From cjfields at illinois.edu  Fri Aug  1 01:47:14 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 1 Aug 2014 01:47:14 +0000
Subject: [Bioperl-l] Bio::SearchIO::infernal.pm
In-Reply-To: <53D9B72C.2000902@gmail.com>
References: <53D9B72C.2000902@gmail.com>
Message-ID: <3F204F01-61A9-4FF4-A002-542DF332849D@illinois.edu>

Let us know if you manage to get it working, we?ll be glad to accept a patch!

chris

On Jul 30, 2014, at 10:25 PM, Ashton Trey Belew <abelew at gmail.com> wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
>  Good evening,
>  I was fiddling with cmsearch this evening and discovered that the
> current infernal parser does not play well with the new version (1.1)
> of infernal.  I am currently hacking on the function parse_latest() in
> an attempt to handle the differences in formats but have hit a bit of
> a wall in picking up the accessions and descriptions from the cmsearch
> output.
>  In a peculiar turn of events, if parse_latest does not find the
> accession/description fields, it seems to repeat the PARSER: loop
> indefinitely, in my case repeating $self->_readline on the the 10th hit.
> 
>  I will keep poking at it this evening, but if anyone has made
> greater headway, I would love some pointers.
> 
>  Thank you for your time,
> -Trey
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1
> 
> iD8DBQFT2bcsF9UIceSIYeoRArqPAKCR4ueCEKhamjkQzwHcyXWix9hy7QCgwaIf
> Icd5hZI3yARPRUpkcpHtZ2U=
> =brNJ
> -----END PGP SIGNATURE-----
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Mon Aug  4 21:05:04 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 4 Aug 2014 21:05:04 +0000
Subject: [Bioperl-l] help!
In-Reply-To: <010da15a-eecf-43d8-854c-e12134e6cd88@googlegroups.com>
References: <8DFE8929-F3F7-4D0A-AD9E-A11983020EDF@gmail.com>
	<CA+JTaox--hBLMDb6Fe=b5p0yC-ZMTGzjxfe1c-DxqM8FVQnKOQ@mail.gmail.com>
	<4F31917A.9030804@illinois.edu>
	<CA+JTaowDXGvvCJz=Jm8DbOk6urcFrzNc+4rRUKO4zqAzZRV1EA@mail.gmail.com>
	<CAM3TQQViA2jqp0qkLu+Cei30bq_=2afTESWTnUebkb1vLyrVJA@mail.gmail.com>
	<010da15a-eecf-43d8-854c-e12134e6cd88@googlegroups.com>
Message-ID: <7CF75534-70D3-4EBC-9AB0-12D5EB68783B@illinois.edu>

All,

The master branch on github is undergoing significant changes that will break your code; in short, it is missing several modules that were removed due to our work on modularization.  If you really need to grab the latest stable code, I recommend either getting the latest CPAN release (v1.6.924, just released a month ago) or using the ?v1.6.x? branch on GitHub, which we have been routinely patching with fixes to the main branch.

If needed we can switch the default checkout branch to ?v1.6.x' to make things easier (so far there has been no consensus about this, so I am leaving it as is for the time being).

chris

On Aug 1, 2014, at 1:20 PM, Tess Cherlin <tess.cherlin at gmail.com<mailto:tess.cherlin at gmail.com>> wrote:

Hi Dave, Chris, Cassandra and others,

I was following the wonderful directions that Dave wrote and have made it to an almost similar end as Cassandra.


ncfa-2-3502-ap3:~ Vi$ perl -e "use Bio::SeqIO;"
Base class package "Bio::Root::Root" is empty.
    (Perhaps you need to 'use' the module which defines that package first.)
 at /Users/Vi/bioperl-live/Bio/Location/WidestCoordPolicy.pm line 80
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Location/WidestCoordPolicy.pm line 80.
Compilation failed in require at /Users/Vi/bioperl-live/Bio/Location/Atomic.pm line 79.
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Location/Atomic.pm line 79.
Compilation failed in require at (eval 1) line 3.
    ...propagated at /System/Library/Perl/5.8.8/base.pm line 85.
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Location/Simple.pm line 87.
Compilation failed in require at /Users/Vi/bioperl-live/Bio/Factory/FTLocationFactory.pm line 97.
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Factory/FTLocationFactory.pm line 97.
Compilation failed in require at /Users/Vi/bioperl-live/Bio/SeqIO.pm line 330.
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/SeqIO.pm line 330.
Compilation failed in require at -e line 1.
BEGIN failed--compilation aborted at -e line 1.
ncfa-2-3502-ap3:~ Vi$


I see that there are many items that were not compiled "aborted", is that something I need to do separately? I'm sorry but I got lost when Dave and Chris began discussing the stuff at the bottom of this chain. So if someone could explain a solution simply I would greatly appreciate it!

Thank you!

Tess

On Tuesday, February 7, 2012 3:38:12 PM UTC-6, Dave Messina wrote:
I will take the opportunity to shamelessly pimp my no-install install
instructions (below and http://seqxml.org/xml/BioPerl.html). IMHO if
Casandra is just looking to get started with BioPerl, messing with external
libs and configs is probably overkill.

Best,
Dave


 There?s a quickie, ?zero-install? way to get BioPerl on your system.

    1) Okay, click here to download bioperl as a zip file:

    https://github.com/bioperl/bioperl-live/zipball/master

    when it's done downloading, unzip it if your computer hasn?t done it
automatically. On the
    command line, you would do:

         unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip

    or whatever the file is called. You should then have a folder with some
ugly name like

    bioperl-bioperl-live-558467a

    3) rename that to

    bioperl-live

    4) move that folder to wherever you want to keep it. I keep mine in a
directory called src in my
        home directory.

    So on my computer if I go to the command line and cd to that folder and
type pwd I get:

    /Users/dave/src/bioperl-live

    5) in the terminal, cd to your home directory.

    6) see if you have a file named .bash_profile by typing

    ls -l ~/.bash_profile

    7) if so, open that file in your favorite editor. if the file doesn't
exist, just create the file.

    8) put this line in your .bash_profile

             export PERL5LIB=/Users/dave/src/bioperl-live

    (obviously replacing my path info with wherever you chose to put
bioperl)

    9) save and close your .bash_profile

  10) open a new terminal window so that the change will take effect.

  11) on the command line of the new terminal, type

               perl -e "use Bio::SeqIO;"

    If that works, then you have "installed" bioperl. Yay!






On Tue, Feb 7, 2012 at 22:12, Scott Cain <sc... at scottcain.net<http://scottcain.net/>> wrote:

> Yes, but those doc don't address exactly the problem Cassandra is
> having, that she wants to use local::lib, but there need to be some
> prereqs installed, but they can't be because she chose to use
> local::lib, and it's not installed.  That's all fine if you're not a
> newbie and know how to properly install the prereqs before using the
> cpan shell, but when following instructions that say "use local::lib",
> I find that the instructions are completely insufficient in actually
> getting the desired software installed.  Thus the need for a good
> tutorial.
>
> Scott
>
>
> On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <cjfi... at illinois.edu<http://illinois.edu/>>
> wrote:
> > I guess one key question is where these CPAN installation instructions
> come
> > from.  They're a bit odd, and if this is from the wiki we need to do some
> > updating.
> >
> > Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
> > single perl version.
> >
> > https://metacpan.org/module/local::lib#The-bootstrapping-technique
> >
> > In my case I use perlbrew (which is all local by default, and allows
> > switching between perl versions).  Highly recommend using either simple
> > local::lib or perlbrew in combination with cpanm.
> >
> > https://metacpan.org/module/perlbrew
> > https://metacpan.org/module/cpanm
> >
> > chris
> >
> >
> >
> > On 02/07/2012 02:55 PM, Scott Cain wrote:
> >>
> >> hi Cassandra,
> >>
> >> I don't have an answer for you at the moment.  It seems to me that
> >> using local::lib is a good idea, but I've never found a good tutorial
> >> for using it, so I haven't.  Perhaps someone else on the list can
> >> suggest one.
> >>
> >> The other thing I just wanted to mention as the admin that approved
> >> your message--I came very close to deleting it from the queue without
> >> looking at it because it is not unusual for spam messages to have
> >> generic subjects like "help!"  (just for future reference :-)
> >>
> >> Scott
> >>
> >>
> >> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<kasa... at gmail.com<http://gmail.com/>>  wrote:
> >>>
> >>> Hi,
> >>>
> >>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
> >>> installed becaused I have already write some scripts but I'm biologist
> >>> so...
> >>> not pretty sure about what messages say.
> >>>
> >>> My perl version:
> >>> This is perl, v5.8.8 built for darwin-thread-multi-2level
> >>> My computer:
> >>> Mac OS X Vesion 10.5.8
> >>>
> >>> I was following this preliminary steps:
> >>>
> >>> --------------
> >>>
> >>> PRELIMINARY PREPARATION
> >>>
> >>>    This is optional, but regardless of your subsequent choice of
> >>>    installation method, it will help to carry out the following steps.
> >>>    They will increase the likelyhood of installation success
> >>>    (especially of optional dependencies).
> >>>
> >>>      * Upgrade CPAN:
> >>>
> >>>  >perl -MCPAN -e shell
> >>>  cpan>install Bundle::CPAN
> >>>  cpan>q
> >>>
> >>>      * Install/upgrade Module::Build, and make it your preferred
> >>>        installer:
> >>>
> >>>  >cpan
> >>>  cpan>install Module::Build
> >>>  cpan>o conf prefer_installer MB
> >>>  cpan>o conf commit
> >>>  cpan>q
> >>>
> >>>      * Install the expat library by whatever method is
> >>>        appropriate for your system.
> >>>
> >>>      * If your expat library is installed in a non-standard location,
> >>>        tell CPAN about it:
> >>>
> >>>  >cpan
> >>>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
> >>> EXPATINCPATH=/non-standard/include"
> >>>  cpan>o conf commit
> >>>
> >>> --------------
> >>>
> >>> And I think I did "Upgrade CPAN properly" but when I tried the next one
> >>> it
> >>> started asking too many things to me, and finally it stopped due to
> "some
> >>> problems". In text file you can see the whole process.
> >>> What did I do wrong?
> >>>
> >>>
> >>> After solving these preliminary steps, what should I do? What exactly
> >>> .tar
> >>> or .whatever should I download to install?
> >>>
> >>> I don't see the difference between installing it through "built.PL" or
> >>>  CPAN. And I don't know if I should do this or that "Fink*" stuff for
> >>> MAC.
> >>>
> >>> * I went to Fink webpage and what I expected to see was "hello!
> download
> >>> Bioperl simply clicking here!" but far from this, what it seems is that
> >>> first I have to download some kinf of Fink-program before starting with
> >>> Bioperl... is it something close to this?
> >>>
> >>> I'm sorry, too many questions... But I really want to learn to use
> >>> Bioperl
> >>> but I have no people to ask it face to face.
> >>>
> >>> Thank you so much,
> >>>
> >>> Casandra
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Biop... at lists.open-bio.org<http://lists.open-bio.org/>
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >>
> >>
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Biop... at lists.open-bio.org<http://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
> Biop... at lists.open-bio.org<http://lists.open-bio.org/>
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

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

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From antony.vincent.1 at ulaval.ca  Fri Aug  8 00:47:34 2014
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Thu, 7 Aug 2014 17:47:34 -0700 (PDT)
Subject: [Bioperl-l] fasta36 bug report
Message-ID: <1407458854921-17620.post@n3.nabble.com>

Hello,

There is a problem when I try to parse a fasta36 report. I got this error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Unrecognized alignment line (3) '>--'
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:486
STACK: Bio::SearchIO::fasta::next_result
/usr/share/perl5/Bio/SearchIO/fasta.pm:1148
STACK: ./Auto_Annot.pl:123
-----------------------------------------------------------

There is a '>--' after each alignment in fasta36 but not in fasta35. 

Consequently, I tried to parse a fasta35 alignment. There is no problem with
bioperl. However, the result is clearly not the same between both (fasta35
and fasta36).

fasta35 gives only 1 alignment: http://pastebin.com/f4NdYJCt

while fasta36 gives 3 alignments: http://pastebin.com/ADeKJ4GC

What I'm doing wrong with fasta35? It is probably not normal that it misses
almost 2 perfect alignments on 3.

Thanks you!




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From cjfields at illinois.edu  Fri Aug  8 01:46:28 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 8 Aug 2014 01:46:28 +0000
Subject: [Bioperl-l] fasta36 bug report
In-Reply-To: <1407458854921-17620.post@n3.nabble.com>
References: <1407458854921-17620.post@n3.nabble.com>
Message-ID: <95D0322A-8629-4727-8888-E182947D0A8B@illinois.edu>

Looks as if there have been major changes to fasta36, see here:

    http://faculty.virginia.edu/wrpearson/fasta/fasta36/

Note in particular point 2:


  *   Display of all significant alignments between query and library sequence. BLAST has always displayed multiple high-scoring alignments (HSPs) between the query and library sequence; previous versions of the FASTA programs displayed only the best alignment, even when other high-scoring alignments were present. This is the major change in FASTA36. For most programs (fasta36, ssearch36, [t]fast[xy]36), if the library sequence contains additional significant alignments, they will be displayed with the alignment output, and as part of -m 9 output (the initial list of high scores).

By default, the statistical threshold for alternate alignments (HSPs) is the E()-threshold / 10.0. For proteins, the default expect threshold is E()< 10.0, the secondary threshold for showing alternate alignments is thus E() < 1.0. Fror translated comparisons, the E()-thresholds are 5.0/0.5; for DNA:DNA 2.0/0.2.

Both the primary and secondary E()-thresholds are set with the -E "prim sec" command line option. If the secondary value is betwee zero and 1.0, it is taken as the actual threshold. If it is > 1.0, it is taken as a divisor for the primary threshold. If it is negative, alternative alignments are disabled and only the best alignment is shown.

I suggest submitting this as a bug report to GitHub along with the examples (use a gist, not pastebin as the latter are not around forever).  We could add support for this (it?s not very high on our priority list of fixes), but having example files helps tremendously along that path.  We also will acept any help/patches that get this working again :)

chris

On Aug 7, 2014, at 7:47 PM, Antony03 <antony.vincent.1 at ulaval.ca<mailto:antony.vincent.1 at ulaval.ca>> wrote:

Hello,

There is a problem when I try to parse a fasta36 report. I got this error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Unrecognized alignment line (3) '>--'
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:486
STACK: Bio::SearchIO::fasta::next_result
/usr/share/perl5/Bio/SearchIO/fasta.pm:1148
STACK: ./Auto_Annot.pl:123
-----------------------------------------------------------

There is a '>--' after each alignment in fasta36 but not in fasta35.

Consequently, I tried to parse a fasta35 alignment. There is no problem with
bioperl. However, the result is clearly not the same between both (fasta35
and fasta36).

fasta35 gives only 1 alignment: http://pastebin.com/f4NdYJCt

while fasta36 gives 3 alignments: http://pastebin.com/ADeKJ4GC

What I'm doing wrong with fasta35? It is probably not normal that it misses
almost 2 perfect alignments on 3.

Thanks you!




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From antony.vincent.1 at ulaval.ca  Fri Aug  8 02:29:52 2014
From: antony.vincent.1 at ulaval.ca (Antony03)
Date: Thu, 7 Aug 2014 19:29:52 -0700 (PDT)
Subject: [Bioperl-l] fasta36 bug report
In-Reply-To: <95D0322A-8629-4727-8888-E182947D0A8B@illinois.edu>
References: <1407458854921-17620.post@n3.nabble.com>
	<95D0322A-8629-4727-8888-E182947D0A8B@illinois.edu>
Message-ID: <1407464992449-17622.post@n3.nabble.com>

Thank you for the answer. Do you if I can get more significant results with
fasta35?



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From cjfields at illinois.edu  Fri Aug  8 18:18:02 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 8 Aug 2014 18:18:02 +0000
Subject: [Bioperl-l] fasta36 bug report
In-Reply-To: <1407464992449-17622.post@n3.nabble.com>
References: <1407458854921-17620.post@n3.nabble.com>
	<95D0322A-8629-4727-8888-E182947D0A8B@illinois.edu>
	<1407464992449-17622.post@n3.nabble.com>
Message-ID: <5C83FE8E-491B-454B-8D29-F4C21AC824B3@illinois.edu>

Depends on what you mean by ?significant?; this is a question that probably belongs on a forum like Biostar or seqanswers.

The main thing is that the output is different enough that the latest releases will require additional work to get parsing working, but in the end may likely be more informative.  On the other hand if you have highly repetitive data then it could generate a lot of noise.  fasta35 may be completely sufficient depending what you are trying to do (which isn?t obvious here).

chris

On Aug 7, 2014, at 9:29 PM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:

> Thank you for the answer. Do you if I can get more significant results with
> fasta35?
> 
> 
> 
> --
> View this message in context: http://bioperl.996286.n3.nabble.com/fasta36-bug-report-tp17620p17622.html
> Sent from the Bioperl-L mailing list archive at Nabble.com.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l



From sosippus at gmail.com  Mon Aug 11 13:31:37 2014
From: sosippus at gmail.com (RB)
Date: Mon, 11 Aug 2014 06:31:37 -0700 (PDT)
Subject: [Bioperl-l] 500 Can't connect to www.ncbi.nlm.nih.gov:80 (Bad
	hostname)
Message-ID: <1407763897276-17624.post@n3.nabble.com>

Hello!

I'm trying to connect to a NCBI page and retrieve some information.
Basically I want to retrieve what is under "Representative" in 
http://www.ncbi.nlm.nih.gov/genome/?term=Xylella_fastidiosa
<http://www.ncbi.nlm.nih.gov/genome/?term=Xylella_fastidiosa>  . For this
I'm trying to use LWP::Simple or LWP::UserAgent, but in no way am I able to
retrieve the HTML.

Here is my code:
-------------------------------------------------------
#!/usr/local/bin/perl
use strict;
use warnings;
use autodie;
use Data::Dump;
use LWP::Simple qw(get);

my
$content=get('http://www.ncbi.nlm.nih.gov/genome/?term=Xylella_fastidiosa');

dd $content;
-------------------------------------------------------

But I get an undef from this code. I read through  this post
<http://bioperl.996286.n3.nabble.com/Bio-Tools-Run-RemoteBlast-error-500-Can-t-connect-to-www-ncbi-nlm-nih-gov-80-td10210.html>  
and here is the result of two different pings:
-------------------------------------------------------
Pinging www.wip.ncbi.nlm.nih.gov [130.14.29.110] with 32 bytes of data:
Request timed out.
Request timed out.
Request timed out.
Request timed out.

Ping statistics for 130.14.29.110:
    Packets: Sent = 4, Received = 0, Lost = 4 (100% loss),

-------------------------------------------------------
Pinging www.google.com [173.194.112.240] with 32 bytes of data:
Reply from 173.194.112.240: bytes=32 time=46ms TTL=53
Reply from 173.194.112.240: bytes=32 time=46ms TTL=52
Reply from 173.194.112.240: bytes=32 time=45ms TTL=53
Reply from 173.194.112.240: bytes=32 time=45ms TTL=53

Ping statistics for 173.194.112.240:
    Packets: Sent = 4, Received = 4, Lost = 0 (0% loss),
Approximate round trip times in milli-seconds:
    Minimum = 45ms, Maximum = 46ms, Average = 45ms
-------------------------------------------------------

So I guess this means there is something wrong on my side? What am I doing
wrong? Thanks for all the help




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From cjfields at illinois.edu  Mon Aug 11 15:17:09 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 11 Aug 2014 15:17:09 +0000
Subject: [Bioperl-l] 500 Can't connect to www.ncbi.nlm.nih.gov:80
	(Bad	hostname)
In-Reply-To: <1407763897276-17624.post@n3.nabble.com>
References: <1407763897276-17624.post@n3.nabble.com>
Message-ID: <EAFF0984-F621-4C63-BCF0-CA4C409BB0ED@illinois.edu>

According to your script you aren?t using BioPerl but straight LWP::Simple. If you are retrieving data using NCBI eutils I suggest reading up on their documentation (which includes simple scripts to get raw data):

http://www.ncbi.nlm.nih.gov/books/NBK25500/

NCBI also allows queries via a REST API but very little of it is documented (BLAST and PubChem have some info).  I don?t suggest using that route unless you can find concrete docs describing how to query properly for your database of interest.

chris

On Aug 11, 2014, at 8:31 AM, RB <sosippus at gmail.com> wrote:

> Hello!
> 
> I'm trying to connect to a NCBI page and retrieve some information.
> Basically I want to retrieve what is under "Representative" in 
> http://www.ncbi.nlm.nih.gov/genome/?term=Xylella_fastidiosa
> <http://www.ncbi.nlm.nih.gov/genome/?term=Xylella_fastidiosa>  . For this
> I'm trying to use LWP::Simple or LWP::UserAgent, but in no way am I able to
> retrieve the HTML.
> 
> Here is my code:
> -------------------------------------------------------
> #!/usr/local/bin/perl
> use strict;
> use warnings;
> use autodie;
> use Data::Dump;
> use LWP::Simple qw(get);
> 
> my
> $content=get('http://www.ncbi.nlm.nih.gov/genome/?term=Xylella_fastidiosa');
> 
> dd $content;
> -------------------------------------------------------
> 
> But I get an undef from this code. I read through  this post
> <http://bioperl.996286.n3.nabble.com/Bio-Tools-Run-RemoteBlast-error-500-Can-t-connect-to-www-ncbi-nlm-nih-gov-80-td10210.html>  
> and here is the result of two different pings:
> -------------------------------------------------------
> Pinging www.wip.ncbi.nlm.nih.gov [130.14.29.110] with 32 bytes of data:
> Request timed out.
> Request timed out.
> Request timed out.
> Request timed out.
> 
> Ping statistics for 130.14.29.110:
>    Packets: Sent = 4, Received = 0, Lost = 4 (100% loss),
> 
> -------------------------------------------------------
> Pinging www.google.com [173.194.112.240] with 32 bytes of data:
> Reply from 173.194.112.240: bytes=32 time=46ms TTL=53
> Reply from 173.194.112.240: bytes=32 time=46ms TTL=52
> Reply from 173.194.112.240: bytes=32 time=45ms TTL=53
> Reply from 173.194.112.240: bytes=32 time=45ms TTL=53
> 
> Ping statistics for 173.194.112.240:
>    Packets: Sent = 4, Received = 4, Lost = 0 (0% loss),
> Approximate round trip times in milli-seconds:
>    Minimum = 45ms, Maximum = 46ms, Average = 45ms
> -------------------------------------------------------
> 
> So I guess this means there is something wrong on my side? What am I doing
> wrong? Thanks for all the help
> 
> 
> 
> 
> --
> View this message in context: http://bioperl.996286.n3.nabble.com/500-Can-t-connect-to-www-ncbi-nlm-nih-gov-80-Bad-hostname-tp17624.html
> Sent from the Bioperl-L mailing list archive at Nabble.com.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l



From cacaucenturion2 at gmail.com  Tue Aug 12 19:10:47 2014
From: cacaucenturion2 at gmail.com (Cacau Centurion)
Date: Tue, 12 Aug 2014 11:10:47 -0800
Subject: [Bioperl-l] Extract sequences of CDS regions from Genbank formatted
	file
Message-ID: <CA+SvvBVmmG-Ck=hYycLJhxQR0UD1O0weiX-2PqLLR6bH=1dTHA@mail.gmail.com>

Hi all,

I was wondering if there is a way to directly extract all sequences of CDS
regions from a Genbank formatted file using bioperl?

Yours,
Cacau
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From andreas.leimbach at uni-wuerzburg.de  Tue Aug 12 19:17:09 2014
From: andreas.leimbach at uni-wuerzburg.de (Andreas Leimbach)
Date: Tue, 12 Aug 2014 21:17:09 +0200
Subject: [Bioperl-l] Extract sequences of CDS regions from Genbank
 formatted file
In-Reply-To: <CA+SvvBVmmG-Ck=hYycLJhxQR0UD1O0weiX-2PqLLR6bH=1dTHA@mail.gmail.com>
References: <CA+SvvBVmmG-Ck=hYycLJhxQR0UD1O0weiX-2PqLLR6bH=1dTHA@mail.gmail.com>
Message-ID: <53EA6835.2080703@uni-wuerzburg.de>

Hi Cacau,

there are plenty. The EMBOSS package e.g. has one:
http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/extractfeat.html

There's FeatureExtract from the CBS:
http://www.cbs.dtu.dk/services/FeatureExtract/

I also wrote a script that does that with BioPerl:
https://github.com/aleimba/bac-genomics-scripts/tree/master/cds_extractor

For BioPerl, have a look at the Feature-Annotation HowTo:
http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

Best,
Andreas


--
Andreas Leimbach
Universit?t M?nster
Institut f?r Hygiene
Mendelstr. 7
D-48149 M?nster
Germany

Tel.: +49 (0)551 39 33843
E-Mail: andreas.leimbach at uni-wuerzburg.de

On 12.08.2014 21:10, Cacau Centurion wrote:
> Hi all,
>
> I was wondering if there is a way to directly extract all sequences of CDS
> regions from a Genbank formatted file using bioperl?
>
> Yours,
> Cacau
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>

From abelew at gmail.com  Tue Aug 12 19:05:33 2014
From: abelew at gmail.com (Ashton Trey Belew)
Date: Tue, 12 Aug 2014 15:05:33 -0400
Subject: [Bioperl-l] Extract sequences of CDS regions from Genbank
 formatted file
In-Reply-To: <CA+SvvBVmmG-Ck=hYycLJhxQR0UD1O0weiX-2PqLLR6bH=1dTHA@mail.gmail.com>
References: <CA+SvvBVmmG-Ck=hYycLJhxQR0UD1O0weiX-2PqLLR6bH=1dTHA@mail.gmail.com>
Message-ID: <53EA657D.4070703@gmail.com>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

  Hello Cacau,
  Attached is a script I use for exactly this purpose.  It also makes
a gff and some other stuff which might be of interest.

  It makes use of Getopt::Long and assumes you will feed it --input or
- -i followed by the genbank file.  If you forget (as I often do), it
will ask you for the genbank filename.
  If you provide -o or --output, that will be the basename of the
following output files:

  1.  A gff of all entries
  2.  A gff of all the gene entries
  3.  A gff of CDS entries
  4.  A gff of the inter-cds regions
  5.  A fasta file of all the coding sequences
  6.  A fasta file of the coding sequences as peptide sequence.

 Good luck,
 -Trey

On 08/12/2014 03:10 PM, Cacau Centurion wrote:
> Hi all,
> 
> I was wondering if there is a way to directly extract all sequences
> of CDS regions from a Genbank formatted file using bioperl?
> 
> Yours, Cacau
> 
> 
> _______________________________________________ Bioperl-l mailing
> list Bioperl-l at mailman.open-bio.org 
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
> 
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Version: GnuPG v1

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qm8OHl3RvL5+DweWcCeLSA0=
=vYIR
-----END PGP SIGNATURE-----
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From bosborne11 at verizon.net  Tue Aug 12 19:32:29 2014
From: bosborne11 at verizon.net (Brian Osborne)
Date: Tue, 12 Aug 2014 15:32:29 -0400
Subject: [Bioperl-l] Extract sequences of CDS regions from Genbank
 formatted file
In-Reply-To: <CA+SvvBVmmG-Ck=hYycLJhxQR0UD1O0weiX-2PqLLR6bH=1dTHA@mail.gmail.com>
References: <CA+SvvBVmmG-Ck=hYycLJhxQR0UD1O0weiX-2PqLLR6bH=1dTHA@mail.gmail.com>
Message-ID: <8F466787-00C0-4909-8604-B01AF1D5604D@verizon.net>

Cacau,

Oh yes, all of the Bio* languages can do this.

For an introduction to the concepts and some relevant code see:

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

Brian O.


On Aug 12, 2014, at 3:10 PM, Cacau Centurion <cacaucenturion2 at gmail.com> wrote:

> Hi all,
> 
> I was wondering if there is a way to directly extract all sequences of CDS regions from a Genbank formatted file using bioperl?
> 
> Yours,
> Cacau
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l

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From maj at fortinbras.us  Fri Aug 22 01:49:42 2014
From: maj at fortinbras.us (Mark A. Jensen)
Date: Fri, 22 Aug 2014 01:49:42 +0000
Subject: [Bioperl-l] Proposal for bioperl-run
Message-ID: <fc33cd9a3ee3903686fd2dbf32970764@mail.fortinbras.us>

All,
I'm starting to look at cleaning up bioperl-run so that, e.g., tests 
don't bork without a reasonable error message, are skipped 
appropriately, etc. As I do this, I'm finding that to fix certain 
issues, I need to consider mods to Bio::Tools::Run::WrapperBase and 
friends. Alas, these are in the bioperl-live distro!

Now, grepping for 'WrapperBase' in bioperl-live modules reveals only 
two that mention it:

Bio/Tools/Run/WrapperBase/CommandExts.pm
Bio/Tools/Run/StandAloneBlast.pm
Bio/Tools/Run/WrapperBase.pm

My simple proposal is to move these three modules from bioperl-live to 
bioperl-run. (Only AlignIO/bl2seq.pm depends on StandAloneBlast, btw).

Thoughts?
MAJ


From hartzell at alerce.com  Fri Aug 22 02:37:41 2014
From: hartzell at alerce.com (George Hartzell)
Date: Thu, 21 Aug 2014 19:37:41 -0700
Subject: [Bioperl-l] Proposal for bioperl-run
In-Reply-To: <fc33cd9a3ee3903686fd2dbf32970764@mail.fortinbras.us>
References: <fc33cd9a3ee3903686fd2dbf32970764@mail.fortinbras.us>
Message-ID: <21494.44277.720415.951390@alacrity.local>

Mark A. Jensen writes:
  > [...]
 > My simple proposal is to move these three modules from bioperl-live to 
 > bioperl-run. (Only AlignIO/bl2seq.pm depends on StandAloneBlast, btw).
 > 
 > Thoughts?
 > [...]

Speaking from a safe distance, that sounds *wonderful*.

g.


From cjfields at illinois.edu  Fri Aug 22 03:50:10 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 22 Aug 2014 03:50:10 +0000
Subject: [Bioperl-l] Proposal for bioperl-run
In-Reply-To: <21494.44277.720415.951390@alacrity.local>
References: <fc33cd9a3ee3903686fd2dbf32970764@mail.fortinbras.us>
	<21494.44277.720415.951390@alacrity.local>
Message-ID: <2B3DE68B-4BA3-4AE9-B074-1175BF62D3FA@illinois.edu>

On Aug 21, 2014, at 9:37 PM, George Hartzell <hartzell at alerce.com> wrote:

> Mark A. Jensen writes:
>> [...]
>> My simple proposal is to move these three modules from bioperl-live to 
>> bioperl-run. (Only AlignIO/bl2seq.pm depends on StandAloneBlast, btw).
>> 
>> Thoughts?
>> [...]
> 
> Speaking from a safe distance, that sounds *wonderful*.
> 
> g.

Agreed.  Also, I think you mean that StandAloneBlast has a dependency on AlignIO::bl2seq, not the other way around, correct? At least, I didn?t see anything there.

If no one objects to it (give it a day), I say go ahead and move it over.

chris

From maj at fortinbras.us  Fri Aug 22 12:09:11 2014
From: maj at fortinbras.us (Mark A. Jensen)
Date: Fri, 22 Aug 2014 08:09:11 -0400
Subject: [Bioperl-l] Proposal for bioperl-run
In-Reply-To: <2B3DE68B-4BA3-4AE9-B074-1175BF62D3FA@illinois.edu>
References: <fc33cd9a3ee3903686fd2dbf32970764@mail.fortinbras.us>
	<21494.44277.720415.951390@alacrity.local>
	<2B3DE68B-4BA3-4AE9-B074-1175BF62D3FA@illinois.edu>
Message-ID: <db64f3acf9ccda8c8748b43f97eb9fc5@mail.fortinbras.us>

Thanks Chris-- yes, you must be right. I just did a quick grep for 
"StandAloneBlast" in the modules. I will verify and leave bl2seq alone.
Will do everything in branches and then give the signal-
cheers MAJ
On 2014-08-21 23:50, Fields, Christopher J wrote:
> On Aug 21, 2014, at 9:37 PM, George Hartzell <hartzell at alerce.com> 
> wrote:
>
>> Mark A. Jensen writes:
>>> [...]
>>> My simple proposal is to move these three modules from bioperl-live 
>>> to
>>> bioperl-run. (Only AlignIO/bl2seq.pm depends on StandAloneBlast, 
>>> btw).
>>>
>>> Thoughts?
>>> [...]
>>
>> Speaking from a safe distance, that sounds *wonderful*.
>>
>> g.
>
> Agreed.  Also, I think you mean that StandAloneBlast has a dependency
> on AlignIO::bl2seq, not the other way around, correct? At least, I
> didn?t see anything there.
>
> If no one objects to it (give it a day), I say go ahead and move it 
> over.
>
> chris


From cjfields at illinois.edu  Fri Aug 22 15:38:31 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 22 Aug 2014 15:38:31 +0000
Subject: [Bioperl-l] Proposal for bioperl-run
In-Reply-To: <db64f3acf9ccda8c8748b43f97eb9fc5@mail.fortinbras.us>
References: <fc33cd9a3ee3903686fd2dbf32970764@mail.fortinbras.us>
	<21494.44277.720415.951390@alacrity.local>
	<2B3DE68B-4BA3-4AE9-B074-1175BF62D3FA@illinois.edu>
	<db64f3acf9ccda8c8748b43f97eb9fc5@mail.fortinbras.us>
Message-ID: <983AEACC-66D4-4CC4-9871-82D6FF23B628@illinois.edu>

Actually, it might be better to have all the BLAST-related stuff as one distribution, unless we can get bioperl-run installing much more cleanly (little overhead with few dependencies).  Is that what you want to do?  If so: cool!

You should have commit to bioperl-run BTW, you are listed as part of the developer team.

chris

On Aug 22, 2014, at 7:09 AM, Mark A. Jensen <maj at fortinbras.us> wrote:

> Thanks Chris-- yes, you must be right. I just did a quick grep for "StandAloneBlast" in the modules. I will verify and leave bl2seq alone.
> Will do everything in branches and then give the signal-
> cheers MAJ
> On 2014-08-21 23:50, Fields, Christopher J wrote:
>> On Aug 21, 2014, at 9:37 PM, George Hartzell <hartzell at alerce.com> wrote:
>> 
>>> Mark A. Jensen writes:
>>>> [...]
>>>> My simple proposal is to move these three modules from bioperl-live to
>>>> bioperl-run. (Only AlignIO/bl2seq.pm depends on StandAloneBlast, btw).
>>>> 
>>>> Thoughts?
>>>> [...]
>>> 
>>> Speaking from a safe distance, that sounds *wonderful*.
>>> 
>>> g.
>> 
>> Agreed.  Also, I think you mean that StandAloneBlast has a dependency
>> on AlignIO::bl2seq, not the other way around, correct? At least, I
>> didn?t see anything there.
>> 
>> If no one objects to it (give it a day), I say go ahead and move it over.
>> 
>> chris
> 



From fossandonc at hotmail.com  Fri Aug 22 15:50:49 2014
From: fossandonc at hotmail.com (=?UTF-8?Q?Francisco_J._Ossand=C3=B3n?=)
Date: Fri, 22 Aug 2014 11:50:49 -0400
Subject: [Bioperl-l] Proposal for bioperl-run
In-Reply-To: <001501cfbe15$c605c010$52114030$@fortinbras.us>
References: <fc33cd9a3ee3903686fd2dbf32970764@mail.fortinbras.us>	<21494.44277.720415.951390@alacrity.local>	<2B3DE68B-4BA3-4AE9-B074-1175BF62D3FA@illinois.edu>
	<001501cfbe15$c605c010$52114030$@fortinbras.us>
Message-ID: <SNT149-DS94D5913F66D0009EA08C8CFD00@phx.gbl>

I have also looked 

I don't mind the moving of those modules but I would like to ask something. Any future updates to the moved modules should also be added, if possible, to the modules that will remain v1.6.x branch? Or their development would be freezed?? Or should they also be removed from there too??

I've been keeping the synchronicity of updated modules that were moved out of -live into their own repo with their versions in v1.6.x branch (like Root and Coordinate), but the synch of WrapperBase when mixed into other existing repo like Run will depend on if it start to depend on code of other Run modules or not.

On a side note, I just realized that there is an empty "hmmer3.pm" file in "bioperl-live/Bio/Tools/Run"... It seems to have been added already empty in https://github.com/bioperl/bioperl-live/commit/64ab09ecd40abb8cd06e9b80aafcda323d1dc47e, maybe by mistake. It appears to be the only empty file in the repo. Should I delete it??

Cheers,

Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org [mailto:bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org] En nombre de Mark A. Jensen
Enviado el: viernes, 22 de agosto de 2014 8:09
Para: Fields, Christopher J
CC: George Hartzell; bioperl-l at mailman.open-bio.org
Asunto: Re: [Bioperl-l] Proposal for bioperl-run

Thanks Chris-- yes, you must be right. I just did a quick grep for "StandAloneBlast" in the modules. I will verify and leave bl2seq alone.
Will do everything in branches and then give the signal- cheers MAJ On 2014-08-21 23:50, Fields, Christopher J wrote:
> On Aug 21, 2014, at 9:37 PM, George Hartzell <hartzell at alerce.com>
> wrote:
>
>> Mark A. Jensen writes:
>>> [...]
>>> My simple proposal is to move these three modules from bioperl-live 
>>> to bioperl-run. (Only AlignIO/bl2seq.pm depends on StandAloneBlast, 
>>> btw).
>>>
>>> Thoughts?
>>> [...]
>>
>> Speaking from a safe distance, that sounds *wonderful*.
>>
>> g.
>
> Agreed.  Also, I think you mean that StandAloneBlast has a dependency 
> on AlignIO::bl2seq, not the other way around, correct? At least, I 
> didn?t see anything there.
>
> If no one objects to it (give it a day), I say go ahead and move it 
> over.
>
> chris

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



From maj at fortinbras.us  Fri Aug 22 15:51:48 2014
From: maj at fortinbras.us (Mark A Jensen)
Date: Fri, 22 Aug 2014 11:51:48 -0400
Subject: [Bioperl-l] Proposal for bioperl-run
In-Reply-To: <983AEACC-66D4-4CC4-9871-82D6FF23B628@illinois.edu>
References: <fc33cd9a3ee3903686fd2dbf32970764@mail.fortinbras.us>
	<21494.44277.720415.951390@alacrity.local>
	<2B3DE68B-4BA3-4AE9-B074-1175BF62D3FA@illinois.edu>
	<db64f3acf9ccda8c8748b43f97eb9fc5@mail.fortinbras.us>
	<983AEACC-66D4-4CC4-9871-82D6FF23B628@illinois.edu>
Message-ID: <c2a6ae0b0afeba6845c2a7cd4e2b94@ip-10-0-3-56>

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From cjfields at illinois.edu  Fri Aug 22 16:59:05 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 22 Aug 2014 16:59:05 +0000
Subject: [Bioperl-l] Proposal for bioperl-run
In-Reply-To: <SNT149-DS94D5913F66D0009EA08C8CFD00@phx.gbl>
References: <fc33cd9a3ee3903686fd2dbf32970764@mail.fortinbras.us>
	<21494.44277.720415.951390@alacrity.local>
	<2B3DE68B-4BA3-4AE9-B074-1175BF62D3FA@illinois.edu>
	<001501cfbe15$c605c010$52114030$@fortinbras.us>
	<SNT149-DS94D5913F66D0009EA08C8CFD00@phx.gbl>
Message-ID: <E33C56B2-1D11-4FC4-B287-5EF102358EF5@illinois.edu>

On Aug 22, 2014, at 10:50 AM, Francisco J. Ossand?n <fossandonc at hotmail.com> wrote:

> I have also looked 
> 
> I don't mind the moving of those modules but I would like to ask something. Any future updates to the moved modules should also be added, if possible, to the modules that will remain v1.6.x branch? Or their development would be freezed?? Or should they also be removed from there too??

No updates to 1.6.x if they have been moved out (with the exception of Bio::Root).

We need to end-of-life 1.6.x at some point.  It's worth having a meeting to talk about what needs to be done and to maybe discuss 1.7.x(Google or IRC).  IRC may be easier.I can set up a poll, maybe see who wants to participate...

> I've been keeping the synchronicity of updated modules that were moved out of -live into their own repo with their versions in v1.6.x branch (like Root and Coordinate), but the synch of WrapperBase when mixed into other existing repo like Run will depend on if it start to depend on code of other Run modules or not.

WrapperBase is essentially the common core for all the wrappers (a few don?t use it, but most do).  So it really belongs in bioperl-run, as well as StandAloneBlast.  The only real reason this and the other Tool::Run modules were in bioperl-live was legacy, but I think this hampers bioperl-run development frankly, as it relies on bioperl-live (via WrapperBase).  If all the wrapper code were part of bioperl-run fixes would be much easier to make and release independently.

> On a side note, I just realized that there is an empty "hmmer3.pm" file in "bioperl-live/Bio/Tools/Run"... It seems to have been added already empty in https://github.com/bioperl/bioperl-live/commit/64ab09ecd40abb8cd06e9b80aafcda323d1dc47e, maybe by mistake. It appears to be the only empty file in the repo. Should I delete it??

Yes, go ahead and do that.

-c

> Cheers,
> 
> Francisco J. Ossandon
> 
> -----Mensaje original-----
> De: bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org [mailto:bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org] En nombre de Mark A. Jensen
> Enviado el: viernes, 22 de agosto de 2014 8:09
> Para: Fields, Christopher J
> CC: George Hartzell; bioperl-l at mailman.open-bio.org
> Asunto: Re: [Bioperl-l] Proposal for bioperl-run
> 
> Thanks Chris-- yes, you must be right. I just did a quick grep for "StandAloneBlast" in the modules. I will verify and leave bl2seq alone.
> Will do everything in branches and then give the signal- cheers MAJ On 2014-08-21 23:50, Fields, Christopher J wrote:
>> On Aug 21, 2014, at 9:37 PM, George Hartzell <hartzell at alerce.com>
>> wrote:
>> 
>>> Mark A. Jensen writes:
>>>> [...]
>>>> My simple proposal is to move these three modules from bioperl-live 
>>>> to bioperl-run. (Only AlignIO/bl2seq.pm depends on StandAloneBlast, 
>>>> btw).
>>>> 
>>>> Thoughts?
>>>> [...]
>>> 
>>> Speaking from a safe distance, that sounds *wonderful*.
>>> 
>>> g.
>> 
>> Agreed.  Also, I think you mean that StandAloneBlast has a dependency 
>> on AlignIO::bl2seq, not the other way around, correct? At least, I 
>> didn?t see anything there.
>> 
>> If no one objects to it (give it a day), I say go ahead and move it 
>> over.
>> 
>> chris
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
> 



From maj at fortinbras.us  Sat Aug 23 19:29:12 2014
From: maj at fortinbras.us (Mark A. Jensen)
Date: Sat, 23 Aug 2014 15:29:12 -0400
Subject: [Bioperl-l] Proposal for bioperl-run
In-Reply-To: <E33C56B2-1D11-4FC4-B287-5EF102358EF5@illinois.edu>
References: <fc33cd9a3ee3903686fd2dbf32970764@mail.fortinbras.us>
	<21494.44277.720415.951390@alacrity.local>
	<2B3DE68B-4BA3-4AE9-B074-1175BF62D3FA@illinois.edu>
	<001501cfbe15$c605c010$52114030$@fortinbras.us>
	<SNT149-DS94D5913F66D0009EA08C8CFD00@phx.gbl>
	<E33C56B2-1D11-4FC4-B287-5EF102358EF5@illinois.edu>
Message-ID: <c9f5e888085f581b0b8afceeeabe9854@mail.fortinbras.us>

All,
Can people have a look at bioperl/bioperl-run branch 
topic/move_WrapperBase 
(https://github.com/bioperl/bioperl-run/tree/topic/move_WrapperBase) and 
see what they think. I used filter-branch to generate a (local clone of) 
bioperl-live containing only Bio/Tools/Run and t/tools, then merged this 
into a topic/move_WrapperBase branch of bioperl-run. If this looks ok, 
give me the signal and I will merge into master. Next step would be to 
remove these items from bioperl-live.

thanks MAJ


On 2014-08-22 12:59, Fields, Christopher J wrote:
> On Aug 22, 2014, at 10:50 AM, Francisco J. Ossand?n
> <fossandonc at hotmail.com> wrote:
>
>> I have also looked
>>
>> I don't mind the moving of those modules but I would like to ask 
>> something. Any future updates to the moved modules should also be 
>> added, if possible, to the modules that will remain v1.6.x branch? Or 
>> their development would be freezed?? Or should they also be removed 
>> from there too??
>
> No updates to 1.6.x if they have been moved out (with the exception
> of Bio::Root).
>
> We need to end-of-life 1.6.x at some point.  It's worth having a
> meeting to talk about what needs to be done and to maybe discuss
> 1.7.x(Google or IRC).  IRC may be easier.I can set up a poll, maybe
> see who wants to participate...
>
>> I've been keeping the synchronicity of updated modules that were 
>> moved out of -live into their own repo with their versions in v1.6.x 
>> branch (like Root and Coordinate), but the synch of WrapperBase when 
>> mixed into other existing repo like Run will depend on if it start to 
>> depend on code of other Run modules or not.
>
> WrapperBase is essentially the common core for all the wrappers (a
> few don?t use it, but most do).  So it really belongs in bioperl-run,
> as well as StandAloneBlast.  The only real reason this and the other
> Tool::Run modules were in bioperl-live was legacy, but I think this
> hampers bioperl-run development frankly, as it relies on bioperl-live
> (via WrapperBase).  If all the wrapper code were part of bioperl-run
> fixes would be much easier to make and release independently.
>
>> On a side note, I just realized that there is an empty "hmmer3.pm" 
>> file in "bioperl-live/Bio/Tools/Run"... It seems to have been added 
>> already empty in 
>> https://github.com/bioperl/bioperl-live/commit/64ab09ecd40abb8cd06e9b80aafcda323d1dc47e, 
>> maybe by mistake. It appears to be the only empty file in the repo. 
>> Should I delete it??
>
> Yes, go ahead and do that.
>
> -c
>
>> Cheers,
>>
>> Francisco J. Ossandon
>>
>> -----Mensaje original-----
>> De: bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org 
>> [mailto:bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org] 
>> En nombre de Mark A. Jensen
>> Enviado el: viernes, 22 de agosto de 2014 8:09
>> Para: Fields, Christopher J
>> CC: George Hartzell; bioperl-l at mailman.open-bio.org
>> Asunto: Re: [Bioperl-l] Proposal for bioperl-run
>>
>> Thanks Chris-- yes, you must be right. I just did a quick grep for 
>> "StandAloneBlast" in the modules. I will verify and leave bl2seq 
>> alone.
>> Will do everything in branches and then give the signal- cheers MAJ 
>> On 2014-08-21 23:50, Fields, Christopher J wrote:
>>> On Aug 21, 2014, at 9:37 PM, George Hartzell <hartzell at alerce.com>
>>> wrote:
>>>
>>>> Mark A. Jensen writes:
>>>>> [...]
>>>>> My simple proposal is to move these three modules from 
>>>>> bioperl-live
>>>>> to bioperl-run. (Only AlignIO/bl2seq.pm depends on 
>>>>> StandAloneBlast,
>>>>> btw).
>>>>>
>>>>> Thoughts?
>>>>> [...]
>>>>
>>>> Speaking from a safe distance, that sounds *wonderful*.
>>>>
>>>> g.
>>>
>>> Agreed.  Also, I think you mean that StandAloneBlast has a 
>>> dependency
>>> on AlignIO::bl2seq, not the other way around, correct? At least, I
>>> didn?t see anything there.
>>>
>>> If no one objects to it (give it a day), I say go ahead and move it
>>> over.
>>>
>>> chris
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l


From maj at fortinbras.us  Tue Aug 26 02:08:35 2014
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 25 Aug 2014 22:08:35 -0400
Subject: [Bioperl-l] Proposal for bioperl-run
In-Reply-To: <c9f5e888085f581b0b8afceeeabe9854@mail.fortinbras.us>
References: <fc33cd9a3ee3903686fd2dbf32970764@mail.fortinbras.us>
	<21494.44277.720415.951390@alacrity.local>
	<2B3DE68B-4BA3-4AE9-B074-1175BF62D3FA@illinois.edu>
	<001501cfbe15$c605c010$52114030$@fortinbras.us>
	<SNT149-DS94D5913F66D0009EA08C8CFD00@phx.gbl>
	<E33C56B2-1D11-4FC4-B287-5EF102358EF5@illinois.edu>
	<c9f5e888085f581b0b8afceeeabe9854@mail.fortinbras.us>
Message-ID: <5708c66779ccebc4b205b8b441db6518@mail.fortinbras.us>

Hearing no objections, I've merged topic/move_WrapperBase with master. 
I will proceed to remove WrapperBase and friends from bioperl-live.
MAJ
On 2014-08-23 15:29, Mark A. Jensen wrote:
> All,
> Can people have a look at bioperl/bioperl-run branch
> topic/move_WrapperBase
> (https://github.com/bioperl/bioperl-run/tree/topic/move_WrapperBase)
> and see what they think. I used filter-branch to generate a (local
> clone of) bioperl-live containing only Bio/Tools/Run and t/tools, 
> then
> merged this into a topic/move_WrapperBase branch of bioperl-run. If
> this looks ok, give me the signal and I will merge into master. Next
> step would be to remove these items from bioperl-live.
>
> thanks MAJ
>
>
> On 2014-08-22 12:59, Fields, Christopher J wrote:
>> On Aug 22, 2014, at 10:50 AM, Francisco J. Ossand?n
>> <fossandonc at hotmail.com> wrote:
>>
>>> I have also looked
>>>
>>> I don't mind the moving of those modules but I would like to ask 
>>> something. Any future updates to the moved modules should also be 
>>> added, if possible, to the modules that will remain v1.6.x branch? Or 
>>> their development would be freezed?? Or should they also be removed 
>>> from there too??
>>
>> No updates to 1.6.x if they have been moved out (with the exception
>> of Bio::Root).
>>
>> We need to end-of-life 1.6.x at some point.  It's worth having a
>> meeting to talk about what needs to be done and to maybe discuss
>> 1.7.x(Google or IRC).  IRC may be easier.I can set up a poll, maybe
>> see who wants to participate...
>>
>>> I've been keeping the synchronicity of updated modules that were 
>>> moved out of -live into their own repo with their versions in v1.6.x 
>>> branch (like Root and Coordinate), but the synch of WrapperBase when 
>>> mixed into other existing repo like Run will depend on if it start to 
>>> depend on code of other Run modules or not.
>>
>> WrapperBase is essentially the common core for all the wrappers (a
>> few don?t use it, but most do).  So it really belongs in 
>> bioperl-run,
>> as well as StandAloneBlast.  The only real reason this and the other
>> Tool::Run modules were in bioperl-live was legacy, but I think this
>> hampers bioperl-run development frankly, as it relies on 
>> bioperl-live
>> (via WrapperBase).  If all the wrapper code were part of bioperl-run
>> fixes would be much easier to make and release independently.
>>
>>> On a side note, I just realized that there is an empty "hmmer3.pm" 
>>> file in "bioperl-live/Bio/Tools/Run"... It seems to have been added 
>>> already empty in 
>>> https://github.com/bioperl/bioperl-live/commit/64ab09ecd40abb8cd06e9b80aafcda323d1dc47e, 
>>> maybe by mistake. It appears to be the only empty file in the repo. 
>>> Should I delete it??
>>
>> Yes, go ahead and do that.
>>
>> -c
>>
>>> Cheers,
>>>
>>> Francisco J. Ossandon
>>>
>>> -----Mensaje original-----
>>> De: bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org 
>>> [mailto:bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org] 
>>> En nombre de Mark A. Jensen
>>> Enviado el: viernes, 22 de agosto de 2014 8:09
>>> Para: Fields, Christopher J
>>> CC: George Hartzell; bioperl-l at mailman.open-bio.org
>>> Asunto: Re: [Bioperl-l] Proposal for bioperl-run
>>>
>>> Thanks Chris-- yes, you must be right. I just did a quick grep for 
>>> "StandAloneBlast" in the modules. I will verify and leave bl2seq 
>>> alone.
>>> Will do everything in branches and then give the signal- cheers MAJ 
>>> On 2014-08-21 23:50, Fields, Christopher J wrote:
>>>> On Aug 21, 2014, at 9:37 PM, George Hartzell <hartzell at alerce.com>
>>>> wrote:
>>>>
>>>>> Mark A. Jensen writes:
>>>>>> [...]
>>>>>> My simple proposal is to move these three modules from 
>>>>>> bioperl-live
>>>>>> to bioperl-run. (Only AlignIO/bl2seq.pm depends on 
>>>>>> StandAloneBlast,
>>>>>> btw).
>>>>>>
>>>>>> Thoughts?
>>>>>> [...]
>>>>>
>>>>> Speaking from a safe distance, that sounds *wonderful*.
>>>>>
>>>>> g.
>>>>
>>>> Agreed.  Also, I think you mean that StandAloneBlast has a 
>>>> dependency
>>>> on AlignIO::bl2seq, not the other way around, correct? At least, I
>>>> didn?t see anything there.
>>>>
>>>> If no one objects to it (give it a day), I say go ahead and move 
>>>> it
>>>> over.
>>>>
>>>> chris
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at mailman.open-bio.org
>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l


From maj at fortinbras.us  Tue Aug 26 02:46:02 2014
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 25 Aug 2014 22:46:02 -0400
Subject: [Bioperl-l] Proposal for bioperl-run
In-Reply-To: <5708c66779ccebc4b205b8b441db6518@mail.fortinbras.us>
References: <fc33cd9a3ee3903686fd2dbf32970764@mail.fortinbras.us>
	<21494.44277.720415.951390@alacrity.local>
	<2B3DE68B-4BA3-4AE9-B074-1175BF62D3FA@illinois.edu>
	<001501cfbe15$c605c010$52114030$@fortinbras.us>
	<SNT149-DS94D5913F66D0009EA08C8CFD00@phx.gbl>
	<E33C56B2-1D11-4FC4-B287-5EF102358EF5@illinois.edu>
	<c9f5e888085f581b0b8afceeeabe9854@mail.fortinbras.us>
	<5708c66779ccebc4b205b8b441db6518@mail.fortinbras.us>
Message-ID: <844a45aadf5aab2d19d2555bbfb4c35f@mail.fortinbras.us>

WrapperBase and friends removed from bioperl-live; Travis built 
successfully at #486.
MAJ
On 2014-08-25 22:08, Mark A. Jensen wrote:
> Hearing no objections, I've merged topic/move_WrapperBase with
> master. I will proceed to remove WrapperBase and friends from
> bioperl-live.
> MAJ
> On 2014-08-23 15:29, Mark A. Jensen wrote:
>> All,
>> Can people have a look at bioperl/bioperl-run branch
>> topic/move_WrapperBase
>> (https://github.com/bioperl/bioperl-run/tree/topic/move_WrapperBase)
>> and see what they think. I used filter-branch to generate a (local
>> clone of) bioperl-live containing only Bio/Tools/Run and t/tools, 
>> then
>> merged this into a topic/move_WrapperBase branch of bioperl-run. If
>> this looks ok, give me the signal and I will merge into master. Next
>> step would be to remove these items from bioperl-live.
>>
>> thanks MAJ
>>
>>
>> On 2014-08-22 12:59, Fields, Christopher J wrote:
>>> On Aug 22, 2014, at 10:50 AM, Francisco J. Ossand?n
>>> <fossandonc at hotmail.com> wrote:
>>>
>>>> I have also looked
>>>>
>>>> I don't mind the moving of those modules but I would like to ask 
>>>> something. Any future updates to the moved modules should also be 
>>>> added, if possible, to the modules that will remain v1.6.x branch? 
>>>> Or their development would be freezed?? Or should they also be 
>>>> removed from there too??
>>>
>>> No updates to 1.6.x if they have been moved out (with the exception
>>> of Bio::Root).
>>>
>>> We need to end-of-life 1.6.x at some point.  It's worth having a
>>> meeting to talk about what needs to be done and to maybe discuss
>>> 1.7.x(Google or IRC).  IRC may be easier.I can set up a poll, maybe
>>> see who wants to participate...
>>>
>>>> I've been keeping the synchronicity of updated modules that were 
>>>> moved out of -live into their own repo with their versions in v1.6.x 
>>>> branch (like Root and Coordinate), but the synch of WrapperBase when 
>>>> mixed into other existing repo like Run will depend on if it start 
>>>> to depend on code of other Run modules or not.
>>>
>>> WrapperBase is essentially the common core for all the wrappers (a
>>> few don?t use it, but most do).  So it really belongs in 
>>> bioperl-run,
>>> as well as StandAloneBlast.  The only real reason this and the 
>>> other
>>> Tool::Run modules were in bioperl-live was legacy, but I think this
>>> hampers bioperl-run development frankly, as it relies on 
>>> bioperl-live
>>> (via WrapperBase).  If all the wrapper code were part of 
>>> bioperl-run
>>> fixes would be much easier to make and release independently.
>>>
>>>> On a side note, I just realized that there is an empty "hmmer3.pm" 
>>>> file in "bioperl-live/Bio/Tools/Run"... It seems to have been added 
>>>> already empty in 
>>>> https://github.com/bioperl/bioperl-live/commit/64ab09ecd40abb8cd06e9b80aafcda323d1dc47e, 
>>>> maybe by mistake. It appears to be the only empty file in the repo. 
>>>> Should I delete it??
>>>
>>> Yes, go ahead and do that.
>>>
>>> -c
>>>
>>>> Cheers,
>>>>
>>>> Francisco J. Ossandon
>>>>
>>>> -----Mensaje original-----
>>>> De: bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org 
>>>> [mailto:bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org] 
>>>> En nombre de Mark A. Jensen
>>>> Enviado el: viernes, 22 de agosto de 2014 8:09
>>>> Para: Fields, Christopher J
>>>> CC: George Hartzell; bioperl-l at mailman.open-bio.org
>>>> Asunto: Re: [Bioperl-l] Proposal for bioperl-run
>>>>
>>>> Thanks Chris-- yes, you must be right. I just did a quick grep for 
>>>> "StandAloneBlast" in the modules. I will verify and leave bl2seq 
>>>> alone.
>>>> Will do everything in branches and then give the signal- cheers 
>>>> MAJ On 2014-08-21 23:50, Fields, Christopher J wrote:
>>>>> On Aug 21, 2014, at 9:37 PM, George Hartzell 
>>>>> <hartzell at alerce.com>
>>>>> wrote:
>>>>>
>>>>>> Mark A. Jensen writes:
>>>>>>> [...]
>>>>>>> My simple proposal is to move these three modules from 
>>>>>>> bioperl-live
>>>>>>> to bioperl-run. (Only AlignIO/bl2seq.pm depends on 
>>>>>>> StandAloneBlast,
>>>>>>> btw).
>>>>>>>
>>>>>>> Thoughts?
>>>>>>> [...]
>>>>>>
>>>>>> Speaking from a safe distance, that sounds *wonderful*.
>>>>>>
>>>>>> g.
>>>>>
>>>>> Agreed.  Also, I think you mean that StandAloneBlast has a 
>>>>> dependency
>>>>> on AlignIO::bl2seq, not the other way around, correct? At least, 
>>>>> I
>>>>> didn?t see anything there.
>>>>>
>>>>> If no one objects to it (give it a day), I say go ahead and move 
>>>>> it
>>>>> over.
>>>>>
>>>>> chris
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at mailman.open-bio.org
>>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at mailman.open-bio.org
>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l


From cjfields at illinois.edu  Tue Aug 26 04:27:55 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 26 Aug 2014 04:27:55 +0000
Subject: [Bioperl-l] Proposal for bioperl-run
In-Reply-To: <844a45aadf5aab2d19d2555bbfb4c35f@mail.fortinbras.us>
References: <fc33cd9a3ee3903686fd2dbf32970764@mail.fortinbras.us>
	<21494.44277.720415.951390@alacrity.local>
	<2B3DE68B-4BA3-4AE9-B074-1175BF62D3FA@illinois.edu>
	<001501cfbe15$c605c010$52114030$@fortinbras.us>
	<SNT149-DS94D5913F66D0009EA08C8CFD00@phx.gbl>
	<E33C56B2-1D11-4FC4-B287-5EF102358EF5@illinois.edu>
	<c9f5e888085f581b0b8afceeeabe9854@mail.fortinbras.us>
	<5708c66779ccebc4b205b8b441db6518@mail.fortinbras.us>
	<844a45aadf5aab2d19d2555bbfb4c35f@mail.fortinbras.us>
Message-ID: <52B90240-3B5C-4216-B871-2682191D7B3C@illinois.edu>

\o/

Not sure but we should probably set up Travis-CI tests for bioperl-run; lots of apps available via apt.

-c

On Aug 25, 2014, at 9:46 PM, Mark A. Jensen <maj at fortinbras.us> wrote:

> WrapperBase and friends removed from bioperl-live; Travis built successfully at #486.
> MAJ
> On 2014-08-25 22:08, Mark A. Jensen wrote:
>> Hearing no objections, I've merged topic/move_WrapperBase with
>> master. I will proceed to remove WrapperBase and friends from
>> bioperl-live.
>> MAJ
>> On 2014-08-23 15:29, Mark A. Jensen wrote:
>>> All,
>>> Can people have a look at bioperl/bioperl-run branch
>>> topic/move_WrapperBase
>>> (https://github.com/bioperl/bioperl-run/tree/topic/move_WrapperBase)
>>> and see what they think. I used filter-branch to generate a (local
>>> clone of) bioperl-live containing only Bio/Tools/Run and t/tools, then
>>> merged this into a topic/move_WrapperBase branch of bioperl-run. If
>>> this looks ok, give me the signal and I will merge into master. Next
>>> step would be to remove these items from bioperl-live.
>>> 
>>> thanks MAJ
>>> 
>>> 
>>> On 2014-08-22 12:59, Fields, Christopher J wrote:
>>>> On Aug 22, 2014, at 10:50 AM, Francisco J. Ossand?n
>>>> <fossandonc at hotmail.com> wrote:
>>>> 
>>>>> I have also looked
>>>>> 
>>>>> I don't mind the moving of those modules but I would like to ask something. Any future updates to the moved modules should also be added, if possible, to the modules that will remain v1.6.x branch? Or their development would be freezed?? Or should they also be removed from there too??
>>>> 
>>>> No updates to 1.6.x if they have been moved out (with the exception
>>>> of Bio::Root).
>>>> 
>>>> We need to end-of-life 1.6.x at some point.  It's worth having a
>>>> meeting to talk about what needs to be done and to maybe discuss
>>>> 1.7.x(Google or IRC).  IRC may be easier.I can set up a poll, maybe
>>>> see who wants to participate...
>>>> 
>>>>> I've been keeping the synchronicity of updated modules that were moved out of -live into their own repo with their versions in v1.6.x branch (like Root and Coordinate), but the synch of WrapperBase when mixed into other existing repo like Run will depend on if it start to depend on code of other Run modules or not.
>>>> 
>>>> WrapperBase is essentially the common core for all the wrappers (a
>>>> few don?t use it, but most do).  So it really belongs in bioperl-run,
>>>> as well as StandAloneBlast.  The only real reason this and the other
>>>> Tool::Run modules were in bioperl-live was legacy, but I think this
>>>> hampers bioperl-run development frankly, as it relies on bioperl-live
>>>> (via WrapperBase).  If all the wrapper code were part of bioperl-run
>>>> fixes would be much easier to make and release independently.
>>>> 
>>>>> On a side note, I just realized that there is an empty "hmmer3.pm" file in "bioperl-live/Bio/Tools/Run"... It seems to have been added already empty in https://github.com/bioperl/bioperl-live/commit/64ab09ecd40abb8cd06e9b80aafcda323d1dc47e, maybe by mistake. It appears to be the only empty file in the repo. Should I delete it??
>>>> 
>>>> Yes, go ahead and do that.
>>>> 
>>>> -c
>>>> 
>>>>> Cheers,
>>>>> 
>>>>> Francisco J. Ossandon
>>>>> 
>>>>> -----Mensaje original-----
>>>>> De: bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org [mailto:bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org] En nombre de Mark A. Jensen
>>>>> Enviado el: viernes, 22 de agosto de 2014 8:09
>>>>> Para: Fields, Christopher J
>>>>> CC: George Hartzell; bioperl-l at mailman.open-bio.org
>>>>> Asunto: Re: [Bioperl-l] Proposal for bioperl-run
>>>>> 
>>>>> Thanks Chris-- yes, you must be right. I just did a quick grep for "StandAloneBlast" in the modules. I will verify and leave bl2seq alone.
>>>>> Will do everything in branches and then give the signal- cheers MAJ On 2014-08-21 23:50, Fields, Christopher J wrote:
>>>>>> On Aug 21, 2014, at 9:37 PM, George Hartzell <hartzell at alerce.com>
>>>>>> wrote:
>>>>>> 
>>>>>>> Mark A. Jensen writes:
>>>>>>>> [...]
>>>>>>>> My simple proposal is to move these three modules from bioperl-live
>>>>>>>> to bioperl-run. (Only AlignIO/bl2seq.pm depends on StandAloneBlast,
>>>>>>>> btw).
>>>>>>>> 
>>>>>>>> Thoughts?
>>>>>>>> [...]
>>>>>>> 
>>>>>>> Speaking from a safe distance, that sounds *wonderful*.
>>>>>>> 
>>>>>>> g.
>>>>>> 
>>>>>> Agreed.  Also, I think you mean that StandAloneBlast has a dependency
>>>>>> on AlignIO::bl2seq, not the other way around, correct? At least, I
>>>>>> didn?t see anything there.
>>>>>> 
>>>>>> If no one objects to it (give it a day), I say go ahead and move it
>>>>>> over.
>>>>>> 
>>>>>> chris
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at mailman.open-bio.org
>>>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at mailman.open-bio.org
>>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at mailman.open-bio.org
>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l



From maj at fortinbras.us  Tue Aug 26 15:57:47 2014
From: maj at fortinbras.us (Mark A. Jensen)
Date: Tue, 26 Aug 2014 11:57:47 -0400
Subject: [Bioperl-l] Proposal for bioperl-run
In-Reply-To: <52B90240-3B5C-4216-B871-2682191D7B3C@illinois.edu>
References: <fc33cd9a3ee3903686fd2dbf32970764@mail.fortinbras.us>
	<21494.44277.720415.951390@alacrity.local>
	<2B3DE68B-4BA3-4AE9-B074-1175BF62D3FA@illinois.edu>
	<001501cfbe15$c605c010$52114030$@fortinbras.us>
	<SNT149-DS94D5913F66D0009EA08C8CFD00@phx.gbl>
	<E33C56B2-1D11-4FC4-B287-5EF102358EF5@illinois.edu>
	<c9f5e888085f581b0b8afceeeabe9854@mail.fortinbras.us>
	<5708c66779ccebc4b205b8b441db6518@mail.fortinbras.us>
	<844a45aadf5aab2d19d2555bbfb4c35f@mail.fortinbras.us>
	<52B90240-3B5C-4216-B871-2682191D7B3C@illinois.edu>
Message-ID: <349d4bf5b9134d413a5c2a35e2bd0a07@mail.fortinbras.us>

That's a great thought. For my next trick, I was planning ot think 
about https://github.com/bioperl/bioperl-run/issues/11 - how to deal 
with dependencies within BioPerl given the splits. I can include setting 
up travis to test in these thoughts (and perhaps actions)-- unless 
someone else is already working on this...
MAJ

On 2014-08-26 00:27, Fields, Christopher J wrote:
> \o/
>
> Not sure but we should probably set up Travis-CI tests for
> bioperl-run; lots of apps available via apt.
>
> -c
>
> On Aug 25, 2014, at 9:46 PM, Mark A. Jensen <maj at fortinbras.us> 
> wrote:
>
>> WrapperBase and friends removed from bioperl-live; Travis built 
>> successfully at #486.
>> MAJ
>> On 2014-08-25 22:08, Mark A. Jensen wrote:
>>> Hearing no objections, I've merged topic/move_WrapperBase with
>>> master. I will proceed to remove WrapperBase and friends from
>>> bioperl-live.
>>> MAJ
>>> On 2014-08-23 15:29, Mark A. Jensen wrote:
>>>> All,
>>>> Can people have a look at bioperl/bioperl-run branch
>>>> topic/move_WrapperBase
>>>> 
>>>> (https://github.com/bioperl/bioperl-run/tree/topic/move_WrapperBase)
>>>> and see what they think. I used filter-branch to generate a (local
>>>> clone of) bioperl-live containing only Bio/Tools/Run and t/tools, 
>>>> then
>>>> merged this into a topic/move_WrapperBase branch of bioperl-run. 
>>>> If
>>>> this looks ok, give me the signal and I will merge into master. 
>>>> Next
>>>> step would be to remove these items from bioperl-live.
>>>>
>>>> thanks MAJ
>>>>
>>>>
>>>> On 2014-08-22 12:59, Fields, Christopher J wrote:
>>>>> On Aug 22, 2014, at 10:50 AM, Francisco J. Ossand?n
>>>>> <fossandonc at hotmail.com> wrote:
>>>>>
>>>>>> I have also looked
>>>>>>
>>>>>> I don't mind the moving of those modules but I would like to ask 
>>>>>> something. Any future updates to the moved modules should also be 
>>>>>> added, if possible, to the modules that will remain v1.6.x branch? 
>>>>>> Or their development would be freezed?? Or should they also be 
>>>>>> removed from there too??
>>>>>
>>>>> No updates to 1.6.x if they have been moved out (with the 
>>>>> exception
>>>>> of Bio::Root).
>>>>>
>>>>> We need to end-of-life 1.6.x at some point.  It's worth having a
>>>>> meeting to talk about what needs to be done and to maybe discuss
>>>>> 1.7.x(Google or IRC).  IRC may be easier.I can set up a poll, 
>>>>> maybe
>>>>> see who wants to participate...
>>>>>
>>>>>> I've been keeping the synchronicity of updated modules that were 
>>>>>> moved out of -live into their own repo with their versions in 
>>>>>> v1.6.x branch (like Root and Coordinate), but the synch of 
>>>>>> WrapperBase when mixed into other existing repo like Run will 
>>>>>> depend on if it start to depend on code of other Run modules or 
>>>>>> not.
>>>>>
>>>>> WrapperBase is essentially the common core for all the wrappers 
>>>>> (a
>>>>> few don?t use it, but most do).  So it really belongs in 
>>>>> bioperl-run,
>>>>> as well as StandAloneBlast.  The only real reason this and the 
>>>>> other
>>>>> Tool::Run modules were in bioperl-live was legacy, but I think 
>>>>> this
>>>>> hampers bioperl-run development frankly, as it relies on 
>>>>> bioperl-live
>>>>> (via WrapperBase).  If all the wrapper code were part of 
>>>>> bioperl-run
>>>>> fixes would be much easier to make and release independently.
>>>>>
>>>>>> On a side note, I just realized that there is an empty 
>>>>>> "hmmer3.pm" file in "bioperl-live/Bio/Tools/Run"... It seems to 
>>>>>> have been added already empty in 
>>>>>> https://github.com/bioperl/bioperl-live/commit/64ab09ecd40abb8cd06e9b80aafcda323d1dc47e, 
>>>>>> maybe by mistake. It appears to be the only empty file in the 
>>>>>> repo. Should I delete it??
>>>>>
>>>>> Yes, go ahead and do that.
>>>>>
>>>>> -c
>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> Francisco J. Ossandon
>>>>>>
>>>>>> -----Mensaje original-----
>>>>>> De: 
>>>>>> bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org 
>>>>>> [mailto:bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org] 
>>>>>> En nombre de Mark A. Jensen
>>>>>> Enviado el: viernes, 22 de agosto de 2014 8:09
>>>>>> Para: Fields, Christopher J
>>>>>> CC: George Hartzell; bioperl-l at mailman.open-bio.org
>>>>>> Asunto: Re: [Bioperl-l] Proposal for bioperl-run
>>>>>>
>>>>>> Thanks Chris-- yes, you must be right. I just did a quick grep 
>>>>>> for "StandAloneBlast" in the modules. I will verify and leave 
>>>>>> bl2seq alone.
>>>>>> Will do everything in branches and then give the signal- cheers 
>>>>>> MAJ On 2014-08-21 23:50, Fields, Christopher J wrote:
>>>>>>> On Aug 21, 2014, at 9:37 PM, George Hartzell 
>>>>>>> <hartzell at alerce.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Mark A. Jensen writes:
>>>>>>>>> [...]
>>>>>>>>> My simple proposal is to move these three modules from 
>>>>>>>>> bioperl-live
>>>>>>>>> to bioperl-run. (Only AlignIO/bl2seq.pm depends on 
>>>>>>>>> StandAloneBlast,
>>>>>>>>> btw).
>>>>>>>>>
>>>>>>>>> Thoughts?
>>>>>>>>> [...]
>>>>>>>>
>>>>>>>> Speaking from a safe distance, that sounds *wonderful*.
>>>>>>>>
>>>>>>>> g.
>>>>>>>
>>>>>>> Agreed.  Also, I think you mean that StandAloneBlast has a 
>>>>>>> dependency
>>>>>>> on AlignIO::bl2seq, not the other way around, correct? At 
>>>>>>> least, I
>>>>>>> didn?t see anything there.
>>>>>>>
>>>>>>> If no one objects to it (give it a day), I say go ahead and 
>>>>>>> move it
>>>>>>> over.
>>>>>>>
>>>>>>> chris
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at mailman.open-bio.org
>>>>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at mailman.open-bio.org
>>>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at mailman.open-bio.org
>>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at mailman.open-bio.org
>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l


From bosborne11 at verizon.net  Thu Aug 28 14:21:04 2014
From: bosborne11 at verizon.net (Brian Osborne)
Date: Thu, 28 Aug 2014 10:21:04 -0400
Subject: [Bioperl-l] Add to SeqFeature::Generic?
Message-ID: <B15D1DD8-4DB5-4584-BE71-6C295C57C829@verizon.net>

All,

Some SeqFeature modules (e.g. SeqFeature::Computation) allow things like this:

my @sourcefeats = $seq->remove_SeqFeatures(?source?)

my @sourcefeats = $seq->get_SeqFeatures(?source?)

SeqFeature::Generic can?t do this. Any objection to my adding this capability to Generic?

Thanks again,

Brian O.
?



From maj at fortinbras.us  Thu Aug 28 15:13:04 2014
From: maj at fortinbras.us (Mark A Jensen)
Date: Thu, 28 Aug 2014 11:13:04 -0400
Subject: [Bioperl-l] Add to SeqFeature::Generic?
In-Reply-To: <B15D1DD8-4DB5-4584-BE71-6C295C57C829@verizon.net>
References: <B15D1DD8-4DB5-4584-BE71-6C295C57C829@verizon.net>
Message-ID: <4ed7fd8307b8e9238148658eb5aac0@ip-10-0-3-56>

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From cjfields at illinois.edu  Thu Aug 28 21:43:55 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 28 Aug 2014 21:43:55 +0000
Subject: [Bioperl-l] Add to SeqFeature::Generic?
In-Reply-To: <B15D1DD8-4DB5-4584-BE71-6C295C57C829@verizon.net>
References: <B15D1DD8-4DB5-4584-BE71-6C295C57C829@verizon.net>
Message-ID: <85A255F1-C495-44D2-8AC8-E962D0FB8C67@illinois.edu>

Seems fine; it?s essentially a convenience method that shouldn?t affect the API.

chris

On Aug 28, 2014, at 9:21 AM, Brian Osborne <bosborne11 at verizon.net> wrote:

> All,
> 
> Some SeqFeature modules (e.g. SeqFeature::Computation) allow things like this:
> 
> my @sourcefeats = $seq->remove_SeqFeatures(?source?)
> 
> my @sourcefeats = $seq->get_SeqFeatures(?source?)
> 
> SeqFeature::Generic can?t do this. Any objection to my adding this capability to Generic?
> 
> Thanks again,
> 
> Brian O.
> ?
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Sun Aug 31 01:57:46 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sun, 31 Aug 2014 01:57:46 +0000
Subject: [Bioperl-l] Whither Bio::FeatureIO?
In-Reply-To: <EC5050FA-995A-48E5-9167-6592A3A0BB75@illinois.edu>
References: <0193E1DB-1057-4974-ABEA-CF97AE9EAB1A@alerce.com>
	<36A84142-EB26-4980-B503-D20B1C8E085F@illinois.edu>
	<CA+JTaoxgv6gU5cxb1F-hQgaLwHdaOpnX3KiGqe+Xtgm2MzsRUQ@mail.gmail.com>
	<EC5050FA-995A-48E5-9167-6592A3A0BB75@illinois.edu>
Message-ID: <D44B272F-3195-486E-AD80-CBD9039DE743@illinois.edu>

Just a quick update on this: I released a separate Bio::FeatureIO release to CPAN that represents the code split out from the core modules:

   https://metacpan.org/pod/Bio::FeatureIO

I had to do some cleanup to get code to work and tests passing with some sanity.  A *lot* of things were not passing tests when we moved this over.

This should represent what was last working with Chado though.  However, I haven?t officially announced anything yet b/c I would like to shake bugs out of it. Can either of you try this out on a Chado run to make sure everything is up to snuff (or at least point out issues)?  Time depending, I would like to get something running on (for instance) Travis-CI, maybe including some optional Chado-related stuff.  This would also help so that we can work on merging what has been done on master so that these pass the same tests.

chris

On Jul 25, 2014, at 2:59 PM, Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> wrote:

The commit history is all there I believe; we could simply commit a tag pointing to the last commit prior to all the major code changes and make that a separate release (probably with a separate version, 1.7 at least).

chris

On Jul 24, 2014, at 1:53 PM, Scott Cain <scott at scottcain.net<mailto:scott at scottcain.net>> wrote:

Hi Chris,

I almost forgot about this thread.  Yes, there are still tools in the GMOD distribution (including the GFF bulk loader) that use Bio::FeatureIO.  I'm still using 1.6.901 for most things, so I've not been bitten by its being gone.  A distribution on CPAN would probably be best, and a corresponding new release of Chado (because I have all the time in the world to work on that!) to go with it.

I haven't looked--what's the state of it now?

Scott



On Thu, Jul 17, 2014 at 5:58 PM, Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> wrote:
It?s been moved to a separate github distribution, namely Bio-FeatureIO, but it was also being largely rewritten as the original implementation was never completed.  We can probably set up a branch with the relevant version of the code that should work with the script.

Scott, is this the recommended way of loading Chado data in still?  Do we need a working version of Bio::FeatureIO on CPAN so it?s available?  For some reason I thought users started going with Bio::Chado::Schema...

chris

On Jul 17, 2014, at 12:23 PM, George Hartzell <hartzell at alerce.com<mailto:hartzell at alerce.com>> wrote:

> I'm following instructions on the GMOD site to install the Chado schema and related tools.
>
> I used cpanm to install BioPerl, which gives me the current version.
>
> Various Chado-related tools, e.g. load/bin/gmod_bulk_load_gff3, require Bio::FeatureIO, which is no longer in the BioPerl distribution.
>
> I've found a GitHub repo for it, but I can't find any sign of it on CPAN.
>
> Has it ever been released?
>
> Thanks.
>
> g.
>
> Sent from a device that makes me type with two fingers.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org<mailto:Bioperl-l at mailman.open-bio.org>
> http://mailman.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

_______________________________________________
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From hartzell at alerce.com  Sun Aug 31 04:24:10 2014
From: hartzell at alerce.com (George Hartzell)
Date: Sat, 30 Aug 2014 21:24:10 -0700
Subject: [Bioperl-l] Whither Bio::FeatureIO?
In-Reply-To: <D44B272F-3195-486E-AD80-CBD9039DE743@illinois.edu>
References: <0193E1DB-1057-4974-ABEA-CF97AE9EAB1A@alerce.com>
	<36A84142-EB26-4980-B503-D20B1C8E085F@illinois.edu>
	<CA+JTaoxgv6gU5cxb1F-hQgaLwHdaOpnX3KiGqe+Xtgm2MzsRUQ@mail.gmail.com>
	<EC5050FA-995A-48E5-9167-6592A3A0BB75@illinois.edu>
	<D44B272F-3195-486E-AD80-CBD9039DE743@illinois.edu>
Message-ID: <21506.41834.519236.301093@alacrity.local>

Fields, Christopher J writes:
 > Just a quick update on this: I released a separate Bio::FeatureIO
 > release to CPAN that represents the code split out from the core
 > modules: 
 > 
 >    https://metacpan.org/pod/Bio::FeatureIO
 > 
 > I had to do some cleanup to get code to work and tests passing with
 > some sanity.  A *lot* of things were not passing tests when we
 > moved this over. 
 > 
 > This should represent what was last working with Chado though.
 > However, I haven?t officially announced anything yet b/c I would
 > like to shake bugs out of it. Can either of you try this out on a
 > Chado run to make sure everything is up to snuff (or at least point
 > out issues)?  Time depending, I would like to get something running
 > on (for instance) Travis-CI, maybe including some optional
 > Chado-related stuff.  This would also help so that we can work on
 > merging what has been done on master so that these pass the same
 > tests. 

I can't do anything until Tuesday, but will be happy to run it through
the standard Chado build process when I get back to work.

Thanks for digging into it.

g.


From lovevandu08 at gmail.com  Sun Aug 31 05:08:01 2014
From: lovevandu08 at gmail.com (vandana Baranwal)
Date: Sun, 31 Aug 2014 10:38:01 +0530
Subject: [Bioperl-l] Converting pdb files to dssp file
Message-ID: <CAPdEJuXi0drHPCU_wiN2ez-GxCSkW3572kE_PbrL30snpc_r=g@mail.gmail.com>

Hello
Is is possible to convert a pdb file int dssp file using bioperl. I
searched a lot but didn't get a fruitful answer.
I want to convert approximately 1000 pdb files into dssp files.

Any help will be highly appreciated

-- 
Thanks & Regards
Vandana Kumari
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