu.hk> wrote:
>>>> 
>>>> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile', -format =>
>>>> 'Fasta');
>>>> $allseqobj = $gb->get_Stream_by_acc("A3ZI37");
>>>>            l
>>>> print "HEELO";
>>>> while ($seqobj = $allseqobj->next_seq) {
>>>>                    #$seqobj = $allseqobj->next_seq;
>>>> 
>>>>                    $seq=$seqobj->seq;
>>>> 
>>>>                    }
>>>> 
>>>>                print "222   HEELO";
>>>> 
>>>> 
>>>> 
>>>> I find that the 1st HEELO can be printed while the 2nd one can't. Google
>>>> does not return checking success/failure or null/exist of the Seq Object. As
>>>> the 1st HEELO can be executed, so no throw/exception occurs for the
>>>> get_Stream_by_acc. So what can I do? The real case is not hard-coding this
>>>> A3ZI37 but reading a file that may contain a lot of these "illegitimate"
>>>> accession numbers.
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054





From cjfields at illinois.edu  Wed Mar 16 17:58:23 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 12:58:23 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
Message-ID: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>

(apologies if you receive multiple copies of this)

All,

We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:

http://redmine.open-bio.org/

All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.

For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:

1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.

2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.

Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.

Let us know if you have any questions.  

chris

Christopher Fields
IGB Postdoctoral Fellow
Genomics of Neural & Behavioral Plasticity
University of Illinois Urbana-Champaign
Institute for Genomic Biology
1206 W. Gregory Dr. , MC-195
Urbana, IL 61801


From simon.noel.2 at ulaval.ca  Wed Mar 16 19:40:09 2011
From: simon.noel.2 at ulaval.ca (=?iso-8859-1?Q?Simon_No=EBl?=)
Date: Wed, 16 Mar 2011 15:40:09 -0400
Subject: [Bioperl-l]  Perl/BioPerl
Message-ID: <1C970CA8E580A84394CE5CF42FEC0046DF67A4FA81@EXCH-MBX-E.ulaval.ca>

 Hi, 
 
I don't know if I am on the right mailling list for this.
 
My director say that I should have a class of Perl or BioPerl.  Witch one should be better?  Do you know where I can find such class?


Simon No?l
CdeC


From cjfields at illinois.edu  Wed Mar 16 22:30:40 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 17:30:40 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
	<AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
Message-ID: <D6A1291F-898A-4563-8C19-FA2E92D48767@illinois.edu>

Huh, Dave Messina reported something similar earlier.  I actually tested this myself and couldn't reproduce it, maybe I'll try it on Firefox (I was using Chrome).

chris

On Mar 16, 2011, at 3:48 PM, Jonathan Duke Leto wrote:

> Howdy,
> 
> Thanks for working on this Chris!
> 
> I am not sure the password reset works properly.
> 
> Attached is a screenshot of it giving odd errors.
> 
> This was on Firefox 3.6.
> 
> Duke
> 
> On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> (apologies if you receive multiple copies of this)
>> 
>> All,
>> 
>> We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:
>> 
>> http://redmine.open-bio.org/
>> 
>> All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.
>> 
>> For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:
>> 
>> 1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.
>> 
>> 2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.
>> 
>> Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
>> 
>> Let us know if you have any questions.
>> 
>> chris
>> 
>> Christopher Fields
>> IGB Postdoctoral Fellow
>> Genomics of Neural & Behavioral Plasticity
>> University of Illinois Urbana-Champaign
>> Institute for Genomic Biology
>> 1206 W. Gregory Dr. , MC-195
>> Urbana, IL 61801
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> Jonathan "Duke" Leto
> jonathan at leto.net
> http://leto.net
> <obf_redmine.png>




From cjfields at illinois.edu  Wed Mar 16 22:50:18 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 17:50:18 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
	<AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
Message-ID: <F380825D-8F8B-4766-99C3-36FDD8E9C99D@illinois.edu>

I reset the plugins and reloaded the database.  Does that help?  I tested it out again using a test user (using the 'Lost password' link) and it seemed to work.

If not, I can manually reset and send the password to you.

chris

On Mar 16, 2011, at 3:48 PM, Jonathan Duke Leto wrote:

> Howdy,
> 
> Thanks for working on this Chris!
> 
> I am not sure the password reset works properly.
> 
> Attached is a screenshot of it giving odd errors.
> 
> This was on Firefox 3.6.
> 
> Duke
> 
> On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> (apologies if you receive multiple copies of this)
>> 
>> All,
>> 
>> We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:
>> 
>> http://redmine.open-bio.org/
>> 
>> All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.
>> 
>> For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:
>> 
>> 1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.
>> 
>> 2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.
>> 
>> Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
>> 
>> Let us know if you have any questions.
>> 
>> chris
>> 
>> Christopher Fields
>> IGB Postdoctoral Fellow
>> Genomics of Neural & Behavioral Plasticity
>> University of Illinois Urbana-Champaign
>> Institute for Genomic Biology
>> 1206 W. Gregory Dr. , MC-195
>> Urbana, IL 61801
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> Jonathan "Duke" Leto
> jonathan at leto.net
> http://leto.net
> <obf_redmine.png>




From hlapp at drycafe.net  Thu Mar 17 03:05:15 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 16 Mar 2011 23:05:15 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
Message-ID: <1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>


On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:

> Okay, we have bioperl.org set up to use OpenID, works well:

Seems to work mostly - there seems to be some odd small problem with  
ClaimID: typing in my username leads to an OpenID error, whereas  
entering my full ClaimID OpenID works.  Not sure why that would be.

Any chance this can be enabled for BioSQL too (and accordingly account  
creation disabled there, too)?

	-hilmar

>
>
> http://www.bioperl.org/wiki/Special:OpenIDLogin
>
> I have also temporarily shut down new user account creation (new  
> users must now use OpenID); old users can still use the login, but  
> they can also tie their account to an OpenID.  Let's see if it cuts  
> down on the spam.
>
> chris
>
> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>
>> Any update on the OpenID extension?
>>
>> 	-hilmar
>>
>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>
>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit 
>>> ):
>>>
>>> "Unfortunately, reCAPTCHA might be a victim of its own success -  
>>> as of 2011, some spammers appear to have figured out a way to  
>>> bypass it, either through character recognition or by using  
>>> humans. For that reason, it is not necessarily recommended."
>>>
>>> I agree about the barrier to entry issue, but unfortunately with  
>>> the wiki we're facing a reality check re: spam attacks.  We can  
>>> probably set up a new group for users that allows account  
>>> approval, though, which might alleviate the process somewhat.
>>>
>>> chris
>>>
>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>
>>>> Hi Chris,
>>>>
>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>> account, you have the ability to approve other people's  
>>>> accounts.  The
>>>> hope being to distribute the load.  I'm not thrilled about it  
>>>> though:
>>>> I want the barrier to entry to be as low as possible.  We already  
>>>> make
>>>> it so that you have to have an account to edit, passing a  
>>>> recaptcha on
>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu 
>>>> > wrote:
>>>>> All,
>>>>>
>>>>> We have been getting inundated on the wiki with spam lately.  In  
>>>>> order to get on top of this, I'm thinking about having the wiki  
>>>>> set up so wiki admins approve new user accounts, using the  
>>>>> ConfirmAccount plugin:
>>>>>
>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>
>>>>> I wanted to get everyone's opinion on this prior to enforcing  
>>>>> it.  The queue is pretty configurable, and one can set this to  
>>>>> auto-delete old requests.
>>>>>
>>>>> Any thoughts?
>>>>>
>>>>> chris
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>
>>>>
>>>>
>>>> -- 
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at  
>>>> scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                      
>>>> 216-392-3087
>>>> Ontario Institute for Cancer Research
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>> ===========================================================
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From cjfields at illinois.edu  Thu Mar 17 03:08:11 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 22:08:11 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
Message-ID: <E0AD66F8-13FE-4940-A0F5-2E4CC0C02755@illinois.edu>

I can work on that.  Peter, need this for biopython?

chris

On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:

> 
> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
> 
>> Okay, we have bioperl.org set up to use OpenID, works well:
> 
> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works.  Not sure why that would be.
> 
> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
> 
> 	-hilmar
> 
>> 
>> 
>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>> 
>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.
>> 
>> chris
>> 
>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>> 
>>> Any update on the OpenID extension?
>>> 
>>> 	-hilmar
>>> 
>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>> 
>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>> 
>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>> 
>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>> 
>>>> chris
>>>> 
>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>> 
>>>>> Hi Chris,
>>>>> 
>>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>> account, you have the ability to approve other people's accounts.  The
>>>>> hope being to distribute the load.  I'm not thrilled about it though:
>>>>> I want the barrier to entry to be as low as possible.  We already make
>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>> 
>>>>> Scott
>>>>> 
>>>>> 
>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>> All,
>>>>>> 
>>>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>> 
>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>> 
>>>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>> 
>>>>>> Any thoughts?
>>>>>> 
>>>>>> chris
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> -- 
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>> ===========================================================
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 




From cjfields at illinois.edu  Thu Mar 17 03:59:17 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 16 Mar 2011 22:59:17 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
Message-ID: <B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>

Done, for BioSQL.  Let me know about Biopython and the others.

-c 

On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:

> 
> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
> 
>> Okay, we have bioperl.org set up to use OpenID, works well:
> 
> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works.  Not sure why that would be.
> 
> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
> 
> 	-hilmar
> 
>> 
>> 
>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>> 
>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.
>> 
>> chris
>> 
>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>> 
>>> Any update on the OpenID extension?
>>> 
>>> 	-hilmar
>>> 
>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>> 
>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>> 
>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>> 
>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>> 
>>>> chris
>>>> 
>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>> 
>>>>> Hi Chris,
>>>>> 
>>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>> account, you have the ability to approve other people's accounts.  The
>>>>> hope being to distribute the load.  I'm not thrilled about it though:
>>>>> I want the barrier to entry to be as low as possible.  We already make
>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>> 
>>>>> Scott
>>>>> 
>>>>> 
>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>> All,
>>>>>> 
>>>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>> 
>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>> 
>>>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>> 
>>>>>> Any thoughts?
>>>>>> 
>>>>>> chris
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> -- 
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>> ===========================================================
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 




From hlapp at drycafe.net  Thu Mar 17 04:07:45 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Thu, 17 Mar 2011 00:07:45 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
Message-ID: <6747C6EA-27BC-43C1-89B4-0F3AEF18BFA4@drycafe.net>


On Mar 16, 2011, at 11:59 PM, Chris Fields wrote:

> Done, for BioSQL.  Let me know about Biopython and the others.

Great, works! -hilmar


-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From p.j.a.cock at googlemail.com  Thu Mar 17 08:27:22 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 17 Mar 2011 08:27:22 +0000
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
Message-ID: <AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>

Yes please - thanks Chris!

Peter

On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu> wrote:
> Done, for BioSQL. ?Let me know about Biopython and the others.
>
> -c
>
> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>
>>
>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>
>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>
>> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works. ?Not sure why that would be.
>>
>> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
>>
>> ? ? ? -hilmar
>>
>>>
>>>
>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>
>>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID. ?Let's see if it cuts down on the spam.
>>>
>>> chris
>>>
>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>
>>>> Any update on the OpenID extension?
>>>>
>>>> ? ? -hilmar
>>>>
>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>
>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>>>
>>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>>>
>>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks. ?We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>>>
>>>>> chris
>>>>>
>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>
>>>>>> Hi Chris,
>>>>>>
>>>>>> The GMOD wiki has been getting hit similarly. ?I've been thinking
>>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>>> account, you have the ability to approve other people's accounts. ?The
>>>>>> hope being to distribute the load. ?I'm not thrilled about it though:
>>>>>> I want the barrier to entry to be as low as possible. ?We already make
>>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>>> the way. ?Apparently that barrier is already a little too low :-/
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>>> All,
>>>>>>>
>>>>>>> We have been getting inundated on the wiki with spam lately. ?In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>>>
>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>
>>>>>>> I wanted to get everyone's opinion on this prior to enforcing it. ?The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>>>
>>>>>>> Any thoughts?
>>>>>>>
>>>>>>> chris
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> ------------------------------------------------------------------------
>>>>>> Scott Cain, Ph. D.



From David.Messina at sbc.su.se  Thu Mar 17 08:51:21 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 17 Mar 2011 09:51:21 +0100
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <F380825D-8F8B-4766-99C3-36FDD8E9C99D@illinois.edu>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
	<AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
	<F380825D-8F8B-4766-99C3-36FDD8E9C99D@illinois.edu>
Message-ID: <AANLkTik8oYG1yJ7HdV119K08NsbqpDTUpDAtKUPSKUMF@mail.gmail.com>

Works for me now ? I was able to reset the password and log in.

Thanks, Chris!

Dave




On Wed, Mar 16, 2011 at 23:50, Chris Fields <cjfields at illinois.edu> wrote:

> I reset the plugins and reloaded the database.  Does that help?  I tested
> it out again using a test user (using the 'Lost password' link) and it
> seemed to work.
>
> If not, I can manually reset and send the password to you.
>
> chris
>
> On Mar 16, 2011, at 3:48 PM, Jonathan Duke Leto wrote:
>
> > Howdy,
> >
> > Thanks for working on this Chris!
> >
> > I am not sure the password reset works properly.
> >
> > Attached is a screenshot of it giving odd errors.
> >
> > This was on Firefox 3.6.
> >
> > Duke
> >
> > On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu>
> wrote:
> >> (apologies if you receive multiple copies of this)
> >>
> >> All,
> >>
> >> We are currently about 95% done with a transition over to our new
> Redmine tracking system, to the point where we feel comfortable in going
> ahead with opening it to developers:
> >>
> >> http://redmine.open-bio.org/
> >>
> >> All edits to bugzilla reports on our old system (
> http://bugzilla.open-bio.org/) are now disabled and the system is now
> read-only.  Any new bugs and comments to old ones should be reported on the
> new Redmine server.
> >>
> >> For current Bugzilla users, we have migrated login IDs to Redmine (this
> is normally an email address), but we have reset user passwords for security
> reasons.  There are two ways to access your account:
> >>
> >> 1) When logging in (http://redmine.open-bio.org/login), click on the
> 'Lost password' link.  You will be prompted for your email address (this
> should be the same as your bugzilla login).  An new email will be sent out
> containing directions for resetting your password and logging in.
> >>
> >> 2) It is possible the above may be automatically detected as spam.  If
> the above doesn't work or the reset email isn't received within a day,
> contact support at helpdesk.open-bio.org to receive your new password.
> >>
> >> Also, note that Redmine has a different syntax for those who want to add
> links to their reports; see
> http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
> >>
> >> Let us know if you have any questions.
> >>
> >> chris
> >>
> >> Christopher Fields
> >> IGB Postdoctoral Fellow
> >> Genomics of Neural & Behavioral Plasticity
> >> University of Illinois Urbana-Champaign
> >> Institute for Genomic Biology
> >> 1206 W. Gregory Dr. , MC-195
> >> Urbana, IL 61801
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> >
> >
> > --
> > Jonathan "Duke" Leto
> > jonathan at leto.net
> > http://leto.net
> > <obf_redmine.png>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From cjfields at illinois.edu  Thu Mar 17 11:36:05 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Mar 2011 06:36:05 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <AANLkTik8oYG1yJ7HdV119K08NsbqpDTUpDAtKUPSKUMF@mail.gmail.com>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
	<AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>
	<F380825D-8F8B-4766-99C3-36FDD8E9C99D@illinois.edu>
	<AANLkTik8oYG1yJ7HdV119K08NsbqpDTUpDAtKUPSKUMF@mail.gmail.com>
Message-ID: <B8AB68C4-0DD8-408E-8C49-D33339E6C6ED@illinois.edu>

I did a little database cleansing; the email notification settings were screwy (why the warnings popped up).

chris

On Mar 17, 2011, at 3:51 AM, Dave Messina wrote:

> Works for me now ? I was able to reset the password and log in.
> 
> Thanks, Chris!
> 
> Dave
> 
> 
> 
> 
> On Wed, Mar 16, 2011 at 23:50, Chris Fields <cjfields at illinois.edu> wrote:
> I reset the plugins and reloaded the database.  Does that help?  I tested it out again using a test user (using the 'Lost password' link) and it seemed to work.
> 
> If not, I can manually reset and send the password to you.
> 
> chris
> 
> On Mar 16, 2011, at 3:48 PM, Jonathan Duke Leto wrote:
> 
> > Howdy,
> >
> > Thanks for working on this Chris!
> >
> > I am not sure the password reset works properly.
> >
> > Attached is a screenshot of it giving odd errors.
> >
> > This was on Firefox 3.6.
> >
> > Duke
> >
> > On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
> >> (apologies if you receive multiple copies of this)
> >>
> >> All,
> >>
> >> We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:
> >>
> >> http://redmine.open-bio.org/
> >>
> >> All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only.  Any new bugs and comments to old ones should be reported on the new Redmine server.
> >>
> >> For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons.  There are two ways to access your account:
> >>
> >> 1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link.  You will be prompted for your email address (this should be the same as your bugzilla login).  An new email will be sent out containing directions for resetting your password and logging in.
> >>
> >> 2) It is possible the above may be automatically detected as spam.  If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.
> >>
> >> Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
> >>
> >> Let us know if you have any questions.
> >>
> >> chris
> >>
> >> Christopher Fields
> >> IGB Postdoctoral Fellow
> >> Genomics of Neural & Behavioral Plasticity
> >> University of Illinois Urbana-Champaign
> >> Institute for Genomic Biology
> >> 1206 W. Gregory Dr. , MC-195
> >> Urbana, IL 61801
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> >
> >
> > --
> > Jonathan "Duke" Leto
> > jonathan at leto.net
> > http://leto.net
> > <obf_redmine.png>
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From cjfields at illinois.edu  Thu Mar 17 16:16:19 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Mar 2011 11:16:19 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
	<AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
Message-ID: <B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>

Peter, 

It's set up for biopython.  Will make an announcement on open-bio-l and post something on the blog when I catch my breath (redmine and this in one week is a little tiring!).

Will also ping biojava and the other wiki groups about switching over.

chris

On Mar 17, 2011, at 3:27 AM, Peter Cock wrote:

> Yes please - thanks Chris!
> 
> Peter
> 
> On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu> wrote:
>> Done, for BioSQL.  Let me know about Biopython and the others.
>> 
>> -c
>> 
>> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>> 
>>> 
>>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>> 
>>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>> 
>>> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works.  Not sure why that would be.
>>> 
>>> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
>>> 
>>>       -hilmar
>>> 
>>>> 
>>>> 
>>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>> 
>>>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.
>>>> 
>>>> chris
>>>> 
>>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>> 
>>>>> Any update on the OpenID extension?
>>>>> 
>>>>>     -hilmar
>>>>> 
>>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>> 
>>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>>>> 
>>>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>>>> 
>>>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>>>> 
>>>>>> chris
>>>>>> 
>>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>> 
>>>>>>> Hi Chris,
>>>>>>> 
>>>>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>>>> account, you have the ability to approve other people's accounts.  The
>>>>>>> hope being to distribute the load.  I'm not thrilled about it though:
>>>>>>> I want the barrier to entry to be as low as possible.  We already make
>>>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>>>> 
>>>>>>> Scott
>>>>>>> 
>>>>>>> 
>>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>>>> All,
>>>>>>>> 
>>>>>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>>>> 
>>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>> 
>>>>>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>>>> 
>>>>>>>> Any thoughts?
>>>>>>>> 
>>>>>>>> chris
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> --
>>>>>>> ------------------------------------------------------------------------
>>>>>>> Scott Cain, Ph. D.




From adam at retchless.us  Thu Mar 17 16:32:37 2011
From: adam at retchless.us (Adam Retchless)
Date: Thu, 17 Mar 2011 12:32:37 -0400
Subject: [Bioperl-l] Wiki login with OpenId
Message-ID: <4D8237A5.4050706@retchless.us>

Greetings all,

First: A "thank you" to everyone who has developed BioPerl and the 
BioPerl Wiki -- I'm new to BioPerl, but have already benefited from its 
ability to simplify tasks that would otherwise be very tedious.

Anyway, I noticed some outdated information on the Wiki, and wanted to 
change it, but had a little trouble figuring out how to do so. 
Basically, it wasn't clear that the way to create an account was to 
click on the "Login with OpenId" button. As someone who doesn't use 
OpenID, I immediately went to the traditional "Login" page, but got 
stumped there. It did not occur to me that the OpenID page would be any 
different. Only after looking at the recent discussion on the mailing 
list did I figure out what I needed to do.

In the interest of eliminating any obstacle to participation, I think it 
would be helpful for the Wiki itself to clearly indicate how to create a 
new account. Either by changing the wording of the "login with OpenID 
link", or placing a message on the traditional "Log In" page telling 
people what they need to do to make an account.

Thanks, and I look forward to participating here.

-Adam

-- 

Adam Retchless
Center for Genomic Sciences
Allegheny-Singer Research Institute



From cjfields at illinois.edu  Thu Mar 17 17:13:14 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Mar 2011 12:13:14 -0500
Subject: [Bioperl-l] Wiki login with OpenId
In-Reply-To: <4D8237A5.4050706@retchless.us>
References: <4D8237A5.4050706@retchless.us>
Message-ID: <62E050E8-E567-4117-B14C-1F613CC81016@illinois.edu>

Adam, 

We're in the process of doing so; the addition of OpenID logins is a few days old.  I'm actually writing a blog post right now on the problems we've had and the use of OpenID, and will add a few things to the wiki pages so the login is clearer (including adding text to the normal login page).

chris

On Mar 17, 2011, at 11:32 AM, Adam Retchless wrote:

> Greetings all,
> 
> First: A "thank you" to everyone who has developed BioPerl and the BioPerl Wiki -- I'm new to BioPerl, but have already benefited from its ability to simplify tasks that would otherwise be very tedious.
> 
> Anyway, I noticed some outdated information on the Wiki, and wanted to change it, but had a little trouble figuring out how to do so. Basically, it wasn't clear that the way to create an account was to click on the "Login with OpenId" button. As someone who doesn't use OpenID, I immediately went to the traditional "Login" page, but got stumped there. It did not occur to me that the OpenID page would be any different. Only after looking at the recent discussion on the mailing list did I figure out what I needed to do.
> 
> In the interest of eliminating any obstacle to participation, I think it would be helpful for the Wiki itself to clearly indicate how to create a new account. Either by changing the wording of the "login with OpenID link", or placing a message on the traditional "Log In" page telling people what they need to do to make an account.
> 
> Thanks, and I look forward to participating here.
> 
> -Adam
> 
> -- 
> 
> Adam Retchless
> Center for Genomic Sciences
> Allegheny-Singer Research Institute
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hlapp at drycafe.net  Thu Mar 17 19:38:01 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Thu, 17 Mar 2011 15:38:01 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
	<AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
	<B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>
Message-ID: <A95A687E-25DD-4325-983D-BE9A5F45FA23@drycafe.net>

Just a thought towards the future - OpenIDs are so easy to obtain that  
the way it is right now (any OpenID will do) is built on the premise  
that it's not used widely enough (yet!) to make it worth the spammers'  
time.  Same story as with reCaptcha, probably. So once OpenID is used  
widely, we'll probably have to restrict the OpenID providers that we  
permit.

	-hilmar

On Mar 17, 2011, at 12:16 PM, Chris Fields wrote:

> Peter,
>
> It's set up for biopython.  Will make an announcement on open-bio-l  
> and post something on the blog when I catch my breath (redmine and  
> this in one week is a little tiring!).
>
> Will also ping biojava and the other wiki groups about switching over.
>
> chris
>
> On Mar 17, 2011, at 3:27 AM, Peter Cock wrote:
>
>> Yes please - thanks Chris!
>>
>> Peter
>>
>> On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu>  
>> wrote:
>>> Done, for BioSQL.  Let me know about Biopython and the others.
>>>
>>> -c
>>>
>>> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>>>
>>>>
>>>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>>>
>>>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>>>
>>>> Seems to work mostly - there seems to be some odd small problem  
>>>> with ClaimID: typing in my username leads to an OpenID error,  
>>>> whereas entering my full ClaimID OpenID works.  Not sure why that  
>>>> would be.
>>>>
>>>> Any chance this can be enabled for BioSQL too (and accordingly  
>>>> account creation disabled there, too)?
>>>>
>>>>      -hilmar
>>>>
>>>>>
>>>>>
>>>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>>>
>>>>> I have also temporarily shut down new user account creation (new  
>>>>> users must now use OpenID); old users can still use the login,  
>>>>> but they can also tie their account to an OpenID.  Let's see if  
>>>>> it cuts down on the spam.
>>>>>
>>>>> chris
>>>>>
>>>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>>>
>>>>>> Any update on the OpenID extension?
>>>>>>
>>>>>>    -hilmar
>>>>>>
>>>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>>>
>>>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit 
>>>>>>> ):
>>>>>>>
>>>>>>> "Unfortunately, reCAPTCHA might be a victim of its own success  
>>>>>>> - as of 2011, some spammers appear to have figured out a way  
>>>>>>> to bypass it, either through character recognition or by using  
>>>>>>> humans. For that reason, it is not necessarily recommended."
>>>>>>>
>>>>>>> I agree about the barrier to entry issue, but unfortunately  
>>>>>>> with the wiki we're facing a reality check re: spam attacks.   
>>>>>>> We can probably set up a new group for users that allows  
>>>>>>> account approval, though, which might alleviate the process  
>>>>>>> somewhat.
>>>>>>>
>>>>>>> chris
>>>>>>>
>>>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>>>
>>>>>>>> Hi Chris,
>>>>>>>>
>>>>>>>> The GMOD wiki has been getting hit similarly.  I've been  
>>>>>>>> thinking
>>>>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>>>>> account, you have the ability to approve other people's  
>>>>>>>> accounts.  The
>>>>>>>> hope being to distribute the load.  I'm not thrilled about it  
>>>>>>>> though:
>>>>>>>> I want the barrier to entry to be as low as possible.  We  
>>>>>>>> already make
>>>>>>>> it so that you have to have an account to edit, passing a  
>>>>>>>> recaptcha on
>>>>>>>> the way.  Apparently that barrier is already a little too  
>>>>>>>> low :-/
>>>>>>>>
>>>>>>>> Scott
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu 
>>>>>>>> > wrote:
>>>>>>>>> All,
>>>>>>>>>
>>>>>>>>> We have been getting inundated on the wiki with spam  
>>>>>>>>> lately.  In order to get on top of this, I'm thinking about  
>>>>>>>>> having the wiki set up so wiki admins approve new user  
>>>>>>>>> accounts, using the ConfirmAccount plugin:
>>>>>>>>>
>>>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>>>
>>>>>>>>> I wanted to get everyone's opinion on this prior to  
>>>>>>>>> enforcing it.  The queue is pretty configurable, and one can  
>>>>>>>>> set this to auto-delete old requests.
>>>>>>>>>
>>>>>>>>> Any thoughts?
>>>>>>>>>
>>>>>>>>> chris
>>>>>>>>> _______________________________________________
>>>>>>>>> Bioperl-l mailing list
>>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> Scott Cain, Ph. D.
>

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From cjfields at illinois.edu  Thu Mar 17 19:40:47 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 17 Mar 2011 14:40:47 -0500
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <A95A687E-25DD-4325-983D-BE9A5F45FA23@drycafe.net>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
	<AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
	<B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>
	<A95A687E-25DD-4325-983D-BE9A5F45FA23@drycafe.net>
Message-ID: <2E6327AD-4CD3-45CE-A105-66FA3A474294@illinois.edu>

That's easy enough to do with the OpenID plugin settings:

$wgOpenIDConsumerAllow
an array of regular expressions that match OpenIDs you want to allow to log in. For example, "@^(http://)?wikitravel.org/@" will allow OpenIDs from the Wikitravel domain.
$wgOpenIDConsumerDeny
an array of regular expressions that match OpenIDs you want to deny access to. This is mostly useful for servers that are known to be bad. Example: "#^(http://)?example.com/#".

chris

On Mar 17, 2011, at 2:38 PM, Hilmar Lapp wrote:

> Just a thought towards the future - OpenIDs are so easy to obtain that the way it is right now (any OpenID will do) is built on the premise that it's not used widely enough (yet!) to make it worth the spammers' time.  Same story as with reCaptcha, probably. So once OpenID is used widely, we'll probably have to restrict the OpenID providers that we permit.
> 
> 	-hilmar
> 
> On Mar 17, 2011, at 12:16 PM, Chris Fields wrote:
> 
>> Peter,
>> 
>> It's set up for biopython.  Will make an announcement on open-bio-l and post something on the blog when I catch my breath (redmine and this in one week is a little tiring!).
>> 
>> Will also ping biojava and the other wiki groups about switching over.
>> 
>> chris
>> 
>> On Mar 17, 2011, at 3:27 AM, Peter Cock wrote:
>> 
>>> Yes please - thanks Chris!
>>> 
>>> Peter
>>> 
>>> On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu> wrote:
>>>> Done, for BioSQL.  Let me know about Biopython and the others.
>>>> 
>>>> -c
>>>> 
>>>> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>>>> 
>>>>> 
>>>>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>>>> 
>>>>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>>>> 
>>>>> Seems to work mostly - there seems to be some odd small problem with ClaimID: typing in my username leads to an OpenID error, whereas entering my full ClaimID OpenID works.  Not sure why that would be.
>>>>> 
>>>>> Any chance this can be enabled for BioSQL too (and accordingly account creation disabled there, too)?
>>>>> 
>>>>>     -hilmar
>>>>> 
>>>>>> 
>>>>>> 
>>>>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>>>> 
>>>>>> I have also temporarily shut down new user account creation (new users must now use OpenID); old users can still use the login, but they can also tie their account to an OpenID.  Let's see if it cuts down on the spam.
>>>>>> 
>>>>>> chris
>>>>>> 
>>>>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>>>> 
>>>>>>> Any update on the OpenID extension?
>>>>>>> 
>>>>>>>   -hilmar
>>>>>>> 
>>>>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>>>> 
>>>>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit):
>>>>>>>> 
>>>>>>>> "Unfortunately, reCAPTCHA might be a victim of its own success - as of 2011, some spammers appear to have figured out a way to bypass it, either through character recognition or by using humans. For that reason, it is not necessarily recommended."
>>>>>>>> 
>>>>>>>> I agree about the barrier to entry issue, but unfortunately with the wiki we're facing a reality check re: spam attacks.  We can probably set up a new group for users that allows account approval, though, which might alleviate the process somewhat.
>>>>>>>> 
>>>>>>>> chris
>>>>>>>> 
>>>>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>>>> 
>>>>>>>>> Hi Chris,
>>>>>>>>> 
>>>>>>>>> The GMOD wiki has been getting hit similarly.  I've been thinking
>>>>>>>>> about the "vampire" model that EcoliWiki uses: once you have an
>>>>>>>>> account, you have the ability to approve other people's accounts.  The
>>>>>>>>> hope being to distribute the load.  I'm not thrilled about it though:
>>>>>>>>> I want the barrier to entry to be as low as possible.  We already make
>>>>>>>>> it so that you have to have an account to edit, passing a recaptcha on
>>>>>>>>> the way.  Apparently that barrier is already a little too low :-/
>>>>>>>>> 
>>>>>>>>> Scott
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>>>>>>>> All,
>>>>>>>>>> 
>>>>>>>>>> We have been getting inundated on the wiki with spam lately.  In order to get on top of this, I'm thinking about having the wiki set up so wiki admins approve new user accounts, using the ConfirmAccount plugin:
>>>>>>>>>> 
>>>>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>>>> 
>>>>>>>>>> I wanted to get everyone's opinion on this prior to enforcing it.  The queue is pretty configurable, and one can set this to auto-delete old requests.
>>>>>>>>>> 
>>>>>>>>>> Any thoughts?
>>>>>>>>>> 
>>>>>>>>>> chris
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Bioperl-l mailing list
>>>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> --
>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>> Scott Cain, Ph. D.
>> 
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 




From hlapp at drycafe.net  Thu Mar 17 20:01:42 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Thu, 17 Mar 2011 16:01:42 -0400
Subject: [Bioperl-l] bioperl wiki spam
In-Reply-To: <2E6327AD-4CD3-45CE-A105-66FA3A474294@illinois.edu>
References: <04C85CDE-E84B-4F75-9BA9-A9EBEA5F0368@illinois.edu>
	<AANLkTikWL7qmcmOW50SmU3pcdaOoQKivwhvmmjiq3qCt@mail.gmail.com>
	<5F984097-8C59-43D7-AC4D-EF2B1F8A4917@illinois.edu>
	<6C31D549-F686-4B1D-9C78-1DD6385E0C41@drycafe.net>
	<84E2CC2E-8E41-478F-8C69-0DAF3D4148A0@illinois.edu>
	<1A9061E2-1220-43C5-A122-970DF56323C9@drycafe.net>
	<B3C49157-B7F3-46CE-81BD-0FE01524F262@illinois.edu>
	<AANLkTi=17TonomDt8UE03ojLd2WoksEGdEzbSkpUxcJi@mail.gmail.com>
	<B75A7501-937C-43E2-862C-D1677C380F91@illinois.edu>
	<A95A687E-25DD-4325-983D-BE9A5F45FA23@drycafe.net>
	<2E6327AD-4CD3-45CE-A105-66FA3A474294@illinois.edu>
Message-ID: <14304AC6-1AAA-44C3-A169-F0111BA59AC2@drycafe.net>

Indeed. And I guess we can add "bad" providers incrementally as we  
spam from them trickle in. I can imagine that at some point there'll  
also be a blacklist of spam OpenID providers.

	-hilmar

On Mar 17, 2011, at 3:40 PM, Chris Fields wrote:

> That's easy enough to do with the OpenID plugin settings:
>
> $wgOpenIDConsumerAllow
> an array of regular expressions that match OpenIDs you want to allow  
> to log in. For example, "@^(http://)?wikitravel.org/@" will allow  
> OpenIDs from the Wikitravel domain.
> $wgOpenIDConsumerDeny
> an array of regular expressions that match OpenIDs you want to deny  
> access to. This is mostly useful for servers that are known to be  
> bad. Example: "#^(http://)?example.com/#".
>
> chris
>
> On Mar 17, 2011, at 2:38 PM, Hilmar Lapp wrote:
>
>> Just a thought towards the future - OpenIDs are so easy to obtain  
>> that the way it is right now (any OpenID will do) is built on the  
>> premise that it's not used widely enough (yet!) to make it worth  
>> the spammers' time.  Same story as with reCaptcha, probably. So  
>> once OpenID is used widely, we'll probably have to restrict the  
>> OpenID providers that we permit.
>>
>> 	-hilmar
>>
>> On Mar 17, 2011, at 12:16 PM, Chris Fields wrote:
>>
>>> Peter,
>>>
>>> It's set up for biopython.  Will make an announcement on open-bio- 
>>> l and post something on the blog when I catch my breath (redmine  
>>> and this in one week is a little tiring!).
>>>
>>> Will also ping biojava and the other wiki groups about switching  
>>> over.
>>>
>>> chris
>>>
>>> On Mar 17, 2011, at 3:27 AM, Peter Cock wrote:
>>>
>>>> Yes please - thanks Chris!
>>>>
>>>> Peter
>>>>
>>>> On Thursday, March 17, 2011, Chris Fields <cjfields at illinois.edu>  
>>>> wrote:
>>>>> Done, for BioSQL.  Let me know about Biopython and the others.
>>>>>
>>>>> -c
>>>>>
>>>>> On Mar 16, 2011, at 10:05 PM, Hilmar Lapp wrote:
>>>>>
>>>>>>
>>>>>> On Mar 14, 2011, at 11:01 PM, Chris Fields wrote:
>>>>>>
>>>>>>> Okay, we have bioperl.org set up to use OpenID, works well:
>>>>>>
>>>>>> Seems to work mostly - there seems to be some odd small problem  
>>>>>> with ClaimID: typing in my username leads to an OpenID error,  
>>>>>> whereas entering my full ClaimID OpenID works.  Not sure why  
>>>>>> that would be.
>>>>>>
>>>>>> Any chance this can be enabled for BioSQL too (and accordingly  
>>>>>> account creation disabled there, too)?
>>>>>>
>>>>>>    -hilmar
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> http://www.bioperl.org/wiki/Special:OpenIDLogin
>>>>>>>
>>>>>>> I have also temporarily shut down new user account creation  
>>>>>>> (new users must now use OpenID); old users can still use the  
>>>>>>> login, but they can also tie their account to an OpenID.   
>>>>>>> Let's see if it cuts down on the spam.
>>>>>>>
>>>>>>> chris
>>>>>>>
>>>>>>> On Mar 14, 2011, at 1:48 PM, Hilmar Lapp wrote:
>>>>>>>
>>>>>>>> Any update on the OpenID extension?
>>>>>>>>
>>>>>>>>  -hilmar
>>>>>>>>
>>>>>>>> On Mar 14, 2011, at 2:25 PM, Chris Fields wrote:
>>>>>>>>
>>>>>>>>> On use of Recaptcha: according to the ConfirmEdit page (http://www.mediawiki.org/wiki/Extension:ConfirmEdit 
>>>>>>>>> ):
>>>>>>>>>
>>>>>>>>> "Unfortunately, reCAPTCHA might be a victim of its own  
>>>>>>>>> success - as of 2011, some spammers appear to have figured  
>>>>>>>>> out a way to bypass it, either through character recognition  
>>>>>>>>> or by using humans. For that reason, it is not necessarily  
>>>>>>>>> recommended."
>>>>>>>>>
>>>>>>>>> I agree about the barrier to entry issue, but unfortunately  
>>>>>>>>> with the wiki we're facing a reality check re: spam  
>>>>>>>>> attacks.  We can probably set up a new group for users that  
>>>>>>>>> allows account approval, though, which might alleviate the  
>>>>>>>>> process somewhat.
>>>>>>>>>
>>>>>>>>> chris
>>>>>>>>>
>>>>>>>>> On Mar 14, 2011, at 1:12 PM, Scott Cain wrote:
>>>>>>>>>
>>>>>>>>>> Hi Chris,
>>>>>>>>>>
>>>>>>>>>> The GMOD wiki has been getting hit similarly.  I've been  
>>>>>>>>>> thinking
>>>>>>>>>> about the "vampire" model that EcoliWiki uses: once you  
>>>>>>>>>> have an
>>>>>>>>>> account, you have the ability to approve other people's  
>>>>>>>>>> accounts.  The
>>>>>>>>>> hope being to distribute the load.  I'm not thrilled about  
>>>>>>>>>> it though:
>>>>>>>>>> I want the barrier to entry to be as low as possible.  We  
>>>>>>>>>> already make
>>>>>>>>>> it so that you have to have an account to edit, passing a  
>>>>>>>>>> recaptcha on
>>>>>>>>>> the way.  Apparently that barrier is already a little too  
>>>>>>>>>> low :-/
>>>>>>>>>>
>>>>>>>>>> Scott
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Mon, Mar 14, 2011 at 1:44 PM, Chris Fields <cjfields at illinois.edu 
>>>>>>>>>> > wrote:
>>>>>>>>>>> All,
>>>>>>>>>>>
>>>>>>>>>>> We have been getting inundated on the wiki with spam  
>>>>>>>>>>> lately.  In order to get on top of this, I'm thinking  
>>>>>>>>>>> about having the wiki set up so wiki admins approve new  
>>>>>>>>>>> user accounts, using the ConfirmAccount plugin:
>>>>>>>>>>>
>>>>>>>>>>> http://www.mediawiki.org/wiki/Extension:ConfirmAccount
>>>>>>>>>>>
>>>>>>>>>>> I wanted to get everyone's opinion on this prior to  
>>>>>>>>>>> enforcing it.  The queue is pretty configurable, and one  
>>>>>>>>>>> can set this to auto-delete old requests.
>>>>>>>>>>>
>>>>>>>>>>> Any thoughts?
>>>>>>>>>>>
>>>>>>>>>>> chris
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Bioperl-l mailing list
>>>>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>> Scott Cain, Ph. D.
>>>
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>> ===========================================================
>>
>>
>>
>>
>

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From tzhu at mail.bnu.edu.cn  Fri Mar 18 04:33:32 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Fri, 18 Mar 2011 12:33:32 +0800
Subject: [Bioperl-l] What's wrong with the script about module
 Bio::SeqFeature::Gene::GeneStructure
Message-ID: <1300422812.12949.5.camel@ubuntu>

I wrote my script like this,

#!/usr/bin/perl -w
use Bio::SeqIO;
my $catch_seq = Bio::SeqIO -> new(-file => 'test.gbk',-format=>
'genbank');
while( my $seq_obj = $catch_seq -> next_seq)
{
	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
get_SeqFeatures;
	for my $mRNA_feature (@all_mRNA_features)
	{
			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
		{
			@exons=$mRNA_feature->exons;
			$exon_number = scalar(@exons);
			print "$exon_number\n";
		}
	}
}

I hope to count exon number in every mRNA. But it print nothing(You can
arbitrarily get a genbank file to test it). What's wrong?


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)




From hrh at fmi.ch  Fri Mar 18 09:17:30 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Fri, 18 Mar 2011 10:17:30 +0100
Subject: [Bioperl-l] What's wrong with the script about module
	Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300422812.12949.5.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu>
Message-ID: <4D83232A.9050502@fmi.ch>

Hi Tao

I don't fully understand your script, but I do see a major problem:

why do you select for "primary_tag eq 'mRNA'" first?


this simple loop will probably do what you want:

while( my $seq_obj = $catch_seq -> next_seq) {

	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
$seq_obj ->get_SeqFeatures;
	$exon_number = scalar(@all_exon_features);
	print "$exon_number\n";
}


Alternatively, I recommend to read the HOWTO page:

http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

which has a nice example to print out all 'primary_tag' (ie the 'feature 
keys' in a GenBank formated file)

I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
definition:
http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html


Regards, Hans



On 03/18/2011 05:33 AM, Tao Zhu wrote:
> I wrote my script like this,
>
> #!/usr/bin/perl -w
> use Bio::SeqIO;
> my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
> 'genbank');
> while( my $seq_obj = $catch_seq ->  next_seq)
> {
> 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
> get_SeqFeatures;
> 	for my $mRNA_feature (@all_mRNA_features)
> 	{
> 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
> 		{
> 			@exons=$mRNA_feature->exons;
> 			$exon_number = scalar(@exons);
> 			print "$exon_number\n";
> 		}
> 	}
> }
>
> I hope to count exon number in every mRNA. But it print nothing(You can
> arbitrarily get a genbank file to test it). What's wrong?
>
>


From tzhu at mail.bnu.edu.cn  Fri Mar 18 11:32:00 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Fri, 18 Mar 2011 19:32:00 +0800
Subject: [Bioperl-l] What's wrong with the script about module
 Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <4D83232A.9050502@fmi.ch>
References: <1300422812.12949.5.camel@ubuntu>  <4D83232A.9050502@fmi.ch>
Message-ID: <1300447920.16670.2.camel@ubuntu>

Of course that's OK. But what I really want to know is how to use module
Bio::SeqFeature::Gene::GeneStructure. 

? 2011-03-18?? 10:17 +0100?Hans-Rudolf Hotz???
> Hi Tao
> 
> I don't fully understand your script, but I do see a major problem:
> 
> why do you select for "primary_tag eq 'mRNA'" first?
> 
> 
> this simple loop will probably do what you want:
> 
> while( my $seq_obj = $catch_seq -> next_seq) {
> 
> 	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
> $seq_obj ->get_SeqFeatures;
> 	$exon_number = scalar(@all_exon_features);
> 	print "$exon_number\n";
> }
> 
> 
> Alternatively, I recommend to read the HOWTO page:
> 
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> 
> which has a nice example to print out all 'primary_tag' (ie the 'feature 
> keys' in a GenBank formated file)
> 
> I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
> definition:
> http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
> 
> 
> Regards, Hans
> 
> 
> 
> On 03/18/2011 05:33 AM, Tao Zhu wrote:
> > I wrote my script like this,
> >
> > #!/usr/bin/perl -w
> > use Bio::SeqIO;
> > my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
> > 'genbank');
> > while( my $seq_obj = $catch_seq ->  next_seq)
> > {
> > 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
> > get_SeqFeatures;
> > 	for my $mRNA_feature (@all_mRNA_features)
> > 	{
> > 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
> > 		{
> > 			@exons=$mRNA_feature->exons;
> > 			$exon_number = scalar(@exons);
> > 			print "$exon_number\n";
> > 		}
> > 	}
> > }
> >
> > I hope to count exon number in every mRNA. But it print nothing(You can
> > arbitrarily get a genbank file to test it). What's wrong?
> >
> >

-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)




From cjfields at illinois.edu  Fri Mar 18 13:04:34 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 18 Mar 2011 08:04:34 -0500
Subject: [Bioperl-l] What's wrong with the script about module
	Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300447920.16670.2.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu> <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
Message-ID: <2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>

The SeqFeatures derived from a GenBank file are simple Bio::SeqFeature::Generic instances.  I don't think there is a straightforward way to have the parser return Bio::SeqFeature::Gene::GeneStructure instances.

chris

On Mar 18, 2011, at 6:32 AM, Tao Zhu wrote:

> Of course that's OK. But what I really want to know is how to use module
> Bio::SeqFeature::Gene::GeneStructure. 
> 
> ? 2011-03-18?? 10:17 +0100?Hans-Rudolf Hotz???
>> Hi Tao
>> 
>> I don't fully understand your script, but I do see a major problem:
>> 
>> why do you select for "primary_tag eq 'mRNA'" first?
>> 
>> 
>> this simple loop will probably do what you want:
>> 
>> while( my $seq_obj = $catch_seq -> next_seq) {
>> 
>> 	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
>> $seq_obj ->get_SeqFeatures;
>> 	$exon_number = scalar(@all_exon_features);
>> 	print "$exon_number\n";
>> }
>> 
>> 
>> Alternatively, I recommend to read the HOWTO page:
>> 
>> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
>> 
>> which has a nice example to print out all 'primary_tag' (ie the 'feature 
>> keys' in a GenBank formated file)
>> 
>> I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
>> definition:
>> http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
>> 
>> 
>> Regards, Hans
>> 
>> 
>> 
>> On 03/18/2011 05:33 AM, Tao Zhu wrote:
>>> I wrote my script like this,
>>> 
>>> #!/usr/bin/perl -w
>>> use Bio::SeqIO;
>>> my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
>>> 'genbank');
>>> while( my $seq_obj = $catch_seq ->  next_seq)
>>> {
>>> 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
>>> get_SeqFeatures;
>>> 	for my $mRNA_feature (@all_mRNA_features)
>>> 	{
>>> 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
>>> 		{
>>> 			@exons=$mRNA_feature->exons;
>>> 			$exon_number = scalar(@exons);
>>> 			print "$exon_number\n";
>>> 		}
>>> 	}
>>> }
>>> 
>>> I hope to count exon number in every mRNA. But it print nothing(You can
>>> arbitrarily get a genbank file to test it). What's wrong?
>>> 
>>> 
> 
> -- 
> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> 100875, China
> Email: tzhu at mail.bnu.edu.cn
> Website: http://bnuzt.org (mainly written in Chinese)
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From ross at cuhk.edu.hk  Fri Mar 18 13:22:40 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Fri, 18 Mar 2011 21:22:40 +0800
Subject: [Bioperl-l]  failure in unsubscription
In-Reply-To: <1300447920.16670.2.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu> <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
Message-ID: <018101cbe56f$8ec755f0$ac5601d0$@edu.hk>

unable to unsubscribe bioperl mailing list, anybody can help? the web link, after clicking "unsubscribe", there is no confirmation email sent to my email account and I keep receiving emails from bioperl mailing list.




From tzhu at mail.bnu.edu.cn  Fri Mar 18 13:57:21 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Fri, 18 Mar 2011 21:57:21 +0800
Subject: [Bioperl-l] What's wrong with the script about module
 Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
References: <1300422812.12949.5.camel@ubuntu>  <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
	<2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
Message-ID: <1300456641.18688.4.camel@ubuntu>

Yes. But in the document
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
Bio::SeqFeature::Generic. I wonder how to do such inheritance.

? 2011-03-18?? 08:04 -0500?Chris Fields???
> The SeqFeatures derived from a GenBank file are simple Bio::SeqFeature::Generic instances.  I don't think there is a straightforward way to have the parser return Bio::SeqFeature::Gene::GeneStructure instances.
> 
> chris
> 
> On Mar 18, 2011, at 6:32 AM, Tao Zhu wrote:
> 
> > Of course that's OK. But what I really want to know is how to use module
> > Bio::SeqFeature::Gene::GeneStructure. 
> > 
> > ? 2011-03-18?? 10:17 +0100?Hans-Rudolf Hotz???
> >> Hi Tao
> >> 
> >> I don't fully understand your script, but I do see a major problem:
> >> 
> >> why do you select for "primary_tag eq 'mRNA'" first?
> >> 
> >> 
> >> this simple loop will probably do what you want:
> >> 
> >> while( my $seq_obj = $catch_seq -> next_seq) {
> >> 
> >> 	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
> >> $seq_obj ->get_SeqFeatures;
> >> 	$exon_number = scalar(@all_exon_features);
> >> 	print "$exon_number\n";
> >> }
> >> 
> >> 
> >> Alternatively, I recommend to read the HOWTO page:
> >> 
> >> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> >> 
> >> which has a nice example to print out all 'primary_tag' (ie the 'feature 
> >> keys' in a GenBank formated file)
> >> 
> >> I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
> >> definition:
> >> http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
> >> 
> >> 
> >> Regards, Hans
> >> 
> >> 
> >> 
> >> On 03/18/2011 05:33 AM, Tao Zhu wrote:
> >>> I wrote my script like this,
> >>> 
> >>> #!/usr/bin/perl -w
> >>> use Bio::SeqIO;
> >>> my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
> >>> 'genbank');
> >>> while( my $seq_obj = $catch_seq ->  next_seq)
> >>> {
> >>> 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
> >>> get_SeqFeatures;
> >>> 	for my $mRNA_feature (@all_mRNA_features)
> >>> 	{
> >>> 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
> >>> 		{
> >>> 			@exons=$mRNA_feature->exons;
> >>> 			$exon_number = scalar(@exons);
> >>> 			print "$exon_number\n";
> >>> 		}
> >>> 	}
> >>> }
> >>> 
> >>> I hope to count exon number in every mRNA. But it print nothing(You can
> >>> arbitrarily get a genbank file to test it). What's wrong?
> >>> 
> >>> 
> > 
> > -- 
> > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> > 100875, China
> > Email: tzhu at mail.bnu.edu.cn
> > Website: http://bnuzt.org (mainly written in Chinese)
> > 
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 





From fs5 at sanger.ac.uk  Fri Mar 18 15:05:29 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Fri, 18 Mar 2011 15:05:29 +0000
Subject: [Bioperl-l] What's wrong with the script about
	module	Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300456641.18688.4.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu>  <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
	<2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
	<1300456641.18688.4.camel@ubuntu>
Message-ID: <1300460730.12411.50.camel@deskpro15336.internal.sanger.ac.uk>

maybe I'm missing the point here but I think an "mRNA" feature should
not be a Bio::SeqFeature::Gene::GeneStructure and it should not have
exons - it would not make sense biologically.

Frank


On Fri, 2011-03-18 at 21:57 +0800, Tao Zhu wrote:
> Yes. But in the document
> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
> It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
> Bio::SeqFeature::Generic. I wonder how to do such inheritance.
> 
> ? 2011-03-18?? 08:04 -0500?Chris Fields???
> > The SeqFeatures derived from a GenBank file are simple Bio::SeqFeature::Generic instances.  I don't think there is a straightforward way to have the parser return Bio::SeqFeature::Gene::GeneStructure instances.
> > 
> > chris
> > 
> > On Mar 18, 2011, at 6:32 AM, Tao Zhu wrote:
> > 
> > > Of course that's OK. But what I really want to know is how to use module
> > > Bio::SeqFeature::Gene::GeneStructure. 
> > > 
> > > ? 2011-03-18?? 10:17 +0100?Hans-Rudolf Hotz???
> > >> Hi Tao
> > >> 
> > >> I don't fully understand your script, but I do see a major problem:
> > >> 
> > >> why do you select for "primary_tag eq 'mRNA'" first?
> > >> 
> > >> 
> > >> this simple loop will probably do what you want:
> > >> 
> > >> while( my $seq_obj = $catch_seq -> next_seq) {
> > >> 
> > >> 	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
> > >> $seq_obj ->get_SeqFeatures;
> > >> 	$exon_number = scalar(@all_exon_features);
> > >> 	print "$exon_number\n";
> > >> }
> > >> 
> > >> 
> > >> Alternatively, I recommend to read the HOWTO page:
> > >> 
> > >> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> > >> 
> > >> which has a nice example to print out all 'primary_tag' (ie the 'feature 
> > >> keys' in a GenBank formated file)
> > >> 
> > >> I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
> > >> definition:
> > >> http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
> > >> 
> > >> 
> > >> Regards, Hans
> > >> 
> > >> 
> > >> 
> > >> On 03/18/2011 05:33 AM, Tao Zhu wrote:
> > >>> I wrote my script like this,
> > >>> 
> > >>> #!/usr/bin/perl -w
> > >>> use Bio::SeqIO;
> > >>> my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
> > >>> 'genbank');
> > >>> while( my $seq_obj = $catch_seq ->  next_seq)
> > >>> {
> > >>> 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
> > >>> get_SeqFeatures;
> > >>> 	for my $mRNA_feature (@all_mRNA_features)
> > >>> 	{
> > >>> 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
> > >>> 		{
> > >>> 			@exons=$mRNA_feature->exons;
> > >>> 			$exon_number = scalar(@exons);
> > >>> 			print "$exon_number\n";
> > >>> 		}
> > >>> 	}
> > >>> }
> > >>> 
> > >>> I hope to count exon number in every mRNA. But it print nothing(You can
> > >>> arbitrarily get a genbank file to test it). What's wrong?
> > >>> 
> > >>> 
> > > 
> > > -- 
> > > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> > > 100875, China
> > > Email: tzhu at mail.bnu.edu.cn
> > > Website: http://bnuzt.org (mainly written in Chinese)
> > > 
> > > 
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 



From chapmanb at 50mail.com  Fri Mar  4 12:37:28 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Fri, 4 Mar 2011 07:37:28 -0500
Subject: [Bioperl-l] Bioinformatics Open Source Conference (BOSC 2011)--Call
 for Abstracts
Message-ID: <20110304123728.GD27839@sobchak>

We invite you to submit an abstract to BOSC 2011! Please forward this
message as appropriate, and forgive multiple postings.

Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference (BOSC 2011)
An ISMB 2011 Special Interest Group (SIG)

Dates: July 15-16, 2011
Location: Vienna, Austria
Web site: http://www.open-bio.org/wiki/BOSC_2011
Email: bosc at open-bio.org
BOSC announcements mailing list:  http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:
April 18, 2011: Deadline for submitting abstracts to BOSC 2011
May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors
July 13-14, 2011: Codefest 2011 programming session (see http://www.open-bio.org/wiki/Codefest_2011 for details)
July 15-16, 2011: BOSC 2011
July 17-19, 2011: ISMB 2011

The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.

We invite you to submit abstracts for talks and posters.  Sessions include:
- Approaches to parallel processing
- Cloud-based approaches to improving software and data accessibility
- The Semantic Web in open source bioinformatics
- Data visualization
- Tools for next-generation sequencing
- Other Open Source software

In addition to the above sessions, there will be a panel discussion
about "Meeting the challenges of inter-institutional collaboration". We
are also working to arrange a joint session with one of the other ISMB
SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student Travel
Awards for BOSC 2011. Each winner will be awarded $250 to defray the
costs of travel to BOSC 2011.
 
For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee:
Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor 


From bill_zt at sina.com  Fri Mar 18 00:48:19 2011
From: bill_zt at sina.com (Tao Zhu)
Date: Fri, 18 Mar 2011 08:48:19 +0800
Subject: [Bioperl-l] Perl/BioPerl (Simon No?l)
Message-ID: <1300409299.2349.5.camel@ubuntu>

In order to learn BioPerl, you should first learn and master Perl. If
you are not majoring in Bioinformatics, learning Perl is just OK.
Otherwise you should learn both Perl and BioPerl.


> Message: 2
> Date: Wed, 16 Mar 2011 15:40:09 -0400
> From: Simon No?l <simon.noel.2 at ulaval.ca>
> Subject: [Bioperl-l]  Perl/BioPerl
> To: "bioperl-l at lists.open-bio.org" <bioperl-l at lists.open-bio.org>
> Message-ID:
>         <1C970CA8E580A84394CE5CF42FEC0046DF67A4FA81 at EXCH-MBX-E.ulaval.ca>
> Content-Type: text/plain; charset="iso-8859-1"
> 
>  Hi, 
>  
> I don't know if I am on the right mailling list for this.
>  
> My director say that I should have a class of Perl or BioPerl.  Witch
> one should be better?  Do you know where I can find such class?
> 
> 
> Simon No?l
> CdeC
> 


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)



From bio.justin100 at gmail.com  Fri Mar  4 20:24:51 2011
From: bio.justin100 at gmail.com (justin100)
Date: Fri, 4 Mar 2011 12:24:51 -0800 (PST)
Subject: [Bioperl-l] Please recommend Perl module to parse phylogentic trees
Message-ID: <2e94f0bb-0282-4d53-b205-56ff895665de@w7g2000pre.googlegroups.com>

Hi,

I am writing a script to parse phylogenetic trees. The input will be
trees in Newick format for now (maybe NEXUS in the future).

Quite a few Perl modules can parse phylogenetic trees. For Newick
format, there are Bio::TreeIO and  Bio::Phylo::Parsers. For NEXUS
format, there is Bio::NEXUS. From my understanding, it's not difficult
to convert from Newick to NEXUS or vice versa, if only for the purpose
of parsing trees.

I'd to know the advantages and disadvantages of these modules when
compared with each other. Please recommend one that you think is the
most capable parser (and hopefully has the least bugs).

Thanks.

Justin


From jonathan at leto.net  Wed Mar 16 20:48:24 2011
From: jonathan at leto.net (Jonathan "Duke" Leto)
Date: Wed, 16 Mar 2011 13:48:24 -0700
Subject: [Bioperl-l] [ANNOUNCEMENT] Bugzilla to Redmine migration
In-Reply-To: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
References: <34C8C0CB-9273-468E-86D7-74B22464F181@illinois.edu>
Message-ID: <AANLkTim-x8NwKk9rUA2rK2c5CG2ps16QR5ASqdsCxhPA@mail.gmail.com>

Howdy,

Thanks for working on this Chris!

I am not sure the password reset works properly.

Attached is a screenshot of it giving odd errors.

This was on Firefox 3.6.

Duke

On Wed, Mar 16, 2011 at 10:58 AM, Chris Fields <cjfields at illinois.edu> wrote:
> (apologies if you receive multiple copies of this)
>
> All,
>
> We are currently about 95% done with a transition over to our new Redmine tracking system, to the point where we feel comfortable in going ahead with opening it to developers:
>
> http://redmine.open-bio.org/
>
> All edits to bugzilla reports on our old system (http://bugzilla.open-bio.org/) are now disabled and the system is now read-only. ?Any new bugs and comments to old ones should be reported on the new Redmine server.
>
> For current Bugzilla users, we have migrated login IDs to Redmine (this is normally an email address), but we have reset user passwords for security reasons. ?There are two ways to access your account:
>
> 1) When logging in (http://redmine.open-bio.org/login), click on the 'Lost password' link. ?You will be prompted for your email address (this should be the same as your bugzilla login). ?An new email will be sent out containing directions for resetting your password and logging in.
>
> 2) It is possible the above may be automatically detected as spam. ?If the above doesn't work or the reset email isn't received within a day, contact support at helpdesk.open-bio.org to receive your new password.
>
> Also, note that Redmine has a different syntax for those who want to add links to their reports; see http://www.redmine.org/projects/redmine/wiki/RedmineTextFormatting.
>
> Let us know if you have any questions.
>
> chris
>
> Christopher Fields
> IGB Postdoctoral Fellow
> Genomics of Neural & Behavioral Plasticity
> University of Illinois Urbana-Champaign
> Institute for Genomic Biology
> 1206 W. Gregory Dr. , MC-195
> Urbana, IL 61801
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Jonathan "Duke" Leto
jonathan at leto.net
http://leto.net
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From rutgeraldo at gmail.com  Fri Mar 18 14:16:25 2011
From: rutgeraldo at gmail.com (Rutger Vos)
Date: Fri, 18 Mar 2011 14:16:25 +0000
Subject: [Bioperl-l] Please forward: collecting support for Japanese
	scientists
Message-ID: <AANLkTiksWdna1MLpbBWk2nDv0LAyrXdU7xV3Fs5gSHkF@mail.gmail.com>

Dear colleagues,

A web page has been launched to collect support for Japanese
(bio-)scientists: http://biohelpathon.org - please forward this
address widely.

The purpose of the web page is to establish a knowledge base of
available support for our colleagues in Japan. You are invited to
submit any tips, ideas and offers including accommodation, funding
resources, exchange schemes, lab space, server space and open
positions for visiting students and research personnel from Japan.

We will collect your suggestions and offers and will share them with
whoever is best placed to disseminate them. This initiative originates
with the attendees of the BioHackathons (the Japanese website
http://hackathon.dbcls.jp is offline due to the earthquake), but
anyone is very welcome to contribute. To get in touch, join
http://groups.google.com/group/biohelpathon.

This initiative is no alternative to first responders who are helping
out in Japan right now. The rescue operation and food and shelter
support comes first. If you can only do one thing, it should be a
donation to something like the Red Cross. This comes later.

See also:
A different initiative, with which we're in touch:
http://www.nipponsciencesupport.net/
More info on Nature blogs:
http://blogs.nature.com/news/thegreatbeyond/2011/03/helping_hand_for_scientistrefu.html

PLEASE NOTE: WE ARE NOT HANDLING MONEY. This is simply a way to
crowdsource information about available resources.

Thank you.

Rutger Vos


From spotforever at tiscali.it  Sun Mar 13 18:15:54 2011
From: spotforever at tiscali.it (marcocirilli)
Date: Sun, 13 Mar 2011 11:15:54 -0700 (PDT)
Subject: [Bioperl-l]  slit sequence with BioPerl by ID-query
Message-ID: <31138653.post@talk.nabble.com>


Hello, I have 2 fasta file with similar sequences and I want to compare them
and eliminate sequences with the same IDquery (or extract only different
ID-query). How can I do it with BioPerl? Thanks 
-- 
View this message in context: http://old.nabble.com/slit-sequence-with-BioPerl-by-ID-query-tp31138653p31138653.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From suhail.mn12 at yahoo.co.uk  Fri Mar 18 16:18:49 2011
From: suhail.mn12 at yahoo.co.uk (Suhail M)
Date: Fri, 18 Mar 2011 16:18:49 +0000 (GMT)
Subject: [Bioperl-l] RemoteBlast
Message-ID: <988359.99459.qm@web132309.mail.ird.yahoo.com>

Dear Sir or Madam,
I am using a remote blast and encounter either a too many hsp or CPU overload 
problem with my specific gene. The gene itself is not that big so I was 
wondering is there a parameter I can pass when using the submit option to 
restrict number of hsp and to avoid the cpu and too many hsp problem? (I know I 
can use repeat masking and change the e-value but I need something that does not 
require those changes)

my $prog = 'blastn';
#my $db   = 'swissprot';
my $e_val= '1e-10';

my @params = ( '-prog'       => $prog,
#       '-data'       => $db,
               '-expect'     => $e_val,
               '-readmethod' => 'SearchIO'
            );

my $factory = Bio::Tools::Run::RemoteBlast->new(@params);

$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens [ORGN]';

delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};

my $str = Bio::SeqIO->new(-file            =>'temporary.fa' , 
 '-format'         => 'fasta');

my $r = $factory->submit_blast('temporary.fa');

Thank you for your help.
Suhail


      


From shalabh.sharma7 at gmail.com  Fri Mar 18 16:41:42 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Fri, 18 Mar 2011 12:41:42 -0400
Subject: [Bioperl-l] RemoteBlast
In-Reply-To: <988359.99459.qm@web132309.mail.ird.yahoo.com>
References: <988359.99459.qm@web132309.mail.ird.yahoo.com>
Message-ID: <AANLkTikLD+A9o0Nujg9ThGbFL3HvtaAGXaihoEX5OmTE@mail.gmail.com>

Suhail,
         You can restrict the number of hits by using "-v" and "-b"
parameters.

-Shalabh


On Fri, Mar 18, 2011 at 12:18 PM, Suhail M <suhail.mn12 at yahoo.co.uk> wrote:

> Dear Sir or Madam,
> I am using a remote blast and encounter either a too many hsp or CPU
> overload
> problem with my specific gene. The gene itself is not that big so I was
> wondering is there a parameter I can pass when using the submit option to
> restrict number of hsp and to avoid the cpu and too many hsp problem? (I
> know I
> can use repeat masking and change the e-value but I need something that
> does not
> require those changes)
>
> my $prog = 'blastn';
> #my $db   = 'swissprot';
> my $e_val= '1e-10';
>
> my @params = ( '-prog'       => $prog,
> #       '-data'       => $db,
>               '-expect'     => $e_val,
>               '-readmethod' => 'SearchIO'
>            );
>
> my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
>
> $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens
> [ORGN]';
>
> delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};
>
> my $str = Bio::SeqIO->new(-file            =>'temporary.fa' ,
>  '-format'         => 'fasta');
>
> my $r = $factory->submit_blast('temporary.fa');
>
> Thank you for your help.
> Suhail
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


From rmb32 at cornell.edu  Fri Mar 18 19:24:03 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Fri, 18 Mar 2011 15:24:03 -0400
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
Message-ID: <4D83B153.6010006@cornell.edu>

Hi all,

Great news: Google announced today that the Open Bioinformatics
Foundation has been accepted as a mentoring organization for this
summer's Google Summer of Code!

GSoC is a Google-sponsored student internship program for open-source
projects, open to students from around the world (not just US
residents).   Students are paid a $5000 USD stipend to work as a
developer on an open-source project for the summer. For more on GSoC,
see GSoC 2011 FAQ at http://bit.ly/hpoz8W

Student applications are due April 8, 2011 at 19:00 UTC.  Students who
are interested in participating should look at the OBF's GSoC page at
http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
ideas, and whom to contact about applying.

For current developers on OBF projects, please consider volunteering to
be a mentor if you have not already, and contribute project ideas.  Just
list your name and project ideas on OBF wiki and on the relevant
project's GSoC wiki page.

Thanks to all who helped make OBF's application to GSoC a success, and
let's have a great, productive summer of code!

Rob Buels
OBF GSoC 2011 Administrator




From cjfields at illinois.edu  Fri Mar 18 20:06:36 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 18 Mar 2011 15:06:36 -0500
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <4D83B153.6010006@cornell.edu>
References: <4D83B153.6010006@cornell.edu>
Message-ID: <AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>

Congrats Rob!

chris

On Mar 18, 2011, at 2:24 PM, Robert Buels wrote:

> Hi all,
> 
> Great news: Google announced today that the Open Bioinformatics
> Foundation has been accepted as a mentoring organization for this
> summer's Google Summer of Code!
> 
> GSoC is a Google-sponsored student internship program for open-source
> projects, open to students from around the world (not just US
> residents).   Students are paid a $5000 USD stipend to work as a
> developer on an open-source project for the summer. For more on GSoC,
> see GSoC 2011 FAQ at http://bit.ly/hpoz8W
> 
> Student applications are due April 8, 2011 at 19:00 UTC.  Students who
> are interested in participating should look at the OBF's GSoC page at
> http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
> ideas, and whom to contact about applying.
> 
> For current developers on OBF projects, please consider volunteering to
> be a mentor if you have not already, and contribute project ideas.  Just
> list your name and project ideas on OBF wiki and on the relevant
> project's GSoC wiki page.
> 
> Thanks to all who helped make OBF's application to GSoC a success, and
> let's have a great, productive summer of code!
> 
> Rob Buels
> OBF GSoC 2011 Administrator
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From ross at cuhk.edu.hk  Fri Mar 18 23:28:51 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Sat, 19 Mar 2011 07:28:51 +0800
Subject: [Bioperl-l]  failure in unsubscription
In-Reply-To: <AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
Message-ID: <018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>

unable to unsubscribe bioperl mailing list, can anybody help? the web link,
after clicking "unsubscribe" at
http://lists.open-bio.org/mailman/options/bioperl-announce-l, there is no
confirmation email sent to my email account and I keep receiving emails from
bioperl mailing list.



From Kevin.M.Brown at asu.edu  Fri Mar 18 23:35:37 2011
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Fri, 18 Mar 2011 16:35:37 -0700
Subject: [Bioperl-l] failure in unsubscription
In-Reply-To: <018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>
References: <4D83B153.6010006@cornell.edu><AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
	<018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>
Message-ID: <1A4207F8295607498283FE9E93B775B407816AC4@EX02.asurite.ad.asu.edu>

Looks like you're unsubscribing to the wrong list. That is for the
Bioperl ANNOUNCE list. See the signature at the bottom of the emails for
the correct link to remove yourself from the Bioperl-l list.

Kevin Brown
Center for Innovations in Medicine
Biodesign Institute
Arizona State University 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Ross KK Leung
> Sent: Friday, March 18, 2011 4:29 PM
> To: 'Chris Fields'; 'Robert Buels'
> Cc: 'BioPerl List'
> Subject: [Bioperl-l] failure in unsubscription
> 
> unable to unsubscribe bioperl mailing list, can anybody help? the web
> link,
> after clicking "unsubscribe" at
> http://lists.open-bio.org/mailman/options/bioperl-announce-l, there is
> no
> confirmation email sent to my email account and I keep receiving
emails
> from
> bioperl mailing list.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From David.Messina at sbc.su.se  Fri Mar 18 23:55:08 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Sat, 19 Mar 2011 00:55:08 +0100
Subject: [Bioperl-l] failure in unsubscription
In-Reply-To: <018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
	<018f01cbe5c4$3d8b6f50$b8a24df0$@edu.hk>
Message-ID: <AANLkTin6k3AfwYFxgRKLGWbL5BhqxkQr7Vv6MebhObzY@mail.gmail.com>

Looks like you accidentally found the page for the wrong email list. This is
bioperl-l, not bioperl-announce-l.

Try clicking unsubscribe on this page:
http://lists.open-bio.org/mailman/listinfo/bioperl-l



On Sat, Mar 19, 2011 at 00:28, Ross KK Leung <ross at cuhk.edu.hk> wrote:

> unable to unsubscribe bioperl mailing list, can anybody help? the web link,
> after clicking "unsubscribe" at
> http://lists.open-bio.org/mailman/options/bioperl-announce-l, there is no
> confirmation email sent to my email account and I keep receiving emails
> from
> bioperl mailing list.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From David.Messina at sbc.su.se  Fri Mar 18 23:56:12 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Sat, 19 Mar 2011 00:56:12 +0100
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
Message-ID: <AANLkTikTsPeJvs0StBPzicxM55XgfvGbjrZMrwX9mwNo@mail.gmail.com>

Hear, hear! Thanks again Rob for leading this effort. You rock!

Dave



On Fri, Mar 18, 2011 at 21:06, Chris Fields <cjfields at illinois.edu> wrote:

> Congrats Rob!
>
> chris
>
> On Mar 18, 2011, at 2:24 PM, Robert Buels wrote:
>
> > Hi all,
> >
> > Great news: Google announced today that the Open Bioinformatics
> > Foundation has been accepted as a mentoring organization for this
> > summer's Google Summer of Code!
> >
> > GSoC is a Google-sponsored student internship program for open-source
> > projects, open to students from around the world (not just US
> > residents).   Students are paid a $5000 USD stipend to work as a
> > developer on an open-source project for the summer. For more on GSoC,
> > see GSoC 2011 FAQ at http://bit.ly/hpoz8W
> >
> > Student applications are due April 8, 2011 at 19:00 UTC.  Students who
> > are interested in participating should look at the OBF's GSoC page at
> > http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
> > ideas, and whom to contact about applying.
> >
> > For current developers on OBF projects, please consider volunteering to
> > be a mentor if you have not already, and contribute project ideas.  Just
> > list your name and project ideas on OBF wiki and on the relevant
> > project's GSoC wiki page.
> >
> > Thanks to all who helped make OBF's application to GSoC a success, and
> > let's have a great, productive summer of code!
> >
> > Rob Buels
> > OBF GSoC 2011 Administrator
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From hlapp at drycafe.net  Sat Mar 19 02:04:28 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Fri, 18 Mar 2011 22:04:28 -0400
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <AANLkTikTsPeJvs0StBPzicxM55XgfvGbjrZMrwX9mwNo@mail.gmail.com>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
	<AANLkTikTsPeJvs0StBPzicxM55XgfvGbjrZMrwX9mwNo@mail.gmail.com>
Message-ID: <19636599-D2B1-49E5-B557-3E406B405523@drycafe.net>

Yes! -hilmar

On Mar 18, 2011, at 7:56 PM, Dave Messina wrote:

> Hear, hear! Thanks again Rob for leading this effort. You rock!
>
> Dave
>
>
>
> On Fri, Mar 18, 2011 at 21:06, Chris Fields <cjfields at illinois.edu>  
> wrote:
>
>> Congrats Rob!
>>
>> chris
>>
>> On Mar 18, 2011, at 2:24 PM, Robert Buels wrote:
>>
>>> Hi all,
>>>
>>> Great news: Google announced today that the Open Bioinformatics
>>> Foundation has been accepted as a mentoring organization for this
>>> summer's Google Summer of Code!
>>>
>>> GSoC is a Google-sponsored student internship program for open- 
>>> source
>>> projects, open to students from around the world (not just US
>>> residents).   Students are paid a $5000 USD stipend to work as a
>>> developer on an open-source project for the summer. For more on  
>>> GSoC,
>>> see GSoC 2011 FAQ at http://bit.ly/hpoz8W
>>>
>>> Student applications are due April 8, 2011 at 19:00 UTC.  Students  
>>> who
>>> are interested in participating should look at the OBF's GSoC page  
>>> at
>>> http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
>>> ideas, and whom to contact about applying.
>>>
>>> For current developers on OBF projects, please consider  
>>> volunteering to
>>> be a mentor if you have not already, and contribute project  
>>> ideas.  Just
>>> list your name and project ideas on OBF wiki and on the relevant
>>> project's GSoC wiki page.
>>>
>>> Thanks to all who helped make OBF's application to GSoC a success,  
>>> and
>>> let's have a great, productive summer of code!
>>>
>>> Rob Buels
>>> OBF GSoC 2011 Administrator
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From chiragmatkarbioinfo at gmail.com  Sat Mar 19 03:44:32 2011
From: chiragmatkarbioinfo at gmail.com (Chirag Matkar)
Date: Sat, 19 Mar 2011 10:44:32 +0700
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <19636599-D2B1-49E5-B557-3E406B405523@drycafe.net>
References: <4D83B153.6010006@cornell.edu>
	<AF36D21E-FFB0-4625-9E95-A9BF94A2FE8A@illinois.edu>
	<AANLkTikTsPeJvs0StBPzicxM55XgfvGbjrZMrwX9mwNo@mail.gmail.com>
	<19636599-D2B1-49E5-B557-3E406B405523@drycafe.net>
Message-ID: <AANLkTin6_H-T7Eq2jxU-SM4CuMF=nBZpXoM_n6joFfmn@mail.gmail.com>

Great News

On Sat, Mar 19, 2011 at 9:04 AM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> Yes! -hilmar
>
>
> On Mar 18, 2011, at 7:56 PM, Dave Messina wrote:
>
>  Hear, hear! Thanks again Rob for leading this effort. You rock!
>>
>> Dave
>>
>>
>>
>> On Fri, Mar 18, 2011 at 21:06, Chris Fields <cjfields at illinois.edu>
>> wrote:
>>
>>  Congrats Rob!
>>>
>>> chris
>>>
>>> On Mar 18, 2011, at 2:24 PM, Robert Buels wrote:
>>>
>>>  Hi all,
>>>>
>>>> Great news: Google announced today that the Open Bioinformatics
>>>> Foundation has been accepted as a mentoring organization for this
>>>> summer's Google Summer of Code!
>>>>
>>>> GSoC is a Google-sponsored student internship program for open-source
>>>> projects, open to students from around the world (not just US
>>>> residents).   Students are paid a $5000 USD stipend to work as a
>>>> developer on an open-source project for the summer. For more on GSoC,
>>>> see GSoC 2011 FAQ at http://bit.ly/hpoz8W
>>>>
>>>> Student applications are due April 8, 2011 at 19:00 UTC.  Students who
>>>> are interested in participating should look at the OBF's GSoC page at
>>>> http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
>>>> ideas, and whom to contact about applying.
>>>>
>>>> For current developers on OBF projects, please consider volunteering to
>>>> be a mentor if you have not already, and contribute project ideas.  Just
>>>> list your name and project ideas on OBF wiki and on the relevant
>>>> project's GSoC wiki page.
>>>>
>>>> Thanks to all who helped make OBF's application to GSoC a success, and
>>>> let's have a great, productive summer of code!
>>>>
>>>> Rob Buels
>>>> OBF GSoC 2011 Administrator
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>  _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Regards,
Chirag Matkar


From tzhu at mail.bnu.edu.cn  Sat Mar 19 09:49:22 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Sat, 19 Mar 2011 17:49:22 +0800
Subject: [Bioperl-l] What's wrong with the script about module
 Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300460730.12411.50.camel@deskpro15336.internal.sanger.ac.uk>
References: <1300422812.12949.5.camel@ubuntu>  <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
	<2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
	<1300456641.18688.4.camel@ubuntu>
	<1300460730.12411.50.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <1300528162.5998.4.camel@ubuntu>

But I think an "mRNA" feature should have exons. For example:


     mRNA            complement(join(1031434..1031901,1031940..1032269,
                     1032329..1032418,1032472..1032489))
                     /locus_tag="SPCC825.05c"
                     /transcript_id="NM_001023047.1"
                     /db_xref="GI:68021105"
                     /db_xref="GeneID:2539459"

Such mRNA should have 4 exons and 3 introns, right? And I just want to
calculate the lengths of every exons and introns quickly.

Besides, in the document of module Bio::SeqFeature::Gene::GeneStructure,
it writes like these:

@exons = $gene->exons();
@introns = $gene->introns();
@utr_sites = $gene->utrs();

Then where does the object "$gene" come from? I've searched through all
the google sites but found nothing.

? 2011-03-18?? 15:05 +0000?Frank Schwach??? 
> maybe I'm missing the point here but I think an "mRNA" feature should
> not be a Bio::SeqFeature::Gene::GeneStructure and it should not have
> exons - it would not make sense biologically.
> 
> Frank
> 
> 
> On Fri, 2011-03-18 at 21:57 +0800, Tao Zhu wrote:
> > Yes. But in the document
> > http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
> > It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
> > Bio::SeqFeature::Generic. I wonder how to do such inheritance.


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)





From manju.rawat2 at gmail.com  Sat Mar 19 10:29:32 2011
From: manju.rawat2 at gmail.com (manju rawat)
Date: Sat, 19 Mar 2011 15:59:32 +0530
Subject: [Bioperl-l] bio-scf installation error
Message-ID: <AANLkTikQwcqs0YyaHvddq9yjowOpoe_YDRj4Z03zXRdv@mail.gmail.com>

Hello ,

I want to install Bio-SCF module on windows..But i am unable to do this bcs
to install bio-scf i have to install io_lib oe zlib on windows..
I download both from the described url in install file of bio-scf....i also
indtalled MinGW ..but now i dont know how to install it???
pls help to install it..

Thanks in Advance
Manju Rawat


From jason.stajich at gmail.com  Sat Mar 19 18:19:23 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 19 Mar 2011 11:19:23 -0700
Subject: [Bioperl-l] Google Summer of Code is *ON* for OBF projects!
In-Reply-To: <4D83B153.6010006@cornell.edu>
References: <4D83B153.6010006@cornell.edu>
Message-ID: <6387373A-E17F-4CE2-9B19-E296A2668018@gmail.com>

Nice work Rob. Thanks for leading the effort and thanks to those who agreed to mentor. 

Sent from my iPhone-please excuse typos

--
Jason Stajich

On Mar 18, 2011, at 12:24 PM, Robert Buels <rmb32 at cornell.edu> wrote:

> Hi all,
> 
> Great news: Google announced today that the Open Bioinformatics
> Foundation has been accepted as a mentoring organization for this
> summer's Google Summer of Code!
> 
> GSoC is a Google-sponsored student internship program for open-source
> projects, open to students from around the world (not just US
> residents).   Students are paid a $5000 USD stipend to work as a
> developer on an open-source project for the summer. For more on GSoC,
> see GSoC 2011 FAQ at http://bit.ly/hpoz8W
> 
> Student applications are due April 8, 2011 at 19:00 UTC.  Students who
> are interested in participating should look at the OBF's GSoC page at
> http://open-bio.org/wiki/Google_Summer_of_Code, which lists project
> ideas, and whom to contact about applying.
> 
> For current developers on OBF projects, please consider volunteering to
> be a mentor if you have not already, and contribute project ideas.  Just
> list your name and project ideas on OBF wiki and on the relevant
> project's GSoC wiki page.
> 
> Thanks to all who helped make OBF's application to GSoC a success, and
> let's have a great, productive summer of code!
> 
> Rob Buels
> OBF GSoC 2011 Administrator
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jason.stajich at gmail.com  Sat Mar 19 18:31:17 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 19 Mar 2011 11:31:17 -0700
Subject: [Bioperl-l] What's wrong with the script about module
	Bio::SeqFeature::Gene::GeneStructure
In-Reply-To: <1300528162.5998.4.camel@ubuntu>
References: <1300422812.12949.5.camel@ubuntu> <4D83232A.9050502@fmi.ch>
	<1300447920.16670.2.camel@ubuntu>
	<2BF7C2E2-B15F-4889-A58C-B496E689DDB0@illinois.edu>
	<1300456641.18688.4.camel@ubuntu>
	<1300460730.12411.50.camel@deskpro15336.internal.sanger.ac.uk>
	<1300528162.5998.4.camel@ubuntu>
Message-ID: <093660B8-458E-4617-8D12-228985CA88CD@gmail.com>

You have to instantiate the gene structure and copy the exon objects into the substructure. Unless you have specific methods in the GeneStructure I would just pull out the data from the generic objects. 

See the genbank to gff script and the Unflattener for ways to more simply destruct the mRNA feature into gene->mRNA->CDS,Exons 

If you are just wanting to count Exons 
You can see example on slide 27 or so. 

http://jason.open-bio.org/Bioperl_Tutorials/ProgrammingBiology2008/ProgBiology_BioPerl_I.pdf

Sent from my iPhone-please excuse typos

--
Jason Stajich

On Mar 19, 2011, at 2:49 AM, Tao Zhu <tzhu at mail.bnu.edu.cn> wrote:

> But I think an "mRNA" feature should have exons. For example:
> 
> 
>     mRNA            complement(join(1031434..1031901,1031940..1032269,
>                     1032329..1032418,1032472..1032489))
>                     /locus_tag="SPCC825.05c"
>                     /transcript_id="NM_001023047.1"
>                     /db_xref="GI:68021105"
>                     /db_xref="GeneID:2539459"
> 
> Such mRNA should have 4 exons and 3 introns, right? And I just want to
> calculate the lengths of every exons and introns quickly.
> 
> Besides, in the document of module Bio::SeqFeature::Gene::GeneStructure,
> it writes like these:
> 
> @exons = $gene->exons();
> @introns = $gene->introns();
> @utr_sites = $gene->utrs();
> 
> Then where does the object "$gene" come from? I've searched through all
> the google sites but found nothing.
> 
> ? 2011-03-18?? 15:05 +0000?Frank Schwach??? 
>> maybe I'm missing the point here but I think an "mRNA" feature should
>> not be a Bio::SeqFeature::Gene::GeneStructure and it should not have
>> exons - it would not make sense biologically.
>> 
>> Frank
>> 
>> 
>> On Fri, 2011-03-18 at 21:57 +0800, Tao Zhu wrote:
>>> Yes. But in the document
>>> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
>>> It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
>>> Bio::SeqFeature::Generic. I wonder how to do such inheritance.
> 
> 
> -- 
> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> 100875, China
> Email: tzhu at mail.bnu.edu.cn
> Website: http://bnuzt.org (mainly written in Chinese)
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jason.stajich at gmail.com  Sat Mar 19 18:36:49 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 19 Mar 2011 11:36:49 -0700
Subject: [Bioperl-l] Please recommend Perl module to parse phylogentic
	trees
In-Reply-To: <2e94f0bb-0282-4d53-b205-56ff895665de@w7g2000pre.googlegroups.com>
References: <2e94f0bb-0282-4d53-b205-56ff895665de@w7g2000pre.googlegroups.com>
Message-ID: <447BFFD2-06E6-41E0-81BF-B03EB919316C@gmail.com>

Nexus is richer and we only parse the trees from that format. Since the format is a newick tree embedded within it relies on the same code in the newick parser. 

Knowing what you want to do would more likely lead to better answer.  As for bugs - you can search the redmine big tracker to see whether they are reported issues that are unresolved and you can examine the tests in the t directory to see what compliance is tested. 

Jason
Sent from my iPhone-please excuse typos

--
Jason Stajich

On Mar 4, 2011, at 12:24 PM, justin100 <bio.justin100 at gmail.com> wrote:

> Hi,
> 
> I am writing a script to parse phylogenetic trees. The input will be
> trees in Newick format for now (maybe NEXUS in the future).
> 
> Quite a few Perl modules can parse phylogenetic trees. For Newick
> format, there are Bio::TreeIO and  Bio::Phylo::Parsers. For NEXUS
> format, there is Bio::NEXUS. From my understanding, it's not difficult
> to convert from Newick to NEXUS or vice versa, if only for the purpose
> of parsing trees.
> 
> I'd to know the advantages and disadvantages of these modules when
> compared with each other. Please recommend one that you think is the
> most capable parser (and hopefully has the least bugs).
> 
> Thanks.
> 
> Justin
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From veer_lovepune at yahoo.co.in  Sat Mar 19 20:56:06 2011
From: veer_lovepune at yahoo.co.in (virendra patil)
Date: Sun, 20 Mar 2011 02:26:06 +0530 (IST)
Subject: [Bioperl-l] Bioperl-l Digest, Vol 95, Issue 19
In-Reply-To: <mailman.21.1300550405.26148.bioperl-l@lists.open-bio.org>
Message-ID: <790813.91588.qm@web137312.mail.in.yahoo.com>

hi can some one help me i tried to install ?bioperl many time but it show message likeCan't locate Bio/Seq.pm in @INC (@INC contains: E:/JAVA1/.metadata/.plugins/org.epic.debug E:/JAVA1/PERL EXAM D:/Perl/site/lib D:/Perl/lib .) at E:/JAVA1/PERL EXAM/PERLEXAM.pl line 2.BEGIN failed--compilation aborted at E:/JAVA1/PERL EXAM/PERLEXAM.pl line 2.?

---i try with java perl intgration my perl is working but bioperl show upper message




From ngoodman at systemsbiology.org  Tue Mar 22 13:57:50 2011
From: ngoodman at systemsbiology.org (Nathan (Nat) Goodman)
Date: Tue, 22 Mar 2011 06:57:50 -0700
Subject: [Bioperl-l] Ensembl stable_id_event table
Message-ID: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>

With apologies, this is not technically a bioperl question, but hopefully close enough.  I'm trying to map old Ensembl IDs to current ones.  Table stable_id_event on their ftp site seems to be the place to get this information, but the data in that table (for human build 61) is cyclic, meaning that old IDs are sometimes mapped to new ones which in turn are mapped back to the old one.  This seems wrong...  And, it's not a rare occurrence: 18% of IDs in the table lie on cycles, the largest of which contains more than 6000 IDs!

To see one short cycle, run this query (against human build 61).

mysql> select * from stable_id_event where 
    ->     (old_stable_id='ENSP00000399673' or new_stable_id='ENSP00000399673')
    -> and (old_stable_id='ENSP00000365536' or new_stable_id='ENSP00000365536');

The results are

+-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
| old_stable_id   | old_version | new_stable_id   | new_version | mapping_session_id | type        | score |
+-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
| ENSP00000399673 |           2 | ENSP00000365536 |           3 |                380 | translation |     1 | 
| ENSP00000399673 |           2 | ENSP00000365536 |           3 |                381 | translation |     1 | 
| ENSP00000365536 |           3 | ENSP00000399673 |           2 |                381 | translation |     1 | 
| ENSP00000399673 |           2 | ENSP00000365536 |           3 |                382 | translation |     1 | 
| ENSP00000365536 |           3 | ENSP00000399673 |           2 |                382 | translation |     1 | 
+-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+

The first and last lines reveal the cycle:

line 1) ENSP00000399673-> ENSP00000365536
line 5) ENSP00000365536-> ENSP00000399673

If anyone can shed some light, I would be most grateful.

Thanks very much,
Nat Goodman




From molecules at cpan.org  Wed Mar 23 18:44:15 2011
From: molecules at cpan.org (Christopher Bottoms)
Date: Wed, 23 Mar 2011 13:44:15 -0500
Subject: [Bioperl-l] Ensembl stable_id_event table
In-Reply-To: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>
References: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>
Message-ID: <AANLkTi=acb_oG6-PiDLeh373LkYUz9K=XDhUimv922qz@mail.gmail.com>

Hi Nat,

Have you tried contacting someone at Ensembl about it? That is the
first place I would try.

--Christopher Bottoms


On Tue, Mar 22, 2011 at 8:57 AM, Nathan (Nat) Goodman
<ngoodman at systemsbiology.org> wrote:
> With apologies, this is not technically a bioperl question, but hopefully close enough. ?I'm trying to map old Ensembl IDs to current ones. ?Table stable_id_event on their ftp site seems to be the place to get this information, but the data in that table (for human build 61) is cyclic, meaning that old IDs are sometimes mapped to new ones which in turn are mapped back to the old one. ?This seems wrong... ?And, it's not a rare occurrence: 18% of IDs in the table lie on cycles, the largest of which contains more than 6000 IDs!
>
> To see one short cycle, run this query (against human build 61).
>
> mysql> select * from stable_id_event where
> ? ?-> ? ? (old_stable_id='ENSP00000399673' or new_stable_id='ENSP00000399673')
> ? ?-> and (old_stable_id='ENSP00000365536' or new_stable_id='ENSP00000365536');
>
> The results are
>
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> | old_stable_id ? | old_version | new_stable_id ? | new_version | mapping_session_id | type ? ? ? ?| score |
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> | ENSP00000399673 | ? ? ? ? ? 2 | ENSP00000365536 | ? ? ? ? ? 3 | ? ? ? ? ? ? ? ?380 | translation | ? ? 1 |
> | ENSP00000399673 | ? ? ? ? ? 2 | ENSP00000365536 | ? ? ? ? ? 3 | ? ? ? ? ? ? ? ?381 | translation | ? ? 1 |
> | ENSP00000365536 | ? ? ? ? ? 3 | ENSP00000399673 | ? ? ? ? ? 2 | ? ? ? ? ? ? ? ?381 | translation | ? ? 1 |
> | ENSP00000399673 | ? ? ? ? ? 2 | ENSP00000365536 | ? ? ? ? ? 3 | ? ? ? ? ? ? ? ?382 | translation | ? ? 1 |
> | ENSP00000365536 | ? ? ? ? ? 3 | ENSP00000399673 | ? ? ? ? ? 2 | ? ? ? ? ? ? ? ?382 | translation | ? ? 1 |
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
>
> The first and last lines reveal the cycle:
>
> line 1) ENSP00000399673-> ENSP00000365536
> line 5) ENSP00000365536-> ENSP00000399673
>
> If anyone can shed some light, I would be most grateful.
>
> Thanks very much,
> Nat Goodman
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From cjfields at illinois.edu  Wed Mar 23 22:23:47 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 23 Mar 2011 17:23:47 -0500
Subject: [Bioperl-l] Ensembl stable_id_event table
In-Reply-To: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>
References: <6C188BB3-2A7C-4BFF-B268-BCAE0AB31E97@systemsbiology.org>
Message-ID: <890FA151-63D4-4EAF-8141-8975911126E4@illinois.edu>

Odd, wonder what the ensembl folks have to say about it.  Have you asked them?

chris

On Mar 22, 2011, at 8:57 AM, Nathan (Nat) Goodman wrote:

> With apologies, this is not technically a bioperl question, but hopefully close enough.  I'm trying to map old Ensembl IDs to current ones.  Table stable_id_event on their ftp site seems to be the place to get this information, but the data in that table (for human build 61) is cyclic, meaning that old IDs are sometimes mapped to new ones which in turn are mapped back to the old one.  This seems wrong...  And, it's not a rare occurrence: 18% of IDs in the table lie on cycles, the largest of which contains more than 6000 IDs!
> 
> To see one short cycle, run this query (against human build 61).
> 
> mysql> select * from stable_id_event where 
>    ->     (old_stable_id='ENSP00000399673' or new_stable_id='ENSP00000399673')
>    -> and (old_stable_id='ENSP00000365536' or new_stable_id='ENSP00000365536');
> 
> The results are
> 
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> | old_stable_id   | old_version | new_stable_id   | new_version | mapping_session_id | type        | score |
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> | ENSP00000399673 |           2 | ENSP00000365536 |           3 |                380 | translation |     1 | 
> | ENSP00000399673 |           2 | ENSP00000365536 |           3 |                381 | translation |     1 | 
> | ENSP00000365536 |           3 | ENSP00000399673 |           2 |                381 | translation |     1 | 
> | ENSP00000399673 |           2 | ENSP00000365536 |           3 |                382 | translation |     1 | 
> | ENSP00000365536 |           3 | ENSP00000399673 |           2 |                382 | translation |     1 | 
> +-----------------+-------------+-----------------+-------------+--------------------+-------------+-------+
> 
> The first and last lines reveal the cycle:
> 
> line 1) ENSP00000399673-> ENSP00000365536
> line 5) ENSP00000365536-> ENSP00000399673
> 
> If anyone can shed some light, I would be most grateful.
> 
> Thanks very much,
> Nat Goodman
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From roy.chaudhuri at gmail.com  Thu Mar 24 13:47:27 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Thu, 24 Mar 2011 13:47:27 +0000
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
Message-ID: <4D8B4B6F.7010407@gmail.com>

Hi all,

I have discovered a possible bug in Bioperl, although maybe it's my 
expectations that are wrong, not the code.

I noticed that when calculating molecular weights for a bunch of protein 
sequences using Bio::Tools::SeqStats->get_mol_wt, the values I was 
getting were slightly different from the ones given by Emboss pepstats. 
This was due to my protein sequences ending with *, since they were 
derived from translating annotated genes including the stop codon. 
Surprisingly (to me, at least) Bio::Seq->length gives a value that 
counts the terminal *, so one greater than the number of amino acids. 
SeqStats->get_mol_wt calls Bio::Seq->length to determine the number of 
water molecules to subtract from the total molecular weight, so the 
reported weights for my sequence were the weight of one water molecule 
less than they should have been. I'm not sure if this is a bug in 
get_mol_wt, in Bio::Seq->length, or if it's bad practice to use protein 
sequences with a terminal asterisk (I've never had a problem doing so 
before).

Cheers,
Roy.


From adsj at novozymes.com  Thu Mar 24 15:01:25 2011
From: adsj at novozymes.com (Adam =?utf-8?Q?Sj=C3=B8gren?=)
Date: Thu, 24 Mar 2011 16:01:25 +0100
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
In-Reply-To: <4D8B4B6F.7010407@gmail.com> (Roy Chaudhuri's message of "Thu, 24
	Mar 2011 13:47:27 +0000")
References: <4D8B4B6F.7010407@gmail.com>
Message-ID: <87mxkkbm0q.fsf@topper.koldfront.dk>

On Thu, 24 Mar 2011 13:47:27 +0000, Roy wrote:

> This was due to my protein sequences ending with *, since they were
> derived from translating annotated genes including the stop codon.

If you give ->translate() the -complete=>1 option, the stop codon will
not be included in the resulting protein sequence.

 * http://bioperl.org/cgi-bin/deob_detail.cgi?method=Bio::PrimarySeqI::translate


  Best regards,

    Adam

-- 
                                                          Adam Sj?gren
                                                    adsj at novozymes.com



From roy.chaudhuri at gmail.com  Thu Mar 24 15:27:36 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Thu, 24 Mar 2011 15:27:36 +0000
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
In-Reply-To: <87mxkkbm0q.fsf@topper.koldfront.dk>
References: <4D8B4B6F.7010407@gmail.com> <87mxkkbm0q.fsf@topper.koldfront.dk>
Message-ID: <4D8B62E8.2050902@gmail.com>

On 24/03/2011 15:01, Adam Sj?gren wrote:
> If you give ->translate() the -complete=>1 option, the stop codon will
> not be included in the resulting protein sequence.

Ah, that's useful to know, thanks Adam. I still think that get_mol_wt 
should deal with such sequences without giving an incorrect weight, though.


From cjfields at illinois.edu  Thu Mar 24 15:47:29 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 24 Mar 2011 10:47:29 -0500
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
In-Reply-To: <4D8B4B6F.7010407@gmail.com>
References: <4D8B4B6F.7010407@gmail.com>
Message-ID: <2F1303AE-4678-4901-A33C-A7811FF8F309@illinois.edu>


On Mar 24, 2011, at 8:47 AM, Roy Chaudhuri wrote:

> Hi all,
> 
> I have discovered a possible bug in Bioperl, although maybe it's my expectations that are wrong, not the code.
> 
> I noticed that when calculating molecular weights for a bunch of protein sequences using Bio::Tools::SeqStats->get_mol_wt, the values I was getting were slightly different from the ones given by Emboss pepstats. This was due to my protein sequences ending with *, since they were derived from translating annotated genes including the stop codon. Surprisingly (to me, at least) Bio::Seq->length gives a value that counts the terminal *, so one greater than the number of amino acids. SeqStats->get_mol_wt calls Bio::Seq->length to determine the number of water molecules to subtract from the total molecular weight, so the reported weights for my sequence were the weight of one water molecule less than they should have been. I'm not sure if this is a bug in get_mol_wt, in Bio::Seq->length, or if it's bad practice to use protein sequences with a terminal asterisk (I've never had a problem doing so before).

The method should account for the possibility that '*' is present; should be easy enough to fix with something like:

my $len = $seq =~ tr/A-Za-z/A-Za-z/;

I'm not able to do this right away (on fam vacation), can you file this on our new bug server?

http://redmine.open-bio.org

> Cheers,
> Roy.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

chris


From roy.chaudhuri at gmail.com  Thu Mar 24 16:08:22 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Thu, 24 Mar 2011 16:08:22 +0000
Subject: [Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
In-Reply-To: <2F1303AE-4678-4901-A33C-A7811FF8F309@illinois.edu>
References: <4D8B4B6F.7010407@gmail.com>
	<2F1303AE-4678-4901-A33C-A7811FF8F309@illinois.edu>
Message-ID: <4D8B6C76.6090401@gmail.com>

Done:
http://redmine.open-bio.org/issues/3185

Have a good break,
Roy.

On 24/03/2011 15:47, Chris Fields wrote:
>
> On Mar 24, 2011, at 8:47 AM, Roy Chaudhuri wrote:
>
>> Hi all,
>>
>> I have discovered a possible bug in Bioperl, although maybe it's my
>> expectations that are wrong, not the code.
>>
>> I noticed that when calculating molecular weights for a bunch of
>> protein sequences using Bio::Tools::SeqStats->get_mol_wt, the
>> values I was getting were slightly different from the ones given by
>> Emboss pepstats. This was due to my protein sequences ending with
>> *, since they were derived from translating annotated genes
>> including the stop codon. Surprisingly (to me, at least)
>> Bio::Seq->length gives a value that counts the terminal *, so one
>> greater than the number of amino acids. SeqStats->get_mol_wt calls
>> Bio::Seq->length to determine the number of water molecules to
>> subtract from the total molecular weight, so the reported weights
>> for my sequence were the weight of one water molecule less than
>> they should have been. I'm not sure if this is a bug in get_mol_wt,
>> in Bio::Seq->length, or if it's bad practice to use protein
>> sequences with a terminal asterisk (I've never had a problem doing
>> so before).
>
> The method should account for the possibility that '*' is present;
> should be easy enough to fix with something like:
>
> my $len = $seq =~ tr/A-Za-z/A-Za-z/;
>
> I'm not able to do this right away (on fam vacation), can you file
> this on our new bug server?
>
> http://redmine.open-bio.org
>
>> Cheers, Roy. _______________________________________________
>> Bioperl-l mailing list Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> chris



From rachitasharma at gmail.com  Thu Mar 24 17:12:43 2011
From: rachitasharma at gmail.com (Rachita Sharma)
Date: Thu, 24 Mar 2011 11:12:43 -0600
Subject: [Bioperl-l] Genbank to gff3 format
Message-ID: <AANLkTimarbmi3XnFZ9VjT2GMHUoS6COkVGnbtawYh2a+@mail.gmail.com>

I am having trouble using the perl script bp_genbank2gff3.pl for
converting my genbank file into gff3 format. Unique IDs are not
created by the Bioperl converter so I cannot get the gff3 file
validated on the official GFF validator I want to use the final gff3
file on Gbrowse without errors. Will appreciate your suggestions.

Thanks!
Rachita


From dan.bolser at gmail.com  Fri Mar 25 11:21:57 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Fri, 25 Mar 2011 11:21:57 +0000
Subject: [Bioperl-l] from SimpleAlign to SAM/BAM
In-Reply-To: <AANLkTinEo3Ac8h5Gh-l4aqiKE0C1-iPiP96XilazQ4Hd@mail.gmail.com>
References: <AANLkTilHpBojt1AoAR6qe8YgqXrt8vp_dl64GOblTH3h@mail.gmail.com>
	<CF66A9BB040D49189BB80C9E057422AC@NewLife>
	<AANLkTinEo3Ac8h5Gh-l4aqiKE0C1-iPiP96XilazQ4Hd@mail.gmail.com>
Message-ID: <AANLkTikk4jNjG203Lw764Exdb9VBoZPVkXki8n8jVwLO@mail.gmail.com>

On 19 May 2010 17:40, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Bio::Samtools, which is separate from bioperl but compatible with it,
> provides read/write access to SAM and BAM via Heng's C library.

If I understand correctly, Bio::Samtools is a meta package that
encompasses Bio::DB::Sam and friends. However, when I look at
Bio::DB::Sam, I only see "Read SAM/BAM database files", not write, and
I don't see how to write SAM files from the docs there.

I just looked at the pod for Bio::Assembly::IO::sam (how come this
isn't documented in CPAN?), and I read:

This is a (currently) read-only IO module designed to convert
Sequence/Alignment Map (SAM) ...

I guess this is what was being discussed on in this thread (the fact
that IO doesn't yet write, but XS can be used to get it writing).

Did I understand correctly, or is there some way to write SAM from BioPerl?


Cheers,
Dan..

> Lincoln
>
> On Wed, May 19, 2010 at 9:34 AM, Mark A. Jensen <maj at fortinbras.us> wrote:
>
>> Albert-- have a look at Bio::Tools::Run::Samtools which incorporates the
>> use of Bio::Assembly::IO::sam (I think). I know there is only read
>> capability for B:A:I:sam, but Samtools may give you the appropriate wrapper
>> for doing writes (some assembly (so to speak) required...)-- cheers MAJ
>> ----- Original Message ----- From: "Albert Vilella" <avilella at gmail.com>
>>
>> To: <bioperl-l at bioperl.org>
>> Sent: Wednesday, May 19, 2010 4:36 AM
>>
>> Subject: [Bioperl-l] from SimpleAlign to SAM/BAM
>>
>>
>> ?Hi,
>>>
>>> I would like to know what would be the best way to generate a SAM/BAM file
>>> with cDNA alignments against the human reference from a bunch of
>>> Bio::SimpleAlign
>>> cDNA multiple sequence alignment objects.
>>>
>>> Considering I've got a way to map the cDNAs to chromosome coordinates,
>>> how can I generate a SAM/BAM file with ~1,000,000 entries against ~23.000
>>> human
>>> coordinates?
>>>
>>> As far as I can see, there is an Bio::Assembly::IO::sam.pm which loads
>>> assemblies.
>>> Should I be using some other tool existing not in bioperl?
>>>
>>> Cheers,
>>>
>>> Albert.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From dan.bolser at gmail.com  Sun Mar 27 00:11:27 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Sun, 27 Mar 2011 00:11:27 +0000
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
Message-ID: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>

Hi all,

I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm uses:
    if (length $source_tag) {

within the '_types_sql' function to test if $source_tag is defined
(and has a length). This obviously fails when $source_tag it isn't
defined, and I see the above error message from my script when I call
the 'features' function (as shown below).

>From tests (thanks to rbuels in #bioperl) it seems the value of $type
is simply 'fwd link intensity', so:
      ($primary_tag,$source_tag) = split ':',$type,2;

on line 1047 leaves $source_tag undefined.

Here is my proposed fix:

diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
index 00103c2..dfc70c0 100644
--- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
+++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
@@ -1057,8 +1057,8 @@ sub _types_sql {
       ($primary_tag,$source_tag) = split ':',$type,2;
     }

-    if (length $source_tag) {
-      if (length($primary_tag)) {
+    if (defined $source_tag && length $source_tag) {
+      if (defined $primary_tag && length($primary_tag)) {
         push @matches,"tl.tag=?";
         push @args,"$primary_tag:$source_tag";
       }


which seems to work. I'd write some tests, but an old bug that I can't
track down prevents me from running tests on this package
(http://bugzilla.open-bio.org/show_bug.cgi?id=2899).

Cheers,
Dan.


Here are some snippets of code to give context:

my $intensities = Bio::DB::SeqFeature::Store->
  new( -adaptor => 'DBI::mysql',
	-dsn => 'db:mysql.server.ac.uk',
	-user => 'me',
	-pass => 'secret',
       -verbose => $verbose,
     );

my @fwd_intensity = $intensities->
    features( -seqid => 'some-id', -type => 'fwd link intensity',
              -start => 10,
              -end   => 200,
    );


From hufeiyc at gmail.com  Tue Mar 22 19:14:54 2011
From: hufeiyc at gmail.com (Fei Hu)
Date: Tue, 22 Mar 2011 15:14:54 -0400
Subject: [Bioperl-l] GSoC 2011
Message-ID: <AANLkTim6o3bJ6NkBRmoUC5e76GaGzpjP5+xE+ZrWcEdc@mail.gmail.com>

Hi, All.

My name is Fei Hu from U. of South Carolina. I am currently a second-year
Ph.D student in computer science focusing on gene order and sequence(DNA &
AA) phylogeny as well as whole genome alignment. I am instreseted in joining
bioperl project of GSoC 2011. I have two ideas that would like to share.

My first idea is to extend the bioperl so that it can process and analysis
gene order data using published package such as MGR, GRAPPA and distance
estimator. This is a relatively new type of data and many great researchers
have contributed to this type of phylogeny reconstruction (Dr. Pavel Penzer,
Dr. Bernard Moret and Dr. David Sankoff).

Secondly as maximum likelihood becomes more and more popular, especially
RAxML has been widely recognized and used(over 1000 citations). I think it's
time to integrate that as well as GARLI into the Bio::Tools. I extensively
used and explored RAxML in my last publication on gene order phylogeny.

Those are just my preliminary thoughts, not even a plan and any suggestion
is greatly appreciated!!! I use perl on daily bases for data processing and
composing testing scripts, but not much OOP involved.

PS: Rest api for CIPRES is no longer available. So this following task can't
be finished right now:
Development of a
Bio::Tools::Run::RemoteBlast<http://bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast>-like
interface to CIPRES remote analyses; for more see this
thread<http://thread.gmane.org/gmane.comp.lang.perl.bio.general/16524>
.

And Thank you all.
Best

Fei

-- 
*Fei Hu
Bioinformatics Lab
3D-11 Swearingen Building
U of South Carolina
Tel: 803-397-5240*


From Dallas.Thomas at AGR.GC.CA  Wed Mar 23 17:08:12 2011
From: Dallas.Thomas at AGR.GC.CA (Thomas, Dallas)
Date: Wed, 23 Mar 2011 11:08:12 -0600
Subject: [Bioperl-l] Bio::Tools::Protparam
Message-ID: <DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>

Need help.  I am trying to use the Bio::Tools::Protparam perl module.

 

For testing purposes I have copied and pasted the example in the module,
I have set:

 

use strict;

use Bio::Tools::Protparam;

use Bio::DB::GenBank;

 

Every time I try and run the script I get the following error:

                        

                              Can't locate object method "new" via
package "Protparam" (perhaps you forgot to load "Protparam"?) at ...

 

Do you have any ideas?  Any help would be very much appreciated.

 

Sincerely

Dallas Thomas

 




From ravimbt at gmail.com  Thu Mar 24 12:33:55 2011
From: ravimbt at gmail.com (=?UTF-8?B?wrbigKLil4/guYvigKLgrofgrrDgrrXgrr/Rj86xzr3OueKXj+C5i+KAouKAosK2?=)
Date: Thu, 24 Mar 2011 18:03:55 +0530
Subject: [Bioperl-l] Bioperl installation doubt
Message-ID: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>

Hi,

Could you please help me installing bioperl-db, bioperl-run & other packages
using ppm on windows 7? Please find the attachment for the error message I
get. I would really appreciate if you help me fix this issue.

Thanks,

With regards,
Ravi.
-------------- next part --------------
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From abualiga at gmail.com  Sun Mar 27 13:34:05 2011
From: abualiga at gmail.com (Galeb Abu-Ali)
Date: Sun, 27 Mar 2011 06:34:05 -0700 (PDT)
Subject: [Bioperl-l] CDS complement statements from GenBank
Message-ID: <cdf62961-ac89-4274-91ed-9a233d2de15c@k10g2000prh.googlegroups.com>

Hi,

I'm trying to parse CDS complement statements from GenBank files of
bacterial genomes. I know it works for 'join' statements with
Bio::Location::SplitLocationI, but there is no spliced genes in
bacterial annotations and therefore no 'join()' statements. When I
replace 'complement' with 'join' in the bacterial GenBank file,
Bio::Location::SplitLocationI gets the coordinates. I took a look at
SplitLocationI.pm and Split.pm to see if I could replace 'join' with
'complement' to get it to work but no luck. At your convenience,
please advise.

cheers,

galeb


From drinmontana at gmail.com  Sun Mar 27 14:37:17 2011
From: drinmontana at gmail.com (Drin)
Date: Sun, 27 Mar 2011 07:37:17 -0700 (PDT)
Subject: [Bioperl-l] Various bioperl build test errors
Message-ID: <799d8933-c2de-4c88-ac2c-03bb1b32dd78@z27g2000prz.googlegroups.com>

Hello BioPerl mailing list!

So I have been successfully building BioPerl (though I thought I was
failing), but have been getting some errors during said builds. I'm
running ubuntu 9.04 and I ran 'perl Build.PL', then './Build test'
using bash. If any other information is desired, please let me know.
And here are some gists to help with some context:
perl Build.PL - https://gist.github.com/e4be0891635463b07812
./Build test - https://gist.github.com/3e9a1cba10ca0e9b087d


From cjfields at illinois.edu  Sun Mar 27 16:43:11 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 27 Mar 2011 11:43:11 -0500
Subject: [Bioperl-l] Bio::Tools::Protparam
In-Reply-To: <DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>
References: <DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>
Message-ID: <851BC032-98F0-441D-9185-5079527CDA3E@illinois.edu>

Dallas,

Can you send a script example?  Hard to judge what is going wrong w/o code.

chris
 
On Mar 23, 2011, at 12:08 PM, Thomas, Dallas wrote:

> Need help.  I am trying to use the Bio::Tools::Protparam perl module.
> 
> 
> 
> For testing purposes I have copied and pasted the example in the module,
> I have set:
> 
> 
> 
> use strict;
> 
> use Bio::Tools::Protparam;
> 
> use Bio::DB::GenBank;
> 
> 
> 
> Every time I try and run the script I get the following error:
> 
> 
> 
>                              Can't locate object method "new" via
> package "Protparam" (perhaps you forgot to load "Protparam"?) at ...
> 
> 
> 
> Do you have any ideas?  Any help would be very much appreciated.
> 
> 
> 
> Sincerely
> 
> Dallas Thomas
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From David.Messina at sbc.su.se  Sun Mar 27 17:05:05 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Sun, 27 Mar 2011 19:05:05 +0200
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
Message-ID: <AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>

Hi Ravi,

The get_sequence and write_sequence methods are in the Bio::Perl module, not
Bio::Seq. So your first line

use Bio::Seq;

should be replaced with

use Bio::Perl;


More examples in the BioPerl Tutorial here:
http://www.bioperl.org/wiki/BioPerl_Tutorial


Dve



2011/3/24 ?????????????????? <ravimbt at gmail.com>

> Hi,
>
> Could you please help me installing bioperl-db, bioperl-run & other
> packages
> using ppm on windows 7? Please find the attachment for the error message I
> get. I would really appreciate if you help me fix this issue.
>
> Thanks,
>
> With regards,
> Ravi.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From jason at bioperl.org  Sun Mar 27 17:28:04 2011
From: jason at bioperl.org (Jason Stajich)
Date: Sun, 27 Mar 2011 10:28:04 -0700
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
Message-ID: <4D8F73A4.8050408@bioperl.org>

Dan - not sure why you would need to do this as length on an undef 
should still return false (an undef).

$ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} 
print "\n"'
no
$ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"} 
print "\n"'
no

Also, having no 'source' is probably not proper GFF3.

BTW bugzilla is dead so the bug that you refer to is here
   http://redmine.open-bio.org/issues/2899
I've assigned the bug to Lincoln to help figure out what should be done 
with it.

Thanks,
jason

Dan Bolser wrote:
> Hi all,
>
> I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm uses:
>      if (length $source_tag) {
>
> within the '_types_sql' function to test if $source_tag is defined
> (and has a length). This obviously fails when $source_tag it isn't
> defined, and I see the above error message from my script when I call
> the 'features' function (as shown below).
>
> > From tests (thanks to rbuels in #bioperl) it seems the value of $type
> is simply 'fwd link intensity', so:
>        ($primary_tag,$source_tag) = split ':',$type,2;
>
> on line 1047 leaves $source_tag undefined.
>
> Here is my proposed fix:
>
> diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
> index 00103c2..dfc70c0 100644
> --- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
> +++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
> @@ -1057,8 +1057,8 @@ sub _types_sql {
>         ($primary_tag,$source_tag) = split ':',$type,2;
>       }
>
> -    if (length $source_tag) {
> -      if (length($primary_tag)) {
> +    if (defined $source_tag&&  length $source_tag) {
> +      if (defined $primary_tag&&  length($primary_tag)) {
>           push @matches,"tl.tag=?";
>           push @args,"$primary_tag:$source_tag";
>         }
>
>
> which seems to work. I'd write some tests, but an old bug that I can't
> track down prevents me from running tests on this package
> (http://bugzilla.open-bio.org/show_bug.cgi?id=2899).
>
> Cheers,
> Dan.
>
>
> Here are some snippets of code to give context:
>
> my $intensities = Bio::DB::SeqFeature::Store->
>    new( -adaptor =>  'DBI::mysql',
> 	-dsn =>  'db:mysql.server.ac.uk',
> 	-user =>  'me',
> 	-pass =>  'secret',
>         -verbose =>  $verbose,
>       );
>
> my @fwd_intensity = $intensities->
>      features( -seqid =>  'some-id', -type =>  'fwd link intensity',
>                -start =>  10,
>                -end   =>  200,
>      );
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki



From dan.bolser at gmail.com  Sun Mar 27 17:55:02 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Sun, 27 Mar 2011 18:55:02 +0100
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <4D8F73A4.8050408@bioperl.org>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
	<4D8F73A4.8050408@bioperl.org>
Message-ID: <AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>

On 27 March 2011 18:28, Jason Stajich <jason at bioperl.org> wrote:
> Dan - not sure why you would need to do this as length on an undef should
> still return false (an undef).
>
> $ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} print
> "\n"'
> no
> $ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"}
> print "\n"'
> no

Doesn't the latter spew a warning? (The output before / after my 'bug
fix' is the same, I just don't see 100s of warnings about undefined
values).


> Also, having no 'source' is probably not proper GFF3.

I'm quite sure it is, but by GFF does have a source. I'm just calling
'features' with only a feature type and not a feature type and a
source (because I only care about source). My call is pretty similar
to the example here:

http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/DB/SeqFeature/Store.pm#features

 @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');


> BTW bugzilla is dead so the bug that you refer to is here
> ?http://redmine.open-bio.org/issues/2899
> I've assigned the bug to Lincoln to help figure out what should be done with
> it.
>
> Thanks,
> jason

Cheers Jason,
Dan.


> Dan Bolser wrote:
>>
>> Hi all,
>>
>> I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm
>> uses:
>> ? ? if (length $source_tag) {
>>
>> within the '_types_sql' function to test if $source_tag is defined
>> (and has a length). This obviously fails when $source_tag it isn't
>> defined, and I see the above error message from my script when I call
>> the 'features' function (as shown below).
>>
>> > From tests (thanks to rbuels in #bioperl) it seems the value of $type
>> is simply 'fwd link intensity', so:
>> ? ? ? ($primary_tag,$source_tag) = split ':',$type,2;
>>
>> on line 1047 leaves $source_tag undefined.
>>
>> Here is my proposed fix:
>>
>> diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
>> index 00103c2..dfc70c0 100644
>> --- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>> +++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>> @@ -1057,8 +1057,8 @@ sub _types_sql {
>> ? ? ? ?($primary_tag,$source_tag) = split ':',$type,2;
>> ? ? ?}
>>
>> - ? ?if (length $source_tag) {
>> - ? ? ?if (length($primary_tag)) {
>> + ? ?if (defined $source_tag&& ?length $source_tag) {
>> + ? ? ?if (defined $primary_tag&& ?length($primary_tag)) {
>> ? ? ? ? ?push @matches,"tl.tag=?";
>> ? ? ? ? ?push @args,"$primary_tag:$source_tag";
>> ? ? ? ?}
>>
>>
>> which seems to work. I'd write some tests, but an old bug that I can't
>> track down prevents me from running tests on this package
>> (http://bugzilla.open-bio.org/show_bug.cgi?id=2899).
>>
>> Cheers,
>> Dan.
>>
>>
>> Here are some snippets of code to give context:
>>
>> my $intensities = Bio::DB::SeqFeature::Store->
>> ? new( -adaptor => ?'DBI::mysql',
>> ? ? ? ?-dsn => ?'db:mysql.server.ac.uk',
>> ? ? ? ?-user => ?'me',
>> ? ? ? ?-pass => ?'secret',
>> ? ? ? ?-verbose => ?$verbose,
>> ? ? ?);
>>
>> my @fwd_intensity = $intensities->
>> ? ? features( -seqid => ?'some-id', -type => ?'fwd link intensity',
>> ? ? ? ? ? ? ? -start => ?10,
>> ? ? ? ? ? ? ? -end ? => ?200,
>> ? ? );
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> jason at bioperl.org
> http://bioperl.org/wiki
>
>



From jason at bioperl.org  Sun Mar 27 17:59:09 2011
From: jason at bioperl.org (Jason Stajich)
Date: Sun, 27 Mar 2011 10:59:09 -0700
Subject: [Bioperl-l] CDS complement statements from GenBank
In-Reply-To: <cdf62961-ac89-4274-91ed-9a233d2de15c@k10g2000prh.googlegroups.com>
References: <cdf62961-ac89-4274-91ed-9a233d2de15c@k10g2000prh.googlegroups.com>
Message-ID: <4D8F7AED.1070705@bioperl.org>

they won't be split locations they will be Bio::Location::Simple 
locations then - I don't understand if that is causing you problems?



Galeb Abu-Ali wrote:
> Hi,
>
> I'm trying to parse CDS complement statements from GenBank files of
> bacterial genomes. I know it works for 'join' statements with
> Bio::Location::SplitLocationI, but there is no spliced genes in
> bacterial annotations and therefore no 'join()' statements. When I
> replace 'complement' with 'join' in the bacterial GenBank file,
> Bio::Location::SplitLocationI gets the coordinates. I took a look at
> SplitLocationI.pm and Split.pm to see if I could replace 'join' with
> 'complement' to get it to work but no luck. At your convenience,
> please advise.
>
> cheers,
>
> galeb
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki



From dan.bolser at gmail.com  Sun Mar 27 18:00:40 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Sun, 27 Mar 2011 19:00:40 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
Message-ID: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>

Hello,

I'm trying to get Bio::DB::BigWig installed again, this time on a different box.

I installed kent from git as described here:
http://genome.ucsc.edu/admin/git.html


I made the following changes, similar to those described previously:

git diff
diff --git a/src/inc/common.mk b/src/inc/common.mk
index c7fc557..5187901 100644
--- a/src/inc/common.mk
+++ b/src/inc/common.mk
@@ -3,7 +3,7 @@ CC=gcc
 ifeq (${COPT},)
     COPT=-O -g
 endif
-CFLAGS=
+CFLAGS=-fPIC
 HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
-DMACHTYPE_${MACHTYPE}
 HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
-I../../../../../inc

diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
index fa2292b..acb97d2 100644
--- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
+++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
@@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
     /* Parse current line. */
     wordCount = chopLine(line, row);
     if (wordCount == ArraySize(row))
-         errAbort("Too many fields (%d max is %lu) line %d of %s",
wordCount, ArraySize(row),
+         errAbort("Too many fields (%d max is %u) line %d of %s",
wordCount, ArraySize(row),
             lf->lineIx, lf->fileName);
     char *chrom = row[0];
     unsigned int start = lineFileNeedNum(lf, row, 1);


After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
-lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
correctly after typing 'make' in kent/src (should I be building it
differently?)



Now when I try to install Bio::DB::BigWig via cpan, things look like this:

cpan

cpan shell -- CPAN exploration and modules installation (v1.9600)
Enter 'h' for help.

cpan[1]> install Bio::DB::BigWig
CPAN: Storable loaded ok (v2.25)
Going to read '/homes/dbolser/.cpan/Metadata'
  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
Running install for module 'Bio::DB::BigWig'
Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
CPAN: Digest::SHA loaded ok (v5.61)
CPAN: Compress::Zlib loaded ok (v2.03)
Checksum for /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
ok
CPAN: Archive::Tar loaded ok (v1.76)
Bio-BigFile-1.05
Bio-BigFile-1.05/Changes
Bio-BigFile-1.05/LICENSE
Bio-BigFile-1.05/DISCLAIMER
Bio-BigFile-1.05/Build.PL
Bio-BigFile-1.05/typemap
Bio-BigFile-1.05/META.yml
Bio-BigFile-1.05/README
Bio-BigFile-1.05/MANIFEST
Bio-BigFile-1.05/ExampleData
Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
Bio-BigFile-1.05/ExampleData/refSeqTest.as
Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
Bio-BigFile-1.05/bin
Bio-BigFile-1.05/bin/bigWigToWig.pl
Bio-BigFile-1.05/bin/wigToBigWig.pl
Bio-BigFile-1.05/bin/index_bigwigset.pl
Bio-BigFile-1.05/lib
Bio-BigFile-1.05/lib/Bio
Bio-BigFile-1.05/lib/Bio/DB
Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
Bio-BigFile-1.05/lib/Bio/DB/BigFile
Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
Bio-BigFile-1.05/t
Bio-BigFile-1.05/t/02.bigbed.t
Bio-BigFile-1.05/t/03.bigwig_high.t
Bio-BigFile-1.05/t/04.bigbed_high.t
Bio-BigFile-1.05/t/05.bigwig_set.t
/bin/tar: Read 9216 bytes from -
Bio-BigFile-1.05/t/01.bigwig.t
Bio-BigFile-1.05/patches
Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
CPAN: File::Temp loaded ok (v0.22)
CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
CPAN: CPAN::Meta loaded ok (v2.110580)
CPAN: Module::CoreList loaded ok (v2.46)
CPAN: Time::HiRes loaded ok (v1.9717)

  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz


This module requires the compiled jkweb.a library from Jim Kent's source tree.
If you haven't already done so, please download the source from
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
contents of the "kent/src/lib" subdirectory as directed in the README. Then
enter the location of the "kent/src" subdirectory at the prompt below.
To prevent
this message from appearing in the future, set the environment
variable KENT_SRC
to point to the "kent/src" subdirectory.

Please enter the location of Kent source tree: /homes/dbolser/build/src/kent/src

Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-BigFile' version '1.05'
Building Bio-BigFile
gcc -I/homes/dbolser/build/src/kent/src/inc
-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
-DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
-c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
-Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
lib/Bio/DB/BigFile.c
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be undefined
lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be undefined
lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be undefined
lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be undefined
lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
lib/Bio/DB/BigFile.xs: In function
?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be undefined
lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
lib/Bio/DB/BigFile.xs: In function
?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be undefined
lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
-mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
/homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
  LDS/Bio-BigFile-1.05.tar.gz
  ./Build -- OK
CPAN: YAML loaded ok (v0.72)
Running Build test
t/01.bigwig.t ....... Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at t/01.bigwig.t line 28
Compilation failed in require at t/01.bigwig.t line 28.
BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
Failed 29/29 subtests
t/02.bigbed.t ....... Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at t/02.bigbed.t line 28
Compilation failed in require at t/02.bigbed.t line 28.
BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
Failed 15/15 subtests
t/03.bigwig_high.t .. Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
Compilation failed in require at t/03.bigwig_high.t line 28.
BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 32/32 subtests
t/04.bigbed_high.t .. Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
line 7.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
line 7.
Compilation failed in require at t/04.bigbed_high.t line 28.
BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 35/35 subtests
t/05.bigwig_set.t ... Can't load
'/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
for module Bio::DB::BigFile:
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
undefined symbol: SSL_library_init at
/usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
line 7.
Compilation failed in require at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
line 177.
BEGIN failed--compilation aborted at
/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
line 177.
Compilation failed in require at t/05.bigwig_set.t line 19.
BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
No subtests run

Test Summary Report
-------------------
t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 29 tests but ran 0.
t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 15 tests but ran 0.
t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 32 tests but ran 0.
t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 35 tests but ran 0.
t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
0.11 csys =  1.09 CPU)
Result: FAIL
Failed 5/5 test programs. 0/0 subtests failed.
  LDS/Bio-BigFile-1.05.tar.gz
  ./Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports LDS/Bio-BigFile-1.05.tar.gz
Running Build install
  make test had returned bad status, won't install without force
Failed during this command:
 LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO

cpan[2]>






Any hints?

Cheers,
Dan.



From roy.chaudhuri at gmail.com  Sun Mar 27 18:26:55 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Sun, 27 Mar 2011 19:26:55 +0100
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>	<4D8F73A4.8050408@bioperl.org>
	<AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
Message-ID: <4D8F816F.5010809@gmail.com>

Hi Dan,

I think your problem is that you are using the outdated -w flag, which 
reports warnings from inside modules that may not have been designed 
with warnings in mind. The "use warnings" pragma is preferred. See:
http://perldoc.perl.org/perllexwarn.html#What%27s-wrong-with-*-w*-and-$^W

Cheers,
Roy.

On 27/03/2011 18:55, Dan Bolser wrote:
> On 27 March 2011 18:28, Jason Stajich<jason at bioperl.org>  wrote:
>> Dan - not sure why you would need to do this as length on an undef should
>> still return false (an undef).
>>
>> $ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} print
>> "\n"'
>> no
>> $ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"}
>> print "\n"'
>> no
>
> Doesn't the latter spew a warning? (The output before / after my 'bug
> fix' is the same, I just don't see 100s of warnings about undefined
> values).
>
>
>> Also, having no 'source' is probably not proper GFF3.
>
> I'm quite sure it is, but by GFF does have a source. I'm just calling
> 'features' with only a feature type and not a feature type and a
> source (because I only care about source). My call is pretty similar
> to the example here:
>
> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/DB/SeqFeature/Store.pm#features
>
>   @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');
>
>
>> BTW bugzilla is dead so the bug that you refer to is here
>>   http://redmine.open-bio.org/issues/2899
>> I've assigned the bug to Lincoln to help figure out what should be done with
>> it.
>>
>> Thanks,
>> jason
>
> Cheers Jason,
> Dan.
>
>
>> Dan Bolser wrote:
>>>
>>> Hi all,
>>>
>>> I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> uses:
>>>      if (length $source_tag) {
>>>
>>> within the '_types_sql' function to test if $source_tag is defined
>>> (and has a length). This obviously fails when $source_tag it isn't
>>> defined, and I see the above error message from my script when I call
>>> the 'features' function (as shown below).
>>>
>>>>  From tests (thanks to rbuels in #bioperl) it seems the value of $type
>>> is simply 'fwd link intensity', so:
>>>        ($primary_tag,$source_tag) = split ':',$type,2;
>>>
>>> on line 1047 leaves $source_tag undefined.
>>>
>>> Here is my proposed fix:
>>>
>>> diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
>>> index 00103c2..dfc70c0 100644
>>> --- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> +++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> @@ -1057,8 +1057,8 @@ sub _types_sql {
>>>         ($primary_tag,$source_tag) = split ':',$type,2;
>>>       }
>>>
>>> -    if (length $source_tag) {
>>> -      if (length($primary_tag)) {
>>> +    if (defined $source_tag&&    length $source_tag) {
>>> +      if (defined $primary_tag&&    length($primary_tag)) {
>>>           push @matches,"tl.tag=?";
>>>           push @args,"$primary_tag:$source_tag";
>>>         }
>>>
>>>
>>> which seems to work. I'd write some tests, but an old bug that I can't
>>> track down prevents me from running tests on this package
>>> (http://bugzilla.open-bio.org/show_bug.cgi?id=2899).
>>>
>>> Cheers,
>>> Dan.
>>>
>>>
>>> Here are some snippets of code to give context:
>>>
>>> my $intensities = Bio::DB::SeqFeature::Store->
>>>    new( -adaptor =>    'DBI::mysql',
>>>         -dsn =>    'db:mysql.server.ac.uk',
>>>         -user =>    'me',
>>>         -pass =>    'secret',
>>>         -verbose =>    $verbose,
>>>       );
>>>
>>> my @fwd_intensity = $intensities->
>>>      features( -seqid =>    'some-id', -type =>    'fwd link intensity',
>>>                -start =>    10,
>>>                -end   =>    200,
>>>      );
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> --
>> Jason Stajich
>> jason at bioperl.org
>> http://bioperl.org/wiki
>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Sun Mar 27 20:13:14 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 27 Mar 2011 15:13:14 -0500
Subject: [Bioperl-l] Use of uninitialized value in length at
	Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
	<4D8F73A4.8050408@bioperl.org>
	<AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
Message-ID: <4960971A-8C61-49F2-B43A-E32BAFC4C59E@illinois.edu>

On Mar 27, 2011, at 12:55 PM, Dan Bolser wrote:

> On 27 March 2011 18:28, Jason Stajich <jason at bioperl.org> wrote:
>> Dan - not sure why you would need to do this as length on an undef should
>> still return false (an undef).
>> 
>> $ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} print
>> "\n"'
>> no
>> $ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"}
>> print "\n"'
>> no
> 
> Doesn't the latter spew a warning? (The output before / after my 'bug
> fix' is the same, I just don't see 100s of warnings about undefined
> values).

Only with later versions of perl (I think perl 5.12).

>> Also, having no 'source' is probably not proper GFF3.
> 
> I'm quite sure it is, but by GFF does have a source. I'm just calling
> 'features' with only a feature type and not a feature type and a
> source (because I only care about source). My call is pretty similar
> to the example here:
> 
> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/DB/SeqFeature/Store.pm#features
> 
> @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');

I think Jason is inferring that the GFF3 is invalid from your statement below re: $source_tag not being defined, which to me means the source attribute for the feature is not defined.

Note: b/c something works with SF::Store does NOT mean the source is proper GFF3; it is quite possible to have invalid GFF3 loaded into the database w/o a hiccup.  I think the loader assumes the data loaded has already been validated; IIRC there is very little validation done on GFF3 loaded into SF::Store, particularly the 'type'.

chris

>> BTW bugzilla is dead so the bug that you refer to is here
>>  http://redmine.open-bio.org/issues/2899
>> I've assigned the bug to Lincoln to help figure out what should be done with
>> it.
>> 
>> Thanks,
>> jason
> 
> Cheers Jason,
> Dan.
> 
> 
>> Dan Bolser wrote:
>>> 
>>> Hi all,
>>> 
>>> I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> uses:
>>>     if (length $source_tag) {
>>> 
>>> within the '_types_sql' function to test if $source_tag is defined
>>> (and has a length). This obviously fails when $source_tag it isn't
>>> defined, and I see the above error message from my script when I call
>>> the 'features' function (as shown below).
>>> 
>>>> From tests (thanks to rbuels in #bioperl) it seems the value of $type
>>> is simply 'fwd link intensity', so:
>>>       ($primary_tag,$source_tag) = split ':',$type,2;
>>> 
>>> on line 1047 leaves $source_tag undefined.
>>> 
>>> Here is my proposed fix:
>>> 
>>> diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
>>> index 00103c2..dfc70c0 100644
>>> --- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> +++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>>> @@ -1057,8 +1057,8 @@ sub _types_sql {
>>>        ($primary_tag,$source_tag) = split ':',$type,2;
>>>      }
>>> 
>>> -    if (length $source_tag) {
>>> -      if (length($primary_tag)) {
>>> +    if (defined $source_tag&&  length $source_tag) {
>>> +      if (defined $primary_tag&&  length($primary_tag)) {
>>>          push @matches,"tl.tag=?";
>>>          push @args,"$primary_tag:$source_tag";
>>>        }
>>> 
>>> 
>>> which seems to work. I'd write some tests, but an old bug that I can't
>>> track down prevents me from running tests on this package
>>> (http://bugzilla.open-bio.org/show_bug.cgi?id=2899).
>>> 
>>> Cheers,
>>> Dan.
>>> 
>>> 
>>> Here are some snippets of code to give context:
>>> 
>>> my $intensities = Bio::DB::SeqFeature::Store->
>>>   new( -adaptor =>  'DBI::mysql',
>>>        -dsn =>  'db:mysql.server.ac.uk',
>>>        -user =>  'me',
>>>        -pass =>  'secret',
>>>        -verbose =>  $verbose,
>>>      );
>>> 
>>> my @fwd_intensity = $intensities->
>>>     features( -seqid =>  'some-id', -type =>  'fwd link intensity',
>>>               -start =>  10,
>>>               -end   =>  200,
>>>     );
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> --
>> Jason Stajich
>> jason at bioperl.org
>> http://bioperl.org/wiki
>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Sun Mar 27 20:13:56 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 27 Mar 2011 15:13:56 -0500
Subject: [Bioperl-l] Various bioperl build test errors
In-Reply-To: <799d8933-c2de-4c88-ac2c-03bb1b32dd78@z27g2000prz.googlegroups.com>
References: <799d8933-c2de-4c88-ac2c-03bb1b32dd78@z27g2000prz.googlegroups.com>
Message-ID: <FFAB293A-555E-4F4B-90C4-A50458AB2B8C@illinois.edu>

Re: the two problems:

1) The build failures are a new one, haven't seen that before.  

2) The failed tests are all related to NeXML and Bio::Phylo; it appears that Bio::Phylo is having versioning problems.  

Feel free to report these on our bug tracker:

http://redmine.open-bio.org/

chris


On Mar 27, 2011, at 9:37 AM, Drin wrote:

> Hello BioPerl mailing list!
> 
> So I have been successfully building BioPerl (though I thought I was
> failing), but have been getting some errors during said builds. I'm
> running ubuntu 9.04 and I ran 'perl Build.PL', then './Build test'
> using bash. If any other information is desired, please let me know.
> And here are some gists to help with some context:
> perl Build.PL - https://gist.github.com/e4be0891635463b07812
> ./Build test - https://gist.github.com/3e9a1cba10ca0e9b087d
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From heikki.lehvaslaiho at gmail.com  Mon Mar 28 06:11:12 2011
From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho)
Date: Mon, 28 Mar 2011 09:11:12 +0300
Subject: [Bioperl-l] Bio::Tools::Protparam
In-Reply-To: <DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>
References: <AcvpfORY7lvf7BT4TLGDgl1oKgOEwg==>
	<DC81B04360E37E49BD00920177F934DEEB866E@skregixms1.AGR.GC.CA>
Message-ID: <AANLkTi=3wtG+7HO4O8vUbdrnVEu-NXofwmZfVHvRLeVH@mail.gmail.com>

The synopsis code should read:

	my $pp = Bio::Tools::Protparam->new(seq=>$seq->seq);

Fixed in the repository.

? ?? -Heikki

Heikki Lehvaslaiho - skype:heikki_lehvaslaiho http://about.me/heikki
cell: +966 545 595 849? office: +966 2 808 2429

Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
4700 King Abdullah University of Science and Technology (KAUST)
Thuwal 23955-6900, Kingdom of Saudi Arabia




On 23 March 2011 20:08, Thomas, Dallas <Dallas.Thomas at agr.gc.ca> wrote:
> Need help. ?I am trying to use the Bio::Tools::Protparam perl module.
>
>
>
> For testing purposes I have copied and pasted the example in the module,
> I have set:
>
>
>
> use strict;
>
> use Bio::Tools::Protparam;
>
> use Bio::DB::GenBank;
>
>
>
> Every time I try and run the script I get the following error:
>
>
>
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?Can't locate object method "new" via
> package "Protparam" (perhaps you forgot to load "Protparam"?) at ...
>
>
>
> Do you have any ideas? ?Any help would be very much appreciated.
>
>
>
> Sincerely
>
> Dallas Thomas
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From David.Messina at sbc.su.se  Mon Mar 28 07:33:25 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 28 Mar 2011 09:33:25 +0200
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
Message-ID: <AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>

Hi Ravi,

Please make sure to "Reply All" so that everyone on the mailing list can
follow (and add to) the discussion.

If you read the first line of the exception, you'll see it states what the
error is:
"WebDBSeqI Error ? check query sequences!"

You'd have no way of knowing this, but that ID and database combination is
not functioning anymore, so that's why in this case you're getting an error.
Please try using the example in the tutorial here:

  http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts

which has been updated to a different ID which should work.

Sorry for the confusion! So that we can prevent other people from having the
same issue, could you tell me where you got that example code?

Dave






2011/3/28 ?????????????????? <ravimbt at gmail.com>

> Hi Dave,
>
> Thanks a lot for your reply. It is really helpful. Please find the
> screenshot after making the change you pointed out. But I am getting
> "Exception: Bio::Root::Exception" error. I think I have to set the
> environment variables but I am not sure how to do that. Could you please
> guide me on this too.
>
> I can go to the "Environment Variable" Window in my pc. But I dont know
> what to enter once I click "New" on that window.
>
> Thanks in advance.
>
> With regards,
> Ravi.
>
>
> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>
>> Hi Ravi,
>>
>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>> not Bio::Seq. So your first line
>>
>> use Bio::Seq;
>>
>> should be replaced with
>>
>> use Bio::Perl;
>>
>>
>> More examples in the BioPerl Tutorial here:
>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>
>>
>> Dve
>>
>>
>>
>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>
>>> Hi,
>>>
>>> Could you please help me installing bioperl-db, bioperl-run & other
>>> packages
>>> using ppm on windows 7? Please find the attachment for the error message
>>> I
>>> get. I would really appreciate if you help me fix this issue.
>>>
>>> Thanks,
>>>
>>> With regards,
>>> Ravi.
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>



From David.Messina at sbc.su.se  Mon Mar 28 11:51:41 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 28 Mar 2011 13:51:41 +0200
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
Message-ID: <AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>

>
> Thank you very much. It is working. I got the program code from the
> following link.
>
> http://www.bioperl.org/Core/Latest/bptutorial.html


Aha, okay. You got there from Google, I guess? That is *way* out of date.

To the other core devs, in order to prevent this confusion in the future,
I'd like to delete the Core/ directory from our website since it's been
superseded at this point by other docs and is not current. I intend to put
up a ticket at Redmine, but I will wait a bit before doing so to allow time
for people to see this and comment ? please do speak up if there's good
reason to keep it.


Could you please give me the link to join this forum to see other
> discussions, which would be more helpful to me?
>

Sure, you can sign up for the mailing list here:

 <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


And the archives are also searchable:

    http://news.gmane.org/gmane.comp.lang.perl.bio.general


Please let me know if you have any suggestion for me to keep learning the
> bioperl.


I would also suggest reading the (current) tutorial and HOWTOs at
www.bioperl.org . Lots of good links on the main page there, particularly
under the Documentation heading.


Dave





> With regards,
> Ravi.
>
>
> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>
>> Hi Ravi,
>>
>> Please make sure to "Reply All" so that everyone on the mailing list can
>> follow (and add to) the discussion.
>>
>> If you read the first line of the exception, you'll see it states what the
>> error is:
>> "WebDBSeqI Error ? check query sequences!"
>>
>> You'd have no way of knowing this, but that ID and database combination is
>> not functioning anymore, so that's why in this case you're getting an error.
>> Please try using the example in the tutorial here:
>>
>>
>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>
>> which has been updated to a different ID which should work.
>>
>> Sorry for the confusion! So that we can prevent other people from having
>> the same issue, could you tell me where you got that example code?
>>
>> Dave
>>
>>
>>
>>
>>
>>
>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>
>>> Hi Dave,
>>>
>>> Thanks a lot for your reply. It is really helpful. Please find the
>>> screenshot after making the change you pointed out. But I am getting
>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>> environment variables but I am not sure how to do that. Could you please
>>> guide me on this too.
>>>
>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>> what to enter once I click "New" on that window.
>>>
>>> Thanks in advance.
>>>
>>> With regards,
>>> Ravi.
>>>
>>>
>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>
>>>> Hi Ravi,
>>>>
>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>> not Bio::Seq. So your first line
>>>>
>>>> use Bio::Seq;
>>>>
>>>> should be replaced with
>>>>
>>>> use Bio::Perl;
>>>>
>>>>
>>>> More examples in the BioPerl Tutorial here:
>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>
>>>>
>>>> Dve
>>>>
>>>>
>>>>
>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>
>>>>> Hi,
>>>>>
>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>> packages
>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>> message I
>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> With regards,
>>>>> Ravi.
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>
>>>>
>>>
>>
>



From David.Messina at sbc.su.se  Mon Mar 28 12:45:34 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 28 Mar 2011 14:45:34 +0200
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTinhqidOd7VBDT+hr6E-VNKwOobtyZ1Zn=A1uPfy@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
	<AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
	<AANLkTinhqidOd7VBDT+hr6E-VNKwOobtyZ1Zn=A1uPfy@mail.gmail.com>
Message-ID: <AANLkTikiN9J28oNWWnQ5hJSWYB_DKTPHPegj+7wZ-ELr@mail.gmail.com>

Again, please "Reply All" so that your messages go to the mailing list.

Ravi, PLEASE read the documentation on the website first and try to figure
out how to solve your problem on your own. BioPerl is a complex system and
requires some effort to learn how to use. I and everyone on this list
volunteers our time answering questions, and we are happy to do so, but you
have to meet us halfway.


Dave




2011/3/28 ?????????????????? <ravimbt at gmail.com>

> Hi Dave,
>
> Thanks for the information. I have also signed up to join the forum.
>
> I could not retrieve the sequence from other databases other than Genbank.
> Could you please do the changes on the below programme to make it working so
> that I can try in my system.
> --------------------
> use Bio::Perl;
>
> $seq_object = get_sequence('genbank',"ECORHO");
>
> write_sequence(">ael.fasta",'fasta',$seq_object);
> ------------------
>
> Thanks once again.
>
> With regards,
> Ravi.
>
>
> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>
>> Thank you very much. It is working. I got the program code from the
>>> following link.
>>>
>>> http://www.bioperl.org/Core/Latest/bptutorial.html
>>
>>
>> Aha, okay. You got there from Google, I guess? That is *way* out of date.
>>
>> To the other core devs, in order to prevent this confusion in the future,
>> I'd like to delete the Core/ directory from our website since it's been
>> superseded at this point by other docs and is not current. I intend to put
>> up a ticket at Redmine, but I will wait a bit before doing so to allow time
>> for people to see this and comment ? please do speak up if there's good
>> reason to keep it.
>>
>>
>> Could you please give me the link to join this forum to see other
>>> discussions, which would be more helpful to me?
>>>
>>
>> Sure, you can sign up for the mailing list here:
>>
>>  <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> And the archives are also searchable:
>>
>>     http://news.gmane.org/gmane.comp.lang.perl.bio.general
>>
>>
>> Please let me know if you have any suggestion for me to keep learning the
>>> bioperl.
>>
>>
>> I would also suggest reading the (current) tutorial and HOWTOs at
>> www.bioperl.org . Lots of good links on the main page there, particularly
>> under the Documentation heading.
>>
>>
>> Dave
>>
>>
>>
>>
>>
>>> With regards,
>>> Ravi.
>>>
>>>
>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>>>
>>>> Hi Ravi,
>>>>
>>>> Please make sure to "Reply All" so that everyone on the mailing list can
>>>> follow (and add to) the discussion.
>>>>
>>>> If you read the first line of the exception, you'll see it states what
>>>> the error is:
>>>> "WebDBSeqI Error ? check query sequences!"
>>>>
>>>> You'd have no way of knowing this, but that ID and database combination
>>>> is not functioning anymore, so that's why in this case you're getting an
>>>> error. Please try using the example in the tutorial here:
>>>>
>>>>
>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>>>
>>>> which has been updated to a different ID which should work.
>>>>
>>>> Sorry for the confusion! So that we can prevent other people from having
>>>> the same issue, could you tell me where you got that example code?
>>>>
>>>> Dave
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>>>
>>>>> Hi Dave,
>>>>>
>>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>>> screenshot after making the change you pointed out. But I am getting
>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>>> environment variables but I am not sure how to do that. Could you please
>>>>> guide me on this too.
>>>>>
>>>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>>>> what to enter once I click "New" on that window.
>>>>>
>>>>> Thanks in advance.
>>>>>
>>>>> With regards,
>>>>> Ravi.
>>>>>
>>>>>
>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>>>
>>>>>> Hi Ravi,
>>>>>>
>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl
>>>>>> module, not Bio::Seq. So your first line
>>>>>>
>>>>>> use Bio::Seq;
>>>>>>
>>>>>> should be replaced with
>>>>>>
>>>>>> use Bio::Perl;
>>>>>>
>>>>>>
>>>>>> More examples in the BioPerl Tutorial here:
>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>>>
>>>>>>
>>>>>> Dve
>>>>>>
>>>>>>
>>>>>>
>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>>>> packages
>>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>>> message I
>>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> With regards,
>>>>>>> Ravi.
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>



From abualiga at gmail.com  Mon Mar 28 13:19:00 2011
From: abualiga at gmail.com (Galeb Abu-Ali)
Date: Mon, 28 Mar 2011 09:19:00 -0400
Subject: [Bioperl-l] CDS complement statements from GenBank
In-Reply-To: <4D8F7AED.1070705@bioperl.org>
References: <cdf62961-ac89-4274-91ed-9a233d2de15c@k10g2000prh.googlegroups.com>
	<4D8F7AED.1070705@bioperl.org>
Message-ID: <AANLkTimpN2sRvrkn86Ges7100ssRizHr5GU7rPhDvyUS@mail.gmail.com>

I was using the wrong module, Bio::Location::Simple was what I needed.
thanks much!

galeb

On Sun, Mar 27, 2011 at 1:59 PM, Jason Stajich <jason at bioperl.org> wrote:

> they won't be split locations they will be Bio::Location::Simple locations
> then - I don't understand if that is causing you problems?
>
>
>
> Galeb Abu-Ali wrote:
>
>> Hi,
>>
>> I'm trying to parse CDS complement statements from GenBank files of
>> bacterial genomes. I know it works for 'join' statements with
>> Bio::Location::SplitLocationI, but there is no spliced genes in
>> bacterial annotations and therefore no 'join()' statements. When I
>> replace 'complement' with 'join' in the bacterial GenBank file,
>> Bio::Location::SplitLocationI gets the coordinates. I took a look at
>> SplitLocationI.pm and Split.pm to see if I could replace 'join' with
>> 'complement' to get it to work but no luck. At your convenience,
>> please advise.
>>
>> cheers,
>>
>> galeb
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> --
> Jason Stajich
> jason at bioperl.org
> http://bioperl.org/wiki
>
>


From cjfields at illinois.edu  Mon Mar 28 13:27:38 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 28 Mar 2011 08:27:38 -0500
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
	<AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
Message-ID: <6CE8AACF-0D78-4BBA-8094-CC189B0FF872@illinois.edu>

Dave,

+1 on removing old docs to prevent confusion.  Or, alternatively, +1 to syncing those to current docs (though I think decreasing the replication effort in keeping docs up-to-date is probably the best tact).

chris

On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:

>> 
>> Thank you very much. It is working. I got the program code from the
>> following link.
>> 
>> http://www.bioperl.org/Core/Latest/bptutorial.html
> 
> 
> Aha, okay. You got there from Google, I guess? That is *way* out of date.
> 
> To the other core devs, in order to prevent this confusion in the future,
> I'd like to delete the Core/ directory from our website since it's been
> superseded at this point by other docs and is not current. I intend to put
> up a ticket at Redmine, but I will wait a bit before doing so to allow time
> for people to see this and comment ? please do speak up if there's good
> reason to keep it.
> 
> 
> Could you please give me the link to join this forum to see other
>> discussions, which would be more helpful to me?
>> 
> 
> Sure, you can sign up for the mailing list here:
> 
> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> And the archives are also searchable:
> 
>    http://news.gmane.org/gmane.comp.lang.perl.bio.general
> 
> 
> Please let me know if you have any suggestion for me to keep learning the
>> bioperl.
> 
> 
> I would also suggest reading the (current) tutorial and HOWTOs at
> www.bioperl.org . Lots of good links on the main page there, particularly
> under the Documentation heading.
> 
> 
> Dave
> 
> 
> 
> 
> 
>> With regards,
>> Ravi.
>> 
>> 
>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>> 
>>> Hi Ravi,
>>> 
>>> Please make sure to "Reply All" so that everyone on the mailing list can
>>> follow (and add to) the discussion.
>>> 
>>> If you read the first line of the exception, you'll see it states what the
>>> error is:
>>> "WebDBSeqI Error ? check query sequences!"
>>> 
>>> You'd have no way of knowing this, but that ID and database combination is
>>> not functioning anymore, so that's why in this case you're getting an error.
>>> Please try using the example in the tutorial here:
>>> 
>>> 
>>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>> 
>>> which has been updated to a different ID which should work.
>>> 
>>> Sorry for the confusion! So that we can prevent other people from having
>>> the same issue, could you tell me where you got that example code?
>>> 
>>> Dave
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>> 
>>>> Hi Dave,
>>>> 
>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>> screenshot after making the change you pointed out. But I am getting
>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>> environment variables but I am not sure how to do that. Could you please
>>>> guide me on this too.
>>>> 
>>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>>> what to enter once I click "New" on that window.
>>>> 
>>>> Thanks in advance.
>>>> 
>>>> With regards,
>>>> Ravi.
>>>> 
>>>> 
>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>> 
>>>>> Hi Ravi,
>>>>> 
>>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>>> not Bio::Seq. So your first line
>>>>> 
>>>>> use Bio::Seq;
>>>>> 
>>>>> should be replaced with
>>>>> 
>>>>> use Bio::Perl;
>>>>> 
>>>>> 
>>>>> More examples in the BioPerl Tutorial here:
>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>> 
>>>>> 
>>>>> Dve
>>>>> 
>>>>> 
>>>>> 
>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>>> packages
>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>> message I
>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>> 
>>>>>> Thanks,
>>>>>> 
>>>>>> With regards,
>>>>>> Ravi.
>>>>>> 
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>> 
>>>>> 
>>>>> 
>>>> 
>>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From dan.bolser at gmail.com  Mon Mar 28 17:15:32 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 28 Mar 2011 18:15:32 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
Message-ID: <AANLkTikQgn2-YU4-4JBdLkSopFFihhJ-=2KG25P0Ugv6@mail.gmail.com>

--- Build.PL~   2011-03-14 20:27:57.000000000 +0000
+++ Build.PL    2011-03-28 18:06:45.503757000 +0100
@@ -16,7 +16,7 @@
     dist_abstract      => "Manipulate Jim Kent's BigWig and BigBed
index files for genomic features.",
     license            => 'perl',
     include_dirs       => [$jk_include],
-    extra_linker_flags => ["$jk_lib/$LibFile",'-lz'],
+    extra_linker_flags => ["$jk_lib/$LibFile",'-lz','-lssl'],

     extra_compiler_flags=>[
        # turn off warnings originating in Perl's Newx* calls

On 27 March 2011 19:00, Dan Bolser <dan.bolser at gmail.com> wrote:
> Hello,
>
> I'm trying to get Bio::DB::BigWig installed again, this time on a different box.
>
> I installed kent from git as described here:
> http://genome.ucsc.edu/admin/git.html
>
>
> I made the following changes, similar to those described previously:
>
> git diff
> diff --git a/src/inc/common.mk b/src/inc/common.mk
> index c7fc557..5187901 100644
> --- a/src/inc/common.mk
> +++ b/src/inc/common.mk
> @@ -3,7 +3,7 @@ CC=gcc
> ?ifeq (${COPT},)
> ? ? COPT=-O -g
> ?endif
> -CFLAGS=
> +CFLAGS=-fPIC
> ?HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> -DMACHTYPE_${MACHTYPE}
> ?HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> -I../../../../../inc
>
> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> index fa2292b..acb97d2 100644
> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
> ? ? /* Parse current line. */
> ? ? wordCount = chopLine(line, row);
> ? ? if (wordCount == ArraySize(row))
> - ? ? ? ? errAbort("Too many fields (%d max is %lu) line %d of %s",
> wordCount, ArraySize(row),
> + ? ? ? ? errAbort("Too many fields (%d max is %u) line %d of %s",
> wordCount, ArraySize(row),
> ? ? ? ? ? ? lf->lineIx, lf->fileName);
> ? ? char *chrom = row[0];
> ? ? unsigned int start = lineFileNeedNum(lf, row, 1);
>
>
> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> correctly after typing 'make' in kent/src (should I be building it
> differently?)
>
>
>
> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>
> cpan
>
> cpan shell -- CPAN exploration and modules installation (v1.9600)
> Enter 'h' for help.
>
> cpan[1]> install Bio::DB::BigWig
> CPAN: Storable loaded ok (v2.25)
> Going to read '/homes/dbolser/.cpan/Metadata'
> ?Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> Running install for module 'Bio::DB::BigWig'
> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> CPAN: Digest::SHA loaded ok (v5.61)
> CPAN: Compress::Zlib loaded ok (v2.03)
> Checksum for /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> ok
> CPAN: Archive::Tar loaded ok (v1.76)
> Bio-BigFile-1.05
> Bio-BigFile-1.05/Changes
> Bio-BigFile-1.05/LICENSE
> Bio-BigFile-1.05/DISCLAIMER
> Bio-BigFile-1.05/Build.PL
> Bio-BigFile-1.05/typemap
> Bio-BigFile-1.05/META.yml
> Bio-BigFile-1.05/README
> Bio-BigFile-1.05/MANIFEST
> Bio-BigFile-1.05/ExampleData
> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> Bio-BigFile-1.05/bin
> Bio-BigFile-1.05/bin/bigWigToWig.pl
> Bio-BigFile-1.05/bin/wigToBigWig.pl
> Bio-BigFile-1.05/bin/index_bigwigset.pl
> Bio-BigFile-1.05/lib
> Bio-BigFile-1.05/lib/Bio
> Bio-BigFile-1.05/lib/Bio/DB
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> Bio-BigFile-1.05/t
> Bio-BigFile-1.05/t/02.bigbed.t
> Bio-BigFile-1.05/t/03.bigwig_high.t
> Bio-BigFile-1.05/t/04.bigbed_high.t
> Bio-BigFile-1.05/t/05.bigwig_set.t
> /bin/tar: Read 9216 bytes from -
> Bio-BigFile-1.05/t/01.bigwig.t
> Bio-BigFile-1.05/patches
> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> CPAN: File::Temp loaded ok (v0.22)
> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> CPAN: CPAN::Meta loaded ok (v2.110580)
> CPAN: Module::CoreList loaded ok (v2.46)
> CPAN: Time::HiRes loaded ok (v1.9717)
>
> ?CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>
>
> This module requires the compiled jkweb.a library from Jim Kent's source tree.
> If you haven't already done so, please download the source from
> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
> contents of the "kent/src/lib" subdirectory as directed in the README. Then
> enter the location of the "kent/src" subdirectory at the prompt below.
> To prevent
> this message from appearing in the future, set the environment
> variable KENT_SRC
> to point to the "kent/src" subdirectory.
>
> Please enter the location of Kent source tree: /homes/dbolser/build/src/kent/src
>
> Created MYMETA.yml and MYMETA.json
> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> Building Bio-BigFile
> gcc -I/homes/dbolser/build/src/kent/src/inc
> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> lib/Bio/DB/BigFile.c
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be undefined
> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be undefined
> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
> ?LDS/Bio-BigFile-1.05.tar.gz
> ?./Build -- OK
> CPAN: YAML loaded ok (v0.72)
> Running Build test
> t/01.bigwig.t ....... Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at t/01.bigwig.t line 28
> Compilation failed in require at t/01.bigwig.t line 28.
> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 29/29 subtests
> t/02.bigbed.t ....... Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at t/02.bigbed.t line 28
> Compilation failed in require at t/02.bigbed.t line 28.
> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 15/15 subtests
> t/03.bigwig_high.t .. Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at t/03.bigwig_high.t line 28.
> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 32/32 subtests
> t/04.bigbed_high.t .. Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> Compilation failed in require at t/04.bigbed_high.t line 28.
> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 35/35 subtests
> t/05.bigwig_set.t ... Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> ?at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> Compilation failed in require at t/05.bigwig_set.t line 19.
> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> No subtests run
>
> Test Summary Report
> -------------------
> t/01.bigwig.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: Bad plan. ?You planned 29 tests but ran 0.
> t/02.bigbed.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: Bad plan. ?You planned 15 tests but ran 0.
> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: Bad plan. ?You planned 32 tests but ran 0.
> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: Bad plan. ?You planned 35 tests but ran 0.
> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
> ?Non-zero exit status: 2
> ?Parse errors: No plan found in TAP output
> Files=5, Tests=0, ?1 wallclock secs ( 0.04 usr ?0.01 sys + ?0.93 cusr
> 0.11 csys = ?1.09 CPU)
> Result: FAIL
> Failed 5/5 test programs. 0/0 subtests failed.
> ?LDS/Bio-BigFile-1.05.tar.gz
> ?./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module, try:
> ?reports LDS/Bio-BigFile-1.05.tar.gz
> Running Build install
> ?make test had returned bad status, won't install without force
> Failed during this command:
> ?LDS/Bio-BigFile-1.05.tar.gz ? ? ? ? ? ? ? ? ?: make_test NO
>
> cpan[2]>
>
>
>
>
>
>
> Any hints?
>
> Cheers,
> Dan.
>



From dan.bolser at gmail.com  Mon Mar 28 20:08:52 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 28 Mar 2011 21:08:52 +0100
Subject: [Bioperl-l] Use of uninitialized value in length at
 Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062
In-Reply-To: <4960971A-8C61-49F2-B43A-E32BAFC4C59E@illinois.edu>
References: <AANLkTi=D_73Bx=K9An=JDwTho1Whc7JJ4-dch9i-tXmb@mail.gmail.com>
	<4D8F73A4.8050408@bioperl.org>
	<AANLkTinv87NF-RRPrrUsspAByrLXZLiKAcGaTmCWrNb7@mail.gmail.com>
	<4960971A-8C61-49F2-B43A-E32BAFC4C59E@illinois.edu>
Message-ID: <AANLkTi=H4opbLx+qv8XM5+VpQNy2Fhxtbyx54iumRcE5@mail.gmail.com>

On 27 March 2011 21:13, Chris Fields <cjfields at illinois.edu> wrote:
> On Mar 27, 2011, at 12:55 PM, Dan Bolser wrote:
>
>> On 27 March 2011 18:28, Jason Stajich <jason at bioperl.org> wrote:
>>> Dan - not sure why you would need to do this as length on an undef should
>>> still return false (an undef).
>>>
>>> $ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} print
>>> "\n"'
>>> no
>>> $ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"}
>>> print "\n"'
>>> no
>>
>> Doesn't the latter spew a warning? (The output before / after my 'bug
>> fix' is the same, I just don't see 100s of warnings about undefined
>> values).
>
> Only with later versions of perl (I think perl 5.12).
>
>>> Also, having no 'source' is probably not proper GFF3.
>>
>> I'm quite sure it is, but by GFF does have a source. I'm just calling
>> 'features' with only a feature type and not a feature type and a
>> source (because I only care about source). My call is pretty similar
>> to the example here:
>>
>> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/DB/SeqFeature/Store.pm#features
>>
>> @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');
>
> I think Jason is inferring that the GFF3 is invalid from your statement below re: $source_tag not being defined, which to me means the source attribute for the feature is not defined.
>
> Note: b/c something works with SF::Store does NOT mean the source is proper GFF3; it is quite possible to have invalid GFF3 loaded into the database w/o a hiccup. ?I think the loader assumes the data loaded has already been validated; IIRC there is very little validation done on GFF3 loaded into SF::Store, particularly the 'type'.

As I said, my GFF3 does have a source. I'll try to put together a test
script, as it seems like the value should not be undef (but thanks for
the tip Roy).

I had a feeling that this relatively trivial fix was a sticking
plaster on a larger problem.


> chris
Dan



From dan.bolser at gmail.com  Mon Mar 28 20:12:19 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 28 Mar 2011 21:12:19 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTikQgn2-YU4-4JBdLkSopFFihhJ-=2KG25P0Ugv6@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTikQgn2-YU4-4JBdLkSopFFihhJ-=2KG25P0Ugv6@mail.gmail.com>
Message-ID: <AANLkTikjJpMcFWvvAt+bJoXJHHaORfecYmz053RScFjn@mail.gmail.com>

Context, this patch in the distro's Build.PL fixes the errors with the
tests, but doesn't fix the warnings.

On 28 March 2011 18:15, Dan Bolser <dan.bolser at gmail.com> wrote:
> --- Build.PL~ ? 2011-03-14 20:27:57.000000000 +0000
> +++ Build.PL ? ?2011-03-28 18:06:45.503757000 +0100
> @@ -16,7 +16,7 @@
> ? ? dist_abstract ? ? ?=> "Manipulate Jim Kent's BigWig and BigBed
> index files for genomic features.",
> ? ? license ? ? ? ? ? ?=> 'perl',
> ? ? include_dirs ? ? ? => [$jk_include],
> - ? ?extra_linker_flags => ["$jk_lib/$LibFile",'-lz'],
> + ? ?extra_linker_flags => ["$jk_lib/$LibFile",'-lz','-lssl'],
>
> ? ? extra_compiler_flags=>[
> ? ? ? ?# turn off warnings originating in Perl's Newx* calls



From cjfields at illinois.edu  Mon Mar 28 20:23:38 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 28 Mar 2011 15:23:38 -0500
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTikjJpMcFWvvAt+bJoXJHHaORfecYmz053RScFjn@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTikQgn2-YU4-4JBdLkSopFFihhJ-=2KG25P0Ugv6@mail.gmail.com>
	<AANLkTikjJpMcFWvvAt+bJoXJHHaORfecYmz053RScFjn@mail.gmail.com>
Message-ID: <91759940-6457-460D-95F5-EF7098A7412C@illinois.edu>

Dan,

Was this using the latest kent src and Bio::DB::BigWig?

chris

PS : cc'ing gbrowse, which is where these seem to get answered a bit faster, context thread here: http://lists.open-bio.org/pipermail/bioperl-l/2011-March/034738.html

On Mar 28, 2011, at 3:12 PM, Dan Bolser wrote:

> Context, this patch in the distro's Build.PL fixes the errors with the
> tests, but doesn't fix the warnings.
> 
> On 28 March 2011 18:15, Dan Bolser <dan.bolser at gmail.com> wrote:
>> --- Build.PL~   2011-03-14 20:27:57.000000000 +0000
>> +++ Build.PL    2011-03-28 18:06:45.503757000 +0100
>> @@ -16,7 +16,7 @@
>>     dist_abstract      => "Manipulate Jim Kent's BigWig and BigBed
>> index files for genomic features.",
>>     license            => 'perl',
>>     include_dirs       => [$jk_include],
>> -    extra_linker_flags => ["$jk_lib/$LibFile",'-lz'],
>> +    extra_linker_flags => ["$jk_lib/$LibFile",'-lz','-lssl'],
>> 
>>     extra_compiler_flags=>[
>>        # turn off warnings originating in Perl's Newx* calls
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From lincoln.stein at gmail.com  Mon Mar 28 21:26:20 2011
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Mon, 28 Mar 2011 17:26:20 -0400
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
Message-ID: <AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>

Hi Dan,

There are two problems that I can see. One is a series of compiler warnings
when compiling the Perl .XS interface file. These are likely nothing to
worry about, but I should fix them. What versions of Perl and gcc do you
have installed? I don't see them when I compile on my system.

The second issue is that the SSL library is not being linked in. Previously
there was no dependency on SSL, but Jim may recently have added this to the
BigWig library in order to allow it to read bigwig files from https servers.
I see that you added a -lssl to Build.PL; does this make the tests work
again?

Lincoln


On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com> wrote:

> Hello,
>
> I'm trying to get Bio::DB::BigWig installed again, this time on a different
> box.
>
> I installed kent from git as described here:
> http://genome.ucsc.edu/admin/git.html
>
>
> I made the following changes, similar to those described previously:
>
> git diff
> diff --git a/src/inc/common.mk b/src/inc/common.mk
> index c7fc557..5187901 100644
> --- a/src/inc/common.mk
> +++ b/src/inc/common.mk
> @@ -3,7 +3,7 @@ CC=gcc
>  ifeq (${COPT},)
>     COPT=-O -g
>  endif
> -CFLAGS=
> +CFLAGS=-fPIC
>  HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> -DMACHTYPE_${MACHTYPE}
>  HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> -I../../../../../inc
>
> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> index fa2292b..acb97d2 100644
> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
>     /* Parse current line. */
>     wordCount = chopLine(line, row);
>     if (wordCount == ArraySize(row))
> -         errAbort("Too many fields (%d max is %lu) line %d of %s",
> wordCount, ArraySize(row),
> +         errAbort("Too many fields (%d max is %u) line %d of %s",
> wordCount, ArraySize(row),
>             lf->lineIx, lf->fileName);
>     char *chrom = row[0];
>     unsigned int start = lineFileNeedNum(lf, row, 1);
>
>
> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> correctly after typing 'make' in kent/src (should I be building it
> differently?)
>
>
>
> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>
> cpan
>
> cpan shell -- CPAN exploration and modules installation (v1.9600)
> Enter 'h' for help.
>
> cpan[1]> install Bio::DB::BigWig
> CPAN: Storable loaded ok (v2.25)
> Going to read '/homes/dbolser/.cpan/Metadata'
>  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> Running install for module 'Bio::DB::BigWig'
> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> CPAN: Digest::SHA loaded ok (v5.61)
> CPAN: Compress::Zlib loaded ok (v2.03)
> Checksum for
> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> ok
> CPAN: Archive::Tar loaded ok (v1.76)
> Bio-BigFile-1.05
> Bio-BigFile-1.05/Changes
> Bio-BigFile-1.05/LICENSE
> Bio-BigFile-1.05/DISCLAIMER
> Bio-BigFile-1.05/Build.PL
> Bio-BigFile-1.05/typemap
> Bio-BigFile-1.05/META.yml
> Bio-BigFile-1.05/README
> Bio-BigFile-1.05/MANIFEST
> Bio-BigFile-1.05/ExampleData
> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> Bio-BigFile-1.05/bin
> Bio-BigFile-1.05/bin/bigWigToWig.pl
> Bio-BigFile-1.05/bin/wigToBigWig.pl
> Bio-BigFile-1.05/bin/index_bigwigset.pl
> Bio-BigFile-1.05/lib
> Bio-BigFile-1.05/lib/Bio
> Bio-BigFile-1.05/lib/Bio/DB
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> Bio-BigFile-1.05/t
> Bio-BigFile-1.05/t/02.bigbed.t
> Bio-BigFile-1.05/t/03.bigwig_high.t
> Bio-BigFile-1.05/t/04.bigbed_high.t
> Bio-BigFile-1.05/t/05.bigwig_set.t
> /bin/tar: Read 9216 bytes from -
> Bio-BigFile-1.05/t/01.bigwig.t
> Bio-BigFile-1.05/patches
> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> CPAN: File::Temp loaded ok (v0.22)
> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> CPAN: CPAN::Meta loaded ok (v2.110580)
> CPAN: Module::CoreList loaded ok (v2.46)
> CPAN: Time::HiRes loaded ok (v1.9717)
>
>  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>
>
> This module requires the compiled jkweb.a library from Jim Kent's source
> tree.
> If you haven't already done so, please download the source from
> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
> contents of the "kent/src/lib" subdirectory as directed in the README. Then
> enter the location of the "kent/src" subdirectory at the prompt below.
> To prevent
> this message from appearing in the future, set the environment
> variable KENT_SRC
> to point to the "kent/src" subdirectory.
>
> Please enter the location of Kent source tree:
> /homes/dbolser/build/src/kent/src
>
> Created MYMETA.yml and MYMETA.json
> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> Building Bio-BigFile
> gcc -I/homes/dbolser/build/src/kent/src/inc
> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> lib/Bio/DB/BigFile.c
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
> undefined
> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
> undefined
> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
>
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build -- OK
> CPAN: YAML loaded ok (v0.72)
> Running Build test
> t/01.bigwig.t ....... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/01.bigwig.t line 28
> Compilation failed in require at t/01.bigwig.t line 28.
> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 29/29 subtests
> t/02.bigbed.t ....... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/02.bigbed.t line 28
> Compilation failed in require at t/02.bigbed.t line 28.
> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 15/15 subtests
> t/03.bigwig_high.t .. Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at t/03.bigwig_high.t line 28.
> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 32/32 subtests
> t/04.bigbed_high.t .. Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> Compilation failed in require at t/04.bigbed_high.t line 28.
> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 35/35 subtests
> t/05.bigwig_set.t ... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> Compilation failed in require at t/05.bigwig_set.t line 19.
> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> No subtests run
>
> Test Summary Report
> -------------------
> t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 29 tests but ran 0.
> t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 32 tests but ran 0.
> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 35 tests but ran 0.
> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: No plan found in TAP output
> Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
> 0.11 csys =  1.09 CPU)
> Result: FAIL
> Failed 5/5 test programs. 0/0 subtests failed.
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module, try:
>  reports LDS/Bio-BigFile-1.05.tar.gz
> Running Build install
>  make test had returned bad status, won't install without force
> Failed during this command:
>  LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO
>
> cpan[2]>
>
>
>
>
>
>
> Any hints?
>
> Cheers,
> Dan.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>



From lincoln.stein at gmail.com  Mon Mar 28 21:26:20 2011
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Mon, 28 Mar 2011 17:26:20 -0400
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
Message-ID: <AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>

Hi Dan,

There are two problems that I can see. One is a series of compiler warnings
when compiling the Perl .XS interface file. These are likely nothing to
worry about, but I should fix them. What versions of Perl and gcc do you
have installed? I don't see them when I compile on my system.

The second issue is that the SSL library is not being linked in. Previously
there was no dependency on SSL, but Jim may recently have added this to the
BigWig library in order to allow it to read bigwig files from https servers.
I see that you added a -lssl to Build.PL; does this make the tests work
again?

Lincoln


On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com> wrote:

> Hello,
>
> I'm trying to get Bio::DB::BigWig installed again, this time on a different
> box.
>
> I installed kent from git as described here:
> http://genome.ucsc.edu/admin/git.html
>
>
> I made the following changes, similar to those described previously:
>
> git diff
> diff --git a/src/inc/common.mk b/src/inc/common.mk
> index c7fc557..5187901 100644
> --- a/src/inc/common.mk
> +++ b/src/inc/common.mk
> @@ -3,7 +3,7 @@ CC=gcc
>  ifeq (${COPT},)
>     COPT=-O -g
>  endif
> -CFLAGS=
> +CFLAGS=-fPIC
>  HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> -DMACHTYPE_${MACHTYPE}
>  HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> -I../../../../../inc
>
> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> index fa2292b..acb97d2 100644
> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
>     /* Parse current line. */
>     wordCount = chopLine(line, row);
>     if (wordCount == ArraySize(row))
> -         errAbort("Too many fields (%d max is %lu) line %d of %s",
> wordCount, ArraySize(row),
> +         errAbort("Too many fields (%d max is %u) line %d of %s",
> wordCount, ArraySize(row),
>             lf->lineIx, lf->fileName);
>     char *chrom = row[0];
>     unsigned int start = lineFileNeedNum(lf, row, 1);
>
>
> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> correctly after typing 'make' in kent/src (should I be building it
> differently?)
>
>
>
> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>
> cpan
>
> cpan shell -- CPAN exploration and modules installation (v1.9600)
> Enter 'h' for help.
>
> cpan[1]> install Bio::DB::BigWig
> CPAN: Storable loaded ok (v2.25)
> Going to read '/homes/dbolser/.cpan/Metadata'
>  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> Running install for module 'Bio::DB::BigWig'
> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> CPAN: Digest::SHA loaded ok (v5.61)
> CPAN: Compress::Zlib loaded ok (v2.03)
> Checksum for
> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> ok
> CPAN: Archive::Tar loaded ok (v1.76)
> Bio-BigFile-1.05
> Bio-BigFile-1.05/Changes
> Bio-BigFile-1.05/LICENSE
> Bio-BigFile-1.05/DISCLAIMER
> Bio-BigFile-1.05/Build.PL
> Bio-BigFile-1.05/typemap
> Bio-BigFile-1.05/META.yml
> Bio-BigFile-1.05/README
> Bio-BigFile-1.05/MANIFEST
> Bio-BigFile-1.05/ExampleData
> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> Bio-BigFile-1.05/bin
> Bio-BigFile-1.05/bin/bigWigToWig.pl
> Bio-BigFile-1.05/bin/wigToBigWig.pl
> Bio-BigFile-1.05/bin/index_bigwigset.pl
> Bio-BigFile-1.05/lib
> Bio-BigFile-1.05/lib/Bio
> Bio-BigFile-1.05/lib/Bio/DB
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> Bio-BigFile-1.05/t
> Bio-BigFile-1.05/t/02.bigbed.t
> Bio-BigFile-1.05/t/03.bigwig_high.t
> Bio-BigFile-1.05/t/04.bigbed_high.t
> Bio-BigFile-1.05/t/05.bigwig_set.t
> /bin/tar: Read 9216 bytes from -
> Bio-BigFile-1.05/t/01.bigwig.t
> Bio-BigFile-1.05/patches
> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> CPAN: File::Temp loaded ok (v0.22)
> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> CPAN: CPAN::Meta loaded ok (v2.110580)
> CPAN: Module::CoreList loaded ok (v2.46)
> CPAN: Time::HiRes loaded ok (v1.9717)
>
>  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>
>
> This module requires the compiled jkweb.a library from Jim Kent's source
> tree.
> If you haven't already done so, please download the source from
> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
> contents of the "kent/src/lib" subdirectory as directed in the README. Then
> enter the location of the "kent/src" subdirectory at the prompt below.
> To prevent
> this message from appearing in the future, set the environment
> variable KENT_SRC
> to point to the "kent/src" subdirectory.
>
> Please enter the location of Kent source tree:
> /homes/dbolser/build/src/kent/src
>
> Created MYMETA.yml and MYMETA.json
> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> Building Bio-BigFile
> gcc -I/homes/dbolser/build/src/kent/src/inc
> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> lib/Bio/DB/BigFile.c
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
> undefined
> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
> undefined
> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be undefined
> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
> lib/Bio/DB/BigFile.xs: In function
> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
>
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build -- OK
> CPAN: YAML loaded ok (v0.72)
> Running Build test
> t/01.bigwig.t ....... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/01.bigwig.t line 28
> Compilation failed in require at t/01.bigwig.t line 28.
> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 29/29 subtests
> t/02.bigbed.t ....... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/02.bigbed.t line 28
> Compilation failed in require at t/02.bigbed.t line 28.
> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 15/15 subtests
> t/03.bigwig_high.t .. Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at t/03.bigwig_high.t line 28.
> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 32/32 subtests
> t/04.bigbed_high.t .. Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> Compilation failed in require at t/04.bigbed_high.t line 28.
> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 35/35 subtests
> t/05.bigwig_set.t ... Can't load
>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> BEGIN failed--compilation aborted at
>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> Compilation failed in require at t/05.bigwig_set.t line 19.
> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> No subtests run
>
> Test Summary Report
> -------------------
> t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 29 tests but ran 0.
> t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 32 tests but ran 0.
> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 35 tests but ran 0.
> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: No plan found in TAP output
> Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
> 0.11 csys =  1.09 CPU)
> Result: FAIL
> Failed 5/5 test programs. 0/0 subtests failed.
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module, try:
>  reports LDS/Bio-BigFile-1.05.tar.gz
> Running Build install
>  make test had returned bad status, won't install without force
> Failed during this command:
>  LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO
>
> cpan[2]>
>
>
>
>
>
>
> Any hints?
>
> Cheers,
> Dan.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>



From bosborne11 at verizon.net  Mon Mar 28 20:43:51 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Mon, 28 Mar 2011 16:43:51 -0400
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <6CE8AACF-0D78-4BBA-8094-CC189B0FF872@illinois.edu>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
	<AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
	<6CE8AACF-0D78-4BBA-8094-CC189B0FF872@illinois.edu>
Message-ID: <63E35F39-D70C-4D6F-A792-D2738B850567@verizon.net>

Chris,

I'll get started on dissembling bptutorial. There's certainly useful text in there but there's also duplicated or outdated material. Looks like there are 3 options for any given section:

- put it into an existing HOWTO
- make it into a new HOWTO
- delete it

BIO

On Mar 28, 2011, at 9:27 AM, Chris Fields wrote:

> Dave,
> 
> +1 on removing old docs to prevent confusion.  Or, alternatively, +1 to syncing those to current docs (though I think decreasing the replication effort in keeping docs up-to-date is probably the best tact).
> 
> chris
> 
> On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:
> 
>>> 
>>> Thank you very much. It is working. I got the program code from the
>>> following link.
>>> 
>>> http://www.bioperl.org/Core/Latest/bptutorial.html
>> 
>> 
>> Aha, okay. You got there from Google, I guess? That is *way* out of date.
>> 
>> To the other core devs, in order to prevent this confusion in the future,
>> I'd like to delete the Core/ directory from our website since it's been
>> superseded at this point by other docs and is not current. I intend to put
>> up a ticket at Redmine, but I will wait a bit before doing so to allow time
>> for people to see this and comment ? please do speak up if there's good
>> reason to keep it.
>> 
>> 
>> Could you please give me the link to join this forum to see other
>>> discussions, which would be more helpful to me?
>>> 
>> 
>> Sure, you can sign up for the mailing list here:
>> 
>> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> And the archives are also searchable:
>> 
>>   http://news.gmane.org/gmane.comp.lang.perl.bio.general
>> 
>> 
>> Please let me know if you have any suggestion for me to keep learning the
>>> bioperl.
>> 
>> 
>> I would also suggest reading the (current) tutorial and HOWTOs at
>> www.bioperl.org . Lots of good links on the main page there, particularly
>> under the Documentation heading.
>> 
>> 
>> Dave
>> 
>> 
>> 
>> 
>> 
>>> With regards,
>>> Ravi.
>>> 
>>> 
>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>>> 
>>>> Hi Ravi,
>>>> 
>>>> Please make sure to "Reply All" so that everyone on the mailing list can
>>>> follow (and add to) the discussion.
>>>> 
>>>> If you read the first line of the exception, you'll see it states what the
>>>> error is:
>>>> "WebDBSeqI Error ? check query sequences!"
>>>> 
>>>> You'd have no way of knowing this, but that ID and database combination is
>>>> not functioning anymore, so that's why in this case you're getting an error.
>>>> Please try using the example in the tutorial here:
>>>> 
>>>> 
>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>>> 
>>>> which has been updated to a different ID which should work.
>>>> 
>>>> Sorry for the confusion! So that we can prevent other people from having
>>>> the same issue, could you tell me where you got that example code?
>>>> 
>>>> Dave
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>>> 
>>>>> Hi Dave,
>>>>> 
>>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>>> screenshot after making the change you pointed out. But I am getting
>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>>> environment variables but I am not sure how to do that. Could you please
>>>>> guide me on this too.
>>>>> 
>>>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>>>> what to enter once I click "New" on that window.
>>>>> 
>>>>> Thanks in advance.
>>>>> 
>>>>> With regards,
>>>>> Ravi.
>>>>> 
>>>>> 
>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>>> 
>>>>>> Hi Ravi,
>>>>>> 
>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>>>> not Bio::Seq. So your first line
>>>>>> 
>>>>>> use Bio::Seq;
>>>>>> 
>>>>>> should be replaced with
>>>>>> 
>>>>>> use Bio::Perl;
>>>>>> 
>>>>>> 
>>>>>> More examples in the BioPerl Tutorial here:
>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>>> 
>>>>>> 
>>>>>> Dve
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>>> 
>>>>>>> Hi,
>>>>>>> 
>>>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>>>> packages
>>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>>> message I
>>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>>> 
>>>>>>> Thanks,
>>>>>>> 
>>>>>>> With regards,
>>>>>>> Ravi.
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Mon Mar 28 22:40:39 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 28 Mar 2011 17:40:39 -0500
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <63E35F39-D70C-4D6F-A792-D2738B850567@verizon.net>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
	<AANLkTinzmM+rFeodTJQnMCqdVZsi84Y0KGp2sCe_vTo2@mail.gmail.com>
	<6CE8AACF-0D78-4BBA-8094-CC189B0FF872@illinois.edu>
	<63E35F39-D70C-4D6F-A792-D2738B850567@verizon.net>
Message-ID: <1569920B-D132-487F-BBC6-9A81A430E6E0@illinois.edu>

Brian,

I think this was started:

http://www.bioperl.org/wiki/Bptutorial.pl

It certainly could be cleaned up, organized, and updated (that and the FAQ).  Makes sense to have it as a HOWTO or maybe split it into several HOWTOs.  Maybe even combine it with the beginner's HOWTO into various sections?

chris

On Mar 28, 2011, at 3:43 PM, Brian Osborne wrote:

> Chris,
> 
> I'll get started on dissembling bptutorial. There's certainly useful text in there but there's also duplicated or outdated material. Looks like there are 3 options for any given section:
> 
> - put it into an existing HOWTO
> - make it into a new HOWTO
> - delete it
> 
> BIO
> 
> On Mar 28, 2011, at 9:27 AM, Chris Fields wrote:
> 
>> Dave,
>> 
>> +1 on removing old docs to prevent confusion.  Or, alternatively, +1 to syncing those to current docs (though I think decreasing the replication effort in keeping docs up-to-date is probably the best tact).
>> 
>> chris
>> 
>> On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:
>> 
>>>> 
>>>> Thank you very much. It is working. I got the program code from the
>>>> following link.
>>>> 
>>>> http://www.bioperl.org/Core/Latest/bptutorial.html
>>> 
>>> 
>>> Aha, okay. You got there from Google, I guess? That is *way* out of date.
>>> 
>>> To the other core devs, in order to prevent this confusion in the future,
>>> I'd like to delete the Core/ directory from our website since it's been
>>> superseded at this point by other docs and is not current. I intend to put
>>> up a ticket at Redmine, but I will wait a bit before doing so to allow time
>>> for people to see this and comment ? please do speak up if there's good
>>> reason to keep it.
>>> 
>>> 
>>> Could you please give me the link to join this forum to see other
>>>> discussions, which would be more helpful to me?
>>>> 
>>> 
>>> Sure, you can sign up for the mailing list here:
>>> 
>>> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>>> And the archives are also searchable:
>>> 
>>>  http://news.gmane.org/gmane.comp.lang.perl.bio.general
>>> 
>>> 
>>> Please let me know if you have any suggestion for me to keep learning the
>>>> bioperl.
>>> 
>>> 
>>> I would also suggest reading the (current) tutorial and HOWTOs at
>>> www.bioperl.org . Lots of good links on the main page there, particularly
>>> under the Documentation heading.
>>> 
>>> 
>>> Dave
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> With regards,
>>>> Ravi.
>>>> 
>>>> 
>>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>>>> 
>>>>> Hi Ravi,
>>>>> 
>>>>> Please make sure to "Reply All" so that everyone on the mailing list can
>>>>> follow (and add to) the discussion.
>>>>> 
>>>>> If you read the first line of the exception, you'll see it states what the
>>>>> error is:
>>>>> "WebDBSeqI Error ? check query sequences!"
>>>>> 
>>>>> You'd have no way of knowing this, but that ID and database combination is
>>>>> not functioning anymore, so that's why in this case you're getting an error.
>>>>> Please try using the example in the tutorial here:
>>>>> 
>>>>> 
>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>>>> 
>>>>> which has been updated to a different ID which should work.
>>>>> 
>>>>> Sorry for the confusion! So that we can prevent other people from having
>>>>> the same issue, could you tell me where you got that example code?
>>>>> 
>>>>> Dave
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>>>> 
>>>>>> Hi Dave,
>>>>>> 
>>>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>>>> screenshot after making the change you pointed out. But I am getting
>>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>>>> environment variables but I am not sure how to do that. Could you please
>>>>>> guide me on this too.
>>>>>> 
>>>>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>>>>> what to enter once I click "New" on that window.
>>>>>> 
>>>>>> Thanks in advance.
>>>>>> 
>>>>>> With regards,
>>>>>> Ravi.
>>>>>> 
>>>>>> 
>>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>>>> 
>>>>>>> Hi Ravi,
>>>>>>> 
>>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>>>>> not Bio::Seq. So your first line
>>>>>>> 
>>>>>>> use Bio::Seq;
>>>>>>> 
>>>>>>> should be replaced with
>>>>>>> 
>>>>>>> use Bio::Perl;
>>>>>>> 
>>>>>>> 
>>>>>>> More examples in the BioPerl Tutorial here:
>>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>>>> 
>>>>>>> 
>>>>>>> Dve
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>>>> 
>>>>>>>> Hi,
>>>>>>>> 
>>>>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>>>>> packages
>>>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>>>> message I
>>>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>>>> 
>>>>>>>> Thanks,
>>>>>>>> 
>>>>>>>> With regards,
>>>>>>>> Ravi.
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From dan.kortschak at adelaide.edu.au  Tue Mar 29 01:12:55 2011
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Tue, 29 Mar 2011 11:42:55 +1030
Subject: [Bioperl-l] GuessSeqFormat GFF vs VCF
Message-ID: <1301361175.4727.17.camel@sueno>

Hi All,

I'm going through the BEDTools wrapper to bring it up to date. A number
BEDTools executables now accept GFF and VCF as well as BED format input
files.

Part of the WrapperBase::CommandExts give acceptable input formats, so
I'm adding to GuessSeqFormat guessers for GFF and VCF, which from the
point of view of a stateless guesser, are indistinguishable unless (and
I don't like this idea), GFF is additionally defined as not VCF and VCF
is additionally defined as not VCF (these can be identified from the
##gff-version and ##fileformat=VCF lines).

Can people provide their thoughts on this?

cheers
Dan



From dan.bolser at gmail.com  Tue Mar 29 08:57:29 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 29 Mar 2011 09:57:29 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
Message-ID: <AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>

On 28 March 2011 22:26, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Hi Dan,
> There are two problems that I can see. One is a series of compiler warnings
> when compiling the Perl .XS interface file. These are likely nothing to
> worry about, but I should fix them. What versions of Perl and gcc do you
> have installed? I don't see them when I compile on my system.

gcc --version # gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
perl --version # v5.8.8 built for i386-linux-thread-multi

uname -a # Linux cricket 2.6.18-194.32.1.el5PAE #1 SMP Wed Jan 5
18:43:13 EST 2011 i686 i686 i386 GNU/Linux



I got kent from git and built it with the following commands:

cd kent/src/lib/
echo $MACHTYPE # i686-redhat-linux-gnu
export MACHTYPE=i686
make
cd ../
export KENT_SRC=`pwd`

# NOTE, both $MACHTYPE and $KENT_SRC should be defined here
cpan -i Bio::DB::BigWig # FAILS AS DESCRIBED

cd /tmp
wget http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
tar zxfv Bio-BigFile-1.05.tar.gz
cd Bio-BigFile-1.05
# PATCH  Build.PL AS DESCRIBED (add -lssl after -lz)
perl Build.PL
./Build # SEE WARNINGS AS BEFORE
./Build test # Files=5, Tests=135, Result: PASS
./Build install


Note, above I didn't patch kent to include -fPIC as suggested
previously. I don't see any noticeable difference if I do on this
arch.

It would be good if the instructions above could make it into the
Bio::DB::BigWig README, as a few people have expressed confusion about
the exact steps (the README in kent is a bit confusing, and mostly
unnecessary for the purposes of building Bio::DB::BigWig).


> The second issue is that the SSL library is not being linked in. Previously
> there was no dependency on SSL, but Jim may recently have added this to the
> BigWig library in order to allow it to read bigwig files from https servers.
> I see that you added a -lssl to Build.PL; does this make the tests work
> again?

Yup, when I add -lssl to Build.PL (as per the previous diff), the
tests pass, but I still see the warnings.

I'm sure I saw the warnings disappear when I was playing with
different versions of Bio::DB::BigWig, but now they occur without
fail... if you pardon the pun.

I have a seeking suspicion that it's related to my perl 'build kit'...
However, since I'm not sure what module versions to report, and since
you promised to fix these issues anyway, I won't dig into it.


Thanks for help, and thanks for the support on
irc://irc.freenode.net/#bioperl, without which I would have probably
give up!

Cheers,
Dan.

> Lincoln
>
> On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com> wrote:
>>
>> Hello,
>>
>> I'm trying to get Bio::DB::BigWig installed again, this time on a
>> different box.
>>
>> I installed kent from git as described here:
>> http://genome.ucsc.edu/admin/git.html
>>
>>
>> I made the following changes, similar to those described previously:
>>
>> git diff
>> diff --git a/src/inc/common.mk b/src/inc/common.mk
>> index c7fc557..5187901 100644
>> --- a/src/inc/common.mk
>> +++ b/src/inc/common.mk
>> @@ -3,7 +3,7 @@ CC=gcc
>> ?ifeq (${COPT},)
>> ? ? COPT=-O -g
>> ?endif
>> -CFLAGS=
>> +CFLAGS=-fPIC
>> ?HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
>> -DMACHTYPE_${MACHTYPE}
>> ?HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
>> -I../../../../../inc
>>
>> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> index fa2292b..acb97d2 100644
>> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
>> ? ? /* Parse current line. */
>> ? ? wordCount = chopLine(line, row);
>> ? ? if (wordCount == ArraySize(row))
>> - ? ? ? ? errAbort("Too many fields (%d max is %lu) line %d of %s",
>> wordCount, ArraySize(row),
>> + ? ? ? ? errAbort("Too many fields (%d max is %u) line %d of %s",
>> wordCount, ArraySize(row),
>> ? ? ? ? ? ? lf->lineIx, lf->fileName);
>> ? ? char *chrom = row[0];
>> ? ? unsigned int start = lineFileNeedNum(lf, row, 1);
>>
>>
>> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
>> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
>> correctly after typing 'make' in kent/src (should I be building it
>> differently?)
>>
>>
>>
>> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>>
>> cpan
>>
>> cpan shell -- CPAN exploration and modules installation (v1.9600)
>> Enter 'h' for help.
>>
>> cpan[1]> install Bio::DB::BigWig
>> CPAN: Storable loaded ok (v2.25)
>> Going to read '/homes/dbolser/.cpan/Metadata'
>> ?Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
>> Running install for module 'Bio::DB::BigWig'
>> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
>> CPAN: Digest::SHA loaded ok (v5.61)
>> CPAN: Compress::Zlib loaded ok (v2.03)
>> Checksum for
>> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
>> ok
>> CPAN: Archive::Tar loaded ok (v1.76)
>> Bio-BigFile-1.05
>> Bio-BigFile-1.05/Changes
>> Bio-BigFile-1.05/LICENSE
>> Bio-BigFile-1.05/DISCLAIMER
>> Bio-BigFile-1.05/Build.PL
>> Bio-BigFile-1.05/typemap
>> Bio-BigFile-1.05/META.yml
>> Bio-BigFile-1.05/README
>> Bio-BigFile-1.05/MANIFEST
>> Bio-BigFile-1.05/ExampleData
>> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
>> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
>> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
>> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
>> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
>> Bio-BigFile-1.05/ExampleData/refSeqTest.as
>> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
>> Bio-BigFile-1.05/bin
>> Bio-BigFile-1.05/bin/bigWigToWig.pl
>> Bio-BigFile-1.05/bin/wigToBigWig.pl
>> Bio-BigFile-1.05/bin/index_bigwigset.pl
>> Bio-BigFile-1.05/lib
>> Bio-BigFile-1.05/lib/Bio
>> Bio-BigFile-1.05/lib/Bio/DB
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
>> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
>> Bio-BigFile-1.05/t
>> Bio-BigFile-1.05/t/02.bigbed.t
>> Bio-BigFile-1.05/t/03.bigwig_high.t
>> Bio-BigFile-1.05/t/04.bigbed_high.t
>> Bio-BigFile-1.05/t/05.bigwig_set.t
>> /bin/tar: Read 9216 bytes from -
>> Bio-BigFile-1.05/t/01.bigwig.t
>> Bio-BigFile-1.05/patches
>> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
>> CPAN: File::Temp loaded ok (v0.22)
>> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
>> CPAN: CPAN::Meta loaded ok (v2.110580)
>> CPAN: Module::CoreList loaded ok (v2.46)
>> CPAN: Time::HiRes loaded ok (v1.9717)
>>
>> ?CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>>
>>
>> This module requires the compiled jkweb.a library from Jim Kent's source
>> tree.
>> If you haven't already done so, please download the source from
>> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
>> contents of the "kent/src/lib" subdirectory as directed in the README.
>> Then
>> enter the location of the "kent/src" subdirectory at the prompt below.
>> To prevent
>> this message from appearing in the future, set the environment
>> variable KENT_SRC
>> to point to the "kent/src" subdirectory.
>>
>> Please enter the location of Kent source tree:
>> /homes/dbolser/build/src/kent/src
>>
>> Created MYMETA.yml and MYMETA.json
>> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
>> Building Bio-BigFile
>> gcc -I/homes/dbolser/build/src/kent/src/inc
>> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
>> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
>> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
>> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
>> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
>> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
>> lib/Bio/DB/BigFile.c
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
>> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
>> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
>> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
>> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
>> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
>> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
>> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
>> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
>> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
>>
>> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
>> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
>> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
>> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
>> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
>> ?LDS/Bio-BigFile-1.05.tar.gz
>> ?./Build -- OK
>> CPAN: YAML loaded ok (v0.72)
>> Running Build test
>> t/01.bigwig.t ....... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at t/01.bigwig.t line 28
>> Compilation failed in require at t/01.bigwig.t line 28.
>> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
>> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 29/29 subtests
>> t/02.bigbed.t ....... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at t/02.bigbed.t line 28
>> Compilation failed in require at t/02.bigbed.t line 28.
>> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
>> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 15/15 subtests
>> t/03.bigwig_high.t .. Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at t/03.bigwig_high.t line 28.
>> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
>> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 32/32 subtests
>> t/04.bigbed_high.t .. Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
>> line 7.
>> Compilation failed in require at t/04.bigbed_high.t line 28.
>> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
>> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 35/35 subtests
>> t/05.bigwig_set.t ... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
>> line 177.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
>> line 177.
>> Compilation failed in require at t/05.bigwig_set.t line 19.
>> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
>> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
>> No subtests run
>>
>> Test Summary Report
>> -------------------
>> t/01.bigwig.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 29 tests but ran 0.
>> t/02.bigbed.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 15 tests but ran 0.
>> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 32 tests but ran 0.
>> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 35 tests but ran 0.
>> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: No plan found in TAP output
>> Files=5, Tests=0, ?1 wallclock secs ( 0.04 usr ?0.01 sys + ?0.93 cusr
>> 0.11 csys = ?1.09 CPU)
>> Result: FAIL
>> Failed 5/5 test programs. 0/0 subtests failed.
>> ?LDS/Bio-BigFile-1.05.tar.gz
>> ?./Build test -- NOT OK
>> //hint// to see the cpan-testers results for installing this module, try:
>> ?reports LDS/Bio-BigFile-1.05.tar.gz
>> Running Build install
>> ?make test had returned bad status, won't install without force
>> Failed during this command:
>> ?LDS/Bio-BigFile-1.05.tar.gz ? ? ? ? ? ? ? ? ?: make_test NO
>>
>> cpan[2]>
>>
>>
>>
>>
>>
>>
>> Any hints?
>>
>> Cheers,
>> Dan.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
>



From dan.bolser at gmail.com  Tue Mar 29 08:57:29 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 29 Mar 2011 09:57:29 +0100
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
Message-ID: <AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>

On 28 March 2011 22:26, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Hi Dan,
> There are two problems that I can see. One is a series of compiler warnings
> when compiling the Perl .XS interface file. These are likely nothing to
> worry about, but I should fix them. What versions of Perl and gcc do you
> have installed? I don't see them when I compile on my system.

gcc --version # gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
perl --version # v5.8.8 built for i386-linux-thread-multi

uname -a # Linux cricket 2.6.18-194.32.1.el5PAE #1 SMP Wed Jan 5
18:43:13 EST 2011 i686 i686 i386 GNU/Linux



I got kent from git and built it with the following commands:

cd kent/src/lib/
echo $MACHTYPE # i686-redhat-linux-gnu
export MACHTYPE=i686
make
cd ../
export KENT_SRC=`pwd`

# NOTE, both $MACHTYPE and $KENT_SRC should be defined here
cpan -i Bio::DB::BigWig # FAILS AS DESCRIBED

cd /tmp
wget http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
tar zxfv Bio-BigFile-1.05.tar.gz
cd Bio-BigFile-1.05
# PATCH  Build.PL AS DESCRIBED (add -lssl after -lz)
perl Build.PL
./Build # SEE WARNINGS AS BEFORE
./Build test # Files=5, Tests=135, Result: PASS
./Build install


Note, above I didn't patch kent to include -fPIC as suggested
previously. I don't see any noticeable difference if I do on this
arch.

It would be good if the instructions above could make it into the
Bio::DB::BigWig README, as a few people have expressed confusion about
the exact steps (the README in kent is a bit confusing, and mostly
unnecessary for the purposes of building Bio::DB::BigWig).


> The second issue is that the SSL library is not being linked in. Previously
> there was no dependency on SSL, but Jim may recently have added this to the
> BigWig library in order to allow it to read bigwig files from https servers.
> I see that you added a -lssl to Build.PL; does this make the tests work
> again?

Yup, when I add -lssl to Build.PL (as per the previous diff), the
tests pass, but I still see the warnings.

I'm sure I saw the warnings disappear when I was playing with
different versions of Bio::DB::BigWig, but now they occur without
fail... if you pardon the pun.

I have a seeking suspicion that it's related to my perl 'build kit'...
However, since I'm not sure what module versions to report, and since
you promised to fix these issues anyway, I won't dig into it.


Thanks for help, and thanks for the support on
irc://irc.freenode.net/#bioperl, without which I would have probably
give up!

Cheers,
Dan.

> Lincoln
>
> On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com> wrote:
>>
>> Hello,
>>
>> I'm trying to get Bio::DB::BigWig installed again, this time on a
>> different box.
>>
>> I installed kent from git as described here:
>> http://genome.ucsc.edu/admin/git.html
>>
>>
>> I made the following changes, similar to those described previously:
>>
>> git diff
>> diff --git a/src/inc/common.mk b/src/inc/common.mk
>> index c7fc557..5187901 100644
>> --- a/src/inc/common.mk
>> +++ b/src/inc/common.mk
>> @@ -3,7 +3,7 @@ CC=gcc
>> ?ifeq (${COPT},)
>> ? ? COPT=-O -g
>> ?endif
>> -CFLAGS=
>> +CFLAGS=-fPIC
>> ?HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
>> -DMACHTYPE_${MACHTYPE}
>> ?HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
>> -I../../../../../inc
>>
>> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> index fa2292b..acb97d2 100644
>> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
>> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
>> ? ? /* Parse current line. */
>> ? ? wordCount = chopLine(line, row);
>> ? ? if (wordCount == ArraySize(row))
>> - ? ? ? ? errAbort("Too many fields (%d max is %lu) line %d of %s",
>> wordCount, ArraySize(row),
>> + ? ? ? ? errAbort("Too many fields (%d max is %u) line %d of %s",
>> wordCount, ArraySize(row),
>> ? ? ? ? ? ? lf->lineIx, lf->fileName);
>> ? ? char *chrom = row[0];
>> ? ? unsigned int start = lineFileNeedNum(lf, row, 1);
>>
>>
>> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
>> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
>> correctly after typing 'make' in kent/src (should I be building it
>> differently?)
>>
>>
>>
>> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>>
>> cpan
>>
>> cpan shell -- CPAN exploration and modules installation (v1.9600)
>> Enter 'h' for help.
>>
>> cpan[1]> install Bio::DB::BigWig
>> CPAN: Storable loaded ok (v2.25)
>> Going to read '/homes/dbolser/.cpan/Metadata'
>> ?Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
>> Running install for module 'Bio::DB::BigWig'
>> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
>> CPAN: Digest::SHA loaded ok (v5.61)
>> CPAN: Compress::Zlib loaded ok (v2.03)
>> Checksum for
>> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
>> ok
>> CPAN: Archive::Tar loaded ok (v1.76)
>> Bio-BigFile-1.05
>> Bio-BigFile-1.05/Changes
>> Bio-BigFile-1.05/LICENSE
>> Bio-BigFile-1.05/DISCLAIMER
>> Bio-BigFile-1.05/Build.PL
>> Bio-BigFile-1.05/typemap
>> Bio-BigFile-1.05/META.yml
>> Bio-BigFile-1.05/README
>> Bio-BigFile-1.05/MANIFEST
>> Bio-BigFile-1.05/ExampleData
>> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
>> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
>> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
>> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
>> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
>> Bio-BigFile-1.05/ExampleData/refSeqTest.as
>> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
>> Bio-BigFile-1.05/bin
>> Bio-BigFile-1.05/bin/bigWigToWig.pl
>> Bio-BigFile-1.05/bin/wigToBigWig.pl
>> Bio-BigFile-1.05/bin/index_bigwigset.pl
>> Bio-BigFile-1.05/lib
>> Bio-BigFile-1.05/lib/Bio
>> Bio-BigFile-1.05/lib/Bio/DB
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
>> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
>> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
>> Bio-BigFile-1.05/t
>> Bio-BigFile-1.05/t/02.bigbed.t
>> Bio-BigFile-1.05/t/03.bigwig_high.t
>> Bio-BigFile-1.05/t/04.bigbed_high.t
>> Bio-BigFile-1.05/t/05.bigwig_set.t
>> /bin/tar: Read 9216 bytes from -
>> Bio-BigFile-1.05/t/01.bigwig.t
>> Bio-BigFile-1.05/patches
>> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
>> CPAN: File::Temp loaded ok (v0.22)
>> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
>> CPAN: CPAN::Meta loaded ok (v2.110580)
>> CPAN: Module::CoreList loaded ok (v2.46)
>> CPAN: Time::HiRes loaded ok (v1.9717)
>>
>> ?CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>>
>>
>> This module requires the compiled jkweb.a library from Jim Kent's source
>> tree.
>> If you haven't already done so, please download the source from
>> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
>> contents of the "kent/src/lib" subdirectory as directed in the README.
>> Then
>> enter the location of the "kent/src" subdirectory at the prompt below.
>> To prevent
>> this message from appearing in the future, set the environment
>> variable KENT_SRC
>> to point to the "kent/src" subdirectory.
>>
>> Please enter the location of Kent source tree:
>> /homes/dbolser/build/src/kent/src
>>
>> Created MYMETA.yml and MYMETA.json
>> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
>> Building Bio-BigFile
>> gcc -I/homes/dbolser/build/src/kent/src/inc
>> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
>> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
>> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
>> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
>> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
>> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
>> lib/Bio/DB/BigFile.c
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
>> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
>> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
>> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be undefined
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
>> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
>> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
>> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
>> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be
>> undefined
>> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
>> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
>> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be undefined
>> lib/Bio/DB/BigFile.xs: In function
>> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
>> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
>>
>> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
>> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
>> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
>> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
>> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
>> ?LDS/Bio-BigFile-1.05.tar.gz
>> ?./Build -- OK
>> CPAN: YAML loaded ok (v0.72)
>> Running Build test
>> t/01.bigwig.t ....... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at t/01.bigwig.t line 28
>> Compilation failed in require at t/01.bigwig.t line 28.
>> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
>> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 29/29 subtests
>> t/02.bigbed.t ....... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at t/02.bigbed.t line 28
>> Compilation failed in require at t/02.bigbed.t line 28.
>> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
>> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 15/15 subtests
>> t/03.bigwig_high.t .. Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at t/03.bigwig_high.t line 28.
>> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
>> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 32/32 subtests
>> t/04.bigbed_high.t .. Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
>> line 7.
>> Compilation failed in require at t/04.bigbed_high.t line 28.
>> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
>> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 35/35 subtests
>> t/05.bigwig_set.t ... Can't load
>>
>> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
>> for module Bio::DB::BigFile:
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
>> undefined symbol: SSL_library_init at
>> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>> ?at
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
>> line 7.
>> Compilation failed in require at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
>> line 177.
>> BEGIN failed--compilation aborted at
>>
>> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
>> line 177.
>> Compilation failed in require at t/05.bigwig_set.t line 19.
>> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
>> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
>> No subtests run
>>
>> Test Summary Report
>> -------------------
>> t/01.bigwig.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 29 tests but ran 0.
>> t/02.bigbed.t ? ? (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 15 tests but ran 0.
>> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 32 tests but ran 0.
>> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: Bad plan. ?You planned 35 tests but ran 0.
>> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
>> ?Non-zero exit status: 2
>> ?Parse errors: No plan found in TAP output
>> Files=5, Tests=0, ?1 wallclock secs ( 0.04 usr ?0.01 sys + ?0.93 cusr
>> 0.11 csys = ?1.09 CPU)
>> Result: FAIL
>> Failed 5/5 test programs. 0/0 subtests failed.
>> ?LDS/Bio-BigFile-1.05.tar.gz
>> ?./Build test -- NOT OK
>> //hint// to see the cpan-testers results for installing this module, try:
>> ?reports LDS/Bio-BigFile-1.05.tar.gz
>> Running Build install
>> ?make test had returned bad status, won't install without force
>> Failed during this command:
>> ?LDS/Bio-BigFile-1.05.tar.gz ? ? ? ? ? ? ? ? ?: make_test NO
>>
>> cpan[2]>
>>
>>
>>
>>
>>
>>
>> Any hints?
>>
>> Cheers,
>> Dan.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
>



From David.Messina at sbc.su.se  Tue Mar 29 09:11:26 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 29 Mar 2011 11:11:26 +0200
Subject: [Bioperl-l] GSoC 2011
In-Reply-To: <AANLkTim6o3bJ6NkBRmoUC5e76GaGzpjP5+xE+ZrWcEdc@mail.gmail.com>
References: <AANLkTim6o3bJ6NkBRmoUC5e76GaGzpjP5+xE+ZrWcEdc@mail.gmail.com>
Message-ID: <AANLkTi=OW4OYGwB1AWRe4TXZTXyLuENxZakArcVoAjHF@mail.gmail.com>

Hi Fei,

Glad to hear you're interested in working on BioPerl!

Just to throw in my two cents, I think it would be great to have a RAxML
wrapper in BioPerl. Although actually any of the projects you mentioned
sound like they're about the right size for a summer project.

I'm not directly involved with GSoC, so I think if you haven't already you
should take a look at our GsOC page here

    http://news.open-bio.org/news/2011/03/obf-gsoc-2011/

and get in touch with Rob Buels, our coordinator (rmb32 at cornell.edu)



Best,
Dave





On Tue, Mar 22, 2011 at 20:14, Fei Hu <hufeiyc at gmail.com> wrote:

> Hi, All.
>
> My name is Fei Hu from U. of South Carolina. I am currently a second-year
> Ph.D student in computer science focusing on gene order and sequence(DNA &
> AA) phylogeny as well as whole genome alignment. I am instreseted in
> joining
> bioperl project of GSoC 2011. I have two ideas that would like to share.
>
> My first idea is to extend the bioperl so that it can process and analysis
> gene order data using published package such as MGR, GRAPPA and distance
> estimator. This is a relatively new type of data and many great researchers
> have contributed to this type of phylogeny reconstruction (Dr. Pavel
> Penzer,
> Dr. Bernard Moret and Dr. David Sankoff).
>
> Secondly as maximum likelihood becomes more and more popular, especially
> RAxML has been widely recognized and used(over 1000 citations). I think
> it's
> time to integrate that as well as GARLI into the Bio::Tools. I extensively
> used and explored RAxML in my last publication on gene order phylogeny.
>
> Those are just my preliminary thoughts, not even a plan and any suggestion
> is greatly appreciated!!! I use perl on daily bases for data processing and
> composing testing scripts, but not much OOP involved.
>
> PS: Rest api for CIPRES is no longer available. So this following task
> can't
> be finished right now:
> Development of a
> Bio::Tools::Run::RemoteBlast<
> http://bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast>-like
> interface to CIPRES remote analyses; for more see this
> thread<http://thread.gmane.org/gmane.comp.lang.perl.bio.general/16524>
> .
>
> And Thank you all.
> Best
>
> Fei
>
> --
> *Fei Hu
> Bioinformatics Lab
> 3D-11 Swearingen Building
> U of South Carolina
> Tel: 803-397-5240*
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From tzhu at mail.bnu.edu.cn  Tue Mar 29 10:33:59 2011
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Tue, 29 Mar 2011 18:33:59 +0800
Subject: [Bioperl-l] How to use module Bio::SeqFeature::Gene::GeneStructure?
Message-ID: <1301394839.6397.1.camel@ubuntu>

I've referred the ducument
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
It says, @transcripts = $gene->transcripts(); @exons = $gene->exons();
The object $gene should mean a Bio::SeqFeature::Gene::GeneStructure
object. But how could I get such object? I hope to see a good example.
Thank you! 


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)




From lincoln.stein at gmail.com  Tue Mar 29 13:59:22 2011
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Tue, 29 Mar 2011 09:59:22 -0400
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
	<AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>
Message-ID: <AANLkTi=Jrw3adAgigbAeG_-KT4VqLBsPBE08x_NQyOHD@mail.gmail.com>

I'll release a new version with a fixed Build.PL and README today.

Lincoln

On Tue, Mar 29, 2011 at 4:57 AM, Dan Bolser <dan.bolser at gmail.com> wrote:

> On 28 March 2011 22:26, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> > Hi Dan,
> > There are two problems that I can see. One is a series of compiler
> warnings
> > when compiling the Perl .XS interface file. These are likely nothing to
> > worry about, but I should fix them. What versions of Perl and gcc do you
> > have installed? I don't see them when I compile on my system.
>
> gcc --version # gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
> perl --version # v5.8.8 built for i386-linux-thread-multi
>
> uname -a # Linux cricket 2.6.18-194.32.1.el5PAE #1 SMP Wed Jan 5
> 18:43:13 EST 2011 i686 i686 i386 GNU/Linux
>
>
>
> I got kent from git and built it with the following commands:
>
> cd kent/src/lib/
> echo $MACHTYPE # i686-redhat-linux-gnu
> export MACHTYPE=i686
> make
> cd ../
> export KENT_SRC=`pwd`
>
> # NOTE, both $MACHTYPE and $KENT_SRC should be defined here
> cpan -i Bio::DB::BigWig # FAILS AS DESCRIBED
>
> cd /tmp
> wget
> http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> tar zxfv Bio-BigFile-1.05.tar.gz
> cd Bio-BigFile-1.05
> # PATCH  Build.PL AS DESCRIBED (add -lssl after -lz)
> perl Build.PL
> ./Build # SEE WARNINGS AS BEFORE
> ./Build test # Files=5, Tests=135, Result: PASS
> ./Build install
>
>
> Note, above I didn't patch kent to include -fPIC as suggested
> previously. I don't see any noticeable difference if I do on this
> arch.
>
> It would be good if the instructions above could make it into the
> Bio::DB::BigWig README, as a few people have expressed confusion about
> the exact steps (the README in kent is a bit confusing, and mostly
> unnecessary for the purposes of building Bio::DB::BigWig).
>
>
> > The second issue is that the SSL library is not being linked in.
> Previously
> > there was no dependency on SSL, but Jim may recently have added this to
> the
> > BigWig library in order to allow it to read bigwig files from https
> servers.
> > I see that you added a -lssl to Build.PL; does this make the tests work
> > again?
>
> Yup, when I add -lssl to Build.PL (as per the previous diff), the
> tests pass, but I still see the warnings.
>
> I'm sure I saw the warnings disappear when I was playing with
> different versions of Bio::DB::BigWig, but now they occur without
> fail... if you pardon the pun.
>
> I have a seeking suspicion that it's related to my perl 'build kit'...
> However, since I'm not sure what module versions to report, and since
> you promised to fix these issues anyway, I won't dig into it.
>
>
> Thanks for help, and thanks for the support on
> irc://irc.freenode.net/#bioperl, without which I would have probably
> give up!
>
> Cheers,
> Dan.
>
> > Lincoln
> >
> > On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com>
> wrote:
> >>
> >> Hello,
> >>
> >> I'm trying to get Bio::DB::BigWig installed again, this time on a
> >> different box.
> >>
> >> I installed kent from git as described here:
> >> http://genome.ucsc.edu/admin/git.html
> >>
> >>
> >> I made the following changes, similar to those described previously:
> >>
> >> git diff
> >> diff --git a/src/inc/common.mk b/src/inc/common.mk
> >> index c7fc557..5187901 100644
> >> --- a/src/inc/common.mk
> >> +++ b/src/inc/common.mk
> >> @@ -3,7 +3,7 @@ CC=gcc
> >>  ifeq (${COPT},)
> >>     COPT=-O -g
> >>  endif
> >> -CFLAGS=
> >> +CFLAGS=-fPIC
> >>  HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> >> -DMACHTYPE_${MACHTYPE}
> >>  HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> >> -I../../../../../inc
> >>
> >> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> index fa2292b..acb97d2 100644
> >> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
> >>     /* Parse current line. */
> >>     wordCount = chopLine(line, row);
> >>     if (wordCount == ArraySize(row))
> >> -         errAbort("Too many fields (%d max is %lu) line %d of %s",
> >> wordCount, ArraySize(row),
> >> +         errAbort("Too many fields (%d max is %u) line %d of %s",
> >> wordCount, ArraySize(row),
> >>             lf->lineIx, lf->fileName);
> >>     char *chrom = row[0];
> >>     unsigned int start = lineFileNeedNum(lf, row, 1);
> >>
> >>
> >> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> >> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> >> correctly after typing 'make' in kent/src (should I be building it
> >> differently?)
> >>
> >>
> >>
> >> Now when I try to install Bio::DB::BigWig via cpan, things look like
> this:
> >>
> >> cpan
> >>
> >> cpan shell -- CPAN exploration and modules installation (v1.9600)
> >> Enter 'h' for help.
> >>
> >> cpan[1]> install Bio::DB::BigWig
> >> CPAN: Storable loaded ok (v2.25)
> >> Going to read '/homes/dbolser/.cpan/Metadata'
> >>  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> >> Running install for module 'Bio::DB::BigWig'
> >> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >> CPAN: Digest::SHA loaded ok (v5.61)
> >> CPAN: Compress::Zlib loaded ok (v2.03)
> >> Checksum for
> >> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >> ok
> >> CPAN: Archive::Tar loaded ok (v1.76)
> >> Bio-BigFile-1.05
> >> Bio-BigFile-1.05/Changes
> >> Bio-BigFile-1.05/LICENSE
> >> Bio-BigFile-1.05/DISCLAIMER
> >> Bio-BigFile-1.05/Build.PL
> >> Bio-BigFile-1.05/typemap
> >> Bio-BigFile-1.05/META.yml
> >> Bio-BigFile-1.05/README
> >> Bio-BigFile-1.05/MANIFEST
> >> Bio-BigFile-1.05/ExampleData
> >> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> >> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> >> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> >> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> >> Bio-BigFile-1.05/bin
> >> Bio-BigFile-1.05/bin/bigWigToWig.pl
> >> Bio-BigFile-1.05/bin/wigToBigWig.pl
> >> Bio-BigFile-1.05/bin/index_bigwigset.pl
> >> Bio-BigFile-1.05/lib
> >> Bio-BigFile-1.05/lib/Bio
> >> Bio-BigFile-1.05/lib/Bio/DB
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> >> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> >> Bio-BigFile-1.05/t
> >> Bio-BigFile-1.05/t/02.bigbed.t
> >> Bio-BigFile-1.05/t/03.bigwig_high.t
> >> Bio-BigFile-1.05/t/04.bigbed_high.t
> >> Bio-BigFile-1.05/t/05.bigwig_set.t
> >> /bin/tar: Read 9216 bytes from -
> >> Bio-BigFile-1.05/t/01.bigwig.t
> >> Bio-BigFile-1.05/patches
> >> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> >> CPAN: File::Temp loaded ok (v0.22)
> >> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> >> CPAN: CPAN::Meta loaded ok (v2.110580)
> >> CPAN: Module::CoreList loaded ok (v2.46)
> >> CPAN: Time::HiRes loaded ok (v1.9717)
> >>
> >>  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >>
> >>
> >> This module requires the compiled jkweb.a library from Jim Kent's source
> >> tree.
> >> If you haven't already done so, please download the source from
> >> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build
> the
> >> contents of the "kent/src/lib" subdirectory as directed in the README.
> >> Then
> >> enter the location of the "kent/src" subdirectory at the prompt below.
> >> To prevent
> >> this message from appearing in the future, set the environment
> >> variable KENT_SRC
> >> to point to the "kent/src" subdirectory.
> >>
> >> Please enter the location of Kent source tree:
> >> /homes/dbolser/build/src/kent/src
> >>
> >> Created MYMETA.yml and MYMETA.json
> >> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> >> Building Bio-BigFile
> >> gcc -I/homes/dbolser/build/src/kent/src/inc
> >> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> >> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> >> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> >> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> >> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> >> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> >> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> >> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> >> lib/Bio/DB/BigFile.c
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> >> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> >> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> >> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> >> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> >> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> >> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> >> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> >> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> >> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
> >>
> >>
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> >> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> >> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> >> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> >> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> >> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
> >>  LDS/Bio-BigFile-1.05.tar.gz
> >>  ./Build -- OK
> >> CPAN: YAML loaded ok (v0.72)
> >> Running Build test
> >> t/01.bigwig.t ....... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at t/01.bigwig.t line 28
> >> Compilation failed in require at t/01.bigwig.t line 28.
> >> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> >> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 29/29 subtests
> >> t/02.bigbed.t ....... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at t/02.bigbed.t line 28
> >> Compilation failed in require at t/02.bigbed.t line 28.
> >> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> >> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 15/15 subtests
> >> t/03.bigwig_high.t .. Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at t/03.bigwig_high.t line 28.
> >> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> >> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 32/32 subtests
> >> t/04.bigbed_high.t .. Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> >> line 7.
> >> Compilation failed in require at t/04.bigbed_high.t line 28.
> >> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> >> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 35/35 subtests
> >> t/05.bigwig_set.t ... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> >> line 177.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> >> line 177.
> >> Compilation failed in require at t/05.bigwig_set.t line 19.
> >> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> >> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> >> No subtests run
> >>
> >> Test Summary Report
> >> -------------------
> >> t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 29 tests but ran 0.
> >> t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> >> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 32 tests but ran 0.
> >> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 35 tests but ran 0.
> >> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: No plan found in TAP output
> >> Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
> >> 0.11 csys =  1.09 CPU)
> >> Result: FAIL
> >> Failed 5/5 test programs. 0/0 subtests failed.
> >>  LDS/Bio-BigFile-1.05.tar.gz
> >>  ./Build test -- NOT OK
> >> //hint// to see the cpan-testers results for installing this module,
> try:
> >>  reports LDS/Bio-BigFile-1.05.tar.gz
> >> Running Build install
> >>  make test had returned bad status, won't install without force
> >> Failed during this command:
> >>  LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO
> >>
> >> cpan[2]>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Any hints?
> >>
> >> Cheers,
> >> Dan.
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
> > --
> > Lincoln D. Stein
> > Director, Informatics and Biocomputing Platform
> > Ontario Institute for Cancer Research
> > 101 College St., Suite 800
> > Toronto, ON, Canada M5G0A3
> > 416 673-8514
> > Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> >
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>



From lincoln.stein at gmail.com  Tue Mar 29 13:59:22 2011
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Tue, 29 Mar 2011 09:59:22 -0400
Subject: [Bioperl-l] install Bio::DB::BigWig ?
In-Reply-To: <AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>
References: <AANLkTik109gYJ6RZRLws_1ES8Raf4LmHtFwtkFYwNbUa@mail.gmail.com>
	<AANLkTinA7jJuiapxkVCg7itzKQQHraKy93H8pK1wOY77@mail.gmail.com>
	<AANLkTi=WfgzirLhMUGac7fhurrFpjmjEQASysq1b_9F3@mail.gmail.com>
Message-ID: <AANLkTi=Jrw3adAgigbAeG_-KT4VqLBsPBE08x_NQyOHD@mail.gmail.com>

I'll release a new version with a fixed Build.PL and README today.

Lincoln

On Tue, Mar 29, 2011 at 4:57 AM, Dan Bolser <dan.bolser at gmail.com> wrote:

> On 28 March 2011 22:26, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> > Hi Dan,
> > There are two problems that I can see. One is a series of compiler
> warnings
> > when compiling the Perl .XS interface file. These are likely nothing to
> > worry about, but I should fix them. What versions of Perl and gcc do you
> > have installed? I don't see them when I compile on my system.
>
> gcc --version # gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
> perl --version # v5.8.8 built for i386-linux-thread-multi
>
> uname -a # Linux cricket 2.6.18-194.32.1.el5PAE #1 SMP Wed Jan 5
> 18:43:13 EST 2011 i686 i686 i386 GNU/Linux
>
>
>
> I got kent from git and built it with the following commands:
>
> cd kent/src/lib/
> echo $MACHTYPE # i686-redhat-linux-gnu
> export MACHTYPE=i686
> make
> cd ../
> export KENT_SRC=`pwd`
>
> # NOTE, both $MACHTYPE and $KENT_SRC should be defined here
> cpan -i Bio::DB::BigWig # FAILS AS DESCRIBED
>
> cd /tmp
> wget
> http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> tar zxfv Bio-BigFile-1.05.tar.gz
> cd Bio-BigFile-1.05
> # PATCH  Build.PL AS DESCRIBED (add -lssl after -lz)
> perl Build.PL
> ./Build # SEE WARNINGS AS BEFORE
> ./Build test # Files=5, Tests=135, Result: PASS
> ./Build install
>
>
> Note, above I didn't patch kent to include -fPIC as suggested
> previously. I don't see any noticeable difference if I do on this
> arch.
>
> It would be good if the instructions above could make it into the
> Bio::DB::BigWig README, as a few people have expressed confusion about
> the exact steps (the README in kent is a bit confusing, and mostly
> unnecessary for the purposes of building Bio::DB::BigWig).
>
>
> > The second issue is that the SSL library is not being linked in.
> Previously
> > there was no dependency on SSL, but Jim may recently have added this to
> the
> > BigWig library in order to allow it to read bigwig files from https
> servers.
> > I see that you added a -lssl to Build.PL; does this make the tests work
> > again?
>
> Yup, when I add -lssl to Build.PL (as per the previous diff), the
> tests pass, but I still see the warnings.
>
> I'm sure I saw the warnings disappear when I was playing with
> different versions of Bio::DB::BigWig, but now they occur without
> fail... if you pardon the pun.
>
> I have a seeking suspicion that it's related to my perl 'build kit'...
> However, since I'm not sure what module versions to report, and since
> you promised to fix these issues anyway, I won't dig into it.
>
>
> Thanks for help, and thanks for the support on
> irc://irc.freenode.net/#bioperl, without which I would have probably
> give up!
>
> Cheers,
> Dan.
>
> > Lincoln
> >
> > On Sun, Mar 27, 2011 at 2:00 PM, Dan Bolser <dan.bolser at gmail.com>
> wrote:
> >>
> >> Hello,
> >>
> >> I'm trying to get Bio::DB::BigWig installed again, this time on a
> >> different box.
> >>
> >> I installed kent from git as described here:
> >> http://genome.ucsc.edu/admin/git.html
> >>
> >>
> >> I made the following changes, similar to those described previously:
> >>
> >> git diff
> >> diff --git a/src/inc/common.mk b/src/inc/common.mk
> >> index c7fc557..5187901 100644
> >> --- a/src/inc/common.mk
> >> +++ b/src/inc/common.mk
> >> @@ -3,7 +3,7 @@ CC=gcc
> >>  ifeq (${COPT},)
> >>     COPT=-O -g
> >>  endif
> >> -CFLAGS=
> >> +CFLAGS=-fPIC
> >>  HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> >> -DMACHTYPE_${MACHTYPE}
> >>  HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> >> -I../../../../../inc
> >>
> >> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> index fa2292b..acb97d2 100644
> >> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> >> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
> >>     /* Parse current line. */
> >>     wordCount = chopLine(line, row);
> >>     if (wordCount == ArraySize(row))
> >> -         errAbort("Too many fields (%d max is %lu) line %d of %s",
> >> wordCount, ArraySize(row),
> >> +         errAbort("Too many fields (%d max is %u) line %d of %s",
> >> wordCount, ArraySize(row),
> >>             lf->lineIx, lf->fileName);
> >>     char *chrom = row[0];
> >>     unsigned int start = lineFileNeedNum(lf, row, 1);
> >>
> >>
> >> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> >> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> >> correctly after typing 'make' in kent/src (should I be building it
> >> differently?)
> >>
> >>
> >>
> >> Now when I try to install Bio::DB::BigWig via cpan, things look like
> this:
> >>
> >> cpan
> >>
> >> cpan shell -- CPAN exploration and modules installation (v1.9600)
> >> Enter 'h' for help.
> >>
> >> cpan[1]> install Bio::DB::BigWig
> >> CPAN: Storable loaded ok (v2.25)
> >> Going to read '/homes/dbolser/.cpan/Metadata'
> >>  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> >> Running install for module 'Bio::DB::BigWig'
> >> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >> CPAN: Digest::SHA loaded ok (v5.61)
> >> CPAN: Compress::Zlib loaded ok (v2.03)
> >> Checksum for
> >> /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >> ok
> >> CPAN: Archive::Tar loaded ok (v1.76)
> >> Bio-BigFile-1.05
> >> Bio-BigFile-1.05/Changes
> >> Bio-BigFile-1.05/LICENSE
> >> Bio-BigFile-1.05/DISCLAIMER
> >> Bio-BigFile-1.05/Build.PL
> >> Bio-BigFile-1.05/typemap
> >> Bio-BigFile-1.05/META.yml
> >> Bio-BigFile-1.05/README
> >> Bio-BigFile-1.05/MANIFEST
> >> Bio-BigFile-1.05/ExampleData
> >> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> >> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> >> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> >> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> >> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> >> Bio-BigFile-1.05/bin
> >> Bio-BigFile-1.05/bin/bigWigToWig.pl
> >> Bio-BigFile-1.05/bin/wigToBigWig.pl
> >> Bio-BigFile-1.05/bin/index_bigwigset.pl
> >> Bio-BigFile-1.05/lib
> >> Bio-BigFile-1.05/lib/Bio
> >> Bio-BigFile-1.05/lib/Bio/DB
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> >> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> >> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> >> Bio-BigFile-1.05/t
> >> Bio-BigFile-1.05/t/02.bigbed.t
> >> Bio-BigFile-1.05/t/03.bigwig_high.t
> >> Bio-BigFile-1.05/t/04.bigbed_high.t
> >> Bio-BigFile-1.05/t/05.bigwig_set.t
> >> /bin/tar: Read 9216 bytes from -
> >> Bio-BigFile-1.05/t/01.bigwig.t
> >> Bio-BigFile-1.05/patches
> >> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> >> CPAN: File::Temp loaded ok (v0.22)
> >> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> >> CPAN: CPAN::Meta loaded ok (v2.110580)
> >> CPAN: Module::CoreList loaded ok (v2.46)
> >> CPAN: Time::HiRes loaded ok (v1.9717)
> >>
> >>  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
> >>
> >>
> >> This module requires the compiled jkweb.a library from Jim Kent's source
> >> tree.
> >> If you haven't already done so, please download the source from
> >> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build
> the
> >> contents of the "kent/src/lib" subdirectory as directed in the README.
> >> Then
> >> enter the location of the "kent/src" subdirectory at the prompt below.
> >> To prevent
> >> this message from appearing in the future, set the environment
> >> variable KENT_SRC
> >> to point to the "kent/src" subdirectory.
> >>
> >> Please enter the location of Kent source tree:
> >> /homes/dbolser/build/src/kent/src
> >>
> >> Created MYMETA.yml and MYMETA.json
> >> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> >> Building Bio-BigFile
> >> gcc -I/homes/dbolser/build/src/kent/src/inc
> >> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> >> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> >> -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> >> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> >> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> >> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> >> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> >> -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o
> >> lib/Bio/DB/BigFile.c
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigIntervalQuery?:
> >> lib/Bio/DB/BigFile.xs:172: warning: operation on ?list? may be undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigSummaryArray?:
> >> lib/Bio/DB/BigFile.xs:193: warning: operation on ?values? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedSummaryArray?:
> >> lib/Bio/DB/BigFile.xs:252: warning: operation on ?values? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigWigSummary?:
> >> lib/Bio/DB/BigFile.xs:296: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:302: warning: operation on ?summaryList? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:290: warning: unused variable ?i?
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_bigBedSummary?:
> >> lib/Bio/DB/BigFile.xs:326: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:332: warning: operation on ?summaryList? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:320: warning: unused variable ?i?
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended?:
> >> lib/Bio/DB/BigFile.xs:358: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:354: warning: unused variable ?summaryList?
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended?:
> >> lib/Bio/DB/BigFile.xs:395: warning: operation on ?summary? may be
> >> undefined
> >> lib/Bio/DB/BigFile.xs:391: warning: unused variable ?summaryList?
> >> lib/Bio/DB/BigFile.xs: In function ?XS_Bio__DB__bbiFile_chromList?:
> >> lib/Bio/DB/BigFile.xs:424: warning: operation on ?RETVAL? may be
> undefined
> >> lib/Bio/DB/BigFile.xs: In function
> >> ?XS_Bio__DB__bbiFile_bigBedIntervalQuery?:
> >> lib/Bio/DB/BigFile.xs:450: warning: operation on ?list? may be undefined
> >>
> >>
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> >> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> >> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
> >> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o
> >> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> >> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
> >>  LDS/Bio-BigFile-1.05.tar.gz
> >>  ./Build -- OK
> >> CPAN: YAML loaded ok (v0.72)
> >> Running Build test
> >> t/01.bigwig.t ....... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at t/01.bigwig.t line 28
> >> Compilation failed in require at t/01.bigwig.t line 28.
> >> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> >> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 29/29 subtests
> >> t/02.bigbed.t ....... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at t/02.bigbed.t line 28
> >> Compilation failed in require at t/02.bigbed.t line 28.
> >> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> >> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 15/15 subtests
> >> t/03.bigwig_high.t .. Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at t/03.bigwig_high.t line 28.
> >> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> >> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 32/32 subtests
> >> t/04.bigbed_high.t .. Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> >> line 7.
> >> Compilation failed in require at t/04.bigbed_high.t line 28.
> >> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> >> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> >> Failed 35/35 subtests
> >> t/05.bigwig_set.t ... Can't load
> >>
> >>
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> >> for module Bio::DB::BigFile:
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> >> undefined symbol: SSL_library_init at
> >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
> >>  at
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> >> line 7.
> >> Compilation failed in require at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> >> line 177.
> >> BEGIN failed--compilation aborted at
> >>
> >>
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> >> line 177.
> >> Compilation failed in require at t/05.bigwig_set.t line 19.
> >> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> >> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> >> No subtests run
> >>
> >> Test Summary Report
> >> -------------------
> >> t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 29 tests but ran 0.
> >> t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> >> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 32 tests but ran 0.
> >> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: Bad plan.  You planned 35 tests but ran 0.
> >> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
> >>  Non-zero exit status: 2
> >>  Parse errors: No plan found in TAP output
> >> Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
> >> 0.11 csys =  1.09 CPU)
> >> Result: FAIL
> >> Failed 5/5 test programs. 0/0 subtests failed.
> >>  LDS/Bio-BigFile-1.05.tar.gz
> >>  ./Build test -- NOT OK
> >> //hint// to see the cpan-testers results for installing this module,
> try:
> >>  reports LDS/Bio-BigFile-1.05.tar.gz
> >> Running Build install
> >>  make test had returned bad status, won't install without force
> >> Failed during this command:
> >>  LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO
> >>
> >> cpan[2]>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Any hints?
> >>
> >> Cheers,
> >> Dan.
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
> > --
> > Lincoln D. Stein
> > Director, Informatics and Biocomputing Platform
> > Ontario Institute for Cancer Research
> > 101 College St., Suite 800
> > Toronto, ON, Canada M5G0A3
> > 416 673-8514
> > Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> >
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>



From ravimbt at gmail.com  Mon Mar 28 09:56:58 2011
From: ravimbt at gmail.com (=?UTF-8?B?wrbigKLil4/guYvigKLgrofgrrDgrrXgrr/Rj86xzr3OueKXj+C5i+KAouKAosK2?=)
Date: Mon, 28 Mar 2011 15:26:58 +0530
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
Message-ID: <AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>

Hi Dave,

Thank you very much. It is working. I got the program code from the
following link.

http://www.bioperl.org/Core/Latest/bptutorial.html

I spent so much time on browsing, downloading and installing programs and
packages. But, it seems like the code error is the reason it dint work.
Thanks Dave.

Could you please give me the link to join this forum to see other
discussions, which would be more helpful to me? Please let me know if you
have any suggestion for me to keep learning the bioperl.

With regards,
Ravi.

2011/3/28 Dave Messina <David.Messina at sbc.su.se>

> Hi Ravi,
>
> Please make sure to "Reply All" so that everyone on the mailing list can
> follow (and add to) the discussion.
>
> If you read the first line of the exception, you'll see it states what the
> error is:
> "WebDBSeqI Error ? check query sequences!"
>
> You'd have no way of knowing this, but that ID and database combination is
> not functioning anymore, so that's why in this case you're getting an error.
> Please try using the example in the tutorial here:
>
>
> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>
> which has been updated to a different ID which should work.
>
> Sorry for the confusion! So that we can prevent other people from having
> the same issue, could you tell me where you got that example code?
>
> Dave
>
>
>
>
>
>
> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>
>> Hi Dave,
>>
>> Thanks a lot for your reply. It is really helpful. Please find the
>> screenshot after making the change you pointed out. But I am getting
>> "Exception: Bio::Root::Exception" error. I think I have to set the
>> environment variables but I am not sure how to do that. Could you please
>> guide me on this too.
>>
>> I can go to the "Environment Variable" Window in my pc. But I dont know
>> what to enter once I click "New" on that window.
>>
>> Thanks in advance.
>>
>> With regards,
>> Ravi.
>>
>>
>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>
>>> Hi Ravi,
>>>
>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>> not Bio::Seq. So your first line
>>>
>>> use Bio::Seq;
>>>
>>> should be replaced with
>>>
>>> use Bio::Perl;
>>>
>>>
>>> More examples in the BioPerl Tutorial here:
>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>
>>>
>>> Dve
>>>
>>>
>>>
>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>
>>>> Hi,
>>>>
>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>> packages
>>>> using ppm on windows 7? Please find the attachment for the error message
>>>> I
>>>> get. I would really appreciate if you help me fix this issue.
>>>>
>>>> Thanks,
>>>>
>>>> With regards,
>>>> Ravi.
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>>
>>
>



From rmb32 at cornell.edu  Tue Mar 29 21:20:41 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Tue, 29 Mar 2011 14:20:41 -0700
Subject: [Bioperl-l] Announcing OBF Summer of Code - please forward!
Message-ID: <4D924D29.3020707@cornell.edu>

Hi all,

Here's an advertising-ready announcement for OBF's Summer of Code, 
thanks to Christian Zmasek and Hilmar Lapp for their excellent writing.

Student applications are due April 8!  Please spread it widely, we need 
to reach lots of students with it!

Rob Buels
OBF GSoC 2011 Admin


============================================================

*** Please disseminate widely at your local institutions ***
*** including posting to message and job boards, so that ***
*** we reach as many students as possible.               ***

============================================================


OPEN BIOINFORMATICS FOUNDATION SUMMER OF CODE 2011

Applications due 19:00 UTC, April 8, 2010.
http://www.open-bio.org/wiki/Google_Summer_of_Code

The Open Bioinformatics Foundation Summer of Code program provides a 
unique opportunity for undergraduate, masters, and PhD students to 
obtain hands-on experience writing and extending open-source software 
for bioinformatics under the mentorship of experienced developers from 
around the world. The program is the participation of the Open 
Bioinformatics Foundation (OBF) as a mentoring organization in the 
Google Summer of Code(tm) (http://code.google.com/soc/).

Students successfully completing the 3 month program receive a $5,000 
USD stipend, and may work entirely from their home or home institution. 
  Participation is open to students from any country in the world except 
countries subject to US trade restrictions.  Each student will have at 
least one dedicated mentor to show them the ropes and help them complete 
their project.

The Open Bioinformatics Foundation is particularly seeking students 
interested in both bioinformatics (computational biology) and software 
development. Some initial project ideas are listed on the website. These 
range from Galaxy phylogenetics pipeline development in Biopython to 
lightweight sequence objects and lazy parsing in BioPerl, a DAS Server 
for large files on local filesystems, and mapping Java libraries to 
Perl/Ruby/Python using Biolib+SWIG+JNI.  All project ideas are flexible 
and many can be adjusted in scope to match the skills of the student. We 
also welcome and encourage students proposing their own project ideas; 
historically some of the most successful Summer of Code projects are 
ones proposed by the students themselves.

TO APPLY: Apply online at the Google Summer of Code website 
(http://socghop.appspot.com/), where you will also find GSoC program 
rules and eligibility requirements. The 12-day application period for 
students runs from Monday, March 28 through Friday, April 8th, 2011.

INQUIRIES:

We strongly encourage all interested students to get in touch with us 
with their ideas as early on as possible.  See the OBF GSoC page for 
contact details.

2011 OBF Summer of Code:
http://www.open-bio.org/wiki/Google_Summer_of_Code

Google Summer of Code FAQ:
http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs





From cjfields at illinois.edu  Wed Mar 30 13:58:00 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 30 Mar 2011 08:58:00 -0500
Subject: [Bioperl-l] Bioperl installation doubt
In-Reply-To: <AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
References: <AANLkTi=mZW4mW1EuDz8+S37ozs=0Tv_HGP3EihHq45Qj@mail.gmail.com>
	<AANLkTimMox3OmeWnR94bsjU28M4STubasjjqZG5Rs91J@mail.gmail.com>
	<AANLkTi=kVKavjOKRPpC_zKHe4PBjOZyp25mtVwayKHhi@mail.gmail.com>
	<AANLkTimRJqRvtsJ3DZQ4K0eodyUpBm5j3kBeUZr0Me3O@mail.gmail.com>
	<AANLkTi=PkbDTvN8GrT_K8upzoF+kO3c96KKrO4BXH9kt@mail.gmail.com>
Message-ID: <9EDCB97E-3256-476C-AA40-EDE27BF96033@illinois.edu>

Ravi,

You can sign up for the email list here:

http://lists.open-bio.org/mailman/listinfo/bioperl-l

Once you are signed up, you should be able to post questions.

chris

On Mar 28, 2011, at 4:56 AM, ?????????????????? wrote:

> Hi Dave,
> 
> Thank you very much. It is working. I got the program code from the
> following link.
> 
> http://www.bioperl.org/Core/Latest/bptutorial.html
> 
> I spent so much time on browsing, downloading and installing programs and
> packages. But, it seems like the code error is the reason it dint work.
> Thanks Dave.
> 
> Could you please give me the link to join this forum to see other
> discussions, which would be more helpful to me? Please let me know if you
> have any suggestion for me to keep learning the bioperl.
> 
> With regards,
> Ravi.
> 
> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
> 
>> Hi Ravi,
>> 
>> Please make sure to "Reply All" so that everyone on the mailing list can
>> follow (and add to) the discussion.
>> 
>> If you read the first line of the exception, you'll see it states what the
>> error is:
>> "WebDBSeqI Error ? check query sequences!"
>> 
>> You'd have no way of knowing this, but that ID and database combination is
>> not functioning anymore, so that's why in this case you're getting an error.
>> Please try using the example in the tutorial here:
>> 
>> 
>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>> 
>> which has been updated to a different ID which should work.
>> 
>> Sorry for the confusion! So that we can prevent other people from having
>> the same issue, could you tell me where you got that example code?
>> 
>> Dave
>> 
>> 
>> 
>> 
>> 
>> 
>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>> 
>>> Hi Dave,
>>> 
>>> Thanks a lot for your reply. It is really helpful. Please find the
>>> screenshot after making the change you pointed out. But I am getting
>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>> environment variables but I am not sure how to do that. Could you please
>>> guide me on this too.
>>> 
>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>> what to enter once I click "New" on that window.
>>> 
>>> Thanks in advance.
>>> 
>>> With regards,
>>> Ravi.
>>> 
>>> 
>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>> 
>>>> Hi Ravi,
>>>> 
>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>> not Bio::Seq. So your first line
>>>> 
>>>> use Bio::Seq;
>>>> 
>>>> should be replaced with
>>>> 
>>>> use Bio::Perl;
>>>> 
>>>> 
>>>> More examples in the BioPerl Tutorial here:
>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>> 
>>>> 
>>>> Dve
>>>> 
>>>> 
>>>> 
>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>> 
>>>>> Hi,
>>>>> 
>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>> packages
>>>>> using ppm on windows 7? Please find the attachment for the error message
>>>>> I
>>>>> get. I would really appreciate if you help me fix this issue.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> With regards,
>>>>> Ravi.
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> 
>>>> 
>>>> 
>>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From dvadell at clustering.com.ar  Wed Mar 30 14:51:38 2011
From: dvadell at clustering.com.ar (Diego M. Vadell)
Date: Wed, 30 Mar 2011 11:51:38 -0300
Subject: [Bioperl-l] Newbie alert: Aligning and printing first position
Message-ID: <201103301151.38752.dvadell@clustering.com.ar>

Hi list,

    I have an alignment ( done with Bio::Tools::Run::Alignment::Clustalw ) 
that I can see ( printing $aln->match_line() along with the sequences ):

        ********* .:                                   (match_line)
.......TDDSFDTDVSSS.........[...].............   ($seq1)
SDKIIHLTDDSFDTDVLKADGA[...]EFLDANLA   ($seq2)

    It looks right ( that "[...]" is mine, it's larger ). Now I want to get 
the position of the match ( the first "T" ), which should be "7". I thought I 
needed to use something like:

my $seq = $aln->get_seq_by_pos(1);
my $loc = $seq->location_from_column(1);
say $loc;

And $loc would be 7, but it's undef. If I try to iterate from 1 to 10, I start 
getting Bio::Location::Simple objects at the 8th place. So, should I loop 
untill I location_from_column() gives me an object? Is it another way of 
finding the position of the match?

As you can see, I'm just starting with bioinformatics. Any pointer will be 
appreciated.

Thanks in advance,
 -- Diego 


From joshearl1 at hotmail.com  Wed Mar 30 15:23:21 2011
From: joshearl1 at hotmail.com (Josh Earl)
Date: Wed, 30 Mar 2011 11:23:21 -0400
Subject: [Bioperl-l] Difficulty downloading biosql schema
Message-ID: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>


Hello all,

I'm trying to download the schema for biosql, however, when I run the command:
svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql-schema

(as per the instructions @ https://github.com/biosql/biosql/blob/master/INSTALL)
I either get no response, or it times out.  I've tried this a couple of times, the last time was a few weeks ago.  Anyone know what's going on?

Here's an example error:
svn: Can't connect to host 'code.open-bio.org': Connection timed out

thanks,
~josh

Center for Genomic Sciences
(412)-359-8341

 		 	   		  


From hlapp at drycafe.net  Wed Mar 30 15:52:22 2011
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 30 Mar 2011 11:52:22 -0400
Subject: [Bioperl-l] Difficulty downloading biosql schema
In-Reply-To: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
References: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
Message-ID: <4C1B95A9-0480-4B9B-91E2-1D35BCB568B4@drycafe.net>

(moving this to BioSQL list)
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From cjfields at illinois.edu  Wed Mar 30 15:54:00 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 30 Mar 2011 10:54:00 -0500
Subject: [Bioperl-l] Difficulty downloading biosql schema
In-Reply-To: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
References: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
Message-ID: <87CBA000-B964-40DA-BF35-BC229CF24BB6@illinois.edu>

BioSQL moved to github a while back:

https://github.com/biosql/biosql

(this might be better asked on the biosql-l list, which I've cc'd)

chris

On Mar 30, 2011, at 10:23 AM, Josh Earl wrote:

> 
> Hello all,
> 
> I'm trying to download the schema for biosql, however, when I run the command:
> svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql-schema
> 
> (as per the instructions @ https://github.com/biosql/biosql/blob/master/INSTALL)
> I either get no response, or it times out.  I've tried this a couple of times, the last time was a few weeks ago.  Anyone know what's going on?
> 
> Here's an example error:
> svn: Can't connect to host 'code.open-bio.org': Connection timed out
> 
> thanks,
> ~josh
> 
> Center for Genomic Sciences
> (412)-359-8341
> 
> 		 	   		  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From p.j.a.cock at googlemail.com  Wed Mar 30 15:55:49 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 30 Mar 2011 16:55:49 +0100
Subject: [Bioperl-l] Difficulty downloading biosql schema
In-Reply-To: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
References: <COL105-W14CC2A5C6E1DADC31BD452FABC0@phx.gbl>
Message-ID: <AANLkTi=v80WkLtJxiDu1MBLoyKD0RTR5eBhmb4NF5zO7@mail.gmail.com>

On Wed, Mar 30, 2011 at 4:23 PM, Josh Earl <joshearl1 at hotmail.com> wrote:
>
> Hello all,
>
> I'm trying to download the schema for biosql, however, when I run the command:
> svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql-schema
>
> (as per the instructions @ https://github.com/biosql/biosql/blob/master/INSTALL)
> I either get no response, or it times out. ?I've tried this a couple of times, the last
> time was a few weeks ago. ?Anyone know what's going on?
>
> Here's an example error:
> svn: Can't connect to host 'code.open-bio.org': Connection timed out
>
> thanks,
> ~josh

Hi Josh

First the code.open-bio.org has been having trouble and is being rebuilt.
Even if it did work, it would give you an out of date copy prior to the move
from SVN to git.

Secondly, the instructions you pointed to are out of date, we'll have to
fix that. Just use git:

git clone git://github.com/biosql/biosql.git

Thanks for the heads up!

Peter

P.S. There is a dedicated BioSQL mailing list.



From roy.chaudhuri at gmail.com  Wed Mar 30 15:43:35 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Wed, 30 Mar 2011 16:43:35 +0100
Subject: [Bioperl-l] Newbie alert: Aligning and printing first position
In-Reply-To: <201103301151.38752.dvadell@clustering.com.ar>
References: <201103301151.38752.dvadell@clustering.com.ar>
Message-ID: <4D934FA7.2080206@gmail.com>

Hi Diego,

Column refers to the position in the alignment, not the individual 
sequence. location_from_column therefore gives the position in the 
individual sequence that corresponds to the requested column (you get 
undef since there is a gap in the first column of the alignment for 
seq1). If I understand correctly, you want the reverse, the position in 
the alignment that corresponds to the first position in your sequence. 
For that you need the opposite function, column_from_residue_number:

my $loc=$seq->column_from_residue_number(1);

$loc will now contain 8 (not 7), since position 1 of your sequence is in 
column 8 of the alignment.

Hope this helps,
Roy.

On 30/03/2011 15:51, Diego M. Vadell wrote:
> Hi list,
>
>      I have an alignment ( done with Bio::Tools::Run::Alignment::Clustalw )
> that I can see ( printing $aln->match_line() along with the sequences ):
>
>          ********* .:                                   (match_line)
> .......TDDSFDTDVSSS.........[...].............   ($seq1)
> SDKIIHLTDDSFDTDVLKADGA[...]EFLDANLA   ($seq2)
>
>      It looks right ( that "[...]" is mine, it's larger ). Now I want to get
> the position of the match ( the first "T" ), which should be "7". I thought I
> needed to use something like:
>
> my $seq = $aln->get_seq_by_pos(1);
> my $loc = $seq->location_from_column(1);
> say $loc;
>
> And $loc would be 7, but it's undef. If I try to iterate from 1 to 10, I start
> getting Bio::Location::Simple objects at the 8th place. So, should I loop
> untill I location_from_column() gives me an object? Is it another way of
> finding the position of the match?
>
> As you can see, I'm just starting with bioinformatics. Any pointer will be
> appreciated.
>
> Thanks in advance,
>   -- Diego
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From zheboyang at gmail.com  Thu Mar 31 12:28:53 2011
From: zheboyang at gmail.com (boyang zhe)
Date: Thu, 31 Mar 2011 14:28:53 +0200
Subject: [Bioperl-l] blast best hit
Message-ID: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>

Hi,

I just want to parse the blast results ,and get the best hit.

One way is to parse the results as usual, then get the first hit and exit
the loop.

I checked the bioperl document, and find that there is a method
best_hit_only in Bio::SearchIO::blast.pm.
But it only return 1/0. So my question is how to use this method to get the
best hit.

Thank you very much!

Boyang


From dvadell at clustering.com.ar  Thu Mar 31 12:59:46 2011
From: dvadell at clustering.com.ar (Diego M. Vadell)
Date: Thu, 31 Mar 2011 09:59:46 -0300
Subject: [Bioperl-l] Newbie alert: Aligning and printing first position
In-Reply-To: <4D934FA7.2080206@gmail.com>
References: <201103301151.38752.dvadell@clustering.com.ar>
	<4D934FA7.2080206@gmail.com>
Message-ID: <201103311000.36567.dvadell@clustering.com.ar>

Hi Roy,

  Thanks!! I can't beleive I didn't see that method in the documentation. 
Thank you very much. It worked perfectly.

Cheers,
 -- Diego

On Wednesday, March 30, 2011 12:43:35 pm Roy Chaudhuri wrote:
> Hi Diego,
> 
> Column refers to the position in the alignment, not the individual
> sequence. location_from_column therefore gives the position in the
> individual sequence that corresponds to the requested column (you get
> undef since there is a gap in the first column of the alignment for
> seq1). If I understand correctly, you want the reverse, the position in
> the alignment that corresponds to the first position in your sequence.
> For that you need the opposite function, column_from_residue_number:
> 
> my $loc=$seq->column_from_residue_number(1);
> 
> $loc will now contain 8 (not 7), since position 1 of your sequence is in
> column 8 of the alignment.
> 
> Hope this helps,
> Roy.
> 
> On 30/03/2011 15:51, Diego M. Vadell wrote:
> > Hi list,
> > 
> >      I have an alignment ( done with Bio::Tools::Run::Alignment::Clustalw
> >      )
> > 
> > that I can see ( printing $aln->match_line() along with the sequences ):
> >          ********* .:                                   (match_line)
> > 
> > .......TDDSFDTDVSSS.........[...].............   ($seq1)
> > SDKIIHLTDDSFDTDVLKADGA[...]EFLDANLA   ($seq2)
> > 
> >      It looks right ( that "[...]" is mine, it's larger ). Now I want to
> >      get
> > 
> > the position of the match ( the first "T" ), which should be "7". I
> > thought I needed to use something like:
> > 
> > my $seq = $aln->get_seq_by_pos(1);
> > my $loc = $seq->location_from_column(1);
> > say $loc;
> > 
> > And $loc would be 7, but it's undef. If I try to iterate from 1 to 10, I
> > start getting Bio::Location::Simple objects at the 8th place. So, should
> > I loop untill I location_from_column() gives me an object? Is it another
> > way of finding the position of the match?
> > 
> > As you can see, I'm just starting with bioinformatics. Any pointer will
> > be appreciated.
> > 
> > Thanks in advance,
> > 
> >   -- Diego
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l


From bosborne11 at verizon.net  Thu Mar 31 13:04:22 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Thu, 31 Mar 2011 09:04:22 -0400
Subject: [Bioperl-l] blast best hit
In-Reply-To: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
References: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
Message-ID: <A29F9EB5-BEC6-4DF3-924F-F8F98F96C6F1@verizon.net>

Boyang,

You can sort the hits, by any criterion you want:

my @hits = $result->hits;
@hits = sort { $a-> bits <=> $b->bits } @hits;

BIO

On Mar 31, 2011, at 8:28 AM, boyang zhe wrote:

> Hi,
> 
> I just want to parse the blast results ,and get the best hit.
> 
> One way is to parse the results as usual, then get the first hit and exit
> the loop.
> 
> I checked the bioperl document, and find that there is a method
> best_hit_only in Bio::SearchIO::blast.pm.
> But it only return 1/0. So my question is how to use this method to get the
> best hit.
> 
> Thank you very much!
> 
> Boyang
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jordi.durban at gmail.com  Thu Mar 31 14:23:54 2011
From: jordi.durban at gmail.com (Jordi Durban)
Date: Thu, 31 Mar 2011 16:23:54 +0200
Subject: [Bioperl-l] blast best hit
In-Reply-To: <A29F9EB5-BEC6-4DF3-924F-F8F98F96C6F1@verizon.net>
References: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
	<A29F9EB5-BEC6-4DF3-924F-F8F98F96C6F1@verizon.net>
Message-ID: <AANLkTimiAanHL89eJ3uKgnGXKbcbJh+jBmw6MRs1VC1t@mail.gmail.com>

Hi,
I did a pair of scripts to parse a blastxml report. I'd like know your
opinion.
First I obtained a file with tab separated results (whatever you want) from
the blast results according to some Bioperl modules as SearchIO. That is:
hit_name    query_name    e-value    score
hit_name    query-name   e-value     score
.
.

Then, I parse that file as an array where:
foreach my $line ($array[0]){ ###### best hit
        next if $seen {$line}++; ##### non-repeated lines
        push @unique , $line[1]; ### best hit outcome in a new array
       }

I hope this helps and I look forward some opinions.






2011/3/31 Brian Osborne <bosborne11 at verizon.net>

> Boyang,
>
> You can sort the hits, by any criterion you want:
>
> my @hits = $result->hits;
> @hits = sort { $a-> bits <=> $b->bits } @hits;
>
> BIO
>
> On Mar 31, 2011, at 8:28 AM, boyang zhe wrote:
>
> > Hi,
> >
> > I just want to parse the blast results ,and get the best hit.
> >
> > One way is to parse the results as usual, then get the first hit and exit
> > the loop.
> >
> > I checked the bioperl document, and find that there is a method
> > best_hit_only in Bio::SearchIO::blast.pm.
> > But it only return 1/0. So my question is how to use this method to get
> the
> > best hit.
> >
> > Thank you very much!
> >
> > Boyang
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Jordi


From fs5 at sanger.ac.uk  Thu Mar 31 14:23:33 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 31 Mar 2011 15:23:33 +0100
Subject: [Bioperl-l] blast best hit
In-Reply-To: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
References: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
Message-ID: <1301581413.12411.188.camel@deskpro15336.internal.sanger.ac.uk>

Yes, best_hit_only is a boolean that can be set to true if you only want
one hit to be returned from the stream of hits (the best hit). I have
never actualyl used this one but you shoud be able to set it in the
constructor as in:
my $blast = Bio::SearchIO->new( ...., -best_hit_only => 1 )



Frank

On Thu, 2011-03-31 at 14:28 +0200, boyang zhe wrote:
> Hi,
> 
> I just want to parse the blast results ,and get the best hit.
> 
> One way is to parse the results as usual, then get the first hit and exit
> the loop.
> 
> I checked the bioperl document, and find that there is a method
> best_hit_only in Bio::SearchIO::blast.pm.
> But it only return 1/0. So my question is how to use this method to get the
> best hit.
> 
> Thank you very much!
> 
> Boyang
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From fs5 at sanger.ac.uk  Thu Mar 31 15:06:41 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 31 Mar 2011 16:06:41 +0100
Subject: [Bioperl-l] blast best hit
In-Reply-To: <AANLkTimXj+D8VQO_Mb4vpgfadXqFfgD1dHQL+fwCMsX5@mail.gmail.com>
References: <AANLkTi=YfRu59phY98bT=E2Hf88qCUcqM=suq_JwiaeQ@mail.gmail.com>
	<1301581413.12411.188.camel@deskpro15336.internal.sanger.ac.uk>
	<AANLkTimXj+D8VQO_Mb4vpgfadXqFfgD1dHQL+fwCMsX5@mail.gmail.com>
Message-ID: <1301584001.12411.202.camel@deskpro15336.internal.sanger.ac.uk>

Hi Boyang,

With best_hit_only set to "true" (as you have done now) you should be
able to use the usual way of parsing the BLAST report with 

while (my $result = $blast_io->next_result) {
  my $hit = $result->next_hit;
  ... (do something with the hit)
}

Because there should be only one hit now. 'best_hit_only' is a flag, an
indicator that tells the parser to limit the output to the best hit. It
does not itself return any hits.

Even if you used the 

while (my $hit=$result->next_hit){..

inner loop (as in the BioPerl HOWTOs) you should now only ever get one
hit retunred from that loop, which is the best hit for the result. I
haven't tried this but it should work.

Personally, I'd not use this option and rather sort or filter the hits
because tomorrow you might want to find out what the next best hit
actually was and how close the e-values and bits were or something like
that. 

Hope this helps,

Frank


On Thu, 2011-03-31 at 16:43 +0200, boyang zhe wrote:
> I try this at the constructor
> 
> my $blast_io = Bio::SearchIO->new(-file => 'test', -format => 'blast',
> -best_hit_only => 1);
> 
> What I need to do in the following steps? It seems that setting
> best_hit_only or not does not change the way of blast parser working.
> 
> In my opinion, if we can use it as a similar way following, it will be
> much better.
> 
> my $blast_io = Bio::SearchIO->new(-file => 'test', -format => 'blast',
> -best_hit_only => 1);
> 
> while (my $blast_result = $blast_io->next_result()) {
>       my $best_hit = $blast_result->best_hit_only();  # just assume it
> working here; in fact, it does not work
>       my $best_hit_name = $best_hit->name();
>       ...................................
> }
> 
> thank you !
> 
> On Thu, Mar 31, 2011 at 4:23 PM, Frank Schwach <fs5 at sanger.ac.uk>
> wrote:
>         Yes, best_hit_only is a boolean that can be set to true if you
>         only want
>         one hit to be returned from the stream of hits (the best hit).
>         I have
>         never actualyl used this one but you shoud be able to set it
>         in the
>         constructor as in:
>         my $blast = Bio::SearchIO->new( ...., -best_hit_only => 1 )
>         
>         
>         
>         Frank
>         
>         
>         On Thu, 2011-03-31 at 14:28 +0200, boyang zhe wrote:
>         > Hi,
>         >
>         > I just want to parse the blast results ,and get the best
>         hit.
>         >
>         > One way is to parse the results as usual, then get the first
>         hit and exit
>         > the loop.
>         >
>         > I checked the bioperl document, and find that there is a
>         method
>         > best_hit_only in Bio::SearchIO::blast.pm.
>         > But it only return 1/0. So my question is how to use this
>         method to get the
>         > best hit.
>         >
>         > Thank you very much!
>         >
>         > Boyang
>         
>         
>         > _______________________________________________
>         > Bioperl-l mailing list
>         > Bioperl-l at lists.open-bio.org
>         > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>         
>         
>         
>         
>         --
>          The Wellcome Trust Sanger Institute is operated by Genome
>         Research
>          Limited, a charity registered in England with number 1021457
>         and a
>          company registered in England with number 2742969, whose
>         registered
>          office is 215 Euston Road, London, NW1 2BE.
> 



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From suy at big.ac.cn  Thu Mar 31 07:24:55 2011
From: suy at big.ac.cn (suy)
Date: Thu, 31 Mar 2011 15:24:55 +0800
Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
Message-ID: <201103311524549534382@big.ac.cn>

I want to use Bio::Tools::HMM, but I can not find it in bioperl 1.6.1. Could anyone tell me how to do it ? 

2011-03-31 



suy 


From cjfields at illinois.edu  Thu Mar 31 17:01:13 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 31 Mar 2011 12:01:13 -0500
Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
In-Reply-To: <201103311524549534382@big.ac.cn>
References: <201103311524549534382@big.ac.cn>
Message-ID: <93E13DE0-5888-4B5C-AC9D-F68623D0D891@illinois.edu>

It's now in it's own distribution, along with the related C code.  See:

https://github.com/bioperl/Bio-Tools-HMM

It hasn't been released to CPAN yet, and (IIRC) it may be failing some tests.

chris

On Mar 31, 2011, at 2:24 AM, suy wrote:

> I want to use Bio::Tools::HMM, but I can not find it in bioperl 1.6.1. Could anyone tell me how to do it ? 
> 
> 2011-03-31 
> 
> 
> 
> suy 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From David.Messina at sbc.su.se  Thu Mar 31 17:07:54 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 31 Mar 2011 19:07:54 +0200
Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
In-Reply-To: <201103311524549534382@big.ac.cn>
References: <201103311524549534382@big.ac.cn>
Message-ID: <AANLkTin2qe1V=2swW1qd8O=s8eQTi5p1LDHc-=sViKPT@mail.gmail.com>

It's distributed separately from BioPerl now. You can get it here:

https://github.com/bioperl/Bio-Tools-HMM


Dave



On Thu, Mar 31, 2011 at 09:24, suy <suy at big.ac.cn> wrote:

> I want to use Bio::Tools::HMM, but I can not find it in bioperl 1.6.1.
> Could anyone tell me how to do it ?
>
> 2011-03-31
>
>
>
> suy
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From Kevin.M.Brown at asu.edu  Thu Mar 31 18:22:06 2011
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Thu, 31 Mar 2011 11:22:06 -0700
Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
In-Reply-To: <201103311524549534382@big.ac.cn>
References: <201103311524549534382@big.ac.cn>
Message-ID: <1A4207F8295607498283FE9E93B775B40781779B@EX02.asurite.ad.asu.edu>

https://github.com/bioperl/Bio-Tools-HMM

"moved Bio::Tools::HMM and Bio::Ext::HMM into their own distro, got them
compiling cleanly. tests not passing yet
svn path=/Bio-Tools-HMM/trunk/; revision=15966"

Kevin Brown
Center for Innovations in Medicine
Biodesign Institute
Arizona State University 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of suy
> Sent: Thursday, March 31, 2011 12:25 AM
> To: bioperl-l
> Subject: [Bioperl-l] Tools::HMM in bioperl 1.6.1
> 
> I want to use Bio::Tools::HMM, but I can not find it in bioperl 1.6.1.
> Could anyone tell me how to do it ?
> 
> 2011-03-31
> 
> 
> 
> suy
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From David.Messina at sbc.su.se  Thu Mar 31 19:43:14 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 31 Mar 2011 21:43:14 +0200
Subject: [Bioperl-l] Old docs cleanup (was Re: Bioperl installation doubt)
Message-ID: <AANLkTikzx+iP6ws0CpwEEA2USiLwYVHTHjZU8KO+3vMo@mail.gmail.com>

Hi,

Just to clarify:

Brian, is it okay with you if I go ahead and remove the Core/ directory from
the website? (and okay with everyone else, too, for that matter? I haven't
heard any nays so far.)


Dave



On Tue, Mar 29, 2011 at 00:40, Chris Fields <cjfields at illinois.edu> wrote:

> Brian,
>
> I think this was started:
>
> http://www.bioperl.org/wiki/Bptutorial.pl
>
> It certainly could be cleaned up, organized, and updated (that and the
> FAQ).  Makes sense to have it as a HOWTO or maybe split it into several
> HOWTOs.  Maybe even combine it with the beginner's HOWTO into various
> sections?
>
> chris
>
> On Mar 28, 2011, at 3:43 PM, Brian Osborne wrote:
>
> > Chris,
> >
> > I'll get started on dissembling bptutorial. There's certainly useful text
> in there but there's also duplicated or outdated material. Looks like there
> are 3 options for any given section:
> >
> > - put it into an existing HOWTO
> > - make it into a new HOWTO
> > - delete it
> >
> > BIO
> >
> > On Mar 28, 2011, at 9:27 AM, Chris Fields wrote:
> >
> >> Dave,
> >>
> >> +1 on removing old docs to prevent confusion.  Or, alternatively, +1 to
> syncing those to current docs (though I think decreasing the replication
> effort in keeping docs up-to-date is probably the best tact).
> >>
> >> chris
> >>
> >> On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:
> >>
> >>>>
> >>>> Thank you very much. It is working. I got the program code from the
> >>>> following link.
> >>>>
> >>>> http://www.bioperl.org/Core/Latest/bptutorial.html
> >>>
> >>>
> >>> Aha, okay. You got there from Google, I guess? That is *way* out of
> date.
> >>>
> >>> To the other core devs, in order to prevent this confusion in the
> future,
> >>> I'd like to delete the Core/ directory from our website since it's been
> >>> superseded at this point by other docs and is not current. I intend to
> put
> >>> up a ticket at Redmine, but I will wait a bit before doing so to allow
> time
> >>> for people to see this and comment ? please do speak up if there's good
> >>> reason to keep it.
> >>>
> >>>
> >>> Could you please give me the link to join this forum to see other
> >>>> discussions, which would be more helpful to me?
> >>>>
> >>>
> >>> Sure, you can sign up for the mailing list here:
> >>>
> >>> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
> >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>>
> >>> And the archives are also searchable:
> >>>
> >>>  http://news.gmane.org/gmane.comp.lang.perl.bio.general
> >>>
> >>>
> >>> Please let me know if you have any suggestion for me to keep learning
> the
> >>>> bioperl.
> >>>
> >>>
> >>> I would also suggest reading the (current) tutorial and HOWTOs at
> >>> www.bioperl.org . Lots of good links on the main page there,
> particularly
> >>> under the Documentation heading.
> >>>
> >>>
> >>> Dave
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>> With regards,
> >>>> Ravi.
> >>>>
> >>>>
> >>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
> >>>>
> >>>>> Hi Ravi,
> >>>>>
> >>>>> Please make sure to "Reply All" so that everyone on the mailing list
> can
> >>>>> follow (and add to) the discussion.
> >>>>>
> >>>>> If you read the first line of the exception, you'll see it states
> what the
> >>>>> error is:
> >>>>> "WebDBSeqI Error ? check query sequences!"
> >>>>>
> >>>>> You'd have no way of knowing this, but that ID and database
> combination is
> >>>>> not functioning anymore, so that's why in this case you're getting an
> error.
> >>>>> Please try using the example in the tutorial here:
> >>>>>
> >>>>>
> >>>>>
> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
> >>>>>
> >>>>> which has been updated to a different ID which should work.
> >>>>>
> >>>>> Sorry for the confusion! So that we can prevent other people from
> having
> >>>>> the same issue, could you tell me where you got that example code?
> >>>>>
> >>>>> Dave
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
> >>>>>
> >>>>>> Hi Dave,
> >>>>>>
> >>>>>> Thanks a lot for your reply. It is really helpful. Please find the
> >>>>>> screenshot after making the change you pointed out. But I am getting
> >>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
> >>>>>> environment variables but I am not sure how to do that. Could you
> please
> >>>>>> guide me on this too.
> >>>>>>
> >>>>>> I can go to the "Environment Variable" Window in my pc. But I dont
> know
> >>>>>> what to enter once I click "New" on that window.
> >>>>>>
> >>>>>> Thanks in advance.
> >>>>>>
> >>>>>> With regards,
> >>>>>> Ravi.
> >>>>>>
> >>>>>>
> >>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
> >>>>>>
> >>>>>>> Hi Ravi,
> >>>>>>>
> >>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl
> module,
> >>>>>>> not Bio::Seq. So your first line
> >>>>>>>
> >>>>>>> use Bio::Seq;
> >>>>>>>
> >>>>>>> should be replaced with
> >>>>>>>
> >>>>>>> use Bio::Perl;
> >>>>>>>
> >>>>>>>
> >>>>>>> More examples in the BioPerl Tutorial here:
> >>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
> >>>>>>>
> >>>>>>>
> >>>>>>> Dve
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
> >>>>>>>
> >>>>>>>> Hi,
> >>>>>>>>
> >>>>>>>> Could you please help me installing bioperl-db, bioperl-run &
> other
> >>>>>>>> packages
> >>>>>>>> using ppm on windows 7? Please find the attachment for the error
> >>>>>>>> message I
> >>>>>>>> get. I would really appreciate if you help me fix this issue.
> >>>>>>>>
> >>>>>>>> Thanks,
> >>>>>>>>
> >>>>>>>> With regards,
> >>>>>>>> Ravi.
> >>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> Bioperl-l mailing list
> >>>>>>>> Bioperl-l at lists.open-bio.org
> >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>



From cjfields at illinois.edu  Thu Mar 31 19:49:08 2011
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 31 Mar 2011 14:49:08 -0500
Subject: [Bioperl-l] Old docs cleanup (was Re: Bioperl installation
	doubt)
In-Reply-To: <AANLkTikzx+iP6ws0CpwEEA2USiLwYVHTHjZU8KO+3vMo@mail.gmail.com>
References: <AANLkTikzx+iP6ws0CpwEEA2USiLwYVHTHjZU8KO+3vMo@mail.gmail.com>
Message-ID: <1D3D2910-F1F9-40A1-9A39-656D3DF17847@illinois.edu>

+1 from me.  Go ahead.  Old misleading documentation is bad to have around.

chris

On Mar 31, 2011, at 2:43 PM, Dave Messina wrote:

> Hi,
> 
> Just to clarify:
> 
> Brian, is it okay with you if I go ahead and remove the Core/ directory from
> the website? (and okay with everyone else, too, for that matter? I haven't
> heard any nays so far.)
> 
> 
> Dave
> 
> 
> 
> On Tue, Mar 29, 2011 at 00:40, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Brian,
>> 
>> I think this was started:
>> 
>> http://www.bioperl.org/wiki/Bptutorial.pl
>> 
>> It certainly could be cleaned up, organized, and updated (that and the
>> FAQ).  Makes sense to have it as a HOWTO or maybe split it into several
>> HOWTOs.  Maybe even combine it with the beginner's HOWTO into various
>> sections?
>> 
>> chris
>> 
>> On Mar 28, 2011, at 3:43 PM, Brian Osborne wrote:
>> 
>>> Chris,
>>> 
>>> I'll get started on dissembling bptutorial. There's certainly useful text
>> in there but there's also duplicated or outdated material. Looks like there
>> are 3 options for any given section:
>>> 
>>> - put it into an existing HOWTO
>>> - make it into a new HOWTO
>>> - delete it
>>> 
>>> BIO
>>> 
>>> On Mar 28, 2011, at 9:27 AM, Chris Fields wrote:
>>> 
>>>> Dave,
>>>> 
>>>> +1 on removing old docs to prevent confusion.  Or, alternatively, +1 to
>> syncing those to current docs (though I think decreasing the replication
>> effort in keeping docs up-to-date is probably the best tact).
>>>> 
>>>> chris
>>>> 
>>>> On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:
>>>> 
>>>>>> 
>>>>>> Thank you very much. It is working. I got the program code from the
>>>>>> following link.
>>>>>> 
>>>>>> http://www.bioperl.org/Core/Latest/bptutorial.html
>>>>> 
>>>>> 
>>>>> Aha, okay. You got there from Google, I guess? That is *way* out of
>> date.
>>>>> 
>>>>> To the other core devs, in order to prevent this confusion in the
>> future,
>>>>> I'd like to delete the Core/ directory from our website since it's been
>>>>> superseded at this point by other docs and is not current. I intend to
>> put
>>>>> up a ticket at Redmine, but I will wait a bit before doing so to allow
>> time
>>>>> for people to see this and comment ? please do speak up if there's good
>>>>> reason to keep it.
>>>>> 
>>>>> 
>>>>> Could you please give me the link to join this forum to see other
>>>>>> discussions, which would be more helpful to me?
>>>>>> 
>>>>> 
>>>>> Sure, you can sign up for the mailing list here:
>>>>> 
>>>>> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> 
>>>>> 
>>>>> And the archives are also searchable:
>>>>> 
>>>>> http://news.gmane.org/gmane.comp.lang.perl.bio.general
>>>>> 
>>>>> 
>>>>> Please let me know if you have any suggestion for me to keep learning
>> the
>>>>>> bioperl.
>>>>> 
>>>>> 
>>>>> I would also suggest reading the (current) tutorial and HOWTOs at
>>>>> www.bioperl.org . Lots of good links on the main page there,
>> particularly
>>>>> under the Documentation heading.
>>>>> 
>>>>> 
>>>>> Dave
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> With regards,
>>>>>> Ravi.
>>>>>> 
>>>>>> 
>>>>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>>>>>> 
>>>>>>> Hi Ravi,
>>>>>>> 
>>>>>>> Please make sure to "Reply All" so that everyone on the mailing list
>> can
>>>>>>> follow (and add to) the discussion.
>>>>>>> 
>>>>>>> If you read the first line of the exception, you'll see it states
>> what the
>>>>>>> error is:
>>>>>>> "WebDBSeqI Error ? check query sequences!"
>>>>>>> 
>>>>>>> You'd have no way of knowing this, but that ID and database
>> combination is
>>>>>>> not functioning anymore, so that's why in this case you're getting an
>> error.
>>>>>>> Please try using the example in the tutorial here:
>>>>>>> 
>>>>>>> 
>>>>>>> 
>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>>>>>>> 
>>>>>>> which has been updated to a different ID which should work.
>>>>>>> 
>>>>>>> Sorry for the confusion! So that we can prevent other people from
>> having
>>>>>>> the same issue, could you tell me where you got that example code?
>>>>>>> 
>>>>>>> Dave
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 2011/3/28 ?????????????????? <ravimbt at gmail.com>
>>>>>>> 
>>>>>>>> Hi Dave,
>>>>>>>> 
>>>>>>>> Thanks a lot for your reply. It is really helpful. Please find the
>>>>>>>> screenshot after making the change you pointed out. But I am getting
>>>>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>>>>>>> environment variables but I am not sure how to do that. Could you
>> please
>>>>>>>> guide me on this too.
>>>>>>>> 
>>>>>>>> I can go to the "Environment Variable" Window in my pc. But I dont
>> know
>>>>>>>> what to enter once I click "New" on that window.
>>>>>>>> 
>>>>>>>> Thanks in advance.
>>>>>>>> 
>>>>>>>> With regards,
>>>>>>>> Ravi.
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>>>>>>> 
>>>>>>>>> Hi Ravi,
>>>>>>>>> 
>>>>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl
>> module,
>>>>>>>>> not Bio::Seq. So your first line
>>>>>>>>> 
>>>>>>>>> use Bio::Seq;
>>>>>>>>> 
>>>>>>>>> should be replaced with
>>>>>>>>> 
>>>>>>>>> use Bio::Perl;
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> More examples in the BioPerl Tutorial here:
>>>>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> Dve
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 2011/3/24 ?????????????????? <ravimbt at gmail.com>
>>>>>>>>> 
>>>>>>>>>> Hi,
>>>>>>>>>> 
>>>>>>>>>> Could you please help me installing bioperl-db, bioperl-run &
>> other
>>>>>>>>>> packages
>>>>>>>>>> using ppm on windows 7? Please find the attachment for the error
>>>>>>>>>> message I
>>>>>>>>>> get. I would really appreciate if you help me fix this issue.
>>>>>>>>>> 
>>>>>>>>>> Thanks,
>>>>>>>>>> 
>>>>>>>>>> With regards,
>>>>>>>>>> Ravi.
>>>>>>>>>> 
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Bioperl-l mailing list
>>>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From rmb32 at cornell.edu  Thu Mar 31 21:58:52 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 31 Mar 2011 14:58:52 -0700
Subject: [Bioperl-l] Reminder: GSoC proposals due in 1 week
Message-ID: <4D94F91C.1080005@cornell.edu>

Hi all,

Just a reminder, Google Summer of Code student applications are due April 8!

If you're a student planning to apply to GSoC with OBF, it's very much 
in your best interest to write your proposal *early*, like now, and get 
it into the hands of the developers and mentors on your subproject 
(BioPerl/Ruby/Python/etc) so that they can give you some feedback on it.

The final proposals must, of course, still be submitted to Google 
through the GSoC web application, as described on the main GSoC site 
(http://www.google-melange.com/gsoc/homepage/google/gsoc2011).

Rob Buels
OBF GSoC 2011 Administrator




From rmb32 at cornell.edu  Thu Mar 31 22:04:49 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 31 Mar 2011 15:04:49 -0700
Subject: [Bioperl-l] GSoC call for mentors
Message-ID: <4D94FA81.5090701@cornell.edu>

Hi all,

For current developers on OBF projects:

If you would not mind being a mentor to a Summer of Code student this 
summer, please make sure you sign up as an OBF mentor in the GSoC web 
app.  There's a link under "mentors: apply now!" midway down the page at 
http://www.google-melange.com/.  If you didn't do last year's summer of 
code, it would be a good idea to drop me an email introducing yourself, 
as well, or I won't know whether to approve your request. :-)

Being signed up as an OBF GSoC mentor will give you access to the 
student proposals, as they come in, and the ability to comment on them 
and assign scores to the ones you think show the most promise.

If you sign up as a mentor, please also add yourself to the two OBF GSoC 
mailing lists: OBF-GSoC and OBF-GSoC-mentors

OBF-GSoC list: http://lists.open-bio.org/mailman/listinfo/gsoc
OBF mentors:   http://lists.open-bio.org/mailman/listinfo/gsoc-mentors


Thanks in advance!

Rob

---
Robert Buels
OBF GSoC 2011 Administrator



From zuz17 at psu.edu  Thu Mar 31 22:18:59 2011
From: zuz17 at psu.edu (Zhenguo Zhang)
Date: Thu, 31 Mar 2011 18:18:59 -0400
Subject: [Bioperl-l] FW: How to specify color for each feature in a track?
In-Reply-To: 1301604855l.1593384l.0l@psu.edu
References: <1301604855l.1593384l.0l@psu.edu>
Message-ID: <1301609939l.901330l.0l@psu.edu>

Dear Dr. Stein,

Sorry for interruption. I found the problems, I used
$f->get_tag_values('color'); to return the tag value, it is not correct. The
list context should be provided. It is my mistake. Thanks.

Best wishes!

Zhenguo

---------------- Forwarded Message ----------------
From: "Zhenguo Zhang" <zuz17 at psu.edu>
Date: Thu, Mar 31, 2011 04:54 PM
Subject: How to specify color for each feature in a track?
To: lstein at cshl.edu, bioperl-l at lists.open-bio.org

Dear Dr. Stein,

I am using your excellent module Bio::Graphics for
programming to show protein domains. I want to put all the domains for a
sequence into one track, and give each domain (one feature here) one designated
color. The following is the cold to add_track:


 75        
$panel->add_track($seq,
 78                 -glyph    =>  'segments',
 81                 -bgcolor  => sub {
 82                     my $f = shift;
 87                     return $f->get_tag_values('color');
 88                 },
 89                 -fgcolor  => 'black',
 90                 -font2color => 'red',
 91                 -key      => "$seq",
 92                 -label    => 1,
 93                 -bump     => +1,
 94                 -height   => 8,
 95                 -description => 1,
 96 #               -part_label_merge => 1
 97                 );

Here $seq is an array reference, each element being one domain feature. I
specify the -bgcolor based on the tag 'color'  defined when domain feature was
constructed. However, it does not work. All the domains in all sequences show
the same color. Based on the document, the -glyph can be changed by calling
back the anonymous functions (I have not tried this). The color might be
changed in a similar way. Thank you in advance!

Best regards!

Zhenguo

**************************************************************
Zhenguo Zhang
Postdoctoral Scholar
Institute of Molecular Evolutionary Genetics
Penn State University
312 Mueller Lab
University Park, PA 16802
Tel: 814-865-2796
Homepage: <http://www.personal.psu.edu/zuz17/>
Lab page:  <http://homes.bio.psu.edu/people/Faculty/Nei/>




**************************************************************
Zhenguo Zhang
Postdoctoral Scholar
Institute of Molecular Evolutionary Genetics
Penn State University
312 Mueller Lab
University Park, PA 16802
Tel: 814-865-2796
Homepage: <http://www.personal.psu.edu/zuz17/>
Lab page:  <http://homes.bio.psu.edu/people/Faculty/Nei/>





From scott at scottcain.net  Thu Mar 31 23:13:06 2011
From: scott at scottcain.net (Scott Cain)
Date: Thu, 31 Mar 2011 19:13:06 -0400
Subject: [Bioperl-l] git help
Message-ID: <AANLkTin9BRdaSY_p-5rKSCFvpUr+rfCSZ8hjVTgyhxC5@mail.gmail.com>

Hi all,

I just want to know if it is safe for me to commit.  Here is what git
said to me:

scott-cains-macbook-pro:bioperl-live cain$ git commit
# On branch master
# Your branch is behind 'origin/master' by 47 commits, and can be
fast-forwarded.
#
# Changed but not updated:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#	modified:   Bio/DB/GFF.pm
#	modified:   Bio/FeatureIO/gff.pm
#	modified:   scripts/Bio-DB-GFF/bulk_load_gff.PLS
#	modified:   scripts/Bio-DB-GFF/fast_load_gff.PLS
#	modified:   t/SeqFeature/FeatureIO.t
#	modified:   t/data/knownGene.gff3
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#	scripts/Bio-DB-GFF/genbank2gff3.diff
no changes added to commit (use "git add" and/or "git commit -a")
----------------------

so should I do a git commit -a?

Also, when I try a git pull, this is what it tells me:

scott-cains-macbook-pro:bioperl-live cain$ git pull
Updating 1c2cf24..d5de022
error: Your local changes to 'Bio/FeatureIO/gff.pm' would be
overwritten by merge.  Aborting.
Please, commit your changes or stash them before you can merge.

Thanks,
Scott



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From dan.kortschak at adelaide.edu.au  Thu Mar 31 23:24:25 2011
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Fri, 01 Apr 2011 09:54:25 +1030
Subject: [Bioperl-l] BEDTools.pm update
Message-ID: <1301613865.3334.35.camel@sueno>

Hi All,

I have completed a revision of the BEDTools module that makes use of the
v2.10.1 BEDTools additions, including the ability to read GFF and VCF
file formats.

Because of the interactions between CommandExts/Config and the way
BEDTools executables can receive input files, I have had to change the
parameter names for a number of the filespecs from -bed* to -bvg* (for
BED/GFF/VCF). The alternative, though possible was much more involved
for little gain in my view.

This change will break BEDTools.pm-using scripts that use the -bed[12]?
filespecs (except for those wrapping genomeCoverageBed which cannot read
bgv and so which see no change).

I just wanted to get an idea if this is going to be a significant
problem for people before I push the changes to bioperl-run.

cheers
Dan



From zuz17 at psu.edu  Thu Mar 31 20:54:15 2011
From: zuz17 at psu.edu (Zhenguo Zhang)
Date: Thu, 31 Mar 2011 16:54:15 -0400
Subject: [Bioperl-l] How to specify color for each feature in a track?
Message-ID: <1301604855l.1593384l.0l@psu.edu>

Dear Dr. Stein,

I am using your excellent module Bio::Graphics for programming to show protein
domains. I want to put all the domains for a sequence into one track, and give
each domain (one feature here) one designated color. The following is the cold
to add_track: 

 75         $panel->add_track($seq,
 78                 -glyph    =>  'segments',
 81                 -bgcolor  => sub {
 82                     my $f = shift;
 87                     return $f->get_tag_values('color');
 88                 },
 89                 -fgcolor  => 'black',
 90                 -font2color => 'red',
 91                 -key      => "$seq",
 92                 -label    => 1,
 93                 -bump     => +1,
 94                 -height   => 8,
 95                 -description => 1,
 96 #               -part_label_merge => 1
 97                 );

Here $seq is an array reference, each element being one domain feature. I
specify the -bgcolor based on the tag 'color'  defined when domain feature was
constructed. However, it does not work. All the domains in all sequences show
the same color. Based on the document, the -glyph can be changed by calling
back the anonymous functions (I have not tried this). The color might be
changed in a similar way. Thank you in advance!

Best regards!

Zhenguo

**************************************************************
Zhenguo Zhang
Postdoctoral Scholar
Institute of Molecular Evolutionary Genetics
Penn State University
312 Mueller Lab
University Park, PA 16802
Tel: 814-865-2796
Homepage: <http://www.personal.psu.edu/zuz17/>
Lab page:  <http://homes.bio.psu.edu/people/Faculty/Nei/>