From scott at scottcain.net  Fri Oct  1 11:45:35 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 1 Oct 2010 11:45:35 -0400
Subject: [Bioperl-l] [Gmod-gbrowse] bp_seqfeature_delete.PL - where
	should I submit a patch?
In-Reply-To: <87782334-E5F5-4DFE-AEBD-64565D5C2F9F@sanger.ac.uk>
References: <87782334-E5F5-4DFE-AEBD-64565D5C2F9F@sanger.ac.uk>
Message-ID: <AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>

Hi Keiran,

Well, I've been told that it is easy for non-bioperl developers to use
git to commit patches, and as if to prove it, there is a very long
wiki page on the bioperl wiki describing how to use git:

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

I'm not sure what the right thing is to do; I'm cc'ing the bioperl
list to get their input.

Scott


On Fri, Oct 1, 2010 at 8:46 AM, Keiran Raine <kr2 at sanger.ac.uk> wrote:
> Hi all,
>
> Does anyone know how I should best get push a patch (new functionality) out
> for this script which is part of the BioPerl package.
>
> I've added a 'fast' option which is useful for when you want to delete a
> whole dataset. ?The problem I was having is I loaded a large set of data
> which had errors. ?To delete it I tried to use the '-t' option but this
> continually fails after several hours (eventually runs out of memory). ?To
> get round this I've added the '-f' flag which tells the script to perform
> the delete/commit on each individual feature (and associated sub-features)
> rather than attempt to do them all in a single commit.
>
> I've attached the modified version (unfortunately the formatting was kind of
> knackered so a patch file will be a bit iffy).
>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a
> charity registered in England with number 1021457 and acompany registered in
> England with number 2742969, whose registeredoffice is 215 Euston Road,
> London, NW1 2BE.
>
>
> Keiran Raine
> Senior Computer Biologist
> The Cancer Genome Project
> Ext: 7703
> kr2 at sanger.ac.uk
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



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


From dan.bolser at gmail.com  Fri Oct  1 15:14:34 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Fri, 1 Oct 2010 20:14:34 +0100
Subject: [Bioperl-l] Spam on the wiki: best way to report it?
Message-ID: <AANLkTik1panWOrmZ_hE3dnXYMCBeOTn=LGg=YSjqB2aa@mail.gmail.com>

Is there something like a spam category to report spam on the wiki?

I'm talking about this:

http://www.bioperl.org/wiki/Special:Contributions/Xiangniant


I figure this list isn't really the best place to report it all, but I
couldn't find any advice on what else to do.

Cheers,
Dan.

From cjfields at illinois.edu  Fri Oct  1 15:53:55 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 1 Oct 2010 14:53:55 -0500
Subject: [Bioperl-l] Spam on the wiki: best way to report it?
In-Reply-To: <AANLkTik1panWOrmZ_hE3dnXYMCBeOTn=LGg=YSjqB2aa@mail.gmail.com>
References: <AANLkTik1panWOrmZ_hE3dnXYMCBeOTn=LGg=YSjqB2aa@mail.gmail.com>
Message-ID: <4EC133B7-60D0-4DF3-B0F7-D1628E431397@illinois.edu>

We can delete spam and block users (I just did for that example and one other).  I'll make you a wiki admin; more hands the better!

chris

On Oct 1, 2010, at 2:14 PM, Dan Bolser wrote:

> Is there something like a spam category to report spam on the wiki?
> 
> I'm talking about this:
> 
> http://www.bioperl.org/wiki/Special:Contributions/Xiangniant
> 
> 
> I figure this list isn't really the best place to report it all, but I
> couldn't find any advice on what else to do.
> 
> 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  Fri Oct  1 15:47:31 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 1 Oct 2010 14:47:31 -0500
Subject: [Bioperl-l] [Gmod-gbrowse] bp_seqfeature_delete.PL - where
	should I submit a patch?
In-Reply-To: <AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>
References: <87782334-E5F5-4DFE-AEBD-64565D5C2F9F@sanger.ac.uk>
	<AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>
Message-ID: <1D851E84-1664-4E72-82F5-D8C75ABA3789@illinois.edu>

Keiran,

We gladly accept patches if this is easier for you.  Using git/github is one way of getting more users involved and opening up the code more; the actual barrier to submit code changes is lowered to the point where one can fork our code and hack away, then submit pull requests for those changes to be merged (all via github, using one's account).  

We are generally doing more code review these days (asking for tests, requiring passing tests for inclusion, etc), but in this case that's probably not a problem.

chris

On Oct 1, 2010, at 10:45 AM, Scott Cain wrote:

> Hi Keiran,
> 
> Well, I've been told that it is easy for non-bioperl developers to use
> git to commit patches, and as if to prove it, there is a very long
> wiki page on the bioperl wiki describing how to use git:
> 
>  http://www.bioperl.org/wiki/Using_Git
> 
> I'm not sure what the right thing is to do; I'm cc'ing the bioperl
> list to get their input.
> 
> Scott
> 
> 
> On Fri, Oct 1, 2010 at 8:46 AM, Keiran Raine <kr2 at sanger.ac.uk> wrote:
>> Hi all,
>> 
>> Does anyone know how I should best get push a patch (new functionality) out
>> for this script which is part of the BioPerl package.
>> 
>> I've added a 'fast' option which is useful for when you want to delete a
>> whole dataset.  The problem I was having is I loaded a large set of data
>> which had errors.  To delete it I tried to use the '-t' option but this
>> continually fails after several hours (eventually runs out of memory).  To
>> get round this I've added the '-f' flag which tells the script to perform
>> the delete/commit on each individual feature (and associated sub-features)
>> rather than attempt to do them all in a single commit.
>> 
>> I've attached the modified version (unfortunately the formatting was kind of
>> knackered so a patch file will be a bit iffy).
>> 
>> 
>> 
>> 
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a
>> charity registered in England with number 1021457 and acompany registered in
>> England with number 2742969, whose registeredoffice is 215 Euston Road,
>> London, NW1 2BE.
>> 
>> 
>> Keiran Raine
>> Senior Computer Biologist
>> The Cancer Genome Project
>> Ext: 7703
>> kr2 at sanger.ac.uk
>> 
>> 
>> 
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> Start uncovering the many advantages of virtual appliances
>> and start using them to simplify application deployment and
>> accelerate your shift to cloud computing.
>> http://p.sf.net/sfu/novell-sfdev2dev
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> 
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> 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 jason at bioperl.org  Fri Oct  1 17:17:36 2010
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 01 Oct 2010 14:17:36 -0700
Subject: [Bioperl-l] Bioperl sim4 parse
In-Reply-To: <A475AF196964604CAEE109F1CA0275AB1578AF1378@SJMEMXMBS10.stjude.sjcrh.local>
References: <A475AF196964604CAEE109F1CA0275AB1578AF1378@SJMEMXMBS10.stjude.sjcrh.local>
Message-ID: <4CA64FF0.2010201@bioperl.org>

Jianmin -

Your question is better addressed to the mailing list bioperl-l at bioperl.org

Please attach an example file that is attached and sample perl code you 
are using so someone can test that your problem exists with the latest code.

-jason

Wang, Jianmin wrote, On 10/1/10 1:59 PM:
> Hi, Jason and Steve,
>
> I checked the code of the sim4.pm and used it in my program.  Unforturnately, it does not work well.  When there is a single hit with a single hsp, the code does not generate the hsp correctly and many of the information are lost.  Could you help me to check the code.  For following is the sim4 output file:
>
> Warning: lowercase letter in d.fa data. Convert sequence to uppercase.
>
> seq1 = d.fa, 203 bp
> seq2 = q.fa (HWI-EAS90_614M9:2:106:16121:11311#0), 12 bp
>
>> chr18:60413870-60414073
>> HWI-EAS90_614M9:2:106:16121:11311#0
>
> 111-122  (1-12)   100%
>
>        0     .    :
>      111 CTCATATAGCTC
>          ||||||||||||
>        1 CTCATATAGCTC
>
> Warning: lowercase letter in q.fa data. Convert sequence to uppercase.
>
> seq1 = d.fa, 203 bp
> seq2 = q.fa (teat), 15 bp
>
>> chr18:60413870-60414073
>> teat
>
> 126-140  (1-15)   100%
>
>        0     .    :    .
>      126 GTGGTATACAGAGTT
>          |||||||||||||||
>        1 GTGGTATACAGAGTT
>
>
>
> I found it's impossible to get the strand and mapping position from the data.
>
> Best.
> Jianmin Wang
>
>
>
>    ________________________________
> Email Disclaimer: www.stjude.org/emaildisclaimer

-- 
Jason Stajich
jason at bioperl.org


From avilella at gmail.com  Tue Oct  5 06:00:28 2010
From: avilella at gmail.com (Albert Vilella)
Date: Tue, 5 Oct 2010 11:00:28 +0100
Subject: [Bioperl-l] bioperl version for ensembl Was: Retrieve Sequence from
	Ensembl gene id
Message-ID: <AANLkTim9rEkgWtyF-E+4pvo1G3YS9qr5fw42uFQGwEMq@mail.gmail.com>

I also tested bioperl 1.6.1 for some scripting with the Ensembl API, and it
produces a few warnings here and there, but it doesn't break anything
obvious...

On Thu, Sep 30, 2010 at 4:16 PM, Chris Fields <cjfields at illinois.edu> wrote:

> On Sep 30, 2010, at 8:36 AM, Jun Yin wrote:
>
> > Hi, Chirag,
> >
> > BioPerl does not have any module to retrieve data from Ensembl. But
> Ensembl
> > provides a BioPerl-like interface on that function.
>
> Actually, BioPerl does have Bio::Tools::Run::Ensembl, which was submitted
> by Sendu Bala a few years back.  I think it stills works rather well, at
> least tests pass.  You might get more out of using the Ensembl API directly
> as Jun states though, YMMV.
>
> BTW, the ensembl API also works with the latest bioperl code, regardless
> what the Ensembl website says (e.g. they only support v1.2.3).  Haven't
> heard more about whether this discrepancy was supposed to be addressed at
> some point.
>
> chris
>
> > You can visit Ensembl's website on how to use that module:
> > http://www.ensembl.org/info/data/api.html
> >
> > Cheers,
> > Jun Yin
> > Ph.D. student in U.C.D.
> >
> > Bioinformatics Laboratory
> > Conway Institute
> > University College Dublin
> >
> >
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org
> > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of chirag matkar
> > Sent: Thursday, September 30, 2010 1:21 PM
> > To: bioperl-l at lists.open-bio.org
> > Subject: [Bioperl-l] Retrieve Sequence from Ensembl gene id
> >
> > Hello all,
> > Is there any module to fetch dna sequence data from ensemble gene id?
> >
> > --
> > Regards,
> > Chirag Matkar
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > __________ Information from ESET Smart Security, version of virus
> signature
> > database 5377 (20100818) __________
> >
> > The message was checked by ESET Smart Security.
> >
> > http://www.eset.com
> >
> >
> >
> >
> > __________ Information from ESET Smart Security, version of virus
> signature
> > database 5377 (20100818) __________
> >
> > The message was checked by ESET Smart Security.
> >
> > http://www.eset.com
> >
> >
> >
> > __________ Information from ESET Smart Security, version of virus
> signature
> > database 5377 (20100818) __________
> >
> > The message was checked by ESET Smart Security.
> >
> > http://www.eset.com
> >
> >
> >
> > _______________________________________________
> > 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  Tue Oct  5 06:07:36 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 5 Oct 2010 11:07:36 +0100
Subject: [Bioperl-l] [Gmod-gbrowse] bp_seqfeature_delete.PL - where
	should I submit a patch?
In-Reply-To: <AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>
References: <87782334-E5F5-4DFE-AEBD-64565D5C2F9F@sanger.ac.uk>
	<AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>
Message-ID: <AANLkTinDK93L8KJZbvL-TVriEw4sNT4uJP45BzZiL9W1@mail.gmail.com>

Here is a nice SVN to GIT conversion course:

http://git.or.cz/course/svn.html


On 1 October 2010 16:45, Scott Cain <scott at scottcain.net> wrote:
> Hi Keiran,
>
> Well, I've been told that it is easy for non-bioperl developers to use
> git to commit patches, and as if to prove it, there is a very long
> wiki page on the bioperl wiki describing how to use git:
>
> ?http://www.bioperl.org/wiki/Using_Git
>
> I'm not sure what the right thing is to do; I'm cc'ing the bioperl
> list to get their input.
>
> Scott
>
>
> On Fri, Oct 1, 2010 at 8:46 AM, Keiran Raine <kr2 at sanger.ac.uk> wrote:
>> Hi all,
>>
>> Does anyone know how I should best get push a patch (new functionality) out
>> for this script which is part of the BioPerl package.
>>
>> I've added a 'fast' option which is useful for when you want to delete a
>> whole dataset. ?The problem I was having is I loaded a large set of data
>> which had errors. ?To delete it I tried to use the '-t' option but this
>> continually fails after several hours (eventually runs out of memory). ?To
>> get round this I've added the '-f' flag which tells the script to perform
>> the delete/commit on each individual feature (and associated sub-features)
>> rather than attempt to do them all in a single commit.
>>
>> I've attached the modified version (unfortunately the formatting was kind of
>> knackered so a patch file will be a bit iffy).
>>
>>
>>
>>
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a
>> charity registered in England with number 1021457 and acompany registered in
>> England with number 2742969, whose registeredoffice is 215 Euston Road,
>> London, NW1 2BE.
>>
>>
>> Keiran Raine
>> Senior Computer Biologist
>> The Cancer Genome Project
>> Ext: 7703
>> kr2 at sanger.ac.uk
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Start uncovering the many advantages of virtual appliances
>> and start using them to simplify application deployment and
>> accelerate your shift to cloud computing.
>> http://p.sf.net/sfu/novell-sfdev2dev
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>


From dan.bolser at gmail.com  Tue Oct  5 06:36:49 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 5 Oct 2010 11:36:49 +0100
Subject: [Bioperl-l] Question about Bio::Coordinate::Pair
Message-ID: <AANLkTi=fmjWt95GWw=Fe+-WVkhQYcuHPDCNxE6iLpN0w@mail.gmail.com>

Hi,

Can someone describe in a bit more detail the purpose of the Gap
sublocations that are sometimes returned by Bio::Coordinate::Pair [1]?

I found that, according to Bio::Location::Split, if the Match and Gap
sublocations have a different strand, the strand method (called via
Bio::Coordinate::Result) returns undef. This is inconsistent with the
way Bio::Coordinate::Result tends to behave. See the test script and
results below, also pasted here [2].

The question is, can I just toggle the strand of the Gap sublocation
to match that of the Match sublocation? Or does the strand of the Gap
sublocation encode some important but as yet undocumented information?
If the strand of the Gap and Match sublocations are made to match
(within Bio::Coordinate::Pair) this will simplify code that uses
Bio::Coordinate::Pair, making it more consistent, and perhaps help
with some other bugs [3].


Cheers,
Dan.

[1] http://www.bioperl.org/wiki/Module:Bio::Coordinate::Pair
[2] http://www.bioperl.org/wiki/Module_Discussion:Bio::Coordinate::Pair
[3] http://tinyurl.com/36na2cp


#!/usr/bin/perl -w

## Stress test Bio::Coordinate::Pair

use strict;
use Data::Dumper;

use Bio::Location::Simple;
use Bio::Coordinate::Pair;

## A contig
my $ctg = Bio::Location::Simple->
  new( -seq_id => 'ctg',
       -start  =>    1,
       -end    => 1001,
       -strand =>   +1,
     );

## The contigs position on a chromosome (forward)
my $ctg_on_chr_f = Bio::Location::Simple->
  new( -seq_id => 'ctg on chr r',
       -start  =>           5001,
       -end    =>           6001,
       -strand =>             +1,
     );

## The contigs position on a chromosome (reverse)
my $ctg_on_chr_r = Bio::Location::Simple->
  new( -seq_id => 'ctg on chr r',
       -start  =>           5001,
       -end    =>           6001,
       -strand =>             -1,
     );

## Coordinate mapping (forward)
my $agp_f = Bio::Coordinate::Pair->
  new( -in  => $ctg,
       -out => $ctg_on_chr_f
     );

## Coordinate mapping (reverse)
my $agp_r = Bio::Coordinate::Pair->
  new( -in  => $ctg,
       -out => $ctg_on_chr_r
     );



## A match, in contig coordinates...
my $match_on_ctg_4 = Bio::Location::Simple->
  new( -seq_id => 'hit 4',
       -start  =>     925,
       -end    =>    1125,
       -strand =>      -1,
     );

## Map it into chromosome coordinates (forward)
my $match_on_chr_4_f =
  $agp_f->map( $match_on_ctg_4 );

print Dumper $match_on_chr_4_f, "\n";

## Map it into chromosome coordinates (reverse)
my $match_on_chr_4_r =
  $agp_r->map( $match_on_ctg_4 );

print Dumper $match_on_chr_4_r, "\n";

__END__

$VAR1 = bless( {
                 '_sublocations' => [
                                      bless( {
                                               '_strand' => -1,
                                               '_seqid' => 'ctg on chr r',
                                               '_start' => 5925,
                                               '_location_type' => 'EXACT',
                                               '_end' => 6001
                                             },
'Bio::Coordinate::Result::Match' ),
                                      bless( {
                                               '_strand' => -1,
                                               '_seqid' => 'ctg',
                                               '_location_type' => 'EXACT',
                                               '_start' => 1002,
                                               '_end' => 1125
                                             }, 'Bio::Coordinate::Result::Gap' )
                                    ],
                 '_gap' => $VAR1->{'_sublocations'}[1],
                 'strand' => -1,
                 '_match' => $VAR1->{'_sublocations'}[0],
                 '_splittype' => 'JOIN'
               }, 'Bio::Coordinate::Result' );
$VAR2 = '
';
$VAR1 = bless( {
                 '_sublocations' => [
                                      bless( {
                                               '_strand' => 1,
                                               '_seqid' => 'ctg on chr r',
                                               '_start' => 5001,
                                               '_location_type' => 'EXACT',
                                               '_end' => 5077
                                             },
'Bio::Coordinate::Result::Match' ),
                                      bless( {
                                               '_strand' => -1,
                                               '_seqid' => 'ctg',
                                               '_location_type' => 'EXACT',
                                               '_start' => 1002,
                                               '_end' => 1125
                                             }, 'Bio::Coordinate::Result::Gap' )
                                    ],
                 '_gap' => $VAR1->{'_sublocations'}[1],
                 'strand' => 1,
                 '_match' => $VAR1->{'_sublocations'}[0],
                 '_splittype' => 'JOIN'
               }, 'Bio::Coordinate::Result' );
$VAR2 = '
';

From gandipalem at gmail.com  Wed Oct  6 01:35:31 2010
From: gandipalem at gmail.com (gandipalem)
Date: Tue, 5 Oct 2010 22:35:31 -0700 (PDT)
Subject: [Bioperl-l] how to identify least degeneracy for a conserved region
 among all conserved regions in an amino acid alignment?
Message-ID: <29893643.post@talk.nabble.com>


Hi,

I am new to this.

I am working on designing primers for a set of highly diverged  proteins.
I designed degenerate primers for all those proteins manually starting from
multiple sequence alignment to reverse translation of conserved regions. But
this process is very time taking and robust. I would like automate this work
PERL. But I am getting a problem were I am unable to getting the logic "how
to measure/find out the least degeneracy for a conserved region among all
conserved regions of a multiple sequence alignment?".

So can anybody tell about how to find out least degenerated conserved region
in PERL?

Thanking you

Suresh
NBPGR

-- 
View this message in context: http://old.nabble.com/how-to-identify-least-degeneracy-for-a-conserved-region-among-all-conserved-regions-in-an-amino-acid-alignment--tp29893643p29893643.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From dan.bolser at gmail.com  Thu Oct  7 10:22:04 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 7 Oct 2010 15:22:04 +0100
Subject: [Bioperl-l] Installing Bio::DB::BigWig ?
In-Reply-To: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
References: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
Message-ID: <AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>

Trying to run make in .../src/kent/src (also CC'ing BP)

Dan.

# fun for everyone!
irc://irc.perl.org/#gmod

#also good!
irc://irc.freenode.net/#bioperl

On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
> Hi,
>
> I'm having trouble installing Bio::DB::BigWig.
>
> I grabbed the jkucsc code as described here [1] and built it
> successfully after setting 'export MACHTYPE=x86_64'.
>
> I then set 'export KENT_SRC=.../src/kent/src' and called:
> cpan[1]> install Bio::DB::BigWig
>
> The error comes:
> ...
> 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: comparison is always false due to
> limited range of data type
> 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: comparison is always false due to
> limited range of data type
> 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 -m64 -mtune=generic -o
> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> .../src/kent/src/lib/x86_64/jkweb.a -lz
> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
> relocation R_X86_64_32S against `a local symbol' can not be used when
> making a shared object; recompile with -fPIC
> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
> lib/Bio/DB/BigFile.o at
> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
> ?LDS/Bio-BigFile-1.03.tar.gz
> ?./Build -- NOT OK
> ...
>
>
> I tried to 'recompile with -fPIC', but saw further errors about
> missing symbols that I can't fix.
>
> Are there some specific applications of the jkucsc package that I
> should build and install first?
>
>
> Thanks for any help,
> Dan.
>
>
> [1] http://genome.ucsc.edu/admin/git.html
>


From dan.bolser at gmail.com  Thu Oct  7 11:01:50 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 7 Oct 2010 16:01:50 +0100
Subject: [Bioperl-l] Installing Bio::DB::BigWig ?
In-Reply-To: <AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>
References: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
	<AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>
Message-ID: <AANLkTikPF=qo8dv-PXEaU71tU8UtDYXjJ6cC9DB8ranV@mail.gmail.com>

I finally found the solution to this install problem. The error
message 'recompile with -fPIC' isn't referring to the Perl code, but
rather the jkucsc code...

In the directory .../src/kent/src/inc I changed the file common.mk to
add the -fPIC option to the CFLAGS...

[me at box inc]$ diff common.mk~ common.mk
6c6
< CFLAGS=
---
> CFLAGS=-fPIC


I then went back to .../src/kent/src/lib and hit 'make clean && make'.
Finally, going back to cpan, and re-installing Bio::DB::BigWig,
everything worked.


Sorry for the confusion, but it's been a long time since I needed to
install anything 'manually' ;-)

Dan.

# fun for everyone!
irc://irc.perl.org/#gmod

#also good!
irc://irc.freenode.net/#bioperl


On 7 October 2010 15:22, Dan Bolser <dan.bolser at gmail.com> wrote:
> Trying to run make in .../src/kent/src (also CC'ing BP)
>
> Dan.
>
> # fun for everyone!
> irc://irc.perl.org/#gmod
>
> #also good!
> irc://irc.freenode.net/#bioperl
>
> On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
>> Hi,
>>
>> I'm having trouble installing Bio::DB::BigWig.
>>
>> I grabbed the jkucsc code as described here [1] and built it
>> successfully after setting 'export MACHTYPE=x86_64'.
>>
>> I then set 'export KENT_SRC=.../src/kent/src' and called:
>> cpan[1]> install Bio::DB::BigWig
>>
>> The error comes:
>> ...
>> 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: comparison is always false due to
>> limited range of data type
>> 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: comparison is always false due to
>> limited range of data type
>> 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 -m64 -mtune=generic -o
>> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
>> .../src/kent/src/lib/x86_64/jkweb.a -lz
>> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
>> relocation R_X86_64_32S against `a local symbol' can not be used when
>> making a shared object; recompile with -fPIC
>> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
>> collect2: ld returned 1 exit status
>> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
>> lib/Bio/DB/BigFile.o at
>> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
>> ?LDS/Bio-BigFile-1.03.tar.gz
>> ?./Build -- NOT OK
>> ...
>>
>>
>> I tried to 'recompile with -fPIC', but saw further errors about
>> missing symbols that I can't fix.
>>
>> Are there some specific applications of the jkucsc package that I
>> should build and install first?
>>
>>
>> Thanks for any help,
>> Dan.
>>
>>
>> [1] http://genome.ucsc.edu/admin/git.html
>>
>


From lincoln.stein at gmail.com  Thu Oct  7 14:52:09 2010
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Thu, 7 Oct 2010 14:52:09 -0400
Subject: [Bioperl-l] [Gmod-gbrowse] Installing Bio::DB::BigWig ?
In-Reply-To: <AANLkTikPF=qo8dv-PXEaU71tU8UtDYXjJ6cC9DB8ranV@mail.gmail.com>
References: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
	<AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>
	<AANLkTikPF=qo8dv-PXEaU71tU8UtDYXjJ6cC9DB8ranV@mail.gmail.com>
Message-ID: <AANLkTinXx94t-RhyYF8_f4=pdj3YZwF_1Bqfe7oJMAh8@mail.gmail.com>

Sorry, I'll fix the installation documentation to warn people about -fPIC.
This seems to be needed on some platforms and not others.

Lincoln

On Thu, Oct 7, 2010 at 11:01 AM, Dan Bolser <dan.bolser at gmail.com> wrote:

> I finally found the solution to this install problem. The error
> message 'recompile with -fPIC' isn't referring to the Perl code, but
> rather the jkucsc code...
>
> In the directory .../src/kent/src/inc I changed the file common.mk to
> add the -fPIC option to the CFLAGS...
>
> [me at box inc]$ diff common.mk~ common.mk
> 6c6
> < CFLAGS=
> ---
> > CFLAGS=-fPIC
>
>
> I then went back to .../src/kent/src/lib and hit 'make clean && make'.
> Finally, going back to cpan, and re-installing Bio::DB::BigWig,
> everything worked.
>
>
> Sorry for the confusion, but it's been a long time since I needed to
> install anything 'manually' ;-)
>
> Dan.
>
> # fun for everyone!
> irc://irc.perl.org/#gmod
>
> #also good!
> irc://irc.freenode.net/#bioperl
>
>
> On 7 October 2010 15:22, Dan Bolser <dan.bolser at gmail.com> wrote:
> > Trying to run make in .../src/kent/src (also CC'ing BP)
> >
> > Dan.
> >
> > # fun for everyone!
> > irc://irc.perl.org/#gmod
> >
> > #also good!
> > irc://irc.freenode.net/#bioperl
> >
> > On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
> >> Hi,
> >>
> >> I'm having trouble installing Bio::DB::BigWig.
> >>
> >> I grabbed the jkucsc code as described here [1] and built it
> >> successfully after setting 'export MACHTYPE=x86_64'.
> >>
> >> I then set 'export KENT_SRC=.../src/kent/src' and called:
> >> cpan[1]> install Bio::DB::BigWig
> >>
> >> The error comes:
> >> ...
> >> 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: comparison is always false due to
> >> limited range of data type
> >> 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: comparison is always false due to
> >> limited range of data type
> >> 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 -m64 -mtune=generic -o
> >> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> >> .../src/kent/src/lib/x86_64/jkweb.a -lz
> >> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
> >> relocation R_X86_64_32S against `a local symbol' can not be used when
> >> making a shared object; recompile with -fPIC
> >> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
> >> collect2: ld returned 1 exit status
> >> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
> >> lib/Bio/DB/BigFile.o at
> >> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
> >>  LDS/Bio-BigFile-1.03.tar.gz
> >>  ./Build -- NOT OK
> >> ...
> >>
> >>
> >> I tried to 'recompile with -fPIC', but saw further errors about
> >> missing symbols that I can't fix.
> >>
> >> Are there some specific applications of the jkucsc package that I
> >> should build and install first?
> >>
> >>
> >> Thanks for any help,
> >> Dan.
> >>
> >>
> >> [1] http://genome.ucsc.edu/admin/git.html
> >>
> >
>
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



-- 
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  Thu Oct  7 15:58:40 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 7 Oct 2010 20:58:40 +0100
Subject: [Bioperl-l] [Gmod-gbrowse] Installing Bio::DB::BigWig ?
In-Reply-To: <AANLkTinXx94t-RhyYF8_f4=pdj3YZwF_1Bqfe7oJMAh8@mail.gmail.com>
References: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
	<AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>
	<AANLkTikPF=qo8dv-PXEaU71tU8UtDYXjJ6cC9DB8ranV@mail.gmail.com>
	<AANLkTinXx94t-RhyYF8_f4=pdj3YZwF_1Bqfe7oJMAh8@mail.gmail.com>
Message-ID: <AANLkTi=1pnkXFf4XE6K1BgQikf40AnTfbRwzV7CAvnrz@mail.gmail.com>

On 7 October 2010 19:52, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Sorry, I'll fix the installation documentation to warn people about -fPIC.
> This seems to be needed on some platforms and not others.

No problem, thanks for the update. Perhaps it should also be added to
the jkucsc code? any harm in adding -fPIC there anyway?

Here are the details of my box:

ge-002 2.6.18-92.1.22.el5 #1 SMP Tue Dec 16 11:57:43 EST 2008 x86_64
x86_64 x86_64 GNU/Linux

gcc --version
gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)
Copyright (C) 2006 Free Software Foundation, Inc.

perl --version
This is perl, v5.8.8 built for x86_64-linux-thread-multi

jkucsc ... git rev-parse HEAD
cb419933fdc44246e6bac605e65ddc27e7683559


I made some other minor changes to the jkucsc code in an attempt to
get the whole lot to compile:

diff --git a/src/inc/common.mk b/src/inc/common.mk
index 65c9f3c..b7b5389 100644
--- a/src/inc/common.mk
+++ b/src/inc/common.mk
@@ -3,7 +3,7 @@ CC=gcc
 ifeq (${COPT},)
     COPT=-O -g
 endif
-CFLAGS=
+CFLAGS=-fPIC
 HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${M
 HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../i

diff --git a/src/oneShot/smoothWindow/smoothWindow.c b/src/oneShot/smoothWindow/
index b062c91..f0d9c49 100644
--- a/src/oneShot/smoothWindow/smoothWindow.c
+++ b/src/oneShot/smoothWindow/smoothWindow.c
@@ -80,9 +80,9 @@ while (lineFileNext(lf, &line, NULL))
     val = words[1];
     dataValue = strtod(val, &valEnd);
     if ((*val == '\0') || (*valEnd != '\0'))
-       errAbort("Not a valid float at line %d: %s\n", lineCount, words[1]);
+       errAbort("Not a valid float at line %llu: %s\n", lineCount, words[1]);
     if (Offset < 1)
-       errAbort("Illegal offset: %llu at line %d, dataValue: %g", Offset,
+       errAbort("Illegal offset: %llu at line %llu, dataValue: %g", Offset,
            lineCount, dataValue);
     verbose(3, "#\tline: %llu, offset: %llu, data: %g\n",
        lineCount, Offset, dataValue);
diff --git a/src/utils/wigAsciiCrunch/wigAsciiCrunch.c b/src/utils/wigAsciiCrunc
index 04f7692..fc86036 100644
--- a/src/utils/wigAsciiCrunch/wigAsciiCrunch.c
+++ b/src/utils/wigAsciiCrunch/wigAsciiCrunch.c
@@ -103,7 +103,7 @@ while ((wordCount = lineFileChop(lf, words)) != 0)
        if (clFixOverlap)
            {
            minPos = lastOffset;
-           verbose(1, "Removing overlap %d-%d line %d of %s\n",
+           verbose(1, "Removing overlap %ld-%ld line %d of %s\n",
                    lastOffset, offset, lf->lineIx, lf->fileName);
            }
        else


Thanks again,
Dan.

# fun for everyone!
irc://irc.perl.org/#gmod

#also good!
irc://irc.freenode.net/#bioperl


> Lincoln
>
> On Thu, Oct 7, 2010 at 11:01 AM, Dan Bolser <dan.bolser at gmail.com> wrote:
>>
>> I finally found the solution to this install problem. The error
>> message 'recompile with -fPIC' isn't referring to the Perl code, but
>> rather the jkucsc code...
>>
>> In the directory .../src/kent/src/inc I changed the file common.mk to
>> add the -fPIC option to the CFLAGS...
>>
>> [me at box inc]$ diff common.mk~ common.mk
>> 6c6
>> < CFLAGS=
>> ---
>> > CFLAGS=-fPIC
>>
>>
>> I then went back to .../src/kent/src/lib and hit 'make clean && make'.
>> Finally, going back to cpan, and re-installing Bio::DB::BigWig,
>> everything worked.
>>
>>
>> Sorry for the confusion, but it's been a long time since I needed to
>> install anything 'manually' ;-)
>>
>> Dan.
>>
>> # fun for everyone!
>> irc://irc.perl.org/#gmod
>>
>> #also good!
>> irc://irc.freenode.net/#bioperl
>>
>>
>> On 7 October 2010 15:22, Dan Bolser <dan.bolser at gmail.com> wrote:
>> > Trying to run make in .../src/kent/src (also CC'ing BP)
>> >
>> > Dan.
>> >
>> > # fun for everyone!
>> > irc://irc.perl.org/#gmod
>> >
>> > #also good!
>> > irc://irc.freenode.net/#bioperl
>> >
>> > On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
>> >> Hi,
>> >>
>> >> I'm having trouble installing Bio::DB::BigWig.
>> >>
>> >> I grabbed the jkucsc code as described here [1] and built it
>> >> successfully after setting 'export MACHTYPE=x86_64'.
>> >>
>> >> I then set 'export KENT_SRC=.../src/kent/src' and called:
>> >> cpan[1]> install Bio::DB::BigWig
>> >>
>> >> The error comes:
>> >> ...
>> >> 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: comparison is always false due to
>> >> limited range of data type
>> >> 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: comparison is always false due to
>> >> limited range of data type
>> >> 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 -m64 -mtune=generic -o
>> >> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
>> >> .../src/kent/src/lib/x86_64/jkweb.a -lz
>> >> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
>> >> relocation R_X86_64_32S against `a local symbol' can not be used when
>> >> making a shared object; recompile with -fPIC
>> >> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
>> >> collect2: ld returned 1 exit status
>> >> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
>> >> lib/Bio/DB/BigFile.o at
>> >> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
>> >> ?LDS/Bio-BigFile-1.03.tar.gz
>> >> ?./Build -- NOT OK
>> >> ...
>> >>
>> >>
>> >> I tried to 'recompile with -fPIC', but saw further errors about
>> >> missing symbols that I can't fix.
>> >>
>> >> Are there some specific applications of the jkucsc package that I
>> >> should build and install first?
>> >>
>> >>
>> >> Thanks for any help,
>> >> Dan.
>> >>
>> >>
>> >> [1] http://genome.ucsc.edu/admin/git.html
>> >>
>> >
>>
>>
>> ------------------------------------------------------------------------------
>> Beautiful is writing same markup. Internet Explorer 9 supports
>> standards for HTML5, CSS3, SVG 1.1, ?ECMAScript5, and DOM L2 & L3.
>> Spend less time writing and ?rewriting code and more time creating great
>> experiences on the web. Be a part of the beta today.
>> http://p.sf.net/sfu/beautyoftheweb
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> 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 timmcilveen at talktalk.net  Fri Oct  8 05:16:48 2010
From: timmcilveen at talktalk.net (tim)
Date: Fri, 8 Oct 2010 10:16:48 +0100
Subject: [Bioperl-l] Getting BioPerl from Github
Message-ID: <201010081016.48460.timmcilveen@talktalk.net>

Hi,
I'm not an experienced Linux user but have been trying to download Bioperl via 
GitHub as I was getting lots of errors using the package installer. It was 
suggested by a list user that I use GitHub instead.

I installed Git using Yast.

I visited this page:
http://www.bioperl.org/wiki/Using_Git 

and used the installation instructions:
$ git clone git://github.com/bioperl/bioperl-live.git
bash: $ export PERL5LIB="$HOME/src/bioperl-live:$PERL5LIB"

I tested the code:
$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;' 
but the install didn't work.
Here is the ouput from my terminal.
tim at linux-oxgy:~> su
Password: 
linux-oxgy:/home/tim # git clone git://github.com/bioperl/bioperl-live.git
Initialized empty Git repository in /home/tim/bioperl-live/.git/
remote: Counting objects: 88288, done.
remote: Compressing objects: 100% (23829/23829), done.
remote: Total 88288 (delta 66885), reused 85264 (delta 63993)
Receiving objects: 100% (88288/88288), 138.20 MiB | 1.19 MiB/s, done.
Resolving deltas: 100% (66885/66885), done.
linux-oxgy:/home/tim # bash
linux-oxgy:/home/tim # export PERL5LIB="$HOME/src/biooperl-live:$PERL5LIB"
linux-oxgy:/home/tim # perl -MBIO::Perl -le 'print Bio::Perl->VERSION;'
Can't locate BIO/Perl.pm in @INC (@INC contains: /root/src/biooperl-live 
/usr/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi 
/usr/lib/perl5/site_perl/5.12.1 /usr/lib/perl5/vendor_perl/5.12.1/x86_64-
linux-thread-multi /usr/lib/perl5/vendor_perl/5.12.1 
/usr/lib/perl5/5.12.1/x86_64-linux-thread-multi /usr/lib/perl5/5.12.1 .).
BEGIN failed--compilation aborted.
linux-oxgy:/home/tim # 

I assume that something has went wrong at this step:
To use this 'live' version of BioPerl, you need to install it (simply tell 
Perl where to find it). Assuming you checked out the code above into 
$HOME/src; set this in your .bash_profile, .profile, or .cshrc: 

How do I set things up so that the code is in $HOME/src? Where is it likely to 
be if I carried out the installation as root?

Any help would be appreciated.

Thanks,
Tim



From scott at scottcain.net  Fri Oct  8 09:14:24 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 8 Oct 2010 09:14:24 -0400
Subject: [Bioperl-l] Getting BioPerl from Github
In-Reply-To: <201010081016.48460.timmcilveen@talktalk.net>
References: <201010081016.48460.timmcilveen@talktalk.net>
Message-ID: <AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>

Hi Tim,

Could it just be that you misspelled "bioperl-live" (as biooperl-live)
in your export statement?

Scott


On Fri, Oct 8, 2010 at 5:16 AM, tim <timmcilveen at talktalk.net> wrote:
> Hi,
> I'm not an experienced Linux user but have been trying to download Bioperl via
> GitHub as I was getting lots of errors using the package installer. It was
> suggested by a list user that I use GitHub instead.
>
> I installed Git using Yast.
>
> I visited this page:
> http://www.bioperl.org/wiki/Using_Git
>
> and used the installation instructions:
> $ git clone git://github.com/bioperl/bioperl-live.git
> bash: $ export PERL5LIB="$HOME/src/bioperl-live:$PERL5LIB"
>
> I tested the code:
> $ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
> but the install didn't work.
> Here is the ouput from my terminal.
> tim at linux-oxgy:~> su
> Password:
> linux-oxgy:/home/tim # git clone git://github.com/bioperl/bioperl-live.git
> Initialized empty Git repository in /home/tim/bioperl-live/.git/
> remote: Counting objects: 88288, done.
> remote: Compressing objects: 100% (23829/23829), done.
> remote: Total 88288 (delta 66885), reused 85264 (delta 63993)
> Receiving objects: 100% (88288/88288), 138.20 MiB | 1.19 MiB/s, done.
> Resolving deltas: 100% (66885/66885), done.
> linux-oxgy:/home/tim # bash
> linux-oxgy:/home/tim # export PERL5LIB="$HOME/src/biooperl-live:$PERL5LIB"
> linux-oxgy:/home/tim # perl -MBIO::Perl -le 'print Bio::Perl->VERSION;'
> Can't locate BIO/Perl.pm in @INC (@INC contains: /root/src/biooperl-live
> /usr/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi
> /usr/lib/perl5/site_perl/5.12.1 /usr/lib/perl5/vendor_perl/5.12.1/x86_64-
> linux-thread-multi /usr/lib/perl5/vendor_perl/5.12.1
> /usr/lib/perl5/5.12.1/x86_64-linux-thread-multi /usr/lib/perl5/5.12.1 .).
> BEGIN failed--compilation aborted.
> linux-oxgy:/home/tim #
>
> I assume that something has went wrong at this step:
> To use this 'live' version of BioPerl, you need to install it (simply tell
> Perl where to find it). Assuming you checked out the code above into
> $HOME/src; set this in your .bash_profile, .profile, or .cshrc:
>
> How do I set things up so that the code is in $HOME/src? Where is it likely to
> be if I carried out the installation as root?
>
> Any help would be appreciated.
>
> Thanks,
> Tim
>
>
> _______________________________________________
> 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 pjayaraman at mcw.edu  Thu Oct  7 16:46:19 2010
From: pjayaraman at mcw.edu (Jayaraman, Pushkala)
Date: Thu, 7 Oct 2010 15:46:19 -0500
Subject: [Bioperl-l] FW: bp_genbank2gff3- Unflattening error
Message-ID: <1448A38A42714048B9C53E473E13CCF00379E83D@davis.hmgc.mcw.edu>

I apologize, 

I should have sent it to the forum first.. 

 

 

FYI.. 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala 
Sent: Thursday, October 07, 2010 3:07 PM
To: 'cjm at fruitfly.org'
Subject: bp_genbank2gff3- Unflattening error

 

Hi Chris, 

I saw your response in a  post about Unflattener.pm here;

http://generic-model-organism-system-database.450254.n5.nabble.com/genba
nk-to-gff3-conversion-problem-td460065.html

 

hence decided to fwd this to you.. 

I have no clue what is going on.. 

 

NT_010799 Unflattening error:

Details: 

------------- EXCEPTION -------------

MSG: PROBLEM, SEVERITY==1

Container feature does not spatially contain subfeature. Perhaps this is
a dicistronic gene? I am expanding the parent feature

SF [Bio::SeqFeature::Generic=HASH(0x149297a0)]: gene; CCL14

 

SF [Bio::SeqFeature::Generic=HASH(0x1492d860)]: mRNA; CCL14; chemokine
(C-C motif) ligand 14 (CCL14), transcript variant 1

 

STACK Bio::SeqFeature::Tools::Unflattener::problem
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:952

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_group
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:2170

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_groups
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1798

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1503

STACK (eval) /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:915

STACK main::unflatten_seq
/usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:914

STACK toplevel /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:411

 

 

 

 

 

I even get another error under Unflattener.pm in another region.. this
is how it is described:

 

PROBLEM:

NT_024524 Unflattening error:

Details: 

------------- EXCEPTION -------------

MSG: 1 there is a conflict with exons; there was an explicitly stated
exon with location 22748456..22748502, yet I cannot generate this exon
from the supplied mRNA locations

 

1 There are some inferred exons that are not in the explicit exon list;
they are the exons at locations:

10982777..10983033

9516278..9517506

1225346..1225429

33491613..33491816

58797942..58798087

7323184..7323367

21253638..21253755

59172140..59172196

54309290..54310329

8988942..8989171

26569087..26569218

6479986..6480032

32266760..32267377

.....

 

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1631

STACK (eval) /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:915

STACK main::unflatten_seq
/usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:914

STACK toplevel /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:411

-------------------------------------

 

 

I do not know what is going on.. is it something that the data has or
something that I am doing wrong? 

the section of the genbank file that gives out this error is pasted
below.. 

 

 

 

 

Please help,

 

 

 

 

 

gene            complement(9047672..9065992)

                     /gene="CCL14-CCL15"

                     /note="chemokine ligand 14, chemokine ligand 15

                     transcription unit"

                     /db_xref="GeneID:348249"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004166.3"

                     /db_xref="GI:34335177"

                     /db_xref="GeneID:6358"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032964.2"

                     /db_xref="GI:34335178"

                     /db_xref="GeneID:6359"

                     /db_xref="MIM:601393"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032962.2"

                     /db_xref="GI:34335175"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004167.3"

                     /db_xref="GI:34335181"

                     /db_xref="GeneID:6359"

                     /db_xref="HGNC:10613"

                     /db_xref="MIM:601393"

     gene            complement(9047672..9050719)

                     /gene="CCL14"

                     /note="chemokine (C-C motif) ligand 14; synonyms:
CC-1,

                     CC-3, CKb1, MCIF, NCC2, SY14, HCC-1, HCC-3, NCC-2,
SCYL2,

                     SCYA14"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050719))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 3"

                     /transcript_id="NM_032963.2"

                     /db_xref="GI:34335176"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     STS             9047707..9047892

                     /standard_name="STS-H22017"

                     /db_xref="UniSTS:13833"

     STS             9047767..9047885

                     /standard_name="GDB:607751"

                     /db_xref="UniSTS:158278"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_116739.1"

                     /db_xref="GI:14589961"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_004157.1"

                     /db_xref="GI:4759070"

                     /db_xref="CCDS:CCDS32624.1"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 2

                     precursor"

                     /protein_id="NP_116738.1"

                     /db_xref="GI:14589959"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

 

 

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala [mailto:pjayaraman at mcw.edu] 
Sent: Thursday, October 07, 2010 2:56 PM
To: gmod-devel at lists.sourceforge.net
Cc: gmod-gbrowse at lists.sourceforge.net
Subject: [Gmod-gbrowse] FW: bp_genbank2gff3- Unflattening error

 

I am providing the section of the genbank file here as I am not able to
attach the entire genbank file here(duh!):

 

     gene            complement(9047672..9065992)

                     /gene="CCL14-CCL15"

                     /note="chemokine ligand 14, chemokine ligand 15

                     transcription unit"

                     /db_xref="GeneID:348249"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004166.3"

                     /db_xref="GI:34335177"

                     /db_xref="GeneID:6358"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032964.2"

                     /db_xref="GI:34335178"

                     /db_xref="GeneID:6359"

                     /db_xref="MIM:601393"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032962.2"

                     /db_xref="GI:34335175"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004167.3"

                     /db_xref="GI:34335181"

                     /db_xref="GeneID:6359"

                     /db_xref="HGNC:10613"

                     /db_xref="MIM:601393"

     gene            complement(9047672..9050719)

                     /gene="CCL14"

                     /note="chemokine (C-C motif) ligand 14; synonyms:
CC-1,

                     CC-3, CKb1, MCIF, NCC2, SY14, HCC-1, HCC-3, NCC-2,
SCYL2,

                     SCYA14"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050719))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 3"

                     /transcript_id="NM_032963.2"

                     /db_xref="GI:34335176"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     STS             9047707..9047892

                     /standard_name="STS-H22017"

                     /db_xref="UniSTS:13833"

     STS             9047767..9047885

                     /standard_name="GDB:607751"

                     /db_xref="UniSTS:158278"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_116739.1"

                     /db_xref="GI:14589961"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_004157.1"

                     /db_xref="GI:4759070"

                     /db_xref="CCDS:CCDS32624.1"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 2

                     precursor"

                     /protein_id="NP_116738.1"

                     /db_xref="GI:14589959"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

 

 

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala 
Sent: Thursday, October 07, 2010 2:43 PM
To: gmod-gbrowse at lists.sourceforge.net
Subject: bp_genbank2gff3- Unflattening error

 

Hello, 

Running the bp_genbank2gff3.pm gives me:

 

NT_010799 Unflattening error:

Details: 

------------- EXCEPTION -------------

MSG: PROBLEM, SEVERITY==1

Container feature does not spatially contain subfeature. Perhaps this is
a dicistronic gene? I am expanding the parent feature

SF [Bio::SeqFeature::Generic=HASH(0x149297a0)]: gene; CCL14

 

SF [Bio::SeqFeature::Generic=HASH(0x1492d860)]: mRNA; CCL14; chemokine
(C-C motif) ligand 14 (CCL14), transcript variant 1

 

STACK Bio::SeqFeature::Tools::Unflattener::problem
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:952

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_group
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:2170

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_groups
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1798

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1503

STACK (eval) /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:915

STACK main::unflatten_seq
/usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:914

STACK toplevel /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:411

 

 

 

Ive never seen this error before and have no clue how to resolve this as
the input is a .gbk file and the script is a BIOPerl script.  Because we
seem to be losing a  lot of gene information in a particular contig. 

Am I doing anything wrong?

 

Thanks,

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

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From kai.blin at biotech.uni-tuebingen.de  Fri Oct  8 09:35:02 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Fri, 08 Oct 2010 15:35:02 +0200
Subject: [Bioperl-l] Getting BioPerl from Github
In-Reply-To: <AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>
References: <201010081016.48460.timmcilveen@talktalk.net>
	<AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>
Message-ID: <4CAF1E06.2090206@biotech.uni-tuebingen.de>

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Hash: SHA1

On 2010-10-08 15:14, Scott Cain wrote:

> Could it just be that you misspelled "bioperl-live" (as biooperl-live)
> in your export statement?

Looks mighty suspicious, indeed. Good Catch.

Also, if you install into your home directory, there's no reason at all
to do this as root, and you probably never want to do the git clone as
root. There more stuff you do as root, the more likely you're going to
shoot yourself into the foot. :)

Cheers,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universit?t T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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From David.Messina at sbc.su.se  Fri Oct  8 10:24:12 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 8 Oct 2010 16:24:12 +0200
Subject: [Bioperl-l] Getting BioPerl from Github
In-Reply-To: <AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>
References: <201010081016.48460.timmcilveen@talktalk.net>
	<AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>
Message-ID: <65D590FA-9102-4406-AA86-462CF7EFFD0C@sbc.su.se>


> Could it just be that you misspelled "bioperl-live" (as biooperl-live)
> in your export statement?


I think also the capitalization in the following statement is important. That is, -MBio::Perl not -MBIO::Perl

>> linux-oxgy:/home/tim # perl -MBIO::Perl -le 'print Bio::Perl->VERSION;'



Dave



From David.Messina at sbc.su.se  Fri Oct  8 10:37:27 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 8 Oct 2010 16:37:27 +0200
Subject: [Bioperl-l] Bio::Matrix::MatrixI
In-Reply-To: <35D95AF6C5D146479C328BBBA554FB76028C367E@mailf.lumcnet.prod.intern>
References: <35D95AF6C5D146479C328BBBA554FB76028C367E@mailf.lumcnet.prod.intern>
Message-ID: <9826175D-4FD0-44CD-9E29-348176A2C117@sbc.su.se>

Hi Anna,

You will want to use Bio::Matrix::IO to read in a Phylip matrix.

Something like:

use Bio::Matrix::IO;
my $parser = Bio::Matrix::IO->new(-format   => 'phylip',
                                  -file     => 'phylipdist.out');
my $matrix = $parser->next_matrix;


Dave


On Sep 29, 2010, at 15:28 , <A.Vakhrusheva at lumc.nl> wrote:

> Bio::Matrix::MatrixI
> 
> I have a question concerning this interface.
> 
> I want to calculate p distances matrix, but what format is acceptable
> for input? Phylip doesn't work
> 
> Anna 


From dan.bolser at gmail.com  Fri Oct  8 11:04:44 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Fri, 8 Oct 2010 16:04:44 +0100
Subject: [Bioperl-l] Question about Bio::Coordinate::Pair
In-Reply-To: <AANLkTi=fmjWt95GWw=Fe+-WVkhQYcuHPDCNxE6iLpN0w@mail.gmail.com>
References: <AANLkTi=fmjWt95GWw=Fe+-WVkhQYcuHPDCNxE6iLpN0w@mail.gmail.com>
Message-ID: <AANLkTim3fvNkvaXftcvRb0SnhATOdugtr3Z=2v8HTxrU@mail.gmail.com>

Well... I tried to toggle the strand of the gap sublocation to match
that of the match sublocation, and overall I ended up failing one test
within t/Coordinate/CoordinateMapper.t, test number 55 (line 119)...

This test actually tests for the strandedness of the gap sublocation
that I'm specifically changing because it leads to the 'unexpected'
(or at least, 'inconsistent') behaviour that I'm calling a bug (test
55 is at the end, with enough preceding context to reproduce it):

# propepide
my $match1 = Bio::Location::Simple->new
    (-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
# peptide
my $match2 = Bio::Location::Simple->new
    (-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );

ok my $pair = Bio::Coordinate::Pair->new(-in => $match1,
					 -out => $match2,
					 -negative => 0, # false, default
					);

...

#
# partial match = gap & match
#
$pos2 = Bio::Location::Simple->new
    (-start => 20, -end => 22, -strand=> -1 );

ok $res = $pair->map($pos2);

...

is $res->gap->strand, -1; # TEST 55.  Fails when I 'fix' Bio::Coordinate::Pair



In the absence of any other information, can I take this to mean that
the strand of the gap sublocations are not used for anything
significant?


Cheers,
Dan.



On 5 October 2010 11:36, Dan Bolser <dan.bolser at gmail.com> wrote:
> Hi,
>
> Can someone describe in a bit more detail the purpose of the Gap
> sublocations that are sometimes returned by Bio::Coordinate::Pair [1]?
>
> I found that, according to Bio::Location::Split, if the Match and Gap
> sublocations have a different strand, the strand method (called via
> Bio::Coordinate::Result) returns undef. This is inconsistent with the
> way Bio::Coordinate::Result tends to behave. See the test script and
> results below, also pasted here [2].
>
> The question is, can I just toggle the strand of the Gap sublocation
> to match that of the Match sublocation? Or does the strand of the Gap
> sublocation encode some important but as yet undocumented information?
> If the strand of the Gap and Match sublocations are made to match
> (within Bio::Coordinate::Pair) this will simplify code that uses
> Bio::Coordinate::Pair, making it more consistent, and perhaps help
> with some other bugs [3].
>
>
> Cheers,
> Dan.
>
> [1] http://www.bioperl.org/wiki/Module:Bio::Coordinate::Pair
> [2] http://www.bioperl.org/wiki/Module_Discussion:Bio::Coordinate::Pair
> [3] http://tinyurl.com/36na2cp
>
>
> #!/usr/bin/perl -w
>
> ## Stress test Bio::Coordinate::Pair
>
> use strict;
> use Data::Dumper;
>
> use Bio::Location::Simple;
> use Bio::Coordinate::Pair;
>
> ## A contig
> my $ctg = Bio::Location::Simple->
> ?new( -seq_id => 'ctg',
> ? ? ? -start ?=> ? ?1,
> ? ? ? -end ? ?=> 1001,
> ? ? ? -strand => ? +1,
> ? ? );
>
> ## The contigs position on a chromosome (forward)
> my $ctg_on_chr_f = Bio::Location::Simple->
> ?new( -seq_id => 'ctg on chr r',
> ? ? ? -start ?=> ? ? ? ? ? 5001,
> ? ? ? -end ? ?=> ? ? ? ? ? 6001,
> ? ? ? -strand => ? ? ? ? ? ? +1,
> ? ? );
>
> ## The contigs position on a chromosome (reverse)
> my $ctg_on_chr_r = Bio::Location::Simple->
> ?new( -seq_id => 'ctg on chr r',
> ? ? ? -start ?=> ? ? ? ? ? 5001,
> ? ? ? -end ? ?=> ? ? ? ? ? 6001,
> ? ? ? -strand => ? ? ? ? ? ? -1,
> ? ? );
>
> ## Coordinate mapping (forward)
> my $agp_f = Bio::Coordinate::Pair->
> ?new( -in ?=> $ctg,
> ? ? ? -out => $ctg_on_chr_f
> ? ? );
>
> ## Coordinate mapping (reverse)
> my $agp_r = Bio::Coordinate::Pair->
> ?new( -in ?=> $ctg,
> ? ? ? -out => $ctg_on_chr_r
> ? ? );
>
>
>
> ## A match, in contig coordinates...
> my $match_on_ctg_4 = Bio::Location::Simple->
> ?new( -seq_id => 'hit 4',
> ? ? ? -start ?=> ? ? 925,
> ? ? ? -end ? ?=> ? ?1125,
> ? ? ? -strand => ? ? ?-1,
> ? ? );
>
> ## Map it into chromosome coordinates (forward)
> my $match_on_chr_4_f =
> ?$agp_f->map( $match_on_ctg_4 );
>
> print Dumper $match_on_chr_4_f, "\n";
>
> ## Map it into chromosome coordinates (reverse)
> my $match_on_chr_4_r =
> ?$agp_r->map( $match_on_ctg_4 );
>
> print Dumper $match_on_chr_4_r, "\n";
>
> __END__
>
> $VAR1 = bless( {
> ? ? ? ? ? ? ? ? '_sublocations' => [
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg on chr r',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 5925,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 6001
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? },
> 'Bio::Coordinate::Result::Match' ),
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 1002,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 1125
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result::Gap' )
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?],
> ? ? ? ? ? ? ? ? '_gap' => $VAR1->{'_sublocations'}[1],
> ? ? ? ? ? ? ? ? 'strand' => -1,
> ? ? ? ? ? ? ? ? '_match' => $VAR1->{'_sublocations'}[0],
> ? ? ? ? ? ? ? ? '_splittype' => 'JOIN'
> ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result' );
> $VAR2 = '
> ';
> $VAR1 = bless( {
> ? ? ? ? ? ? ? ? '_sublocations' => [
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => 1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg on chr r',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 5001,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 5077
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? },
> 'Bio::Coordinate::Result::Match' ),
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 1002,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 1125
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result::Gap' )
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?],
> ? ? ? ? ? ? ? ? '_gap' => $VAR1->{'_sublocations'}[1],
> ? ? ? ? ? ? ? ? 'strand' => 1,
> ? ? ? ? ? ? ? ? '_match' => $VAR1->{'_sublocations'}[0],
> ? ? ? ? ? ? ? ? '_splittype' => 'JOIN'
> ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result' );
> $VAR2 = '
> ';
>


From cjfields at illinois.edu  Fri Oct  8 11:16:21 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 8 Oct 2010 10:16:21 -0500
Subject: [Bioperl-l] Bio::Matrix::MatrixI
In-Reply-To: <9826175D-4FD0-44CD-9E29-348176A2C117@sbc.su.se>
References: <35D95AF6C5D146479C328BBBA554FB76028C367E@mailf.lumcnet.prod.intern>
	<9826175D-4FD0-44CD-9E29-348176A2C117@sbc.su.se>
Message-ID: <D4BC1FC6-2A66-4F26-ABF3-EB6D6CD65FE9@illinois.edu>

Correct, MatrixI (and pretty much any other module 'FooI') are interfaces for API consistency.

chris

On Oct 8, 2010, at 9:37 AM, Dave Messina wrote:

> Hi Anna,
> 
> You will want to use Bio::Matrix::IO to read in a Phylip matrix.
> 
> Something like:
> 
> use Bio::Matrix::IO;
> my $parser = Bio::Matrix::IO->new(-format   => 'phylip',
>                                  -file     => 'phylipdist.out');
> my $matrix = $parser->next_matrix;
> 
> 
> Dave
> 
> 
> On Sep 29, 2010, at 15:28 , <A.Vakhrusheva at lumc.nl> wrote:
> 
>> Bio::Matrix::MatrixI
>> 
>> I have a question concerning this interface.
>> 
>> I want to calculate p distances matrix, but what format is acceptable
>> for input? Phylip doesn't work
>> 
>> Anna 
> 
> _______________________________________________
> 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  Fri Oct  8 11:57:38 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Fri, 8 Oct 2010 16:57:38 +0100
Subject: [Bioperl-l] Question about Bio::Coordinate::Pair
In-Reply-To: <AANLkTim3fvNkvaXftcvRb0SnhATOdugtr3Z=2v8HTxrU@mail.gmail.com>
References: <AANLkTi=fmjWt95GWw=Fe+-WVkhQYcuHPDCNxE6iLpN0w@mail.gmail.com>
	<AANLkTim3fvNkvaXftcvRb0SnhATOdugtr3Z=2v8HTxrU@mail.gmail.com>
Message-ID: <AANLkTimFqsJbpZ802GzKPUAnhKHUgyjRvyg3bJNPEQNL@mail.gmail.com>

Actually, I changed the Strand of the gap in a few more places [1],
and now there are a total of 4 failed tests, however, they all appear
to be of the same form as the one reported below:


not ok 84
#   Failed test at t/Coordinate/CoordinateMapper.t line 229.
#          got: '1'
#     expected: '-1'

not ok 93
#   Failed test at t/Coordinate/CoordinateMapper.t line 246.
#          got: '1'
#     expected: '-1'

not ok 99
#   Failed test at t/Coordinate/CoordinateMapper.t line 262.
#          got: '1'
#     expected: '-1'

not ok 102
#   Failed test at t/Coordinate/CoordinateMapper.t line 265.
#          got: '1'
#     expected: '-1'


So now you know.


Dan.

[1] http://github.com/dbolser/bioperl-live/tree/dbolser_bio_coordinate_pair_tests

On 8 October 2010 16:04, Dan Bolser <dan.bolser at gmail.com> wrote:
> Well... I tried to toggle the strand of the gap sublocation to match
> that of the match sublocation, and overall I ended up failing one test
> within t/Coordinate/CoordinateMapper.t, test number 55 (line 119)...
>
> This test actually tests for the strandedness of the gap sublocation
> that I'm specifically changing because it leads to the 'unexpected'
> (or at least, 'inconsistent') behaviour that I'm calling a bug (test
> 55 is at the end, with enough preceding context to reproduce it):
>
> # propepide
> my $match1 = Bio::Location::Simple->new
> ? ?(-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
> # peptide
> my $match2 = Bio::Location::Simple->new
> ? ?(-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );
>
> ok my $pair = Bio::Coordinate::Pair->new(-in => $match1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -out => $match2,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -negative => 0, # false, default
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?);
>
> ...
>
> #
> # partial match = gap & match
> #
> $pos2 = Bio::Location::Simple->new
> ? ?(-start => 20, -end => 22, -strand=> -1 );
>
> ok $res = $pair->map($pos2);
>
> ...
>
> is $res->gap->strand, -1; # TEST 55. ?Fails when I 'fix' Bio::Coordinate::Pair
>
>
>
> In the absence of any other information, can I take this to mean that
> the strand of the gap sublocations are not used for anything
> significant?
>
>
> Cheers,
> Dan.
>
>
>
> On 5 October 2010 11:36, Dan Bolser <dan.bolser at gmail.com> wrote:
>> Hi,
>>
>> Can someone describe in a bit more detail the purpose of the Gap
>> sublocations that are sometimes returned by Bio::Coordinate::Pair [1]?
>>
>> I found that, according to Bio::Location::Split, if the Match and Gap
>> sublocations have a different strand, the strand method (called via
>> Bio::Coordinate::Result) returns undef. This is inconsistent with the
>> way Bio::Coordinate::Result tends to behave. See the test script and
>> results below, also pasted here [2].
>>
>> The question is, can I just toggle the strand of the Gap sublocation
>> to match that of the Match sublocation? Or does the strand of the Gap
>> sublocation encode some important but as yet undocumented information?
>> If the strand of the Gap and Match sublocations are made to match
>> (within Bio::Coordinate::Pair) this will simplify code that uses
>> Bio::Coordinate::Pair, making it more consistent, and perhaps help
>> with some other bugs [3].
>>
>>
>> Cheers,
>> Dan.
>>
>> [1] http://www.bioperl.org/wiki/Module:Bio::Coordinate::Pair
>> [2] http://www.bioperl.org/wiki/Module_Discussion:Bio::Coordinate::Pair
>> [3] http://tinyurl.com/36na2cp
>>
>>
>> #!/usr/bin/perl -w
>>
>> ## Stress test Bio::Coordinate::Pair
>>
>> use strict;
>> use Data::Dumper;
>>
>> use Bio::Location::Simple;
>> use Bio::Coordinate::Pair;
>>
>> ## A contig
>> my $ctg = Bio::Location::Simple->
>> ?new( -seq_id => 'ctg',
>> ? ? ? -start ?=> ? ?1,
>> ? ? ? -end ? ?=> 1001,
>> ? ? ? -strand => ? +1,
>> ? ? );
>>
>> ## The contigs position on a chromosome (forward)
>> my $ctg_on_chr_f = Bio::Location::Simple->
>> ?new( -seq_id => 'ctg on chr r',
>> ? ? ? -start ?=> ? ? ? ? ? 5001,
>> ? ? ? -end ? ?=> ? ? ? ? ? 6001,
>> ? ? ? -strand => ? ? ? ? ? ? +1,
>> ? ? );
>>
>> ## The contigs position on a chromosome (reverse)
>> my $ctg_on_chr_r = Bio::Location::Simple->
>> ?new( -seq_id => 'ctg on chr r',
>> ? ? ? -start ?=> ? ? ? ? ? 5001,
>> ? ? ? -end ? ?=> ? ? ? ? ? 6001,
>> ? ? ? -strand => ? ? ? ? ? ? -1,
>> ? ? );
>>
>> ## Coordinate mapping (forward)
>> my $agp_f = Bio::Coordinate::Pair->
>> ?new( -in ?=> $ctg,
>> ? ? ? -out => $ctg_on_chr_f
>> ? ? );
>>
>> ## Coordinate mapping (reverse)
>> my $agp_r = Bio::Coordinate::Pair->
>> ?new( -in ?=> $ctg,
>> ? ? ? -out => $ctg_on_chr_r
>> ? ? );
>>
>>
>>
>> ## A match, in contig coordinates...
>> my $match_on_ctg_4 = Bio::Location::Simple->
>> ?new( -seq_id => 'hit 4',
>> ? ? ? -start ?=> ? ? 925,
>> ? ? ? -end ? ?=> ? ?1125,
>> ? ? ? -strand => ? ? ?-1,
>> ? ? );
>>
>> ## Map it into chromosome coordinates (forward)
>> my $match_on_chr_4_f =
>> ?$agp_f->map( $match_on_ctg_4 );
>>
>> print Dumper $match_on_chr_4_f, "\n";
>>
>> ## Map it into chromosome coordinates (reverse)
>> my $match_on_chr_4_r =
>> ?$agp_r->map( $match_on_ctg_4 );
>>
>> print Dumper $match_on_chr_4_r, "\n";
>>
>> __END__
>>
>> $VAR1 = bless( {
>> ? ? ? ? ? ? ? ? '_sublocations' => [
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg on chr r',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 5925,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 6001
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? },
>> 'Bio::Coordinate::Result::Match' ),
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 1002,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 1125
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result::Gap' )
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?],
>> ? ? ? ? ? ? ? ? '_gap' => $VAR1->{'_sublocations'}[1],
>> ? ? ? ? ? ? ? ? 'strand' => -1,
>> ? ? ? ? ? ? ? ? '_match' => $VAR1->{'_sublocations'}[0],
>> ? ? ? ? ? ? ? ? '_splittype' => 'JOIN'
>> ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result' );
>> $VAR2 = '
>> ';
>> $VAR1 = bless( {
>> ? ? ? ? ? ? ? ? '_sublocations' => [
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => 1,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg on chr r',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 5001,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 5077
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? },
>> 'Bio::Coordinate::Result::Match' ),
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 1002,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 1125
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result::Gap' )
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?],
>> ? ? ? ? ? ? ? ? '_gap' => $VAR1->{'_sublocations'}[1],
>> ? ? ? ? ? ? ? ? 'strand' => 1,
>> ? ? ? ? ? ? ? ? '_match' => $VAR1->{'_sublocations'}[0],
>> ? ? ? ? ? ? ? ? '_splittype' => 'JOIN'
>> ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result' );
>> $VAR2 = '
>> ';
>>
>


From mauricio at open-bio.org  Fri Oct  8 12:47:56 2010
From: mauricio at open-bio.org (Mauricio Herrera Cuadra)
Date: Fri, 08 Oct 2010 11:47:56 -0500
Subject: [Bioperl-l] Pdoc documentation & test coverage updated
Message-ID: <4CAF4B3C.1060001@open-bio.org>

The cron scripts that generate the live code Pdoc documentation and the 
test coverage reports are now updated to pull from the GitHub 
repository. Please let me know if you notice anything wonky.

Mauricio.

From cjfields at illinois.edu  Fri Oct  8 16:13:08 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 8 Oct 2010 15:13:08 -0500
Subject: [Bioperl-l] Pdoc documentation & test coverage updated
In-Reply-To: <4CAF4B3C.1060001@open-bio.org>
References: <4CAF4B3C.1060001@open-bio.org>
Message-ID: <DA23CAB1-6A1C-4EC5-9EEF-06ED68C35AE9@illinois.edu>

Thanks Mauricio!  That completely feel off my radar.

chris

On Oct 8, 2010, at 11:47 AM, Mauricio Herrera Cuadra wrote:

> The cron scripts that generate the live code Pdoc documentation and the test coverage reports are now updated to pull from the GitHub repository. Please let me know if you notice anything wonky.
> 
> Mauricio.
> _______________________________________________
> 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  Fri Oct  8 17:08:40 2010
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 08 Oct 2010 14:08:40 -0700
Subject: [Bioperl-l] Pdoc documentation & test coverage updated
In-Reply-To: <DA23CAB1-6A1C-4EC5-9EEF-06ED68C35AE9@illinois.edu>
References: <4CAF4B3C.1060001@open-bio.org>
	<DA23CAB1-6A1C-4EC5-9EEF-06ED68C35AE9@illinois.edu>
Message-ID: <4CAF8858.5090302@bioperl.org>

nice -- thanks for doing that Mauricio.


Chris Fields wrote, On 10/8/10 1:13 PM:
> Thanks Mauricio!  That completely feel off my radar.
>
> chris
>
> On Oct 8, 2010, at 11:47 AM, Mauricio Herrera Cuadra wrote:
>
>> The cron scripts that generate the live code Pdoc documentation and the test coverage reports are now updated to pull from the GitHub repository. Please let me know if you notice anything wonky.
>>
>> Mauricio.
>> _______________________________________________
>> 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

-- 
Jason Stajich
jason at bioperl.org


From avilella at gmail.com  Tue Oct 12 08:34:14 2010
From: avilella at gmail.com (Albert Vilella)
Date: Tue, 12 Oct 2010 13:34:14 +0100
Subject: [Bioperl-l] possible bug in Bio::SeqIO::fastq
Message-ID: <AANLkTi=XNY9skUoTpJYJ=cp8wcpRPiskjFeuc3RquDUk@mail.gmail.com>

Hi,

I found what seems to me could be a bug in the fastq module, which is
that if the
last line of the raw_quality section is a single "0" character, a
"if($line)" isn't
returning it properly, because it should be "if(defined $line)" instead.

Find here a test case and the line in question:

----
use strict;
use Bio::SeqIO;

my $consio = Bio::SeqIO->new
  (-format => 'fastq',
   -fh => \*DATA);

my $onelineconsout = Bio::SeqIO->new
  (-format => 'fastq',
   -fh => \*STDOUT);

while (my $seq = $consio->next_seq) {
  next if ($seq->seq =~ /^n+$/);
  $seq->seq(uc($seq->seq));
  $onelineconsout->write_seq($seq);
}
$consio->close;
$onelineconsout->close;

__DATA__
@SRR031652.634472
agtgcgctgatctgtggcccgtattgcctcaacgcaagctcaatagcttgagtatattaa
a
+
01111111111111100111111--,,011111101111111110111111111111110
0
----

--- /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm
2010-10-12 13:26:06.491743000 +0100
+++ /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm~
2010-10-12 13:07:27.462833000 +0100
@@ -80,7 +80,7 @@
                 last FASTQ
             }
             chomp $line;
-            if (!defined($line)) {
+            if (!$line) {
                 delete $self->{lastline};
                 last FASTQ;
             }

From shalabh.sharma7 at gmail.com  Tue Oct 12 10:20:58 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 12 Oct 2010 10:20:58 -0400
Subject: [Bioperl-l] fastq Problem
Message-ID: <AANLkTikTASuFtDhvwZDpvn4N4k-nMR2S1y9noQ2OcY12@mail.gmail.com>

Hi,
    I have data from illumina, i can read the data by using Bio::SeqIO but
when i am writing it back its writing in fasta format.

Is there anyway i can write it back in fastq format?

Thanks
Shalabh

From avilella at gmail.com  Tue Oct 12 10:54:46 2010
From: avilella at gmail.com (Albert Vilella)
Date: Tue, 12 Oct 2010 15:54:46 +0100
Subject: [Bioperl-l] possible bug in Bio::SeqIO::fastq
In-Reply-To: <76631143-1043-4A02-BF4C-AC7F9D8A3274@illinois.edu>
References: <AANLkTi=XNY9skUoTpJYJ=cp8wcpRPiskjFeuc3RquDUk@mail.gmail.com>
	<76631143-1043-4A02-BF4C-AC7F9D8A3274@illinois.edu>
Message-ID: <AANLkTi=m3-rR4yGLRPLTVW0azSdS3AUwQQ1u1gtvzWoP@mail.gmail.com>

aah! thanks!

On Tue, Oct 12, 2010 at 3:50 PM, Chris Fields <cjfields at illinois.edu> wrote:
> Albert,
>
> Have you tried bioperl-live? ?This is already fixed there.
>
> chris
>
> On Oct 12, 2010, at 7:34 AM, Albert Vilella wrote:
>
>> Hi,
>>
>> I found what seems to me could be a bug in the fastq module, which is
>> that if the
>> last line of the raw_quality section is a single "0" character, a
>> "if($line)" isn't
>> returning it properly, because it should be "if(defined $line)" instead.
>>
>> Find here a test case and the line in question:
>>
>> ----
>> use strict;
>> use Bio::SeqIO;
>>
>> my $consio = Bio::SeqIO->new
>> ?(-format => 'fastq',
>> ? -fh => \*DATA);
>>
>> my $onelineconsout = Bio::SeqIO->new
>> ?(-format => 'fastq',
>> ? -fh => \*STDOUT);
>>
>> while (my $seq = $consio->next_seq) {
>> ?next if ($seq->seq =~ /^n+$/);
>> ?$seq->seq(uc($seq->seq));
>> ?$onelineconsout->write_seq($seq);
>> }
>> $consio->close;
>> $onelineconsout->close;
>>
>> __DATA__
>> @SRR031652.634472
>> agtgcgctgatctgtggcccgtattgcctcaacgcaagctcaatagcttgagtatattaa
>> a
>> +
>> 01111111111111100111111--,,011111101111111110111111111111110
>> 0
>> ----
>>
>> --- /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm
>> 2010-10-12 13:26:06.491743000 +0100
>> +++ /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm~
>> 2010-10-12 13:07:27.462833000 +0100
>> @@ -80,7 +80,7 @@
>> ? ? ? ? ? ? ? ? last FASTQ
>> ? ? ? ? ? ? }
>> ? ? ? ? ? ? chomp $line;
>> - ? ? ? ? ? ?if (!defined($line)) {
>> + ? ? ? ? ? ?if (!$line) {
>> ? ? ? ? ? ? ? ? delete $self->{lastline};
>> ? ? ? ? ? ? ? ? last FASTQ;
>> ? ? ? ? ? ? }
>> _______________________________________________
>> 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 Oct 12 10:50:30 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 12 Oct 2010 09:50:30 -0500
Subject: [Bioperl-l] possible bug in Bio::SeqIO::fastq
In-Reply-To: <AANLkTi=XNY9skUoTpJYJ=cp8wcpRPiskjFeuc3RquDUk@mail.gmail.com>
References: <AANLkTi=XNY9skUoTpJYJ=cp8wcpRPiskjFeuc3RquDUk@mail.gmail.com>
Message-ID: <76631143-1043-4A02-BF4C-AC7F9D8A3274@illinois.edu>

Albert, 

Have you tried bioperl-live?  This is already fixed there.

chris

On Oct 12, 2010, at 7:34 AM, Albert Vilella wrote:

> Hi,
> 
> I found what seems to me could be a bug in the fastq module, which is
> that if the
> last line of the raw_quality section is a single "0" character, a
> "if($line)" isn't
> returning it properly, because it should be "if(defined $line)" instead.
> 
> Find here a test case and the line in question:
> 
> ----
> use strict;
> use Bio::SeqIO;
> 
> my $consio = Bio::SeqIO->new
>  (-format => 'fastq',
>   -fh => \*DATA);
> 
> my $onelineconsout = Bio::SeqIO->new
>  (-format => 'fastq',
>   -fh => \*STDOUT);
> 
> while (my $seq = $consio->next_seq) {
>  next if ($seq->seq =~ /^n+$/);
>  $seq->seq(uc($seq->seq));
>  $onelineconsout->write_seq($seq);
> }
> $consio->close;
> $onelineconsout->close;
> 
> __DATA__
> @SRR031652.634472
> agtgcgctgatctgtggcccgtattgcctcaacgcaagctcaatagcttgagtatattaa
> a
> +
> 01111111111111100111111--,,011111101111111110111111111111110
> 0
> ----
> 
> --- /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm
> 2010-10-12 13:26:06.491743000 +0100
> +++ /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm~
> 2010-10-12 13:07:27.462833000 +0100
> @@ -80,7 +80,7 @@
>                 last FASTQ
>             }
>             chomp $line;
> -            if (!defined($line)) {
> +            if (!$line) {
>                 delete $self->{lastline};
>                 last FASTQ;
>             }
> _______________________________________________
> 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 Oct 12 10:51:41 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 12 Oct 2010 09:51:41 -0500
Subject: [Bioperl-l] fastq Problem
In-Reply-To: <AANLkTikTASuFtDhvwZDpvn4N4k-nMR2S1y9noQ2OcY12@mail.gmail.com>
References: <AANLkTikTASuFtDhvwZDpvn4N4k-nMR2S1y9noQ2OcY12@mail.gmail.com>
Message-ID: <03B2F4BE-4E32-4A28-BB9E-B2B59EAEFE00@illinois.edu>

Yes, but you need to use the latest CPAN release or bioperl-live; anything older than v. 1.6.1 will not convert Illumina reads correctly.

chris

On Oct 12, 2010, at 9:20 AM, shalabh sharma wrote:

> Hi,
>    I have data from illumina, i can read the data by using Bio::SeqIO but
> when i am writing it back its writing in fasta format.
> 
> Is there anyway i can write it back in fastq format?
> 
> Thanks
> Shalabh
> _______________________________________________
> 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  Tue Oct 12 11:09:50 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 12 Oct 2010 11:09:50 -0400
Subject: [Bioperl-l] fastq Problem
In-Reply-To: <03B2F4BE-4E32-4A28-BB9E-B2B59EAEFE00@illinois.edu>
References: <AANLkTikTASuFtDhvwZDpvn4N4k-nMR2S1y9noQ2OcY12@mail.gmail.com>
	<03B2F4BE-4E32-4A28-BB9E-B2B59EAEFE00@illinois.edu>
Message-ID: <AANLkTim3Hx3SLrEoQa8D9Ha_x-ECTOjCCQY4CjHBJOaV@mail.gmail.com>

Thanks Chris,
I realized that after writing that mail. Its working now.

Thanks
Shalabh


On Tue, Oct 12, 2010 at 10:51 AM, Chris Fields <cjfields at illinois.edu>wrote:

> Yes, but you need to use the latest CPAN release or bioperl-live; anything
> older than v. 1.6.1 will not convert Illumina reads correctly.
>
> chris
>
> On Oct 12, 2010, at 9:20 AM, shalabh sharma wrote:
>
> > Hi,
> >    I have data from illumina, i can read the data by using Bio::SeqIO but
> > when i am writing it back its writing in fasta format.
> >
> > Is there anyway i can write it back in fastq format?
> >
> > Thanks
> > Shalabh
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>

From maj at fortinbras.us  Wed Oct 13 23:52:05 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Wed, 13 Oct 2010 23:52:05 -0400
Subject: [Bioperl-l] Next-gen flu informatics
Message-ID: <81299466177D467091763FEA84CA00FD@NewLife>

Hi All, 

Sorry about the job spam, but you are the best talent pool I know. SRA
(the company now interfering with my BioPerl work) is looking for
next-gen experienced bioinformaticists for a new contract with
CDC. Please have a look at http://www.sra.com/careers/search.php,
requisition numbers 31385, 31402 and 31467.

Thanks!
MAJ


From dichmann at berkeley.edu  Thu Oct 14 21:16:29 2010
From: dichmann at berkeley.edu (Darwin Sorento Dichmann)
Date: Thu, 14 Oct 2010 18:16:29 -0700
Subject: [Bioperl-l] Extracting sequences from MySQL DB with Bio::DB::GFF
Message-ID: <36D60149-EEC5-4A45-85B9-E7FD4F3C005C@berkeley.edu>

Greetings, 

I am trying to extract sequences from a MySQL DB with Bio::DB::GFF. The database is the same as I use for my gbrowse2 and it works fine for that. Also, I can extract all sorts of features but not sequence. 

When I run this script I thought I'd get a sequence output but apparently I get the memory address instead. 

I have very little experience with perl or other programming, but I try to follow the directions in the manual. I suspect that I overlook something very basic and any help would be greatly appreciated. 

Thanks,
Darwin 



The script:
------------
#! usr/bin/perl -w
# module to test if Bio::DB::GFF can be used to extract sequences from frog2 database.

use strict;
use Bio::Seq;
use Bio::SeqIO;
use Bio::DB::GFF;

# Open database
my $db = Bio::DB::GFF->
new( 	-adaptor => 'DBI::mysql',
     	-dsn     => 'frog2',
		-user => 'darwin',
		-password => '****',
		);

# fetch scaffold_1 (1-100000)
my $segment = $db->segment('scaffold_1', 1 => 100000) or die;

# get its DNA
 my $dna = $segment->seq or die;
print $segment, "\n";
print $dna,"\n";

# get an iterator on all curated features of type 'exon' or 'intron'
# this prints all exons and intron with transcript name on screen
	my $iterator = $segment->get_seq_stream(-type     => ['mRNA']);
	while (my $s = $iterator->next_seq) {
    print $s,"\n";
}

exit;
---------------

The output:
Macintosh:perlscripts darwin$ perl frog2_parser.pl 
scaffold_1:1,100000
Bio::PrimarySeq=HASH(0x100bb4d68)
mRNA:pick(xt42f011730m)
mRNA:pick(xt42f014902m)
mRNA:pick(xt42f016160m)
mRNA:pick(xt42f017353m)
mRNA:pick(xt42f029332m)
---------------

From scott at scottcain.net  Thu Oct 14 22:01:24 2010
From: scott at scottcain.net (Scott Cain)
Date: Thu, 14 Oct 2010 22:01:24 -0400
Subject: [Bioperl-l] Extracting sequences from MySQL DB with Bio::DB::GFF
In-Reply-To: <36D60149-EEC5-4A45-85B9-E7FD4F3C005C@berkeley.edu>
References: <36D60149-EEC5-4A45-85B9-E7FD4F3C005C@berkeley.edu>
Message-ID: <AANLkTi=i1xAoyeQJGAnT9X5wEmdchJk1v4YWMSqk7fH1@mail.gmail.com>

Hi Darwin,

The "seq" method returns a Bio::PrimarySeq object (I forget why this
is--I think it's to fulfill the contract with the Bio::SeqFeatureI
interface).  To get the sequence, you can do a few things: 1) call the
seq method on the Bio::PrimarySeq object, like this:

  my $dna = $segment->seq->seq;

or 2) use the dna method:

  my $dna = $segment->dna;

The perldoc section from Bio::DB::GFF::Segment is below.

Scott

       seq

        Title   : seq
        Usage   : $s->seq
        Function: get the sequence string for this segment
        Returns : a Bio::PrimarySeq
        Args    : none
        Status  : Public

       Returns the sequence for this segment as a Bio::PrimarySeq.  (-) strand
       segments are automatically reverse complemented

       The method is called dna() return the data as a simple sequence string.

       dna

        Title   : dna
        Usage   : $s->dna
        Function: get the DNA string for this segment
        Returns : a string
        Args    : none
        Status  : Public

       Returns the sequence for this segment as a simple string. (-) strand
       segments are automatically reverse complemented

       The method is also called protein().


On Thu, Oct 14, 2010 at 9:16 PM, Darwin Sorento Dichmann
<dichmann at berkeley.edu> wrote:
> Greetings,
>
> I am trying to extract sequences from a MySQL DB with Bio::DB::GFF. The database is the same as I use for my gbrowse2 and it works fine for that. Also, I can extract all sorts of features but not sequence.
>
> When I run this script I thought I'd get a sequence output but apparently I get the memory address instead.
>
> I have very little experience with perl or other programming, but I try to follow the directions in the manual. I suspect that I overlook something very basic and any help would be greatly appreciated.
>
> Thanks,
> Darwin
>
>
>
> The script:
> ------------
> #! usr/bin/perl -w
> # module to test if Bio::DB::GFF can be used to extract sequences from frog2 database.
>
> use strict;
> use Bio::Seq;
> use Bio::SeqIO;
> use Bio::DB::GFF;
>
> # Open database
> my $db = Bio::DB::GFF->
> new(    -adaptor => 'DBI::mysql',
>        -dsn     => 'frog2',
>                -user => 'darwin',
>                -password => '****',
>                );
>
> # fetch scaffold_1 (1-100000)
> my $segment = $db->segment('scaffold_1', 1 => 100000) or die;
>
> # get its DNA
>  my $dna = $segment->seq or die;
> print $segment, "\n";
> print $dna,"\n";
>
> # get an iterator on all curated features of type 'exon' or 'intron'
> # this prints all exons and intron with transcript name on screen
>        my $iterator = $segment->get_seq_stream(-type     => ['mRNA']);
>        while (my $s = $iterator->next_seq) {
>    print $s,"\n";
> }
>
> exit;
> ---------------
>
> The output:
> Macintosh:perlscripts darwin$ perl frog2_parser.pl
> scaffold_1:1,100000
> Bio::PrimarySeq=HASH(0x100bb4d68)
> mRNA:pick(xt42f011730m)
> mRNA:pick(xt42f014902m)
> mRNA:pick(xt42f016160m)
> mRNA:pick(xt42f017353m)
> mRNA:pick(xt42f029332m)
> ---------------
> _______________________________________________
> 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 dichmann at berkeley.edu  Fri Oct 15 13:34:02 2010
From: dichmann at berkeley.edu (Darwin Sorento Dichmann)
Date: Fri, 15 Oct 2010 10:34:02 -0700
Subject: [Bioperl-l] Extracting sequences from MySQL DB with Bio::DB::GFF
In-Reply-To: <AANLkTi=i1xAoyeQJGAnT9X5wEmdchJk1v4YWMSqk7fH1@mail.gmail.com>
References: <36D60149-EEC5-4A45-85B9-E7FD4F3C005C@berkeley.edu>
	<AANLkTi=i1xAoyeQJGAnT9X5wEmdchJk1v4YWMSqk7fH1@mail.gmail.com>
Message-ID: <9E7B9E6F-9440-4BAC-AD8D-2A739A863C1B@berkeley.edu>

It's a beauty to behold!
Thanks Scott!

Best,
Darwin

On Oct 14, 2010, at 7:01 PM, Scott Cain wrote:

> Hi Darwin,
> 
> The "seq" method returns a Bio::PrimarySeq object (I forget why this
> is--I think it's to fulfill the contract with the Bio::SeqFeatureI
> interface).  To get the sequence, you can do a few things: 1) call the
> seq method on the Bio::PrimarySeq object, like this:
> 
>  my $dna = $segment->seq->seq;
> 
> or 2) use the dna method:
> 
>  my $dna = $segment->dna;
> 
> The perldoc section from Bio::DB::GFF::Segment is below.
> 
> Scott
> 
>       seq
> 
>        Title   : seq
>        Usage   : $s->seq
>        Function: get the sequence string for this segment
>        Returns : a Bio::PrimarySeq
>        Args    : none
>        Status  : Public
> 
>       Returns the sequence for this segment as a Bio::PrimarySeq.  (-) strand
>       segments are automatically reverse complemented
> 
>       The method is called dna() return the data as a simple sequence string.
> 
>       dna
> 
>        Title   : dna
>        Usage   : $s->dna
>        Function: get the DNA string for this segment
>        Returns : a string
>        Args    : none
>        Status  : Public
> 
>       Returns the sequence for this segment as a simple string. (-) strand
>       segments are automatically reverse complemented
> 
>       The method is also called protein().
> 
> 
> On Thu, Oct 14, 2010 at 9:16 PM, Darwin Sorento Dichmann
> <dichmann at berkeley.edu> wrote:
>> Greetings,
>> 
>> I am trying to extract sequences from a MySQL DB with Bio::DB::GFF. The database is the same as I use for my gbrowse2 and it works fine for that. Also, I can extract all sorts of features but not sequence.
>> 
>> When I run this script I thought I'd get a sequence output but apparently I get the memory address instead.
>> 
>> I have very little experience with perl or other programming, but I try to follow the directions in the manual. I suspect that I overlook something very basic and any help would be greatly appreciated.
>> 
>> Thanks,
>> Darwin
>> 
>> 
>> 
>> The script:
>> ------------
>> #! usr/bin/perl -w
>> # module to test if Bio::DB::GFF can be used to extract sequences from frog2 database.
>> 
>> use strict;
>> use Bio::Seq;
>> use Bio::SeqIO;
>> use Bio::DB::GFF;
>> 
>> # Open database
>> my $db = Bio::DB::GFF->
>> new(    -adaptor => 'DBI::mysql',
>>       -dsn     => 'frog2',
>>               -user => 'darwin',
>>               -password => '****',
>>               );
>> 
>> # fetch scaffold_1 (1-100000)
>> my $segment = $db->segment('scaffold_1', 1 => 100000) or die;
>> 
>> # get its DNA
>> my $dna = $segment->seq or die;
>> print $segment, "\n";
>> print $dna,"\n";
>> 
>> # get an iterator on all curated features of type 'exon' or 'intron'
>> # this prints all exons and intron with transcript name on screen
>>       my $iterator = $segment->get_seq_stream(-type     => ['mRNA']);
>>       while (my $s = $iterator->next_seq) {
>>   print $s,"\n";
>> }
>> 
>> exit;
>> ---------------
>> 
>> The output:
>> Macintosh:perlscripts darwin$ perl frog2_parser.pl
>> scaffold_1:1,100000
>> Bio::PrimarySeq=HASH(0x100bb4d68)
>> mRNA:pick(xt42f011730m)
>> mRNA:pick(xt42f014902m)
>> mRNA:pick(xt42f016160m)
>> mRNA:pick(xt42f017353m)
>> mRNA:pick(xt42f029332m)
>> ---------------
>> _______________________________________________
>> 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 mcestep at gmail.com  Fri Oct 15 16:59:57 2010
From: mcestep at gmail.com (Matt Estep)
Date: Fri, 15 Oct 2010 15:59:57 -0500
Subject: [Bioperl-l] Installing BioPerl on New mac 10.6.4
Message-ID: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>

Hi

When running the ./build install script I get an error because it can
not make a directory in /usr/local/share/man/man3  I looked around a
bit and I have a file titled /usr/share/man/man3. I am guessing the
script does not know how to skip the local bit of the first line.

Can you tell me how to run the script so that it will make the file in
the right place. I am guessing the file struture of the new mac is a
little different.

Thanks in advance for any help.

Matt

From scott at scottcain.net  Fri Oct 15 23:41:40 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 15 Oct 2010 23:41:40 -0400
Subject: [Bioperl-l] Installing BioPerl on New mac 10.6.4
In-Reply-To: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>
References: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>
Message-ID: <AANLkTimUSO7ohhN6L80tjYhsrHk+2oQx6JWcRE11g4ob@mail.gmail.com>

Hi Matt,

Usually, when ./Build install fails to create a directory or file it
is because the user that executed the script didn't have permission to
perform that action.  Did you use "sudo" when you executed the install
command?

Scott


On Fri, Oct 15, 2010 at 4:59 PM, Matt Estep <mcestep at gmail.com> wrote:
> Hi
>
> When running the ./build install script I get an error because it can
> not make a directory in /usr/local/share/man/man3 ?I looked around a
> bit and I have a file titled /usr/share/man/man3. I am guessing the
> script does not know how to skip the local bit of the first line.
>
> Can you tell me how to run the script so that it will make the file in
> the right place. I am guessing the file struture of the new mac is a
> little different.
>
> Thanks in advance for any help.
>
> Matt
> _______________________________________________
> 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 fij at elte.hu  Sat Oct 16 07:34:06 2010
From: fij at elte.hu (Farkas, Illes)
Date: Sat, 16 Oct 2010 13:34:06 +0200
Subject: [Bioperl-l] cis-regulatory elements
Message-ID: <AANLkTinCN+qFBZeGtKiYLMWg+yzitkEP497pHMgG-ULn@mail.gmail.com>

Dear All,

Which (BioPerl or other) module/algorithm would you recommend for predicting
cis-regulatory elements (mainly TFBSs) in a variety of organisms? We (= 1
colleague and I) have looked at
http://www.nature.com/nbt/journal/v23/n1/full/nbt1053.html so far.

Thanks,
Illes
--
http://hal.elte.hu/fij

From grapeguy at gmail.com  Sat Oct 16 15:46:32 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Sat, 16 Oct 2010 15:46:32 -0400
Subject: [Bioperl-l] Installing BioPerl on New mac 10.6.4
In-Reply-To: <AANLkTimUSO7ohhN6L80tjYhsrHk+2oQx6JWcRE11g4ob@mail.gmail.com>
References: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>
	<AANLkTimUSO7ohhN6L80tjYhsrHk+2oQx6JWcRE11g4ob@mail.gmail.com>
Message-ID: <AANLkTikbZnnno5oNDi1Q0HYe9QEFhp9xuF3wH5C8NhXG@mail.gmail.com>

Matt,

I just installed on OSX 10.6.3.  Definitely use sudo to perform the install.

I actually used the PPM install.  I used this command to start PPM: sudo
perl -MCPAN -e shell

http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_CPAN

Thanks,
Bill S.
Dept. of Biomedical Informatics
Ohio State University

On Fri, Oct 15, 2010 at 11:41 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Matt,
>
> Usually, when ./Build install fails to create a directory or file it
> is because the user that executed the script didn't have permission to
> perform that action.  Did you use "sudo" when you executed the install
> command?
>
> Scott
>
>
> On Fri, Oct 15, 2010 at 4:59 PM, Matt Estep <mcestep at gmail.com> wrote:
> > Hi
> >
> > When running the ./build install script I get an error because it can
> > not make a directory in /usr/local/share/man/man3  I looked around a
> > bit and I have a file titled /usr/share/man/man3. I am guessing the
> > script does not know how to skip the local bit of the first line.
> >
> > Can you tell me how to run the script so that it will make the file in
> > the right place. I am guessing the file struture of the new mac is a
> > little different.
> >
> > Thanks in advance for any help.
> >
> > Matt
> > _______________________________________________
> > 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
>

From jun.yin at ucd.ie  Sat Oct 16 16:41:37 2010
From: jun.yin at ucd.ie (Jun Yin)
Date: Sat, 16 Oct 2010 21:41:37 +0100
Subject: [Bioperl-l] cis-regulatory elements
In-Reply-To: <AANLkTinCN+qFBZeGtKiYLMWg+yzitkEP497pHMgG-ULn@mail.gmail.com>
References: <AANLkTinCN+qFBZeGtKiYLMWg+yzitkEP497pHMgG-ULn@mail.gmail.com>
Message-ID: <001501cb6d72$8771c2b0$96554810$%yin@ucd.ie>

Hi, Illes,

Sorry I don't know any package in BioPerl predicting TFBS binding motifs. As
far as I know, neither Bio::Align nor Bio::Assembly has such functions,
though Bio::SimpleAlign can be used to manipulate your promoter alignment.
For TFBS prediction, I personally use PScan and TFFind at the moment.

I am also interested in this question. I will wait for the answer in the
mail list with you :)

Cheers,
Jun Yin
Ph.D.?student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Farkas, Illes
Sent: Saturday, October 16, 2010 12:34 PM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] cis-regulatory elements

Dear All,

Which (BioPerl or other) module/algorithm would you recommend for predicting
cis-regulatory elements (mainly TFBSs) in a variety of organisms? We (= 1
colleague and I) have looked at
http://www.nature.com/nbt/journal/v23/n1/full/nbt1053.html so far.

Thanks,
Illes
--
http://hal.elte.hu/fij
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com


 

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com
 
 

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com
 



From cjfields at illinois.edu  Sat Oct 16 23:24:32 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Sat, 16 Oct 2010 22:24:32 -0500
Subject: [Bioperl-l] cis-regulatory elements
In-Reply-To: <001501cb6d72$8771c2b0$96554810$%yin@ucd.ie>
References: <AANLkTinCN+qFBZeGtKiYLMWg+yzitkEP497pHMgG-ULn@mail.gmail.com>
	<001501cb6d72$8771c2b0$96554810$%yin@ucd.ie>
Message-ID: <ECB68538-3F18-4AEB-A097-773A913935B5@illinois.edu>

Sendu Bala delved into this a bit; you can look at a few of his modules in BioPerl, specifically Bio::DB::TFBS (which is only configured for transfac_pro at the moment).

chris

On Oct 16, 2010, at 3:41 PM, Jun Yin wrote:

> Hi, Illes,
> 
> Sorry I don't know any package in BioPerl predicting TFBS binding motifs. As
> far as I know, neither Bio::Align nor Bio::Assembly has such functions,
> though Bio::SimpleAlign can be used to manipulate your promoter alignment.
> For TFBS prediction, I personally use PScan and TFFind at the moment.
> 
> I am also interested in this question. I will wait for the answer in the
> mail list with you :)
> 
> Cheers,
> Jun Yin
> Ph.D. student in U.C.D.
> 
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Farkas, Illes
> Sent: Saturday, October 16, 2010 12:34 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] cis-regulatory elements
> 
> Dear All,
> 
> Which (BioPerl or other) module/algorithm would you recommend for predicting
> cis-regulatory elements (mainly TFBSs) in a variety of organisms? We (= 1
> colleague and I) have looked at
> http://www.nature.com/nbt/journal/v23/n1/full/nbt1053.html so far.
> 
> Thanks,
> Illes
> --
> http://hal.elte.hu/fij
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
> 
> The message was checked by ESET Smart Security.
> 
> http://www.eset.com
> 
> 
> 
> 
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
> 
> The message was checked by ESET Smart Security.
> 
> http://www.eset.com
> 
> 
> 
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
> 
> The message was checked by ESET Smart Security.
> 
> http://www.eset.com
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From grapeguy at gmail.com  Mon Oct 18 09:58:24 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Mon, 18 Oct 2010 09:58:24 -0400
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal alignment
Message-ID: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>

All,

I'm in my first week with bioperl for a class project (although I've used
Perl for years). I've successfully run a clustal alignment of several DNA
sequences to produce the aln and dnd files. Now I would like to generate a
consensus sequence from the alignment.  I see that Pise Cons does this
satisfactorily on my example data (
http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1 distribution
that I installed.

Is this another module that I need to install separately?

"cpan[2]> m /Pise/
Module    Bio::Tools::Run::AnalysisFactory::Pise
(BIRNEY/bioperl-run-1.4.tar.gz)
Module    Bio::Tools::Run::PiseApplication (BIRNEY/bioperl-run-1.4.tar.gz)"

Bill S.

From cjfields at illinois.edu  Mon Oct 18 10:54:32 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 18 Oct 2010 09:54:32 -0500
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
Message-ID: <DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>

Bill,

Actually, the page you reached at Pasteur is not Pise, but Mobyle (their replacement for the older Pise tools).  The Pise modules were in BioPerl-Run, but they were deprecated a few years ago and removed from the latest BioPerl-Run releases b/c the remote service is no longer active; there is no Perl-based replacement for Mobyle interaction.  

Have you thought about just using the functionality within the Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there are methods in place to do that.

chris

On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:

> All,
> 
> I'm in my first week with bioperl for a class project (although I've used
> Perl for years). I've successfully run a clustal alignment of several DNA
> sequences to produce the aln and dnd files. Now I would like to generate a
> consensus sequence from the alignment.  I see that Pise Cons does this
> satisfactorily on my example data (
> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1 distribution
> that I installed.
> 
> Is this another module that I need to install separately?
> 
> "cpan[2]> m /Pise/
> Module    Bio::Tools::Run::AnalysisFactory::Pise
> (BIRNEY/bioperl-run-1.4.tar.gz)
> Module    Bio::Tools::Run::PiseApplication (BIRNEY/bioperl-run-1.4.tar.gz)"
> 
> Bill S.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From grapeguy at gmail.com  Mon Oct 18 11:52:03 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Mon, 18 Oct 2010 11:52:03 -0400
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
Message-ID: <AANLkTimF5N_AnTV380fT5hPAEjjSgSP37+KVaoHNwbXN@mail.gmail.com>

Chris,

Well, That explains it.

I'll take a 2 pronged approach:
1. Try SimpleAlign
2. Driving the Mobyle UI using LWP::UserAgent, HTML::Form and
HTML::TableExtract (I do this for Tm calculations);

Thanks,
Bill S.



On Mon, Oct 18, 2010 at 10:54 AM, Chris Fields <cjfields at illinois.edu>wrote:

> Bill,
>
> Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
> replacement for the older Pise tools).  The Pise modules were in
> BioPerl-Run, but they were deprecated a few years ago and removed from the
> latest BioPerl-Run releases b/c the remote service is no longer active;
> there is no Perl-based replacement for Mobyle interaction.
>
> Have you thought about just using the functionality within the
> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there are
> methods in place to do that.
>
> chris
>
> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
>
> > All,
> >
> > I'm in my first week with bioperl for a class project (although I've used
> > Perl for years). I've successfully run a clustal alignment of several DNA
> > sequences to produce the aln and dnd files. Now I would like to generate
> a
> > consensus sequence from the alignment.  I see that Pise Cons does this
> > satisfactorily on my example data (
> > http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However,
> I'm
> > not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
> distribution
> > that I installed.
> >
> > Is this another module that I need to install separately?
> >
> > "cpan[2]> m /Pise/
> > Module    Bio::Tools::Run::AnalysisFactory::Pise
> > (BIRNEY/bioperl-run-1.4.tar.gz)
> > Module    Bio::Tools::Run::PiseApplication
> (BIRNEY/bioperl-run-1.4.tar.gz)"
> >
> > Bill S.
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>

From jun.yin at ucd.ie  Mon Oct 18 12:09:32 2010
From: jun.yin at ucd.ie (Jun Yin)
Date: Mon, 18 Oct 2010 17:09:32 +0100
Subject: [Bioperl-l] Generating a consensus sequence from a
	Clustal	alignment
In-Reply-To: <DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
Message-ID: <001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>

Hi, Bill,

You may consider to use consensus_iupac or consensus_string methods in
Bio::SimpleAlign to generate consensus sequence.

Cheers,
Jun Yin
Ph.D.?student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Monday, October 18, 2010 3:55 PM
To: Bill Stephens
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
alignment

Bill,

Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
replacement for the older Pise tools).  The Pise modules were in
BioPerl-Run, but they were deprecated a few years ago and removed from the
latest BioPerl-Run releases b/c the remote service is no longer active;
there is no Perl-based replacement for Mobyle interaction.  

Have you thought about just using the functionality within the
Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there are
methods in place to do that.

chris

On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:

> All,
> 
> I'm in my first week with bioperl for a class project (although I've used
> Perl for years). I've successfully run a clustal alignment of several DNA
> sequences to produce the aln and dnd files. Now I would like to generate a
> consensus sequence from the alignment.  I see that Pise Cons does this
> satisfactorily on my example data (
> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
distribution
> that I installed.
> 
> Is this another module that I need to install separately?
> 
> "cpan[2]> m /Pise/
> Module    Bio::Tools::Run::AnalysisFactory::Pise
> (BIRNEY/bioperl-run-1.4.tar.gz)
> Module    Bio::Tools::Run::PiseApplication
(BIRNEY/bioperl-run-1.4.tar.gz)"
> 
> Bill S.
> _______________________________________________
> 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

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com


 

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com
 



From mcestep at gmail.com  Sat Oct 16 22:59:24 2010
From: mcestep at gmail.com (Matt Estep)
Date: Sat, 16 Oct 2010 21:59:24 -0500
Subject: [Bioperl-l] Installing BioPerl on New mac 10.6.4
In-Reply-To: <AANLkTikbZnnno5oNDi1Q0HYe9QEFhp9xuF3wH5C8NhXG@mail.gmail.com>
References: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>
	<AANLkTimUSO7ohhN6L80tjYhsrHk+2oQx6JWcRE11g4ob@mail.gmail.com>
	<AANLkTikbZnnno5oNDi1Q0HYe9QEFhp9xuF3wH5C8NhXG@mail.gmail.com>
Message-ID: <AANLkTimiPDKCFKZwDT1UM-OG=jKqxVMe2fD5hdY_jPW-@mail.gmail.com>

Thank you both. I think this has solved my troubles.

Matt

On Sat, Oct 16, 2010 at 2:46 PM, Bill Stephens <grapeguy at gmail.com> wrote:
> Matt,
>
> I just installed on OSX 10.6.3.? Definitely use sudo to perform the install.
>
> I actually used the PPM install.? I used this command to start PPM: sudo
> perl -MCPAN -e shell
>
> http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_CPAN
>
> Thanks,
> Bill S.
> Dept. of Biomedical Informatics
> Ohio State University
>
> On Fri, Oct 15, 2010 at 11:41 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Matt,
>>
>> Usually, when ./Build install fails to create a directory or file it
>> is because the user that executed the script didn't have permission to
>> perform that action. ?Did you use "sudo" when you executed the install
>> command?
>>
>> Scott
>>
>>
>> On Fri, Oct 15, 2010 at 4:59 PM, Matt Estep <mcestep at gmail.com> wrote:
>> > Hi
>> >
>> > When running the ./build install script I get an error because it can
>> > not make a directory in /usr/local/share/man/man3 ?I looked around a
>> > bit and I have a file titled /usr/share/man/man3. I am guessing the
>> > script does not know how to skip the local bit of the first line.
>> >
>> > Can you tell me how to run the script so that it will make the file in
>> > the right place. I am guessing the file struture of the new mac is a
>> > little different.
>> >
>> > Thanks in advance for any help.
>> >
>> > Matt
>> > _______________________________________________
>> > 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
>
>


From e.cristiano at Dkfz-Heidelberg.de  Mon Oct 18 10:33:05 2010
From: e.cristiano at Dkfz-Heidelberg.de (Cristiano Elena)
Date: Mon, 18 Oct 2010 16:33:05 +0200
Subject: [Bioperl-l] bioperl easy way installation using cpan
Message-ID: <FC756E55-13EF-449F-B324-3BB76032A22B@Dkfz-Heidelberg.de>

Hi,
I am a beginner and i am trying to install bioperl via CPAN following the instructions on wiki.
i have a leopard mac 10.6 and perl version 5.10 i have X11 and i also installed fink (but the installation of bioperl wasn't successful trough fink either).

the error that i got at the end of the installation via CPAN is the following:

 SHAWNPW/PostScript-0.06.tar.gz
  /usr/bin/make install  -- OK
Warning (usually harmless): 'YAML' not installed, will not store persistent state
Running Build for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
  Has already been unwrapped into directory /Users/ecristiano/.cpan/build/BioPerl-1.6.1-66fecx
Could not make: cannot resolve circular dependency
Warning (usually harmless): 'YAML' not installed, will not store persistent state
Running Build test
  Can't test without successful make
Running Build install
  Make had returned bad status, install seems impossible
Could not read '/Users/ecristiano/.cpan/build/GraphViz-2.04-f7G5nl/META.yml'. Falling back to other methods to determine prerequisites
Failed during this command:
 MINGYILIU/Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz: make NO cannot resolve circular dependency
 CJFIELDS/BioPerl-1.6.1.tar.gz                : make NO cannot resolve circular dependency
 LBROCARD/GraphViz-2.04.tar.gz                : writemakefile NO '/usr/bin/perl Makefile.PL' returned status 512


thanks in advance



Elena



From sarahdoom at gmail.com  Mon Oct 18 11:20:25 2010
From: sarahdoom at gmail.com (Sarah Kingan)
Date: Mon, 18 Oct 2010 08:20:25 -0700 (PDT)
Subject: [Bioperl-l] DNAStatistics
Message-ID: <780929ef-4b06-43ae-9d9c-78a62e84a4d7@g18g2000yqk.googlegroups.com>

Hello,
I am trying to calculate Ka/Ks statistics using the
Align:DNAStatistics module. When I use the function, calc_KaKs_pair, I
get a long list of errors. The calculation is performed but I don't
understand the source of the errors. They include:

Use of uninitialized value in addition (+) at /usr/lib/perl5/site_perl/
5.8.8/Bio/Align/DNAStatistics.pm line 1673, <GEN0> line 25.

Use of uninitialized value in addition (+) at /usr/lib/perl5/site_perl/
5.8.8/Bio/Align/DNAStatistics.pm line 1505, <GEN0> line 25.

Use of uninitialized value in subtraction (-) at /usr/lib/perl5/
site_perl/5.8.8/Bio/Align/DNAStatistics.pm line 1506, <GEN0> line 25.

My alignment object has gaps, but I believe this module handles gaps.
The data I am analyzing comes from recently diverged species, so I
wonder if the errors could originate from a lack of substitutions.

Any help would be much appreciated.

Thanks!
Sarah.Kingan at rochester.edu

From scott at scottcain.net  Mon Oct 18 13:26:53 2010
From: scott at scottcain.net (Scott Cain)
Date: Mon, 18 Oct 2010 13:26:53 -0400
Subject: [Bioperl-l] bioperl easy way installation using cpan
In-Reply-To: <FC756E55-13EF-449F-B324-3BB76032A22B@Dkfz-Heidelberg.de>
References: <FC756E55-13EF-449F-B324-3BB76032A22B@Dkfz-Heidelberg.de>
Message-ID: <AANLkTim6NxZx2-MCNJQ190-za6TkCYF_m9WZvPfO+LhC@mail.gmail.com>

Hi Elena,

I would suggest that you answer the question about installing optional
prerequisites with a "no"; I think that will eliminate the circular
dependency problem.  Of course the only problem is if you need
Bio-ASN1-EntrezGene, but even if you do, you can probably install it
after the BioPerl install completes.

Scott


On Mon, Oct 18, 2010 at 10:33 AM, Cristiano Elena
<e.cristiano at dkfz-heidelberg.de> wrote:
> Hi,
> I am a beginner and i am trying to install bioperl via CPAN following the instructions on wiki.
> i have a leopard mac 10.6 and perl version 5.10 i have X11 and i also installed fink (but the installation of bioperl wasn't successful trough fink either).
>
> the error that i got at the end of the installation via CPAN is the following:
>
> ?SHAWNPW/PostScript-0.06.tar.gz
> ?/usr/bin/make install ?-- OK
> Warning (usually harmless): 'YAML' not installed, will not store persistent state
> Running Build for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
> ?Has already been unwrapped into directory /Users/ecristiano/.cpan/build/BioPerl-1.6.1-66fecx
> Could not make: cannot resolve circular dependency
> Warning (usually harmless): 'YAML' not installed, will not store persistent state
> Running Build test
> ?Can't test without successful make
> Running Build install
> ?Make had returned bad status, install seems impossible
> Could not read '/Users/ecristiano/.cpan/build/GraphViz-2.04-f7G5nl/META.yml'. Falling back to other methods to determine prerequisites
> Failed during this command:
> ?MINGYILIU/Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz: make NO cannot resolve circular dependency
> ?CJFIELDS/BioPerl-1.6.1.tar.gz ? ? ? ? ? ? ? ?: make NO cannot resolve circular dependency
> ?LBROCARD/GraphViz-2.04.tar.gz ? ? ? ? ? ? ? ?: writemakefile NO '/usr/bin/perl Makefile.PL' returned status 512
>
>
> thanks in advance
>
>
>
> Elena
>
>
> _______________________________________________
> 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 Oct 18 13:37:02 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 18 Oct 2010 12:37:02 -0500
Subject: [Bioperl-l] bioperl easy way installation using cpan
In-Reply-To: <AANLkTim6NxZx2-MCNJQ190-za6TkCYF_m9WZvPfO+LhC@mail.gmail.com>
References: <FC756E55-13EF-449F-B324-3BB76032A22B@Dkfz-Heidelberg.de>
	<AANLkTim6NxZx2-MCNJQ190-za6TkCYF_m9WZvPfO+LhC@mail.gmail.com>
Message-ID: <6081844C-D4CB-4926-968D-9CACAE017E57@illinois.edu>

Agreed.  Unfortunately, this is an issue that has repeatedly popped up.  The best way I can think of to solve it is to remove Bio::ASN1::EntrezGene 'recommends' from Build.PL file, manually check for it's presence, and indicate the procedure for installing (basically post-bioperl install).

chris

On Oct 18, 2010, at 12:26 PM, Scott Cain wrote:

> Hi Elena,
> 
> I would suggest that you answer the question about installing optional
> prerequisites with a "no"; I think that will eliminate the circular
> dependency problem.  Of course the only problem is if you need
> Bio-ASN1-EntrezGene, but even if you do, you can probably install it
> after the BioPerl install completes.
> 
> Scott
> 
> 
> On Mon, Oct 18, 2010 at 10:33 AM, Cristiano Elena
> <e.cristiano at dkfz-heidelberg.de> wrote:
>> Hi,
>> I am a beginner and i am trying to install bioperl via CPAN following the instructions on wiki.
>> i have a leopard mac 10.6 and perl version 5.10 i have X11 and i also installed fink (but the installation of bioperl wasn't successful trough fink either).
>> 
>> the error that i got at the end of the installation via CPAN is the following:
>> 
>>  SHAWNPW/PostScript-0.06.tar.gz
>>  /usr/bin/make install  -- OK
>> Warning (usually harmless): 'YAML' not installed, will not store persistent state
>> Running Build for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
>>  Has already been unwrapped into directory /Users/ecristiano/.cpan/build/BioPerl-1.6.1-66fecx
>> Could not make: cannot resolve circular dependency
>> Warning (usually harmless): 'YAML' not installed, will not store persistent state
>> Running Build test
>>  Can't test without successful make
>> Running Build install
>>  Make had returned bad status, install seems impossible
>> Could not read '/Users/ecristiano/.cpan/build/GraphViz-2.04-f7G5nl/META.yml'. Falling back to other methods to determine prerequisites
>> Failed during this command:
>>  MINGYILIU/Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz: make NO cannot resolve circular dependency
>>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make NO cannot resolve circular dependency
>>  LBROCARD/GraphViz-2.04.tar.gz                : writemakefile NO '/usr/bin/perl Makefile.PL' returned status 512
>> 
>> 
>> thanks in advance
>> 
>> 
>> 
>> Elena
>> 
>> 
>> _______________________________________________
>> 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



From David.Messina at sbc.su.se  Mon Oct 18 14:23:18 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 18 Oct 2010 14:23:18 -0400
Subject: [Bioperl-l] DNAStatistics
In-Reply-To: <780929ef-4b06-43ae-9d9c-78a62e84a4d7@g18g2000yqk.googlegroups.com>
References: <780929ef-4b06-43ae-9d9c-78a62e84a4d7@g18g2000yqk.googlegroups.com>
Message-ID: <B1ABB50A-0B78-44D9-85C3-4A316B52278F@sbc.su.se>

Hi Sarah,

Usually "unintialized value" errors mean you're not trying to read from an empty variable.

I would check that all of the data you're passing to calc_KaKs_pair does contain a value.


> My alignment object has gaps, but I believe this module handles gaps.

I'm not sure about that; I'd have to check. Did you try handing it some ungapped data to see if the errors go away?



Dave



From grapeguy at gmail.com  Mon Oct 18 20:02:47 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Mon, 18 Oct 2010 20:02:47 -0400
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
Message-ID: <AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>

So, I've got the SimpleAlign running. It looks like it's running the
alignment based upon the input sequence location only (first residue from
each sequence).  This is not what I need.

I'm back to to clustal, tcoffee or dalign.

Bill

On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:

> Hi, Bill,
>
> You may consider to use consensus_iupac or consensus_string methods in
> Bio::SimpleAlign to generate consensus sequence.
>
> Cheers,
> Jun Yin
> Ph.D. student in U.C.D.
>
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Monday, October 18, 2010 3:55 PM
> To: Bill Stephens
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
> alignment
>
> Bill,
>
> Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
> replacement for the older Pise tools).  The Pise modules were in
> BioPerl-Run, but they were deprecated a few years ago and removed from the
> latest BioPerl-Run releases b/c the remote service is no longer active;
> there is no Perl-based replacement for Mobyle interaction.
>
> Have you thought about just using the functionality within the
> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there
> are
> methods in place to do that.
>
> chris
>
> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
>
> > All,
> >
> > I'm in my first week with bioperl for a class project (although I've used
> > Perl for years). I've successfully run a clustal alignment of several DNA
> > sequences to produce the aln and dnd files. Now I would like to generate
> a
> > consensus sequence from the alignment.  I see that Pise Cons does this
> > satisfactorily on my example data (
> > http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However,
> I'm
> > not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
> distribution
> > that I installed.
> >
> > Is this another module that I need to install separately?
> >
> > "cpan[2]> m /Pise/
> > Module    Bio::Tools::Run::AnalysisFactory::Pise
> > (BIRNEY/bioperl-run-1.4.tar.gz)
> > Module    Bio::Tools::Run::PiseApplication
> (BIRNEY/bioperl-run-1.4.tar.gz)"
> >
> > Bill S.
> > _______________________________________________
> > 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
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>

From thomas.sharpton at gmail.com  Mon Oct 18 22:30:40 2010
From: thomas.sharpton at gmail.com (Thomas Sharpton)
Date: Mon, 18 Oct 2010 19:30:40 -0700
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
	<AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
Message-ID: <16917B57-A1EE-495C-A541-D5C666701C31@gmail.com>

While the tools you mention are sufficient, you might be interested to  
know that HMMER can also generate consensus sequences. Briefly, you  
would use the alignment you generated with clustal (or any other  
multiple sequence alignment tool) to build an HMM via the hmmbuild  
function. You can then emit a consensus sequence from the HMM file  
using the hmmemit function:

hmmemit -c HMM_file.hmm

Just FYI.

T

On Oct 18, 2010, at 5:02 PM, Bill Stephens wrote:

> So, I've got the SimpleAlign running. It looks like it's running the
> alignment based upon the input sequence location only (first residue  
> from
> each sequence).  This is not what I need.
>
> I'm back to to clustal, tcoffee or dalign.
>
> Bill
>
> On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:
>
>> Hi, Bill,
>>
>> You may consider to use consensus_iupac or consensus_string methods  
>> in
>> Bio::SimpleAlign to generate consensus sequence.
>>
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>>
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris  
>> Fields
>> Sent: Monday, October 18, 2010 3:55 PM
>> To: Bill Stephens
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] Generating a consensus sequence from a  
>> Clustal
>> alignment
>>
>> Bill,
>>
>> Actually, the page you reached at Pasteur is not Pise, but Mobyle  
>> (their
>> replacement for the older Pise tools).  The Pise modules were in
>> BioPerl-Run, but they were deprecated a few years ago and removed  
>> from the
>> latest BioPerl-Run releases b/c the remote service is no longer  
>> active;
>> there is no Perl-based replacement for Mobyle interaction.
>>
>> Have you thought about just using the functionality within the
>> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure  
>> there
>> are
>> methods in place to do that.
>>
>> chris
>>
>> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
>>
>>> All,
>>>
>>> I'm in my first week with bioperl for a class project (although  
>>> I've used
>>> Perl for years). I've successfully run a clustal alignment of  
>>> several DNA
>>> sequences to produce the aln and dnd files. Now I would like to  
>>> generate
>> a
>>> consensus sequence from the alignment.  I see that Pise Cons does  
>>> this
>>> satisfactorily on my example data (
>>> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) .  
>>> However,
>> I'm
>>> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
>> distribution
>>> that I installed.
>>>
>>> Is this another module that I need to install separately?
>>>
>>> "cpan[2]> m /Pise/
>>> Module    Bio::Tools::Run::AnalysisFactory::Pise
>>> (BIRNEY/bioperl-run-1.4.tar.gz)
>>> Module    Bio::Tools::Run::PiseApplication
>> (BIRNEY/bioperl-run-1.4.tar.gz)"
>>>
>>> Bill S.
>>> _______________________________________________
>>> 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
>>
>> __________ Information from ESET Smart Security, version of virus  
>> signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus  
>> signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From jun.yin at ucd.ie  Tue Oct 19 04:17:58 2010
From: jun.yin at ucd.ie (Jun Yin)
Date: Tue, 19 Oct 2010 09:17:58 +0100
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
 alignment
In-Reply-To: <AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
	<AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
Message-ID: <003501cb6f66$23c37330$6b4a5990$%yin@ucd.ie>

Hi, Bill,

 

There are several methods you can choose from Bio::SimpleAlign to build
subalignment. For example, you can use $aln->slice  to get part of your
alignment, and then you can calculate concensus sequence from subalignment.
Another method $aln->remove_gaps, which can remove gap containing columns.

 

Cheers,

Jun Yin

Ph.D. student in U.C.D.

 

Bioinformatics Laboratory

Conway Institute

University College Dublin

 

From: Bill Stephens [mailto:grapeguy at gmail.com] 
Sent: Tuesday, October 19, 2010 1:03 AM
To: Jun Yin
Cc: Chris Fields; bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
alignment

 

So, I've got the SimpleAlign running. It looks like it's running the
alignment based upon the input sequence location only (first residue from
each sequence).  This is not what I need. 

I'm back to to clustal, tcoffee or dalign.

Bill

On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:

Hi, Bill,

You may consider to use consensus_iupac or consensus_string methods in
Bio::SimpleAlign to generate consensus sequence.

Cheers,
Jun Yin
Ph.D. student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Monday, October 18, 2010 3:55 PM
To: Bill Stephens
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
alignment

Bill,

Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
replacement for the older Pise tools).  The Pise modules were in
BioPerl-Run, but they were deprecated a few years ago and removed from the
latest BioPerl-Run releases b/c the remote service is no longer active;
there is no Perl-based replacement for Mobyle interaction.

Have you thought about just using the functionality within the
Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there are
methods in place to do that.

chris

On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:

> All,
>
> I'm in my first week with bioperl for a class project (although I've used
> Perl for years). I've successfully run a clustal alignment of several DNA
> sequences to produce the aln and dnd files. Now I would like to generate a
> consensus sequence from the alignment.  I see that Pise Cons does this
> satisfactorily on my example data (
> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
distribution
> that I installed.
>
> Is this another module that I need to install separately?
>
> "cpan[2]> m /Pise/
> Module    Bio::Tools::Run::AnalysisFactory::Pise
> (BIRNEY/bioperl-run-1.4.tar.gz)
> Module    Bio::Tools::Run::PiseApplication
(BIRNEY/bioperl-run-1.4.tar.gz)"
>
> Bill S.
> _______________________________________________
> 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

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com




__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com



 


From joseramonblas at gmail.com  Tue Oct 19 05:34:12 2010
From: joseramonblas at gmail.com (=?ISO-8859-1?Q?Jos=E9_Ram=F3n_Blas_Pastor?=)
Date: Tue, 19 Oct 2010 11:34:12 +0200
Subject: [Bioperl-l] correlated mutations analysis
Message-ID: <AANLkTimtudsQqppZtVz2+cCxKZ7gxEKXuHYPg85TC87M@mail.gmail.com>

Hi,

I have 2 protein sequences (or more). I want...
-to perform an analysis of correlated mutations in these proteins
(considering variations across 10 or 20 sps)
-obtain an statistical parameter on the significance of these mutations to
predict/hint interacting residues

Can you help me in this issue?. (Bioperl or not bioperl-based solutions are
welcome)

Thank you very much.

JR

-- 
Jos? Ram?n Blas - PhD
Dept. Biochemistry - Medicine School
University of Castilla-La Mancha

C Almansa, 14
02006 Albacete (Spain)


From cjfields at illinois.edu  Tue Oct 19 11:47:16 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 19 Oct 2010 10:47:16 -0500
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
	<AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
Message-ID: <16EDEBED-BAD4-4D57-B51B-C3234D1E8C39@illinois.edu>

Bio::SimpleAlign is the class that contains the alignment data; it does not generate the alignment for you.  You can use modules from BioPerl-Run that run ClustalW, MUSCLE, T-Coffee, etc to get a Bio::SimpleAlign instance, or parse the already-generated alignment output via Bio::AlignIO.

>From the Bio::Tools::Run::Alignment::ClustalW docs:

=================================================================

  #  Build a clustalw alignment factory
  @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
  $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);

  #  Pass the factory a list of sequences to be aligned.	
  $inputfilename = 't/data/cysprot.fa';
  $aln = $factory->align($inputfilename); # $aln is a SimpleAlign object.

  # ...or
  $seq_array_ref = \@seq_array;

  # where @seq_array is an array of Bio::Seq objects
  $aln = $factory->align($seq_array_ref);

=================================================================

$aln is a Bio::SimpleAlign derived from ClustalW output.  

>From Bio::SimpleAlign (note the use of Bio::AlignIO):

=================================================================

  # Use Bio::AlignIO to read in the alignment
  $str = Bio::AlignIO->new(-file => 't/data/testaln.pfam');
  $aln = $str->next_aln();

  # Describe
  print $aln->length;
  print $aln->num_residues;
  print $aln->is_flush;
  print $aln->num_sequences;
  print $aln->score;
  print $aln->percentage_identity;
  print $aln->consensus_string(50);

=================================================================

Note the consensus_string() method:

 Title     : consensus_string
 Usage     : $str = $ali->consensus_string($threshold_percent)
 Function  : Makes a strict consensus
 Returns   : Consensus string
 Argument  : Optional treshold ranging from 0 to 100.
             The consensus residue has to appear at least threshold %
             of the sequences at a given location, otherwise a '?'
             character will be placed at that location.
             (Default value = 0%)

chris

On Oct 18, 2010, at 7:02 PM, Bill Stephens wrote:

> So, I've got the SimpleAlign running. It looks like it's running the
> alignment based upon the input sequence location only (first residue from
> each sequence).  This is not what I need.
> 
> I'm back to to clustal, tcoffee or dalign.
> 
> Bill
> 
> On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:
> 
>> Hi, Bill,
>> 
>> You may consider to use consensus_iupac or consensus_string methods in
>> Bio::SimpleAlign to generate consensus sequence.
>> 
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>> 
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>> 
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
>> Sent: Monday, October 18, 2010 3:55 PM
>> To: Bill Stephens
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
>> alignment
>> 
>> Bill,
>> 
>> Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
>> replacement for the older Pise tools).  The Pise modules were in
>> BioPerl-Run, but they were deprecated a few years ago and removed from the
>> latest BioPerl-Run releases b/c the remote service is no longer active;
>> there is no Perl-based replacement for Mobyle interaction.
>> 
>> Have you thought about just using the functionality within the
>> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there
>> are
>> methods in place to do that.
>> 
>> chris
>> 
>> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
>> 
>>> All,
>>> 
>>> I'm in my first week with bioperl for a class project (although I've used
>>> Perl for years). I've successfully run a clustal alignment of several DNA
>>> sequences to produce the aln and dnd files. Now I would like to generate
>> a
>>> consensus sequence from the alignment.  I see that Pise Cons does this
>>> satisfactorily on my example data (
>>> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However,
>> I'm
>>> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
>> distribution
>>> that I installed.
>>> 
>>> Is this another module that I need to install separately?
>>> 
>>> "cpan[2]> m /Pise/
>>> Module    Bio::Tools::Run::AnalysisFactory::Pise
>>> (BIRNEY/bioperl-run-1.4.tar.gz)
>>> Module    Bio::Tools::Run::PiseApplication
>> (BIRNEY/bioperl-run-1.4.tar.gz)"
>>> 
>>> Bill S.
>>> _______________________________________________
>>> 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
>> 
>> __________ Information from ESET Smart Security, version of virus signature
>> database 5377 (20100818) __________
>> 
>> The message was checked by ESET Smart Security.
>> 
>> http://www.eset.com
>> 
>> 
>> 
>> 
>> __________ Information from ESET Smart Security, version of virus signature
>> database 5377 (20100818) __________
>> 
>> The message was checked by ESET Smart Security.
>> 
>> http://www.eset.com
>> 
>> 
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From td8pub at gmail.com  Tue Oct 19 13:28:07 2010
From: td8pub at gmail.com (T D)
Date: Tue, 19 Oct 2010 13:28:07 -0400
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
Message-ID: <AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>

Hi,

I'm new to BioPerl and Perl in general, and I'm trying to get
StandAloneBlastPlus to run. I got the latest versions using git and
downloaded bioperl-live  and bioperl-run.  I am having issues with Perl not
finding modules. Here is my error:

Can't locate IPC/Run.pm in @INC

Where is this module located? I am running Windows 7. I did a search for the
Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
Run.pm the older version? I have Perl v5.12.1 installed.

Thanks in advance!
Tracey

From cjfields at illinois.edu  Tue Oct 19 13:33:19 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 19 Oct 2010 12:33:19 -0500
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
	<AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>
Message-ID: <9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>

No, IPC::Run is different than IPC::Run3:

http://search.cpan.org/dist/IPC-Run/
http://search.cpan.org/dist/IPC-Run3/

Both should work under Windows, not sure about Windows7 but I can't see why they wouldn't work.

chris

On Oct 19, 2010, at 12:28 PM, T D wrote:

> Hi,
> 
> I'm new to BioPerl and Perl in general, and I'm trying to get
> StandAloneBlastPlus to run. I got the latest versions using git and
> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl not
> finding modules. Here is my error:
> 
> Can't locate IPC/Run.pm in @INC
> 
> Where is this module located? I am running Windows 7. I did a search for the
> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
> Run.pm the older version? I have Perl v5.12.1 installed.
> 
> Thanks in advance!
> Tracey
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From td8pub at gmail.com  Tue Oct 19 09:27:20 2010
From: td8pub at gmail.com (T D)
Date: Tue, 19 Oct 2010 09:27:20 -0400
Subject: [Bioperl-l] IPC/Run.pm?
Message-ID: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>

Hi,

I'm new to BioPerl and I'm trying to get StandAloneBlastPlus to run. I got
the latest versions using git and downloaded bioperl-live and and
bioperl-run.  I am having issues with Perl not finding modules. Here is my
error:

Can't locate IPC/Run.pm in @INC

Where is this module located? I am running Windows 7. I did a search for the
Run.pm and could only find IPC/*Run3.pm* under my Perl installation.

Thanks in advance!
Tracey

From anjan.purkayastha at gmail.com  Tue Oct 19 13:49:11 2010
From: anjan.purkayastha at gmail.com (ANJAN PURKAYASTHA)
Date: Tue, 19 Oct 2010 13:49:11 -0400
Subject: [Bioperl-l] Help in retrieving the DEFINITION line
Message-ID: <AANLkTimC=1mD3YBys8mOe9AUVZgo3QeNiWSydRRrfrNu@mail.gmail.com>

Hi,
I need to retrieve the DEFINITION line of a GenBank file, given the GenBank
accession ID.
The following code does not seem to do it:

use strict;
use warnings;
use Bio::Perl;
use Bio::DB::GenBank;
my $gb= new Bio::DB::GenBank;

open(F, "test_id");

while(<F>){
chomp;
my $id= $_;
my $seq= $gb->get_Seq_by_acc("$id");
my $anno_collection = $seq->annotation;
my @annotations = $anno_collection->get_Annotations('definition');
print ("@annotations\n");
}

Any thoughts on how to get this done will be deeply appreciated.
Thanks,
Anjan

-- 
===================================
anjan purkayastha, phd.
research associate
fas center for systems biology,
harvard university
52 oxford street
cambridge ma 02138
phone-703.740.6939
===================================

From David.Messina at sbc.su.se  Tue Oct 19 16:03:08 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 19 Oct 2010 16:03:08 -0400
Subject: [Bioperl-l] Help in retrieving the DEFINITION line
In-Reply-To: <AANLkTimC=1mD3YBys8mOe9AUVZgo3QeNiWSydRRrfrNu@mail.gmail.com>
References: <AANLkTimC=1mD3YBys8mOe9AUVZgo3QeNiWSydRRrfrNu@mail.gmail.com>
Message-ID: <0E6779A3-BD3E-469F-8C23-8BFA92135915@sbc.su.se>

Hi Anjan,

You can get to the definition directly, via the desc() method.

So, this works:

use strict;
use warnings;
use Bio::Perl;
use Bio::DB::GenBank;
my $gb= new Bio::DB::GenBank;

open(F, "test_id");

while(<F>){
	chomp;
	my $id= $_;
	my $seq= $gb->get_Seq_by_acc("$id");

	# I added these lines:
	my $definition      = $seq->desc;
        print $definition, "\n";}
}



Dave


From td8pub at gmail.com  Tue Oct 19 16:38:32 2010
From: td8pub at gmail.com (T D)
Date: Tue, 19 Oct 2010 16:38:32 -0400
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
	<AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>
	<9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>
Message-ID: <AANLkTi=LKy-UMPkQkDXN=83sjRFdJMgOn7Du9vVdh6x7@mail.gmail.com>

Thank you. I downloaded IPC::Run and the code seems to be working now. Is
Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?


On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:

> No, IPC::Run is different than IPC::Run3:
>
> http://search.cpan.org/dist/IPC-Run/
> http://search.cpan.org/dist/IPC-Run3/
>
> Both should work under Windows, not sure about Windows7 but I can't see why
> they wouldn't work.
>
> chris
>
> On Oct 19, 2010, at 12:28 PM, T D wrote:
>
> > Hi,
> >
> > I'm new to BioPerl and Perl in general, and I'm trying to get
> > StandAloneBlastPlus to run. I got the latest versions using git and
> > downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
> not
> > finding modules. Here is my error:
> >
> > Can't locate IPC/Run.pm in @INC
> >
> > Where is this module located? I am running Windows 7. I did a search for
> the
> > Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
> > Run.pm the older version? I have Perl v5.12.1 installed.
> >
> > Thanks in advance!
> > Tracey
> > _______________________________________________
> > 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 Oct 19 16:45:55 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 19 Oct 2010 15:45:55 -0500
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <AANLkTi=LKy-UMPkQkDXN=83sjRFdJMgOn7Du9vVdh6x7@mail.gmail.com>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
	<AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>
	<9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>
	<AANLkTi=LKy-UMPkQkDXN=83sjRFdJMgOn7Du9vVdh6x7@mail.gmail.com>
Message-ID: <840CF652-BAE0-4DD6-A375-30A817F20351@illinois.edu>

If you mean IPC::Run, I'm not sure.  I don't think BioPerl-Run was ever a part of Strawberry Perl Pro.

I do know there are some warnings that will pop up with BioPerl when using perl 5.12; these have been fixed in the github repo but haven't made their way into a release yet.

chris

On Oct 19, 2010, at 3:38 PM, T D wrote:

> Thank you. I downloaded IPC::Run and the code seems to be working now. Is
> Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?
> 
> 
> On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> No, IPC::Run is different than IPC::Run3:
>> 
>> http://search.cpan.org/dist/IPC-Run/
>> http://search.cpan.org/dist/IPC-Run3/
>> 
>> Both should work under Windows, not sure about Windows7 but I can't see why
>> they wouldn't work.
>> 
>> chris
>> 
>> On Oct 19, 2010, at 12:28 PM, T D wrote:
>> 
>>> Hi,
>>> 
>>> I'm new to BioPerl and Perl in general, and I'm trying to get
>>> StandAloneBlastPlus to run. I got the latest versions using git and
>>> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
>> not
>>> finding modules. Here is my error:
>>> 
>>> Can't locate IPC/Run.pm in @INC
>>> 
>>> Where is this module located? I am running Windows 7. I did a search for
>> the
>>> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
>>> Run.pm the older version? I have Perl v5.12.1 installed.
>>> 
>>> Thanks in advance!
>>> Tracey
>>> _______________________________________________
>>> 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 shalabh.sharma7 at gmail.com  Wed Oct 20 11:00:26 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 20 Oct 2010 11:00:26 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
Message-ID: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>

Hi All,
        Is there any module for mummer in Bioperl?

Also i need some suggestions and ideas (i think this is the best place to
ask).
I am working with huge data (around 200 million illumina reads), earlier i
was using blastx and other similar approaches to annotate but now i think
thats not possible, i would be very grateful if anyone can give me some idea
regarding this.

Thanks
Shalabh

From David.Messina at sbc.su.se  Wed Oct 20 11:25:02 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Wed, 20 Oct 2010 11:25:02 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
Message-ID: <C3E45590-33DD-4A27-87FF-533D8E8C9C09@sbc.su.se>


> Is there any module for mummer in Bioperl?

Did you try searching for mummer on the bioperl website?



From shalabh.sharma7 at gmail.com  Wed Oct 20 11:31:09 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 20 Oct 2010 11:31:09 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <C3E45590-33DD-4A27-87FF-533D8E8C9C09@sbc.su.se>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
	<C3E45590-33DD-4A27-87FF-533D8E8C9C09@sbc.su.se>
Message-ID: <AANLkTim3ig2Aa+=TUqb0Cr5HsH0f-eHoi+aZCX-pctEp@mail.gmail.com>

Yes , i did but its saying there aren't any modules available so i jsu
wanted to make sure.

-Shalabh


On Wed, Oct 20, 2010 at 11:25 AM, Dave Messina <David.Messina at sbc.su.se>wrote:

>
> > Is there any module for mummer in Bioperl?
>
> Did you try searching for mummer on the bioperl website?
>
>
>

From jimhu at tamu.edu  Wed Oct 20 11:27:08 2010
From: jimhu at tamu.edu (Jim Hu)
Date: Wed, 20 Oct 2010 10:27:08 -0500
Subject: [Bioperl-l] treeio->write_tree problem
Message-ID: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>

Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.

Jim

use Data::Dumper;
use Bio::TreeIO;
my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
                            -format => "newick");
while( my $tree = $treeio->next_tree ) {
	$treeio->write_tree($tree);
	print Dumper($tree);

}

=====================================
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 Oct 20 11:45:45 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 10:45:45 -0500
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
Message-ID: <572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>

On Oct 20, 2010, at 10:00 AM, shalabh sharma wrote:

> Hi All,
>        Is there any module for mummer in Bioperl?
> 
> Also i need some suggestions and ideas (i think this is the best place to
> ask).
> I am working with huge data (around 200 million illumina reads), earlier i
> was using blastx and other similar approaches to annotate but now i think
> thats not possible, i would be very grateful if anyone can give me some idea
> regarding this.
> 
> Thanks
> Shalabh

Hard to say unless we know a little more about what you are attempting to do.  Not sure why you are using mummer here, but...

This is something fairly well-covered in the literature for most use cases, and on places like seqanswers.  If you are doing something like aligning reads to reference genome(s) or set of gene models, you should be using something like bowtie/tophat, bwa, etc., with the output in SAM (BioPerl has perl wrappers for most of these modules).  

You can also do the same for metagenome analyses, but you may need to run BLAST and convert to SAM (maybe that's what you are doing?).  The samtools package comes with perl scripts to do that and can be further used to sort the matches, convert/index a BAM file for fast accession, etc.  From there you can then use tools like Bio::DB::SAM, R/BioConductor/RSamtools, or similar to access the sequences, find coverage statistics, run SNP calls, etc.

And, for the record, we do have an experimental mummer parser, but I believe it lies in a branch at the moment (don't think it has been merged yet):

http://github.com/bioperl/bioperl-live/tree/topic/bug-2701

chris

From cjfields at illinois.edu  Wed Oct 20 11:46:42 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 10:46:42 -0500
Subject: [Bioperl-l] treeio->write_tree problem
In-Reply-To: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
References: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
Message-ID: <112B35F0-77B6-4B46-9E3A-AAB840E7D349@illinois.edu>

Try '-format => "nhx"'.

chris

On Oct 20, 2010, at 10:27 AM, Jim Hu wrote:

> Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.
> 
> Jim
> 
> use Data::Dumper;
> use Bio::TreeIO;
> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>                            -format => "newick");
> while( my $tree = $treeio->next_tree ) {
> 	$treeio->write_tree($tree);
> 	print Dumper($tree);
> 
> }
> 
> =====================================
> Jim Hu
> Associate Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jimhu at tamu.edu  Wed Oct 20 12:16:52 2010
From: jimhu at tamu.edu (Jim Hu)
Date: Wed, 20 Oct 2010 11:16:52 -0500
Subject: [Bioperl-l] treeio->write_tree problem
In-Reply-To: <534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>
References: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
	<534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>
Message-ID: <BADE3FC8-A40F-4832-8C63-B20CB7C40631@tamu.edu>

Doh!  I suspected it was something brain-dead that I was doing.

Thanks very much.  That worked.

Jim

On Oct 20, 2010, at 11:01 AM, Adam Witney wrote:

> 
> you are writing to your input stream. I think you need to create a separate output stream. Maybe something like this (untested):
> 
> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>                           -format => "newick");
> 
> my $treeio_out = new Bio::TreeIO(-fh   => \*STDOUT,
>                           -format => "newick");
> 
> while( my $tree = $treeio->next_tree ) {
> 	$treeio_out->write_tree($tree);
> 	print Dumper($tree);
> }
> 
> 
> 
> On 20 Oct 2010, at 16:27, Jim Hu wrote:
> 
>> Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.
>> 
>> Jim
>> 
>> use Data::Dumper;
>> use Bio::TreeIO;
>> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>>                           -format => "newick");
>> while( my $tree = $treeio->next_tree ) {
>> 	$treeio->write_tree($tree);
>> 	print Dumper($tree);
>> 
>> }
>> 
>> =====================================
>> Jim Hu
>> Associate Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>> 
>> 
>> 
>> _______________________________________________
>> 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 awitney at sgul.ac.uk  Wed Oct 20 12:01:45 2010
From: awitney at sgul.ac.uk (Adam Witney)
Date: Wed, 20 Oct 2010 17:01:45 +0100
Subject: [Bioperl-l] treeio->write_tree problem
In-Reply-To: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
References: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
Message-ID: <534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>


you are writing to your input stream. I think you need to create a separate output stream. Maybe something like this (untested):

my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
                           -format => "newick");

my $treeio_out = new Bio::TreeIO(-fh   => \*STDOUT,
                           -format => "newick");

while( my $tree = $treeio->next_tree ) {
	$treeio_out->write_tree($tree);
	print Dumper($tree);
}



On 20 Oct 2010, at 16:27, Jim Hu wrote:

> Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.
> 
> Jim
> 
> use Data::Dumper;
> use Bio::TreeIO;
> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>                            -format => "newick");
> while( my $tree = $treeio->next_tree ) {
> 	$treeio->write_tree($tree);
> 	print Dumper($tree);
> 
> }
> 
> =====================================
> Jim Hu
> Associate Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
> 
> 
> 
> _______________________________________________
> 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 Oct 20 12:35:40 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 20 Oct 2010 12:35:40 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
	<572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>
Message-ID: <AANLkTimfSXRn1u-wvqSGM+B=j0Ohhnu5SGDcO413pSBm@mail.gmail.com>

Hey Chris,
             Thanks for the reply , it was really useful.
Actually you are right, it is metagenomics sample. The thing is i've never
worked with that huge amount of data, so i am trying to test some alignment
programs (i am just trying to see if i can avoid blastx) so i am trying all
the available programs.

Blasting 200 million reads doesn't seems a right option (may be i will go
with assembly then blasting it).

Thanks
Shalabh


On Wed, Oct 20, 2010 at 11:45 AM, Chris Fields <cjfields at illinois.edu>wrote:

> On Oct 20, 2010, at 10:00 AM, shalabh sharma wrote:
>
> > Hi All,
> >        Is there any module for mummer in Bioperl?
> >
> > Also i need some suggestions and ideas (i think this is the best place to
> > ask).
> > I am working with huge data (around 200 million illumina reads), earlier
> i
> > was using blastx and other similar approaches to annotate but now i think
> > thats not possible, i would be very grateful if anyone can give me some
> idea
> > regarding this.
> >
> > Thanks
> > Shalabh
>
> Hard to say unless we know a little more about what you are attempting to
> do.  Not sure why you are using mummer here, but...
>
> This is something fairly well-covered in the literature for most use cases,
> and on places like seqanswers.  If you are doing something like aligning
> reads to reference genome(s) or set of gene models, you should be using
> something like bowtie/tophat, bwa, etc., with the output in SAM (BioPerl has
> perl wrappers for most of these modules).
>
> You can also do the same for metagenome analyses, but you may need to run
> BLAST and convert to SAM (maybe that's what you are doing?).  The samtools
> package comes with perl scripts to do that and can be further used to sort
> the matches, convert/index a BAM file for fast accession, etc.  From there
> you can then use tools like Bio::DB::SAM, R/BioConductor/RSamtools, or
> similar to access the sequences, find coverage statistics, run SNP calls,
> etc.
>
> And, for the record, we do have an experimental mummer parser, but I
> believe it lies in a branch at the moment (don't think it has been merged
> yet):
>
> http://github.com/bioperl/bioperl-live/tree/topic/bug-2701
>
> chris

From cjfields at illinois.edu  Wed Oct 20 14:15:09 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 13:15:09 -0500
Subject: [Bioperl-l] treeio->write_tree problem
In-Reply-To: <534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>
References: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
	<534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>
Message-ID: <8A7F4396-D88F-438E-B045-F2CD58293DD1@illinois.edu>

Nice catch!  Completely missed that.

chris

On Oct 20, 2010, at 11:01 AM, Adam Witney wrote:

> 
> you are writing to your input stream. I think you need to create a separate output stream. Maybe something like this (untested):
> 
> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>                           -format => "newick");
> 
> my $treeio_out = new Bio::TreeIO(-fh   => \*STDOUT,
>                           -format => "newick");
> 
> while( my $tree = $treeio->next_tree ) {
> 	$treeio_out->write_tree($tree);
> 	print Dumper($tree);
> }
> 
> 
> 
> On 20 Oct 2010, at 16:27, Jim Hu wrote:
> 
>> Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.
>> 
>> Jim
>> 
>> use Data::Dumper;
>> use Bio::TreeIO;
>> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>>                           -format => "newick");
>> while( my $tree = $treeio->next_tree ) {
>> 	$treeio->write_tree($tree);
>> 	print Dumper($tree);
>> 
>> }
>> 
>> =====================================
>> Jim Hu
>> Associate Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>> 
>> 
>> 
>> _______________________________________________
>> 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  Wed Oct 20 14:25:09 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 13:25:09 -0500
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <AANLkTimfSXRn1u-wvqSGM+B=j0Ohhnu5SGDcO413pSBm@mail.gmail.com>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
	<572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>
	<AANLkTimfSXRn1u-wvqSGM+B=j0Ohhnu5SGDcO413pSBm@mail.gmail.com>
Message-ID: <8B2DB10D-0E81-4426-8678-893669DFD0F9@illinois.edu>

I recall there being a lot of tools available for these.  In particular, one of my colleagues has used MEGAN with some success:

http://www-ab.informatik.uni-tuebingen.de/software/megan

If the sample is from a specific host (i.e. gut microbiome, etc), you can set up initial short read runs that act to filter out sequences you might not be interested in (namely those that belong to the host), then run alignments against more focused databases (rRNA, for instance, if one is doing meta-transcriptomic analyses).  Beyond that, I agree that assembly should be included early in the analysis, if it isn't already the initial step.

chris

On Oct 20, 2010, at 11:35 AM, shalabh sharma wrote:

> Hey Chris,
>              Thanks for the reply , it was really useful.
> Actually you are right, it is metagenomics sample. The thing is i've never worked with that huge amount of data, so i am trying to test some alignment programs (i am just trying to see if i can avoid blastx) so i am trying all the available programs.
> 
> Blasting 200 million reads doesn't seems a right option (may be i will go with assembly then blasting it).
> 
> Thanks
> Shalabh
> 
> 
> On Wed, Oct 20, 2010 at 11:45 AM, Chris Fields <cjfields at illinois.edu> wrote:
> On Oct 20, 2010, at 10:00 AM, shalabh sharma wrote:
> 
> > Hi All,
> >        Is there any module for mummer in Bioperl?
> >
> > Also i need some suggestions and ideas (i think this is the best place to
> > ask).
> > I am working with huge data (around 200 million illumina reads), earlier i
> > was using blastx and other similar approaches to annotate but now i think
> > thats not possible, i would be very grateful if anyone can give me some idea
> > regarding this.
> >
> > Thanks
> > Shalabh
> 
> Hard to say unless we know a little more about what you are attempting to do.  Not sure why you are using mummer here, but...
> 
> This is something fairly well-covered in the literature for most use cases, and on places like seqanswers.  If you are doing something like aligning reads to reference genome(s) or set of gene models, you should be using something like bowtie/tophat, bwa, etc., with the output in SAM (BioPerl has perl wrappers for most of these modules).
> 
> You can also do the same for metagenome analyses, but you may need to run BLAST and convert to SAM (maybe that's what you are doing?).  The samtools package comes with perl scripts to do that and can be further used to sort the matches, convert/index a BAM file for fast accession, etc.  From there you can then use tools like Bio::DB::SAM, R/BioConductor/RSamtools, or similar to access the sequences, find coverage statistics, run SNP calls, etc.
> 
> And, for the record, we do have an experimental mummer parser, but I believe it lies in a branch at the moment (don't think it has been merged yet):
> 
> http://github.com/bioperl/bioperl-live/tree/topic/bug-2701
> 
> chris
> 



From shalabh.sharma7 at gmail.com  Wed Oct 20 14:35:54 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 20 Oct 2010 14:35:54 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <8B2DB10D-0E81-4426-8678-893669DFD0F9@illinois.edu>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
	<572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>
	<AANLkTimfSXRn1u-wvqSGM+B=j0Ohhnu5SGDcO413pSBm@mail.gmail.com>
	<8B2DB10D-0E81-4426-8678-893669DFD0F9@illinois.edu>
Message-ID: <AANLkTinxFKdMkOaejxpFDN-qf0pF=Lg7brHHvqYuXk4s@mail.gmail.com>

I have used MEGAN a lot in past, but again it takes blast files as input and
here i just want to avoid blast.
The problem is its environmental sample so i cant throw any of the data.

I know its not a bioperl question but i was just wondering is there any
program that can align my reads against a huge database at amino acid level
(like with refseq or subset of refseq).
or even alignment is a good option?

I really appreciate your input.

Thanks
Shalabh


On Wed, Oct 20, 2010 at 2:25 PM, Chris Fields <cjfields at illinois.edu> wrote:

> I recall there being a lot of tools available for these.  In particular,
> one of my colleagues has used MEGAN with some success:
>
> http://www-ab.informatik.uni-tuebingen.de/software/megan
>
> If the sample is from a specific host (i.e. gut microbiome, etc), you can
> set up initial short read runs that act to filter out sequences you might
> not be interested in (namely those that belong to the host), then run
> alignments against more focused databases (rRNA, for instance, if one is
> doing meta-transcriptomic analyses).  Beyond that, I agree that assembly
> should be included early in the analysis, if it isn't already the initial
> step.
>
> chris
>
> On Oct 20, 2010, at 11:35 AM, shalabh sharma wrote:
>
> > Hey Chris,
> >              Thanks for the reply , it was really useful.
> > Actually you are right, it is metagenomics sample. The thing is i've
> never worked with that huge amount of data, so i am trying to test some
> alignment programs (i am just trying to see if i can avoid blastx) so i am
> trying all the available programs.
> >
> > Blasting 200 million reads doesn't seems a right option (may be i will go
> with assembly then blasting it).
> >
> > Thanks
> > Shalabh
> >
> >
> > On Wed, Oct 20, 2010 at 11:45 AM, Chris Fields <cjfields at illinois.edu>
> wrote:
> > On Oct 20, 2010, at 10:00 AM, shalabh sharma wrote:
> >
> > > Hi All,
> > >        Is there any module for mummer in Bioperl?
> > >
> > > Also i need some suggestions and ideas (i think this is the best place
> to
> > > ask).
> > > I am working with huge data (around 200 million illumina reads),
> earlier i
> > > was using blastx and other similar approaches to annotate but now i
> think
> > > thats not possible, i would be very grateful if anyone can give me some
> idea
> > > regarding this.
> > >
> > > Thanks
> > > Shalabh
> >
> > Hard to say unless we know a little more about what you are attempting to
> do.  Not sure why you are using mummer here, but...
> >
> > This is something fairly well-covered in the literature for most use
> cases, and on places like seqanswers.  If you are doing something like
> aligning reads to reference genome(s) or set of gene models, you should be
> using something like bowtie/tophat, bwa, etc., with the output in SAM
> (BioPerl has perl wrappers for most of these modules).
> >
> > You can also do the same for metagenome analyses, but you may need to run
> BLAST and convert to SAM (maybe that's what you are doing?).  The samtools
> package comes with perl scripts to do that and can be further used to sort
> the matches, convert/index a BAM file for fast accession, etc.  From there
> you can then use tools like Bio::DB::SAM, R/BioConductor/RSamtools, or
> similar to access the sequences, find coverage statistics, run SNP calls,
> etc.
> >
> > And, for the record, we do have an experimental mummer parser, but I
> believe it lies in a branch at the moment (don't think it has been merged
> yet):
> >
> > http://github.com/bioperl/bioperl-live/tree/topic/bug-2701
> >
> > chris
> >
>
>

From rmb32 at cornell.edu  Wed Oct 20 20:27:36 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Wed, 20 Oct 2010 17:27:36 -0700
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <840CF652-BAE0-4DD6-A375-30A817F20351@illinois.edu>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>	<AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>	<9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>	<AANLkTi=LKy-UMPkQkDXN=83sjRFdJMgOn7Du9vVdh6x7@mail.gmail.com>
	<840CF652-BAE0-4DD6-A375-30A817F20351@illinois.edu>
Message-ID: <4CBF88F8.2030601@cornell.edu>

Ah, the joys of optional deps.

You know, bioperl-run does not have that many deps right now.  Why don't 
we just make those optional ones required?

R


Chris Fields wrote:
> If you mean IPC::Run, I'm not sure.  I don't think BioPerl-Run was ever a part of Strawberry Perl Pro.
> 
> I do know there are some warnings that will pop up with BioPerl when using perl 5.12; these have been fixed in the github repo but haven't made their way into a release yet.
> 
> chris
> 
> On Oct 19, 2010, at 3:38 PM, T D wrote:
> 
>> Thank you. I downloaded IPC::Run and the code seems to be working now. Is
>> Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?
>>
>>
>> On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>
>>> No, IPC::Run is different than IPC::Run3:
>>>
>>> http://search.cpan.org/dist/IPC-Run/
>>> http://search.cpan.org/dist/IPC-Run3/
>>>
>>> Both should work under Windows, not sure about Windows7 but I can't see why
>>> they wouldn't work.
>>>
>>> chris
>>>
>>> On Oct 19, 2010, at 12:28 PM, T D wrote:
>>>
>>>> Hi,
>>>>
>>>> I'm new to BioPerl and Perl in general, and I'm trying to get
>>>> StandAloneBlastPlus to run. I got the latest versions using git and
>>>> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
>>> not
>>>> finding modules. Here is my error:
>>>>
>>>> Can't locate IPC/Run.pm in @INC
>>>>
>>>> Where is this module located? I am running Windows 7. I did a search for
>>> the
>>>> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
>>>> Run.pm the older version? I have Perl v5.12.1 installed.
>>>>
>>>> Thanks in advance!
>>>> Tracey
>>>> _______________________________________________
>>>> 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 maj at fortinbras.us  Wed Oct 20 21:21:56 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Thu, 21 Oct 2010 01:21:56 +0000
Subject: [Bioperl-l] IPC/Run.pm?
Message-ID: <W2403825015265021287624116@webmail11>

I would +1 making IPC::Run required. It's got some nice features and it much safer than system(). Might even want to make it a dev recommendation for all system calls. MAJ

>-----Original Message-----
>From: Robert Buels [mailto:rmb32 at cornell.edu]
>Sent: Wednesday, October 20, 2010 08:27 PM
>To: 'Chris Fields'
>Cc: bioperl-l at lists.open-bio.org
>Subject: Re: [Bioperl-l] IPC/Run.pm?
>
>Ah, the joys of optional deps.
>
>You know, bioperl-run does not have that many deps right now.  Why don't 
>we just make those optional ones required?
>
>R
>
>
>Chris Fields wrote:
>> If you mean IPC::Run, I'm not sure.  I don't think BioPerl-Run was ever a part of Strawberry Perl Pro.
>> 
>> I do know there are some warnings that will pop up with BioPerl when using perl 5.12; these have been fixed in the github repo but haven't made their way into a release yet.
>> 
>> chris
>> 
>> On Oct 19, 2010, at 3:38 PM, T D wrote:
>> 
>>> Thank you. I downloaded IPC::Run and the code seems to be working now. Is
>>> Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?
>>>
>>>
>>> On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>
>>>> No, IPC::Run is different than IPC::Run3:
>>>>
>>>> http://search.cpan.org/dist/IPC-Run/
>>>> http://search.cpan.org/dist/IPC-Run3/
>>>>
>>>> Both should work under Windows, not sure about Windows7 but I can't see why
>>>> they wouldn't work.
>>>>
>>>> chris
>>>>
>>>> On Oct 19, 2010, at 12:28 PM, T D wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I'm new to BioPerl and Perl in general, and I'm trying to get
>>>>> StandAloneBlastPlus to run. I got the latest versions using git and
>>>>> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
>>>> not
>>>>> finding modules. Here is my error:
>>>>>
>>>>> Can't locate IPC/Run.pm in @INC
>>>>>
>>>>> Where is this module located? I am running Windows 7. I did a search for
>>>> the
>>>>> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
>>>>> Run.pm the older version? I have Perl v5.12.1 installed.
>>>>>
>>>>> Thanks in advance!
>>>>> Tracey
>>>>> _______________________________________________
>>>>> 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 cjfields at illinois.edu  Wed Oct 20 21:54:48 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 20:54:48 -0500
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <W2403825015265021287624116@webmail11>
References: <W2403825015265021287624116@webmail11>
Message-ID: <697C7C00-5ED9-4A69-9F55-6C8C6F349DF4@illinois.edu>

+1.  Quite a few modules there use it.

chris

On Oct 20, 2010, at 8:21 PM, Mark A. Jensen wrote:

> I would +1 making IPC::Run required. It's got some nice features and it much safer than system(). Might even want to make it a dev recommendation for all system calls. MAJ
> 
>> -----Original Message-----
>> From: Robert Buels [mailto:rmb32 at cornell.edu]
>> Sent: Wednesday, October 20, 2010 08:27 PM
>> To: 'Chris Fields'
>> Cc: bioperl-l at lists.open-bio.org
>> Subject: Re: [Bioperl-l] IPC/Run.pm?
>> 
>> Ah, the joys of optional deps.
>> 
>> You know, bioperl-run does not have that many deps right now.  Why don't 
>> we just make those optional ones required?
>> 
>> R
>> 
>> 
>> Chris Fields wrote:
>>> If you mean IPC::Run, I'm not sure.  I don't think BioPerl-Run was ever a part of Strawberry Perl Pro.
>>> 
>>> I do know there are some warnings that will pop up with BioPerl when using perl 5.12; these have been fixed in the github repo but haven't made their way into a release yet.
>>> 
>>> chris
>>> 
>>> On Oct 19, 2010, at 3:38 PM, T D wrote:
>>> 
>>>> Thank you. I downloaded IPC::Run and the code seems to be working now. Is
>>>> Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?
>>>> 
>>>> 
>>>> On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>> 
>>>>> No, IPC::Run is different than IPC::Run3:
>>>>> 
>>>>> http://search.cpan.org/dist/IPC-Run/
>>>>> http://search.cpan.org/dist/IPC-Run3/
>>>>> 
>>>>> Both should work under Windows, not sure about Windows7 but I can't see why
>>>>> they wouldn't work.
>>>>> 
>>>>> chris
>>>>> 
>>>>> On Oct 19, 2010, at 12:28 PM, T D wrote:
>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I'm new to BioPerl and Perl in general, and I'm trying to get
>>>>>> StandAloneBlastPlus to run. I got the latest versions using git and
>>>>>> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
>>>>> not
>>>>>> finding modules. Here is my error:
>>>>>> 
>>>>>> Can't locate IPC/Run.pm in @INC
>>>>>> 
>>>>>> Where is this module located? I am running Windows 7. I did a search for
>>>>> the
>>>>>> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
>>>>>> Run.pm the older version? I have Perl v5.12.1 installed.
>>>>>> 
>>>>>> Thanks in advance!
>>>>>> Tracey
>>>>>> _______________________________________________
>>>>>> 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 ashwani.iiit at gmail.com  Thu Oct 21 04:39:22 2010
From: ashwani.iiit at gmail.com (ashwani sharma)
Date: Thu, 21 Oct 2010 14:09:22 +0530
Subject: [Bioperl-l] how to download PDB files using Bioperl script
Message-ID: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>

Hi All,


I have around 150 pdb file names and I need to download them from Protein
Data Bank. I wonder if someone could tell me how to do it by using Bioperl.

Thanks in advance.

Regards,
Ashwani

From hanbobio at 126.com  Tue Oct 19 07:50:07 2010
From: hanbobio at 126.com (yusheng liao)
Date: Tue, 19 Oct 2010 11:50:07 +0000 (UTC)
Subject: [Bioperl-l] Can't locate Bio/seqIO.pm in @INC
Message-ID: <loom.20101019T134347-528@post.gmane.org>

Can't locate Bio/seqIO.pm in @INC 
I try to run a .pl file to get multi sequences for t
he GenBank using the
Bioperl. The following were the error message:
linux:/home/liaoy # perl hsv-1.pl
Can't locate Bio/seqIO.pm in @INC (@INC contains:
/usr/lib/perl5/5.8.7/i586-linux-thread-multi /usr/lib/perl5/5.8.7
/usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.7 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .)
 at hsv-1.pl line 4.
BEGIN failed--compilation aborted at hsv-1.pl line 4.

what is the problem? And how to corret it? 


From cgzheng86 at gmail.com  Thu Oct 21 04:45:40 2010
From: cgzheng86 at gmail.com (Chaogu Zheng)
Date: Thu, 21 Oct 2010 01:45:40 -0700 (PDT)
Subject: [Bioperl-l] Failed to load module Bio::SeqIO::swiss
Message-ID: <63e01ab5-99f2-46a0-8901-3bdb24562c5f@g13g2000yqj.googlegroups.com>

I am extremely new to Bioperl and got a problem immediately after I
installed it.

I installed Bioperl-pm5100 and Bioperl-run-pm5100 using fink.
Everything seems to be fine. However, when I tried to retrieve some
sequences from swissprot, I found the following errors.

It seems the module Bio::SeqIO::swiss can not be loaded, though I
indeed found it under the correct directory. By the way, if I change
'swiss' to 'genbank' I can successfully run the program.

I don't know how to fix it. Anyone can help me?


Ryan

>>>>>>>>>>>>>>
Bio::SeqIO: swiss cannot be found
Exception
------------- EXCEPTION -------------
MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/
Stag.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-
multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-
multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/
5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/
Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/
5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/
5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /
Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/
Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/
5.10.0 .) at /sw/lib/perl5/5.10.0/Bio/Annotation/TagTree.pm line 123.
BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/
Annotation/TagTree.pm line 123.
Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/SeqIO/
swiss.pm line 208.
BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/SeqIO/
swiss.pm line 208.
Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/Root/Root.pm
line 439.

STACK Bio::Root::Root::_load_module /sw/lib/perl5/5.10.0/Bio/Root/
Root.pm:441
STACK (eval) /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:570
STACK Bio::SeqIO::_load_format_module /sw/lib/perl5/5.10.0/Bio/
SeqIO.pm:569
STACK Bio::SeqIO::new /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:389
STACK Bio::DB::WebDBSeqI::get_seq_stream /sw/lib/perl5/5.10.0/Bio/DB/
WebDBSeqI.pm:472
STACK Bio::DB::WebDBSeqI::get_Stream_by_acc /sw/lib/perl5/5.10.0/Bio/
DB/WebDBSeqI.pm:314
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
WebDBSeqI.pm:186
STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
STACK toplevel ./Documents/perl-programs/perl_test:8
-------------------------------------


For more information about the SeqIO system please see the SeqIO docs.
This includes ways of checking for formats at compile time, not run
time

------------- EXCEPTION -------------
MSG: acc P11217 does not exist
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
WebDBSeqI.pm:187
STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
STACK toplevel ./Documents/perl-programs/perl_test:8
-------------------------------------

From cjfields at illinois.edu  Thu Oct 21 11:02:35 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 21 Oct 2010 10:02:35 -0500
Subject: [Bioperl-l] Can't locate Bio/seqIO.pm in @INC
In-Reply-To: <loom.20101019T134347-528@post.gmane.org>
References: <loom.20101019T134347-528@post.gmane.org>
Message-ID: <9E5A48C0-4509-429B-8F16-9A1D1A440CC8@illinois.edu>

Check your spelling (note the caps below):

use Bio::SeqIO;

chris

On Oct 19, 2010, at 6:50 AM, yusheng liao wrote:

> Can't locate Bio/seqIO.pm in @INC 
> I try to run a .pl file to get multi sequences for t
> he GenBank using the
> Bioperl. The following were the error message:
> linux:/home/liaoy # perl hsv-1.pl
> Can't locate Bio/seqIO.pm in @INC (@INC contains:
> /usr/lib/perl5/5.8.7/i586-linux-thread-multi /usr/lib/perl5/5.8.7
> /usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.7 /usr/lib/perl5/site_perl
> /usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .)
> at hsv-1.pl line 4.
> BEGIN failed--compilation aborted at hsv-1.pl line 4.
> 
> what is the problem? And how to corret it? 
> 
> _______________________________________________
> 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 Oct 21 11:05:17 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 21 Oct 2010 10:05:17 -0500
Subject: [Bioperl-l] Failed to load module Bio::SeqIO::swiss
In-Reply-To: <63e01ab5-99f2-46a0-8901-3bdb24562c5f@g13g2000yqj.googlegroups.com>
References: <63e01ab5-99f2-46a0-8901-3bdb24562c5f@g13g2000yqj.googlegroups.com>
Message-ID: <23FDD4AF-3E56-4E05-AFD7-21A54DECD1C6@illinois.edu>

Like the error message says, you need to install Data::Stag (so, for some reason, this way left off).  However, I'm not sure why you are using fink as the version in stable is still 1.5.1; bioperl 1.6.1 is in fink-unstable.

chris

On Oct 21, 2010, at 3:45 AM, Chaogu Zheng wrote:

> I am extremely new to Bioperl and got a problem immediately after I
> installed it.
> 
> I installed Bioperl-pm5100 and Bioperl-run-pm5100 using fink.
> Everything seems to be fine. However, when I tried to retrieve some
> sequences from swissprot, I found the following errors.
> 
> It seems the module Bio::SeqIO::swiss can not be loaded, though I
> indeed found it under the correct directory. By the way, if I change
> 'swiss' to 'genbank' I can successfully run the program.
> 
> I don't know how to fix it. Anyone can help me?
> 
> 
> Ryan
> 
>>>>>>>>>>>>>>> 
> Bio::SeqIO: swiss cannot be found
> Exception
> ------------- EXCEPTION -------------
> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/
> Stag.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-
> multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-
> multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/
> 5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/
> Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/
> 5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/
> 5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /
> Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/
> Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/
> 5.10.0 .) at /sw/lib/perl5/5.10.0/Bio/Annotation/TagTree.pm line 123.
> BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/
> Annotation/TagTree.pm line 123.
> Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> swiss.pm line 208.
> BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> swiss.pm line 208.
> Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/Root/Root.pm
> line 439.
> 
> STACK Bio::Root::Root::_load_module /sw/lib/perl5/5.10.0/Bio/Root/
> Root.pm:441
> STACK (eval) /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:570
> STACK Bio::SeqIO::_load_format_module /sw/lib/perl5/5.10.0/Bio/
> SeqIO.pm:569
> STACK Bio::SeqIO::new /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:389
> STACK Bio::DB::WebDBSeqI::get_seq_stream /sw/lib/perl5/5.10.0/Bio/DB/
> WebDBSeqI.pm:472
> STACK Bio::DB::WebDBSeqI::get_Stream_by_acc /sw/lib/perl5/5.10.0/Bio/
> DB/WebDBSeqI.pm:314
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> WebDBSeqI.pm:186
> STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> STACK toplevel ./Documents/perl-programs/perl_test:8
> -------------------------------------
> 
> 
> For more information about the SeqIO system please see the SeqIO docs.
> This includes ways of checking for formats at compile time, not run
> time
> 
> ------------- EXCEPTION -------------
> MSG: acc P11217 does not exist
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> WebDBSeqI.pm:187
> STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> STACK toplevel ./Documents/perl-programs/perl_test:8
> -------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jimhu at tamu.edu  Thu Oct 21 13:52:32 2010
From: jimhu at tamu.edu (Jim Hu)
Date: Thu, 21 Oct 2010 12:52:32 -0500
Subject: [Bioperl-l] Does $tree->remove_Node prune or splice?
Message-ID: <927BEE54-ABC2-428A-AF42-DDEBDEABB878@tamu.edu>

I'm trying to take an unreadable tree from PFAM and prune it down to just show the paralogs from E. coli.

When you run remove_Node on an internal node, is it supposed to reconnect the ancestors to the descendants?  This seems to be way to aggressive in what it's removing.

while( my $tree = $treeio->next_tree ) {
	for my $node ( $tree->get_nodes ) {
		if ($node->id =~ m/_ECOLI/){
			#	leave this node alone
			#	print $node->id."\n";
		}else{
			if ($node->is_Leaf){
				$tree->remove_Node($node);
			}else{
				my $num_children = scalar($node->each_Descendent);
				if ($num_children == 1){ 
					print "removing ".$node->id."\n";
					$tree->remove_Node($node);
				}	
			}	
		}
	}
	$treeio_out->write_tree($tree);
}

The idea is that when I've pruned the non-ECOLI leaves, some internal nodes will not be branches anymore.  But at the end, all the ECOLI nodes are gone, presumably because an ancestor got removed and the whole branch was lost.  Is there a way to remove just a node and graft the tree back together?  My plan, once I get that working is to repeat the traversal until the output stops changing.

Jim


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




From cgzheng86 at gmail.com  Thu Oct 21 13:57:06 2010
From: cgzheng86 at gmail.com (Chaogu Zheng)
Date: Thu, 21 Oct 2010 10:57:06 -0700 (PDT)
Subject: [Bioperl-l] Failed to load module Bio::SeqIO::swiss
In-Reply-To: <23FDD4AF-3E56-4E05-AFD7-21A54DECD1C6@illinois.edu>
References: <63e01ab5-99f2-46a0-8901-3bdb24562c5f@g13g2000yqj.googlegroups.com>
	<23FDD4AF-3E56-4E05-AFD7-21A54DECD1C6@illinois.edu>
Message-ID: <974a993b-fbdf-4ca6-a59b-a7f247669eff@j18g2000yqd.googlegroups.com>

Maybe my reason for this is silly. I am using the Mac OS X 10.6, which
has the pre-installed perl 5.10.0. Fink only has the unstable bioperl
1.6.1 for Mac OS X 10.6. If I want to install bioperl-pm588 that is
the fink-stable 1.5.1 version, I guess I have to install an earlier
version of perl 5.8.8. I did not bother to do that.

So, do you think I really need to uninstall bioperl-pm5100 and get
perl 5.8.8 to try the fink-stable one?

Ryan

On Oct 21, 11:05?am, Chris Fields <cjfie... at illinois.edu> wrote:
> Like the error message says, you need to install Data::Stag (so, for some reason, this way left off). ?However, I'm not sure why you are using fink as the version in stable is still 1.5.1; bioperl 1.6.1 is in fink-unstable.
>
> chris
>
> On Oct 21, 2010, at 3:45 AM, Chaogu Zheng wrote:
>
>
>
>
>
> > I am extremely new to Bioperl and got a problem immediately after I
> > installed it.
>
> > I installed Bioperl-pm5100 and Bioperl-run-pm5100 using fink.
> > Everything seems to be fine. However, when I tried to retrieve some
> > sequences from swissprot, I found the following errors.
>
> > It seems the module Bio::SeqIO::swiss can not be loaded, though I
> > indeed found it under the correct directory. By the way, if I change
> > 'swiss' to 'genbank' I can successfully run the program.
>
> > I don't know how to fix it. Anyone can help me?
>
> > Ryan
>
> > Bio::SeqIO: swiss cannot be found
> > Exception
> > ------------- EXCEPTION -------------
> > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/
> > Stag.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-
> > multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-
> > multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/
> > 5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/
> > Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/
> > 5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/
> > 5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /
> > Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/
> > Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/
> > 5.10.0 .) at /sw/lib/perl5/5.10.0/Bio/Annotation/TagTree.pm line 123.
> > BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/
> > Annotation/TagTree.pm line 123.
> > Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> > swiss.pm line 208.
> > BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> > swiss.pm line 208.
> > Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/Root/Root.pm
> > line 439.
>
> > STACK Bio::Root::Root::_load_module /sw/lib/perl5/5.10.0/Bio/Root/
> > Root.pm:441
> > STACK (eval) /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:570
> > STACK Bio::SeqIO::_load_format_module /sw/lib/perl5/5.10.0/Bio/
> > SeqIO.pm:569
> > STACK Bio::SeqIO::new /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:389
> > STACK Bio::DB::WebDBSeqI::get_seq_stream /sw/lib/perl5/5.10.0/Bio/DB/
> > WebDBSeqI.pm:472
> > STACK Bio::DB::WebDBSeqI::get_Stream_by_acc /sw/lib/perl5/5.10.0/Bio/
> > DB/WebDBSeqI.pm:314
> > STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> > WebDBSeqI.pm:186
> > STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> > STACK toplevel ./Documents/perl-programs/perl_test:8
> > -------------------------------------
>
> > For more information about the SeqIO system please see the SeqIO docs.
> > This includes ways of checking for formats at compile time, not run
> > time
>
> > ------------- EXCEPTION -------------
> > MSG: acc P11217 does not exist
> > STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> > WebDBSeqI.pm:187
> > STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> > STACK toplevel ./Documents/perl-programs/perl_test:8
> > -------------------------------------
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioper... at lists.open-bio.org
> >http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l


From izlowe at ucdavis.edu  Thu Oct 21 22:00:24 2010
From: izlowe at ucdavis.edu (Iago Lowe)
Date: Thu, 21 Oct 2010 22:00:24 -0400
Subject: [Bioperl-l] Specifying the search set in NCBI BLAST
Message-ID: <AANLkTi=s_RstcyKyoGws0ykcK8VAb7DVcLtMrRyt2O4X@mail.gmail.com>

In the "Choose Search Set" tab on the NCBI BLAST webpage, there are some
convenient ways to restrict the size of the database for queries.  In there
a way to apply these restrictions in a remote search via Bioperl?

For example, in our research, we want to search only the "Non-human,
non-mouse ESTs" for the organism "Triticum" rather than the entire NCBI
database.

Thanks very much for any guidance.
Iago Lowe

From David.Messina at sbc.su.se  Fri Oct 22 11:29:36 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 22 Oct 2010 11:29:36 -0400
Subject: [Bioperl-l] Specifying the search set in NCBI BLAST
In-Reply-To: <AANLkTi=s_RstcyKyoGws0ykcK8VAb7DVcLtMrRyt2O4X@mail.gmail.com>
References: <AANLkTi=s_RstcyKyoGws0ykcK8VAb7DVcLtMrRyt2O4X@mail.gmail.com>
Message-ID: <C7922411-92DE-46D0-B4AA-E32A606C7415@sbc.su.se>

Hi Iago,

It is possible to do this with BioPerl, but I would recommend simply downloading Blast+ (note the +) and using the -entrez_query and -remote options.

Dave



From MEC at stowers.org  Fri Oct 22 11:40:24 2010
From: MEC at stowers.org (Cook, Malcolm)
Date: Fri, 22 Oct 2010 10:40:24 -0500
Subject: [Bioperl-l] Specifying the search set in NCBI BLAST
In-Reply-To: <C7922411-92DE-46D0-B4AA-E32A606C7415@sbc.su.se>
References: <AANLkTi=s_RstcyKyoGws0ykcK8VAb7DVcLtMrRyt2O4X@mail.gmail.com>
	<C7922411-92DE-46D0-B4AA-E32A606C7415@sbc.su.se>
Message-ID: <BD62CBAC4395B94096109020651BE2EC138AFB720D@EXCHMB-02.stowers-institute.org>

I agree with Dave.

But, if you must use BioPerl, see http://doc.bioperl.org/releases/bioperl-1.4/Bio/Tools/Run/RemoteBlast.html where it shows this code:

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

You'll probably want to set your database to  est_others (c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html#2 )

--Malcolm
 

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dave Messina
Sent: Friday, October 22, 2010 10:30 AM
To: Iago Lowe
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Specifying the search set in NCBI BLAST

Hi Iago,

It is possible to do this with BioPerl, but I would recommend simply downloading Blast+ (note the +) and using the -entrez_query and -remote options.

Dave


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


From jun.yin at ucd.ie  Fri Oct 22 12:12:45 2010
From: jun.yin at ucd.ie (Jun Yin)
Date: Fri, 22 Oct 2010 17:12:45 +0100
Subject: [Bioperl-l] how to download PDB files using Bioperl script
In-Reply-To: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
Message-ID: <01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>

Hi, Ashwani,

I havenot found any module in BioPerl for downloading PDB files, though
Bio::Structure::IO::pdb can parse PDB files.

However, PDB provides RESTful service
(http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
batch downloading the proteins.

Cheers,
Jun Yin
Ph.D.?student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
Sent: Thursday, October 21, 2010 9:39 AM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] how to download PDB files using Bioperl script

Hi All,


I have around 150 pdb file names and I need to download them from Protein
Data Bank. I wonder if someone could tell me how to do it by using Bioperl.

Thanks in advance.

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

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__________ Information from ESET Smart Security, version of virus signature
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database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com
 



From jason at bioperl.org  Sat Oct 23 11:33:49 2010
From: jason at bioperl.org (Jason Stajich)
Date: Sat, 23 Oct 2010 08:33:49 -0700
Subject: [Bioperl-l] Question on BioPerl modules
In-Reply-To: <1287838391.5784.19.camel@ubuntu>
References: <1287838391.5784.19.camel@ubuntu>
Message-ID: <4CC3005D.1070708@bioperl.org>

Lincoln overloaded the "" method for the objects that are returned from 
Bio::DB::Fasta so that attempts to print them directly will instead 
print out the display_id field.

If you want to know what kind of object you getting back you use 'ref', 
as in:
print ref($seq),"\n";

Tao Zhu wrote, On 10/23/10 5:53 AM:
> Dear Professor Stajich,
>
> Recently I was puzzled when using two BioPerl modules, Bio::Index::Fasta
> and Bio::DB::Fasta;
>
> For example, I have a fasta file: sequence.fa, on my computer. That is:
>
>> ORFN:87
> ATGGAAGCCCCTTCAGAAATTACCGATTCCAA
>
> I hope to make a local index, then I use Bio::Index::Fasta and write:
>
> use Bio::Index::Fasta;
> $file_name = "sequence.fa";
> $id = "ORFN:87";
> $inx = Bio::Index::Fasta->new (-filename =>  $file_name . ".idx", -write_flag =>  1);
> $inx->make_index($file_name);
> $seq_obj = $inx->fetch($id);
> print "$seq_obj\n";
>
> Running the perl script, it prints "Bio::Seq=HASH(0x66590a0)" on screen.
> That means the scalar "$seq_obj" is a Bio::Seq object.
>
> However, I try another method, using Bio::DB::Fasta,
>
> use Bio::DB::Fasta;
> ($file,$id) = ("sequence.fa","ORFN:87");
> $db = Bio::DB::Fasta->new($file);
> $seq_obj = $db->get_Seq_by_id($id);
> print "$seq_obj\n";
>
> I expect it should also print "Bio::Seq=HASH(sth)",because I also get a
> Bio::Seq object. Surprisingly it prints "ORFN:87"
>
> How it comes to be?
>

-- 
Jason Stajich
jason at bioperl.org


From yifangt at hotmail.com  Sat Oct 23 02:21:40 2010
From: yifangt at hotmail.com (yifangt)
Date: Fri, 22 Oct 2010 23:21:40 -0700 (PDT)
Subject: [Bioperl-l] Can't locate Bio/seqIO.pm in @INC
In-Reply-To: <loom.20101019T134347-528@post.gmane.org>
References: <loom.20101019T134347-528@post.gmane.org>
Message-ID: <30034148.post@talk.nabble.com>


Probably your Bioperl installation is not correct. Re-install your bioperl
and try again!

Good luck!




yusheng liao wrote:
> 
> Can't locate Bio/seqIO.pm in @INC 
> I try to run a .pl file to get multi sequences for t
> he GenBank using the
> Bioperl. The following were the error message:
> linux:/home/liaoy # perl hsv-1.pl
> Can't locate Bio/seqIO.pm in @INC (@INC contains:
> /usr/lib/perl5/5.8.7/i586-linux-thread-multi /usr/lib/perl5/5.8.7
> /usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.7 /usr/lib/perl5/site_perl
> /usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .)
>  at hsv-1.pl line 4.
> BEGIN failed--compilation aborted at hsv-1.pl line 4.
> 
> what is the problem? And how to corret it? 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/Can%27t-locate-Bio-seqIO.pm-in-%40INC-tp30019789p30034148.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From timmcilveen at talktalk.net  Sun Oct 24 20:45:15 2010
From: timmcilveen at talktalk.net (Tim)
Date: Mon, 25 Oct 2010 01:45:15 +0100
Subject: [Bioperl-l] Installing Bioperl  from Git Hub
Message-ID: <4CC4D31B.1080905@talktalk.net>

Hi everyone,
A couple of weeks ago, I posted a query about installing Bioperl from 
GitHub. I was getting installation errors and someone on the list had 
picked up on  a typo I had made while trying to install it.
Bioperl is now installed and working properly. I forgot to acknowledge 
your help. Thanks for your advice.

Tim


From edwardsa at cs.man.ac.uk  Mon Oct 25 12:33:21 2010
From: edwardsa at cs.man.ac.uk (Andrea Edwards)
Date: Mon, 25 Oct 2010 17:33:21 +0100
Subject: [Bioperl-l] can't install bioperl 1.6.1
Message-ID: <4CC5B151.8030606@cs.man.ac.uk>

  Hi

I can't install Bioperl 1.6.1 on windows using Active Perl 5.8.8.822

I have added the repositories as mentioned in the user guide but get 
this error message

?ERROR: File conflict for 'C:/Perl/html/bin/bp_aacomp.html'.The package 
BioPerl has already installed a file that package bioperl wants to install.?

I have seen a forum thread which says the problem is due to the 
trouchelle repository.

http://www.perlmonks.org/?node_id=817531

I did remove the trouchelle repository as suggested and bioperl 1.6.1 
does seem to have installed but I don't know enough about Perl to know 
if it will have installed correctly by removing this repository.

I installed BioPerl 1.6 successfully on a different PC running 
ActivePerl 5.8.9.827 without needing to remove the trouchelle so I 'm 
not sure what to think.

Many thanks



From sahasangi at gmail.com  Tue Oct 26 07:41:01 2010
From: sahasangi at gmail.com (sangita saha)
Date: Tue, 26 Oct 2010 17:11:01 +0530
Subject: [Bioperl-l] Fwd: Need Help regarding reciprocal BLAST using BioPerl
In-Reply-To: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>
References: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>
Message-ID: <AANLkTimidEhyj=nJ4U9vwp1He45fgUg-d1LOs+dEYoq=@mail.gmail.com>

---------- Forwarded message ----------
From: sangita saha <sahasangi at gmail.com>
Date: Tue, Oct 26, 2010 at 4:32 PM
Subject: Need Help regarding reciprocal BLAST using BioPerl
To: bioperl-l at lists.open-bio.org


Hello Sir,
I have installed BioPerl and standalone BLAST in my PC.I faced problem in
doing the Reciprocal BLAST.Will anyone kindly tell me how to link between
BioPerl and Standalone BLAST ?How to use Bioperl itself to identify the
ortholog?What is the command to be used for reciprocal Blast?Since I am the
new user of it and need help to your concerned.If anybody have any
experience regarding reciprocal blast please give me a suggestion.

I will be happy to hear you from.

Thank you

With Regards,
Sangita Saha

From shalabh.sharma7 at gmail.com  Tue Oct 26 10:04:31 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 26 Oct 2010 10:04:31 -0400
Subject: [Bioperl-l] Fwd: Need Help regarding reciprocal BLAST using
	BioPerl
In-Reply-To: <AANLkTimidEhyj=nJ4U9vwp1He45fgUg-d1LOs+dEYoq=@mail.gmail.com>
References: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>
	<AANLkTimidEhyj=nJ4U9vwp1He45fgUg-d1LOs+dEYoq=@mail.gmail.com>
Message-ID: <AANLkTinhKE_KTzr3_Xftu96dyhyC4fc0QYm_2FhQ6HPU@mail.gmail.com>

Hey Sangita,
               I am not sure if bioperl has any direct command for
reciprocal blast.
But it is fairly simple, you can use all vs all blast then post process your
results in finding orthologs according to your cutoff parameters.

Other way is to use OrthoMCL :
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403725/?tool=pubmed

Also read this:
http://bioperl.org/wiki/HOWTO:PhylogeneticAnalysisPipeline
 Since you are a beginner it will help you a lot.

Hope this helps.

Shalabh
-----------------------------------
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636
On Tue, Oct 26, 2010 at 7:41 AM, sangita saha <sahasangi at gmail.com> wrote:

> ---------- Forwarded message ----------
> From: sangita saha <sahasangi at gmail.com>
> Date: Tue, Oct 26, 2010 at 4:32 PM
> Subject: Need Help regarding reciprocal BLAST using BioPerl
> To: bioperl-l at lists.open-bio.org
>
>
> Hello Sir,
> I have installed BioPerl and standalone BLAST in my PC.I faced problem in
> doing the Reciprocal BLAST.Will anyone kindly tell me how to link between
> BioPerl and Standalone BLAST ?How to use Bioperl itself to identify the
> ortholog?What is the command to be used for reciprocal Blast?Since I am the
> new user of it and need help to your concerned.If anybody have any
> experience regarding reciprocal blast please give me a suggestion.
>
> I will be happy to hear you from.
>
> Thank you
>
> With Regards,
> Sangita Saha
> _______________________________________________
> 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  Tue Oct 26 10:09:48 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 26 Oct 2010 10:09:48 -0400
Subject: [Bioperl-l] Genome Information
Message-ID: <AANLkTikLfZa-FSFXiriqPGHf63kcTgkY0+rT2Mq=7hCu@mail.gmail.com>

Hi All,
       I have thousands of taxaIds and i need to find out the following
information regarding genomes:
1) Taxonomy information
2) GC%
3) total coding genes %

I can easily find the taxonomy info by using Bio::DB::Taxonomy but for the
other two i am stuck.
Is there any way i can find this info?
I would really appreciate your help.

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

From cjfields at illinois.edu  Tue Oct 26 11:40:02 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 26 Oct 2010 10:40:02 -0500
Subject: [Bioperl-l] Fwd: Need Help regarding reciprocal BLAST using
	BioPerl
In-Reply-To: <AANLkTinhKE_KTzr3_Xftu96dyhyC4fc0QYm_2FhQ6HPU@mail.gmail.com>
References: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>
	<AANLkTimidEhyj=nJ4U9vwp1He45fgUg-d1LOs+dEYoq=@mail.gmail.com>
	<AANLkTinhKE_KTzr3_Xftu96dyhyC4fc0QYm_2FhQ6HPU@mail.gmail.com>
Message-ID: <02B10B6A-5E4A-4889-AACA-A47D8FA39E88@illinois.edu>

BioPerl does have Bio::Tools::Run::TribeMCL in BioPerl-Run, but I don't suggest using that.  mcl has a few tools in-place already within the distribition, but I personally have been using the latest version of OrthoMCL (v2), and have also started setting up a pipeline using InParanoid.

chris

On Oct 26, 2010, at 9:04 AM, shalabh sharma wrote:

> Hey Sangita,
>               I am not sure if bioperl has any direct command for
> reciprocal blast.
> But it is fairly simple, you can use all vs all blast then post process your
> results in finding orthologs according to your cutoff parameters.
> 
> Other way is to use OrthoMCL :
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403725/?tool=pubmed
> 
> Also read this:
> http://bioperl.org/wiki/HOWTO:PhylogeneticAnalysisPipeline
> Since you are a beginner it will help you a lot.
> 
> Hope this helps.
> 
> Shalabh
> -----------------------------------
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
> On Tue, Oct 26, 2010 at 7:41 AM, sangita saha <sahasangi at gmail.com> wrote:
> 
>> ---------- Forwarded message ----------
>> From: sangita saha <sahasangi at gmail.com>
>> Date: Tue, Oct 26, 2010 at 4:32 PM
>> Subject: Need Help regarding reciprocal BLAST using BioPerl
>> To: bioperl-l at lists.open-bio.org
>> 
>> 
>> Hello Sir,
>> I have installed BioPerl and standalone BLAST in my PC.I faced problem in
>> doing the Reciprocal BLAST.Will anyone kindly tell me how to link between
>> BioPerl and Standalone BLAST ?How to use Bioperl itself to identify the
>> ortholog?What is the command to be used for reciprocal Blast?Since I am the
>> new user of it and need help to your concerned.If anybody have any
>> experience regarding reciprocal blast please give me a suggestion.
>> 
>> I will be happy to hear you from.
>> 
>> Thank you
>> 
>> With Regards,
>> Sangita Saha
>> _______________________________________________
>> 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 Oct 26 12:11:05 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 26 Oct 2010 11:11:05 -0500
Subject: [Bioperl-l] Genome Information
In-Reply-To: <AANLkTikLfZa-FSFXiriqPGHf63kcTgkY0+rT2Mq=7hCu@mail.gmail.com>
References: <AANLkTikLfZa-FSFXiriqPGHf63kcTgkY0+rT2Mq=7hCu@mail.gmail.com>
Message-ID: <7A662ADB-506C-439E-9C0C-44F8DE540428@illinois.edu>

Shalabh,

I don't know if there is a quick one-step way of getting this information via NCBI w/o wrangling with query term limit magic, and even then you will be bound to whatever version of the genome is present within the database of interest.  

For instance, via eutils you can get summary information for various taxa, genomes, and genome projects using the following example code (prints the first 10 archaeal genome project summaries; set the '-db' parameter to one of 'genomeprj', 'taxonomy', 'genome'):

=================================

use Bio::DB::EUtilities;

my $term = "Archaea[ORGN]";

my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                     -db    => 'genome',
                                     -email => 'cjfields at bioperl.org',
                                     -usehistory => 'y',
                                     -term  => $term);

my $hist = $eutil->next_History || die "No history returned";

$eutil->set_parameters(-eutil   => 'esummary',
                       -history => $hist,
                       -retmax  => 10);

$eutil->print_all; # print summary info to STDOUT

=================================

GC and coding % don't appear to be stored in any of the above databases, but they are displayed via the genome overview.  You could probably use something like WWW::Mechanize to grab the summary table information displayed using the Genome UID:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=ShowDetailView&TermToSearch=25024

Just don't spam the server with a billion requests (use a timeout!) or you'll find yourself blocked.  I may pop an email to NCBI to see if this information is programmatically accessible.

chris

On Oct 26, 2010, at 9:09 AM, shalabh sharma wrote:

> Hi All,
>       I have thousands of taxaIds and i need to find out the following
> information regarding genomes:
> 1) Taxonomy information
> 2) GC%
> 3) total coding genes %
> 
> I can easily find the taxonomy info by using Bio::DB::Taxonomy but for the
> other two i am stuck.
> Is there any way i can find this info?
> I would really appreciate your help.
> 
> Thanks
> Shalabh
> -------------------------------
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
> _______________________________________________
> 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  Tue Oct 26 12:23:02 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 26 Oct 2010 12:23:02 -0400
Subject: [Bioperl-l] Genome Information
In-Reply-To: <7A662ADB-506C-439E-9C0C-44F8DE540428@illinois.edu>
References: <AANLkTikLfZa-FSFXiriqPGHf63kcTgkY0+rT2Mq=7hCu@mail.gmail.com>
	<7A662ADB-506C-439E-9C0C-44F8DE540428@illinois.edu>
Message-ID: <AANLkTin_JuaAi9Op_T9N9YVzjpOtN1hnXV=X02kPutBA@mail.gmail.com>

Hey Chris,
            This information is really useful.
Actually i was using Bio::DB::Taxonomy for taxonomy information
and Bio::DB::EUtilities to get the genome size (i didn't know that i can
just use Bio::DB::EUtilities for all the information).
I was very confused about getting GC% and coding% info but i
think WWW::Mechanize might help me out.
I really appreciate your help.

-Shalabh


On Tue, Oct 26, 2010 at 12:11 PM, Chris Fields <cjfields at illinois.edu>wrote:

> Shalabh,
>
> I don't know if there is a quick one-step way of getting this information
> via NCBI w/o wrangling with query term limit magic, and even then you will
> be bound to whatever version of the genome is present within the database of
> interest.
>
> For instance, via eutils you can get summary information for various taxa,
> genomes, and genome projects using the following example code (prints the
> first 10 archaeal genome project summaries; set the '-db' parameter to one
> of 'genomeprj', 'taxonomy', 'genome'):
>
> =================================
>
> use Bio::DB::EUtilities;
>
> my $term = "Archaea[ORGN]";
>
> my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
>                                     -db    => 'genome',
>                                     -email => 'cjfields at bioperl.org',
>                                     -usehistory => 'y',
>                                     -term  => $term);
>
> my $hist = $eutil->next_History || die "No history returned";
>
> $eutil->set_parameters(-eutil   => 'esummary',
>                       -history => $hist,
>                       -retmax  => 10);
>
> $eutil->print_all; # print summary info to STDOUT
>
> =================================
>
> GC and coding % don't appear to be stored in any of the above databases,
> but they are displayed via the genome overview.  You could probably use
> something like WWW::Mechanize to grab the summary table information
> displayed using the Genome UID:
>
>
> http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=ShowDetailView&TermToSearch=25024
>
> Just don't spam the server with a billion requests (use a timeout!) or
> you'll find yourself blocked.  I may pop an email to NCBI to see if this
> information is programmatically accessible.
>
> chris
>
> On Oct 26, 2010, at 9:09 AM, shalabh sharma wrote:
>
> > Hi All,
> >       I have thousands of taxaIds and i need to find out the following
> > information regarding genomes:
> > 1) Taxonomy information
> > 2) GC%
> > 3) total coding genes %
> >
> > I can easily find the taxonomy info by using Bio::DB::Taxonomy but for
> the
> > other two i am stuck.
> > Is there any way i can find this info?
> > I would really appreciate your help.
> >
> > Thanks
> > Shalabh
> > -------------------------------
> > Shalabh Sharma
> > Scientific Computing Professional Associate (Bioinformatics Specialist)
> > Department of Marine Sciences
> > University of Georgia
> > Athens, GA 30602-3636
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>

From mconte at umd.edu  Tue Oct 26 14:25:28 2010
From: mconte at umd.edu (Matthew Conte)
Date: Tue, 26 Oct 2010 14:25:28 -0400
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
Message-ID: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>

Hello,

I have a custom script for parsing out UniProt accessions from a GFF3 file
and fetching the description of the UniProt entry using Bio::DB::SwissProt
and *get_Seq_by_acc*.  This script has been working for months without any
problems until now.  The script and the format of the input files has not
changed at all.

I now get an error like this:

*------------- EXCEPTION: Bio::Root::Exception -------------*
*MSG: acc O95342 does not exist*
*STACK: Error::throw*
*STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
*STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
/Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
*STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
*-----------------------------------------------------------*

The relevant portion of my original code looks something like this:

*#!/usr/bin/perl*
*use strict;*
*use Bio::DB::SwissProt;*
*#parse out accession number*
*..*
*my $acc_num = "**O95342";*
*my $db_obj = Bio::DB::SwissProt->new;*
*my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
*
*
Looking at the documentation for Bio::DB::SwissProt, I noticed you can
specify -servertype and -hostlocation.  So I changed my code to look
something like this:

*
#!/usr/bin/perl
use strict;
use Bio::DB::SwissProt;
#parse out accession number
..
my $acc_num = "O95342";
my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
                                                           '-hostlocation'
=> 'us');
my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
*

This fixes my problem and my script works again.

The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
  Both of these urls work in a browser, though the default throws the error
in my script. Interestingly, the 'us' url has a notice that says
"*Notice:* This
page will be replaced with www.uniprot.org. Please send us your
feedback<http://www.uniprot.org/contact>
!", so hopefully it doesn't break soon as well.  Perhaps the default ebi url
was recently changed in some way?  Anyway, I figured I'd post here in case
anyone else ran into this problem.

cheers,
Matt

From grapeguy at gmail.com  Tue Oct 26 15:15:09 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Tue, 26 Oct 2010 15:15:09 -0400
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <16EDEBED-BAD4-4D57-B51B-C3234D1E8C39@illinois.edu>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
	<AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
	<16EDEBED-BAD4-4D57-B51B-C3234D1E8C39@illinois.edu>
Message-ID: <AANLkTim5_UF-AQd8HRD9v4_5SF8T5z+awWN8KAORoUGs@mail.gmail.com>

I've got my script running.

In order to support the identification of degenerate primers I had to create
a new method that would alter the IUPAC consensus. We're interested in
15-30bp sections of the consensus with high, but not 100%, conservation. We
would like to have a couple of "slices" with 2-3 mismatches to allow for the
ordering of a variety of primers.

To be completed:

   - I would *love* to hide the Clustal output that is being printed to the
   screen
   - Primer candidate identification (min_primerlength to max_primerlength)
   based on our scoring matrix
   - Primer melting temperature calculation
   - 3' Clamping identification
   - Self complementary primers

This has been a nice change from Java.

Bill


*Code*

assume: I have already read fasta input, performed Clustal align and
obtained the IUPAC consensus

sub getDegenerateConsensusIupac {
    my ($aln, $maxGapPercent, $iupacConsensus, $numSequences) = @_;

  # convert consensus into array
  my @cons = split(//, $iupacConsensus);

  # loop over the alignment "columns"
  foreach my $position ( 1 .. $aln->length() ) {
      my $consCode = $cons[$position-1];
      my %slice = getSliceHash($aln, $position);

      my $out = _applyGapPercentToConsensus ($maxGapPercent, $consCode,
$numSequences, %slice);

      # Convert consensus value new value
      if ($out ne $consCode) {
          $cons[$position-1] = $out;
      }
  }

  #rebuild consensus
  my $degenerateConsensus = join '', @cons;

  return $degenerateConsensus;
}

sub _applyGapPercentToConsensus {
    my ($maxGapPercent, $consCode, $numSequences, %slice) = @_;

        my $gapCount = $slice{'.'};

        # no gaps!
        if ($gapCount !~ /\d/) {
            return $consCode;
        }

        my $pctGap = ($gapCount / $numSequences) * 100;

        if ($pctGap > $maxGapPercent) {
            if ($consCode =~ /[A-Z]/) {
                return lc $consCode;
            }
            if ($consCode =~ /[a-z]/) {
                return '.';
            }
        }

    return $consCode;
}

sub getSliceHash{
    my ($aln, $position) = @_;

    my %sliceHash;
    foreach my $seq ($aln->each_seq) {
        my $res = $seq->subseq($position, $position);
        $sliceHash{$res}++;
    }

    return %sliceHash;
}


On Tue, Oct 19, 2010 at 11:47 AM, Chris Fields <cjfields at illinois.edu>wrote:

> Bio::SimpleAlign is the class that contains the alignment data; it does not
> generate the alignment for you.  You can use modules from BioPerl-Run that
> run ClustalW, MUSCLE, T-Coffee, etc to get a Bio::SimpleAlign instance, or
> parse the already-generated alignment output via Bio::AlignIO.
>
> From the Bio::Tools::Run::Alignment::ClustalW docs:
>
> =================================================================
>
>  #  Build a clustalw alignment factory
>  @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
>  $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
>
>  #  Pass the factory a list of sequences to be aligned.
>  $inputfilename = 't/data/cysprot.fa';
>  $aln = $factory->align($inputfilename); # $aln is a SimpleAlign object.
>
>  # ...or
>  $seq_array_ref = \@seq_array;
>
>  # where @seq_array is an array of Bio::Seq objects
>  $aln = $factory->align($seq_array_ref);
>
> =================================================================
>
> $aln is a Bio::SimpleAlign derived from ClustalW output.
>
> From Bio::SimpleAlign (note the use of Bio::AlignIO):
>
> =================================================================
>
>  # Use Bio::AlignIO to read in the alignment
>  $str = Bio::AlignIO->new(-file => 't/data/testaln.pfam');
>  $aln = $str->next_aln();
>
>  # Describe
>  print $aln->length;
>  print $aln->num_residues;
>  print $aln->is_flush;
>  print $aln->num_sequences;
>  print $aln->score;
>  print $aln->percentage_identity;
>  print $aln->consensus_string(50);
>
> =================================================================
>
> Note the consensus_string() method:
>
>  Title     : consensus_string
>  Usage     : $str = $ali->consensus_string($threshold_percent)
>  Function  : Makes a strict consensus
>  Returns   : Consensus string
>  Argument  : Optional treshold ranging from 0 to 100.
>             The consensus residue has to appear at least threshold %
>             of the sequences at a given location, otherwise a '?'
>             character will be placed at that location.
>             (Default value = 0%)
>
> chris
>
> On Oct 18, 2010, at 7:02 PM, Bill Stephens wrote:
>
> > So, I've got the SimpleAlign running. It looks like it's running the
> > alignment based upon the input sequence location only (first residue from
> > each sequence).  This is not what I need.
> >
> > I'm back to to clustal, tcoffee or dalign.
> >
> > Bill
> >
> > On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:
> >
> >> Hi, Bill,
> >>
> >> You may consider to use consensus_iupac or consensus_string methods in
> >> Bio::SimpleAlign to generate consensus sequence.
> >>
> >> Cheers,
> >> Jun Yin
> >> Ph.D. student in U.C.D.
> >>
> >> Bioinformatics Laboratory
> >> Conway Institute
> >> University College Dublin
> >>
> >> -----Original Message-----
> >> From: bioperl-l-bounces at lists.open-bio.org
> >> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
> >> Sent: Monday, October 18, 2010 3:55 PM
> >> To: Bill Stephens
> >> Cc: bioperl-l at bioperl.org
> >> Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
> >> alignment
> >>
> >> Bill,
> >>
> >> Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
> >> replacement for the older Pise tools).  The Pise modules were in
> >> BioPerl-Run, but they were deprecated a few years ago and removed from
> the
> >> latest BioPerl-Run releases b/c the remote service is no longer active;
> >> there is no Perl-based replacement for Mobyle interaction.
> >>
> >> Have you thought about just using the functionality within the
> >> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there
> >> are
> >> methods in place to do that.
> >>
> >> chris
> >>
> >> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
> >>
> >>> All,
> >>>
> >>> I'm in my first week with bioperl for a class project (although I've
> used
> >>> Perl for years). I've successfully run a clustal alignment of several
> DNA
> >>> sequences to produce the aln and dnd files. Now I would like to
> generate
> >> a
> >>> consensus sequence from the alignment.  I see that Pise Cons does this
> >>> satisfactorily on my example data (
> >>> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However,
> >> I'm
> >>> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
> >> distribution
> >>> that I installed.
> >>>
> >>> Is this another module that I need to install separately?
> >>>
> >>> "cpan[2]> m /Pise/
> >>> Module    Bio::Tools::Run::AnalysisFactory::Pise
> >>> (BIRNEY/bioperl-run-1.4.tar.gz)
> >>> Module    Bio::Tools::Run::PiseApplication
> >> (BIRNEY/bioperl-run-1.4.tar.gz)"
> >>>
> >>> Bill S.
> >>> _______________________________________________
> >>> 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
> >>
> >> __________ Information from ESET Smart Security, version of virus
> signature
> >> database 5377 (20100818) __________
> >>
> >> The message was checked by ESET Smart Security.
> >>
> >> http://www.eset.com
> >>
> >>
> >>
> >>
> >> __________ Information from ESET Smart Security, version of virus
> signature
> >> database 5377 (20100818) __________
> >>
> >> The message was checked by ESET Smart Security.
> >>
> >> http://www.eset.com
> >>
> >>
> >>
> > _______________________________________________
> > 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 Oct 26 18:02:03 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 26 Oct 2010 17:02:03 -0500
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
Message-ID: <FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>

The default was changed recently in github to 'expasy'.  My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.

chris

On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:

> Hello,
> 
> I have a custom script for parsing out UniProt accessions from a GFF3 file
> and fetching the description of the UniProt entry using Bio::DB::SwissProt
> and *get_Seq_by_acc*.  This script has been working for months without any
> problems until now.  The script and the format of the input files has not
> changed at all.
> 
> I now get an error like this:
> 
> *------------- EXCEPTION: Bio::Root::Exception -------------*
> *MSG: acc O95342 does not exist*
> *STACK: Error::throw*
> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
> *-----------------------------------------------------------*
> 
> The relevant portion of my original code looks something like this:
> 
> *#!/usr/bin/perl*
> *use strict;*
> *use Bio::DB::SwissProt;*
> *#parse out accession number*
> *..*
> *my $acc_num = "**O95342";*
> *my $db_obj = Bio::DB::SwissProt->new;*
> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
> *
> *
> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
> specify -servertype and -hostlocation.  So I changed my code to look
> something like this:
> 
> *
> #!/usr/bin/perl
> use strict;
> use Bio::DB::SwissProt;
> #parse out accession number
> ..
> my $acc_num = "O95342";
> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>                                                           '-hostlocation'
> => 'us');
> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
> *
> 
> This fixes my problem and my script works again.
> 
> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>  Both of these urls work in a browser, though the default throws the error
> in my script. Interestingly, the 'us' url has a notice that says
> "*Notice:* This
> page will be replaced with www.uniprot.org. Please send us your
> feedback<http://www.uniprot.org/contact>
> !", so hopefully it doesn't break soon as well.  Perhaps the default ebi url
> was recently changed in some way?  Anyway, I figured I'd post here in case
> anyone else ran into this problem.
> 
> cheers,
> Matt
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From sahasangi at gmail.com  Tue Oct 26 07:02:04 2010
From: sahasangi at gmail.com (sangita saha)
Date: Tue, 26 Oct 2010 16:32:04 +0530
Subject: [Bioperl-l] Need Help regarding reciprocal BLAST using BioPerl
Message-ID: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>

Hello Sir,
I have installed BioPerl and standalone BLAST in my PC.I faced problem in
doing the Reciprocal BLAST.Will anyone kindly tell me how to link between
BioPerl and Standalone BLAST ?How to use Bioperl itself to identify the
ortholog?What is the command to be used for reciprocal Blast?Since I am the
new user of it and need help to your concerned.If anybody have any
experience regarding reciprocal blast please give me a suggestion.

I will be happy to hear you from.

Thank you

With Regards,
Sangita Saha

From ameet at eecs.berkeley.edu  Tue Oct 26 19:51:17 2010
From: ameet at eecs.berkeley.edu (Ameet Talwalkar)
Date: Tue, 26 Oct 2010 16:51:17 -0700
Subject: [Bioperl-l] TreeIO for NHX format
Message-ID: <AANLkTim2hsO=rRCfa5H4Uu7waF7iVbJo9NDfTq2q8yrN@mail.gmail.com>

Hi,

I would like to use BIOPerl to convert a tree in PhyloXML format to NHX
format, and I have tried the following code:

*use Bio::TreeIO;

my $input = new Bio::TreeIO(-file   => "reconciled_test.xml",
                            -format => "phyloxml");
my $treeout = new Bio::TreeIO(-fh => \*STDOUT,
                              -format => 'nhx');

while (my $tree = $input->next_tree) {
  $treeout->write_tree($tree);
}
*

The output is indeed in NHX format, but the tags (in particular I have a
duplication / speciation tag) does not appear in the output.  Am I doing
something wrong?

Thanks.

-Ameet

From bill_zt at sina.com  Tue Oct 26 21:08:11 2010
From: bill_zt at sina.com (Tao Zhu)
Date: Wed, 27 Oct 2010 09:08:11 +0800
Subject: [Bioperl-l] A problem on BioPerl module Bio::DB::Fasta
Message-ID: <1288141691.2377.1.camel@ubuntu>

Hello, everyone!

I hope it isn't true, but I really find a problem on BioPerl module
Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
Osborne wrote that we could catch sub-sequences like this,


use Bio::DB::Fasta;
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
$db = Bio::DB::Fasta->new($file);
$seqobj = $db->get_Seq_by_id($id,$start,$end);
print $seqobj->seq,"\n";


In fact it didn't work. I only got the whole sequence after running the
script. Therefore I referred to the Pdoc documentation and realized it
should be written as follows,


use Bio::DB::Fasta;
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
$db = Bio::DB::Fasta->new($file);
$seq = $db->seq($id,$start,$end);
print $seq,"\n";


Then it would return the sub-sequence from 6 to 10.

Probably Dr Osborne had made a mistake when writing the use-guide
HOWTO:Beginners.


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
email: tzhu at mail.bnu.edu.cn


From cjfields at illinois.edu  Tue Oct 26 23:41:40 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 26 Oct 2010 22:41:40 -0500
Subject: [Bioperl-l] TreeIO for NHX format
In-Reply-To: <AANLkTim2hsO=rRCfa5H4Uu7waF7iVbJo9NDfTq2q8yrN@mail.gmail.com>
References: <AANLkTim2hsO=rRCfa5H4Uu7waF7iVbJo9NDfTq2q8yrN@mail.gmail.com>
Message-ID: <55546218-9878-421F-B4A7-FADA7760C374@illinois.edu>

Ameet,

You should file this as a bug, along with example code and data (http://bugzilla.open-bio.org/).  It's possible the tags are parsed but the NHX writer is not finding the data somehow.

chris

On Oct 26, 2010, at 6:51 PM, Ameet Talwalkar wrote:

> Hi,
> 
> I would like to use BIOPerl to convert a tree in PhyloXML format to NHX
> format, and I have tried the following code:
> 
> *use Bio::TreeIO;
> 
> my $input = new Bio::TreeIO(-file   => "reconciled_test.xml",
>                            -format => "phyloxml");
> my $treeout = new Bio::TreeIO(-fh => \*STDOUT,
>                              -format => 'nhx');
> 
> while (my $tree = $input->next_tree) {
>  $treeout->write_tree($tree);
> }
> *
> 
> The output is indeed in NHX format, but the tags (in particular I have a
> duplication / speciation tag) does not appear in the output.  Am I doing
> something wrong?
> 
> Thanks.
> 
> -Ameet
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From hamish.mcwilliam at bioinfo-user.org.uk  Wed Oct 27 06:32:22 2010
From: hamish.mcwilliam at bioinfo-user.org.uk (Hamish McWilliam)
Date: Wed, 27 Oct 2010 11:32:22 +0100
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
	<FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
Message-ID: <AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>

Hi Chris,

The dbfetch service at EBI has changed, see
http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010. On
of the effects of this is the main endpoint used for dbfetch has
changed from http://www.ebi.ac.uk/cgi-bin/dbfetch to
http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. With the old endpoints
being supported via a HTTP redirect. It looks like the
Bio::DB::SwissProt module does not support redirects and is thus
getting an empty document back from the service. Looks like the URL
used in the code needs to be updated.

All the best,

Hamish

On 26 October 2010 23:02, Chris Fields <cjfields at illinois.edu> wrote:
> The default was changed recently in github to 'expasy'. ?My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.
>
> chris
>
> On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:
>
>> Hello,
>>
>> I have a custom script for parsing out UniProt accessions from a GFF3 file
>> and fetching the description of the UniProt entry using Bio::DB::SwissProt
>> and *get_Seq_by_acc*. ?This script has been working for months without any
>> problems until now. ?The script and the format of the input files has not
>> changed at all.
>>
>> I now get an error like this:
>>
>> *------------- EXCEPTION: Bio::Root::Exception -------------*
>> *MSG: acc O95342 does not exist*
>> *STACK: Error::throw*
>> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
>> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
>> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
>> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
>> *-----------------------------------------------------------*
>>
>> The relevant portion of my original code looks something like this:
>>
>> *#!/usr/bin/perl*
>> *use strict;*
>> *use Bio::DB::SwissProt;*
>> *#parse out accession number*
>> *..*
>> *my $acc_num = "**O95342";*
>> *my $db_obj = Bio::DB::SwissProt->new;*
>> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
>> *
>> *
>> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
>> specify -servertype and -hostlocation. ?So I changed my code to look
>> something like this:
>>
>> *
>> #!/usr/bin/perl
>> use strict;
>> use Bio::DB::SwissProt;
>> #parse out accession number
>> ..
>> my $acc_num = "O95342";
>> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '-hostlocation'
>> => 'us');
>> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
>> *
>>
>> This fixes my problem and my script works again.
>>
>> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
>> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>> ?Both of these urls work in a browser, though the default throws the error
>> in my script. Interestingly, the 'us' url has a notice that says
>> "*Notice:* This
>> page will be replaced with www.uniprot.org. Please send us your
>> feedback<http://www.uniprot.org/contact>
>> !", so hopefully it doesn't break soon as well. ?Perhaps the default ebi url
>> was recently changed in some way? ?Anyway, I figured I'd post here in case
>> anyone else ran into this problem.
>>
>> cheers,
>> Matt
>> _______________________________________________
>> 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
>



-- 
----
"Saying the internet has changed dramatically over the last five years
is clich? ? the internet is always changing dramatically" - Craig
Labovitz, Arbor Networks.


From cjfields at illinois.edu  Wed Oct 27 10:51:22 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 27 Oct 2010 09:51:22 -0500
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
	<FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
	<AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>
Message-ID: <FAB70AF7-B56C-4DEA-BF4D-AA9F001D6E9F@illinois.edu>

Hamish,

Thanks, but I already caught that and fixed it in main trunk where appropriate yesterday (specifically, both Bio::DB::SwissProt and Bio::DB::BioFetch).  

chris

On Oct 27, 2010, at 5:32 AM, Hamish McWilliam wrote:

> Hi Chris,
> 
> The dbfetch service at EBI has changed, see
> http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010. On
> of the effects of this is the main endpoint used for dbfetch has
> changed from http://www.ebi.ac.uk/cgi-bin/dbfetch to
> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. With the old endpoints
> being supported via a HTTP redirect. It looks like the
> Bio::DB::SwissProt module does not support redirects and is thus
> getting an empty document back from the service. Looks like the URL
> used in the code needs to be updated.
> 
> All the best,
> 
> Hamish
> 
> On 26 October 2010 23:02, Chris Fields <cjfields at illinois.edu> wrote:
>> The default was changed recently in github to 'expasy'.  My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.
>> 
>> chris
>> 
>> On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:
>> 
>>> Hello,
>>> 
>>> I have a custom script for parsing out UniProt accessions from a GFF3 file
>>> and fetching the description of the UniProt entry using Bio::DB::SwissProt
>>> and *get_Seq_by_acc*.  This script has been working for months without any
>>> problems until now.  The script and the format of the input files has not
>>> changed at all.
>>> 
>>> I now get an error like this:
>>> 
>>> *------------- EXCEPTION: Bio::Root::Exception -------------*
>>> *MSG: acc O95342 does not exist*
>>> *STACK: Error::throw*
>>> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
>>> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
>>> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
>>> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
>>> *-----------------------------------------------------------*
>>> 
>>> The relevant portion of my original code looks something like this:
>>> 
>>> *#!/usr/bin/perl*
>>> *use strict;*
>>> *use Bio::DB::SwissProt;*
>>> *#parse out accession number*
>>> *..*
>>> *my $acc_num = "**O95342";*
>>> *my $db_obj = Bio::DB::SwissProt->new;*
>>> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
>>> *
>>> *
>>> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
>>> specify -servertype and -hostlocation.  So I changed my code to look
>>> something like this:
>>> 
>>> *
>>> #!/usr/bin/perl
>>> use strict;
>>> use Bio::DB::SwissProt;
>>> #parse out accession number
>>> ..
>>> my $acc_num = "O95342";
>>> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>>>                                                           '-hostlocation'
>>> => 'us');
>>> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
>>> *
>>> 
>>> This fixes my problem and my script works again.
>>> 
>>> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
>>> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>>>  Both of these urls work in a browser, though the default throws the error
>>> in my script. Interestingly, the 'us' url has a notice that says
>>> "*Notice:* This
>>> page will be replaced with www.uniprot.org. Please send us your
>>> feedback<http://www.uniprot.org/contact>
>>> !", so hopefully it doesn't break soon as well.  Perhaps the default ebi url
>>> was recently changed in some way?  Anyway, I figured I'd post here in case
>>> anyone else ran into this problem.
>>> 
>>> cheers,
>>> Matt
>>> _______________________________________________
>>> 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
>> 
> 
> 
> 
> -- 
> ----
> "Saying the internet has changed dramatically over the last five years
> is clich? ? the internet is always changing dramatically" - Craig
> Labovitz, Arbor Networks.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From hamish.mcwilliam at bioinfo-user.org.uk  Wed Oct 27 11:34:09 2010
From: hamish.mcwilliam at bioinfo-user.org.uk (Hamish McWilliam)
Date: Wed, 27 Oct 2010 16:34:09 +0100
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <FAB70AF7-B56C-4DEA-BF4D-AA9F001D6E9F@illinois.edu>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
	<FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
	<AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>
	<FAB70AF7-B56C-4DEA-BF4D-AA9F001D6E9F@illinois.edu>
Message-ID: <AANLkTik0tKy2B1W8Avd7ap=Fg4prR3p0w9OXpka5PXHP@mail.gmail.com>

Hi Chris,

Although they handle the redirect, the other modules which use dbfetch
should probably have the URLs updated too:

Bio::DB::Biblio::biofetch
Bio::DB::EMBL
Bio::DB::RefSeq

Hamish

On 27 October 2010 15:51, Chris Fields <cjfields at illinois.edu> wrote:
> Hamish,
>
> Thanks, but I already caught that and fixed it in main trunk where appropriate yesterday (specifically, both Bio::DB::SwissProt and Bio::DB::BioFetch).
>
> chris
>
> On Oct 27, 2010, at 5:32 AM, Hamish McWilliam wrote:
>
>> Hi Chris,
>>
>> The dbfetch service at EBI has changed, see
>> http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010. On
>> of the effects of this is the main endpoint used for dbfetch has
>> changed from http://www.ebi.ac.uk/cgi-bin/dbfetch to
>> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. With the old endpoints
>> being supported via a HTTP redirect. It looks like the
>> Bio::DB::SwissProt module does not support redirects and is thus
>> getting an empty document back from the service. Looks like the URL
>> used in the code needs to be updated.
>>
>> All the best,
>>
>> Hamish
>>
>> On 26 October 2010 23:02, Chris Fields <cjfields at illinois.edu> wrote:
>>> The default was changed recently in github to 'expasy'. ?My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.
>>>
>>> chris
>>>
>>> On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:
>>>
>>>> Hello,
>>>>
>>>> I have a custom script for parsing out UniProt accessions from a GFF3 file
>>>> and fetching the description of the UniProt entry using Bio::DB::SwissProt
>>>> and *get_Seq_by_acc*. ?This script has been working for months without any
>>>> problems until now. ?The script and the format of the input files has not
>>>> changed at all.
>>>>
>>>> I now get an error like this:
>>>>
>>>> *------------- EXCEPTION: Bio::Root::Exception -------------*
>>>> *MSG: acc O95342 does not exist*
>>>> *STACK: Error::throw*
>>>> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
>>>> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
>>>> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
>>>> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
>>>> *-----------------------------------------------------------*
>>>>
>>>> The relevant portion of my original code looks something like this:
>>>>
>>>> *#!/usr/bin/perl*
>>>> *use strict;*
>>>> *use Bio::DB::SwissProt;*
>>>> *#parse out accession number*
>>>> *..*
>>>> *my $acc_num = "**O95342";*
>>>> *my $db_obj = Bio::DB::SwissProt->new;*
>>>> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
>>>> *
>>>> *
>>>> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
>>>> specify -servertype and -hostlocation. ?So I changed my code to look
>>>> something like this:
>>>>
>>>> *
>>>> #!/usr/bin/perl
>>>> use strict;
>>>> use Bio::DB::SwissProt;
>>>> #parse out accession number
>>>> ..
>>>> my $acc_num = "O95342";
>>>> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '-hostlocation'
>>>> => 'us');
>>>> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
>>>> *
>>>>
>>>> This fixes my problem and my script works again.
>>>>
>>>> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
>>>> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>>>> ?Both of these urls work in a browser, though the default throws the error
>>>> in my script. Interestingly, the 'us' url has a notice that says
>>>> "*Notice:* This
>>>> page will be replaced with www.uniprot.org. Please send us your
>>>> feedback<http://www.uniprot.org/contact>
>>>> !", so hopefully it doesn't break soon as well. ?Perhaps the default ebi url
>>>> was recently changed in some way? ?Anyway, I figured I'd post here in case
>>>> anyone else ran into this problem.
>>>>
>>>> cheers,
>>>> Matt
>>>> _______________________________________________
>>>> 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
>>>
>>
>>
>>
>> --
>> ----
>> "Saying the internet has changed dramatically over the last five years
>> is clich? ? the internet is always changing dramatically" - Craig
>> Labovitz, Arbor Networks.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
----
"Saying the internet has changed dramatically over the last five years
is clich? ? the internet is always changing dramatically" - Craig
Labovitz, Arbor Networks.


From cjfields at illinois.edu  Wed Oct 27 12:20:48 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 27 Oct 2010 11:20:48 -0500
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <AANLkTik0tKy2B1W8Avd7ap=Fg4prR3p0w9OXpka5PXHP@mail.gmail.com>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
	<FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
	<AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>
	<FAB70AF7-B56C-4DEA-BF4D-AA9F001D6E9F@illinois.edu>
	<AANLkTik0tKy2B1W8Avd7ap=Fg4prR3p0w9OXpka5PXHP@mail.gmail.com>
Message-ID: <BC746329-82A8-4215-BE8D-4CCDE6911FDB@illinois.edu>

Hamish,

Ah, missed those!  That's what I get for relying on tests alone.  Thanks for pointing them out; I'll double-check the various distributions for more, just in case.

chris

On Oct 27, 2010, at 10:34 AM, Hamish McWilliam wrote:

> Hi Chris,
> 
> Although they handle the redirect, the other modules which use dbfetch
> should probably have the URLs updated too:
> 
> Bio::DB::Biblio::biofetch
> Bio::DB::EMBL
> Bio::DB::RefSeq
> 
> Hamish
> 
> On 27 October 2010 15:51, Chris Fields <cjfields at illinois.edu> wrote:
>> Hamish,
>> 
>> Thanks, but I already caught that and fixed it in main trunk where appropriate yesterday (specifically, both Bio::DB::SwissProt and Bio::DB::BioFetch).
>> 
>> chris
>> 
>> On Oct 27, 2010, at 5:32 AM, Hamish McWilliam wrote:
>> 
>>> Hi Chris,
>>> 
>>> The dbfetch service at EBI has changed, see
>>> http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010. On
>>> of the effects of this is the main endpoint used for dbfetch has
>>> changed from http://www.ebi.ac.uk/cgi-bin/dbfetch to
>>> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. With the old endpoints
>>> being supported via a HTTP redirect. It looks like the
>>> Bio::DB::SwissProt module does not support redirects and is thus
>>> getting an empty document back from the service. Looks like the URL
>>> used in the code needs to be updated.
>>> 
>>> All the best,
>>> 
>>> Hamish
>>> 
>>> On 26 October 2010 23:02, Chris Fields <cjfields at illinois.edu> wrote:
>>>> The default was changed recently in github to 'expasy'.  My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.
>>>> 
>>>> chris
>>>> 
>>>> On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:
>>>> 
>>>>> Hello,
>>>>> 
>>>>> I have a custom script for parsing out UniProt accessions from a GFF3 file
>>>>> and fetching the description of the UniProt entry using Bio::DB::SwissProt
>>>>> and *get_Seq_by_acc*.  This script has been working for months without any
>>>>> problems until now.  The script and the format of the input files has not
>>>>> changed at all.
>>>>> 
>>>>> I now get an error like this:
>>>>> 
>>>>> *------------- EXCEPTION: Bio::Root::Exception -------------*
>>>>> *MSG: acc O95342 does not exist*
>>>>> *STACK: Error::throw*
>>>>> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
>>>>> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
>>>>> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
>>>>> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
>>>>> *-----------------------------------------------------------*
>>>>> 
>>>>> The relevant portion of my original code looks something like this:
>>>>> 
>>>>> *#!/usr/bin/perl*
>>>>> *use strict;*
>>>>> *use Bio::DB::SwissProt;*
>>>>> *#parse out accession number*
>>>>> *..*
>>>>> *my $acc_num = "**O95342";*
>>>>> *my $db_obj = Bio::DB::SwissProt->new;*
>>>>> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
>>>>> *
>>>>> *
>>>>> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
>>>>> specify -servertype and -hostlocation.  So I changed my code to look
>>>>> something like this:
>>>>> 
>>>>> *
>>>>> #!/usr/bin/perl
>>>>> use strict;
>>>>> use Bio::DB::SwissProt;
>>>>> #parse out accession number
>>>>> ..
>>>>> my $acc_num = "O95342";
>>>>> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>>>>>                                                           '-hostlocation'
>>>>> => 'us');
>>>>> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
>>>>> *
>>>>> 
>>>>> This fixes my problem and my script works again.
>>>>> 
>>>>> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
>>>>> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>>>>>  Both of these urls work in a browser, though the default throws the error
>>>>> in my script. Interestingly, the 'us' url has a notice that says
>>>>> "*Notice:* This
>>>>> page will be replaced with www.uniprot.org. Please send us your
>>>>> feedback<http://www.uniprot.org/contact>
>>>>> !", so hopefully it doesn't break soon as well.  Perhaps the default ebi url
>>>>> was recently changed in some way?  Anyway, I figured I'd post here in case
>>>>> anyone else ran into this problem.
>>>>> 
>>>>> cheers,
>>>>> Matt
>>>>> _______________________________________________
>>>>> 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
>>>> 
>>> 
>>> 
>>> 
>>> --
>>> ----
>>> "Saying the internet has changed dramatically over the last five years
>>> is clich? ? the internet is always changing dramatically" - Craig
>>> Labovitz, Arbor Networks.
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> ----
> "Saying the internet has changed dramatically over the last five years
> is clich? ? the internet is always changing dramatically" - Craig
> Labovitz, Arbor Networks.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From maizemu at gmail.com  Wed Oct 27 12:53:26 2010
From: maizemu at gmail.com (Christopher Bottoms)
Date: Wed, 27 Oct 2010 11:53:26 -0500
Subject: [Bioperl-l] how to download PDB files using Bioperl script
In-Reply-To: <01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
Message-ID: <AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>

Ashwani,

Do you need to download the files once or does this need to be automated?

If you just need to do it once, check out
http://www.rcsb.org/pdb/download/download.do for downloading multiple
files.

If you need to automate the process, let me know and I'll help you
figure it out. The easiest way I can think of, which I used to do, is
downloading them from the ftp site.

Sincerely,

Christopher Bottoms

On Fri, Oct 22, 2010 at 11:12 AM, Jun Yin <jun.yin at ucd.ie> wrote:
> Hi, Ashwani,
>
> I havenot found any module in BioPerl for downloading PDB files, though
> Bio::Structure::IO::pdb can parse PDB files.
>
> However, PDB provides RESTful service
> (http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
> batch downloading the proteins.
>
> Cheers,
> Jun Yin
> Ph.D.?student in U.C.D.
>
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
> Sent: Thursday, October 21, 2010 9:39 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] how to download PDB files using Bioperl script
>
> Hi All,
>
>
> I have around 150 pdb file names and I need to download them from Protein
> Data Bank. I wonder if someone could tell me how to do it by using Bioperl.
>
> Thanks in advance.
>
> Regards,
> Ashwani
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>
> _______________________________________________
> 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 Oct 27 14:40:02 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 27 Oct 2010 13:40:02 -0500
Subject: [Bioperl-l] A problem on BioPerl module Bio::DB::Fasta
In-Reply-To: <1288141691.2377.1.camel@ubuntu>
References: <1288141691.2377.1.camel@ubuntu>
Message-ID: <25CA46EE-B73B-4C27-9CA6-28BED05C7AEB@illinois.edu>

Tao,

I've made that correction to the HOWTO.  In the future, if you see an error on the wiki you are free to make changes to correct them.  

Thanks!

chris

On Oct 26, 2010, at 8:08 PM, Tao Zhu wrote:

> Hello, everyone!
> 
> I hope it isn't true, but I really find a problem on BioPerl module
> Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
> Osborne wrote that we could catch sub-sequences like this,
> 
> 
> use Bio::DB::Fasta;
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> $db = Bio::DB::Fasta->new($file);
> $seqobj = $db->get_Seq_by_id($id,$start,$end);
> print $seqobj->seq,"\n";
> 
> 
> In fact it didn't work. I only got the whole sequence after running the
> script. Therefore I referred to the Pdoc documentation and realized it
> should be written as follows,
> 
> 
> use Bio::DB::Fasta;
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> $db = Bio::DB::Fasta->new($file);
> $seq = $db->seq($id,$start,$end);
> print $seq,"\n";
> 
> 
> Then it would return the sub-sequence from 6 to 10.
> 
> Probably Dr Osborne had made a mistake when writing the use-guide
> HOWTO:Beginners.
> 
> 
> -- 
> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> 100875, China
> email: tzhu at mail.bnu.edu.cn
> 
> _______________________________________________
> 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 Oct 28 11:10:25 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 28 Oct 2010 10:10:25 -0500
Subject: [Bioperl-l] A problem on BioPerl module Bio::DB::Fasta
In-Reply-To: <1288251535.4408.18.camel@ubuntu>
References: <1288141691.2377.1.camel@ubuntu>
	<25CA46EE-B73B-4C27-9CA6-28BED05C7AEB@illinois.edu>
	<1288251535.4408.18.camel@ubuntu>
Message-ID: <C3335F92-724B-48C7-A05F-17AF27B244D9@illinois.edu>

Very true, didn't catch that; I was just making the correction you mentioned.  That's what happens when I don't have enough coffee!

chris

On Oct 28, 2010, at 2:38 AM, Tao Zhu wrote:

> Dear Chris,
> 
> Thank you for correcting the HOWTO, but in fact it hasn't been
> completely correct yet. I've made some changes to the passage again like
> this,
> 
> ************************
> use Bio::DB::Fasta; 
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
> $db = Bio::DB::Fasta->new($file);
> $seq = $db->seq($id,$start,$end);
> print $seq,"\n";
> ************************
> 
> The original passage is like this,
> ************************
> use Bio::DB::Fasta;
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
> $db = Bio::DB::Fasta->new($file);
> $seqobj = $db->seq($id,$start,$end); 
> print $seqobj->seq;
> ************************
> 
> We should notice that if method '$db->seq()' is called, then it would
> return a simple string, not a Bio::Seq object.
> 
> 
> 
> ? 2010-10-27?? 13:40 -0500?Chris Fields???
>> Tao,
>> 
>> I've made that correction to the HOWTO.  In the future, if you see an error on the wiki you are free to make changes to correct them.  
>> 
>> Thanks!
>> 
>> chris
>> 
>> On Oct 26, 2010, at 8:08 PM, Tao Zhu wrote:
>> 
>>> Hello, everyone!
>>> 
>>> I hope it isn't true, but I really find a problem on BioPerl module
>>> Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
>>> Osborne wrote that we could catch sub-sequences like this,
>>> 
>>> 
>>> use Bio::DB::Fasta;
>>> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
>>> $db = Bio::DB::Fasta->new($file);
>>> $seqobj = $db->get_Seq_by_id($id,$start,$end);
>>> print $seqobj->seq,"\n";
>>> 
>>> 
>>> In fact it didn't work. I only got the whole sequence after running the
>>> script. Therefore I referred to the Pdoc documentation and realized it
>>> should be written as follows,
>>> 
>>> 
>>> use Bio::DB::Fasta;
>>> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
>>> $db = Bio::DB::Fasta->new($file);
>>> $seq = $db->seq($id,$start,$end);
>>> print $seq,"\n";
>>> 
>>> 
>>> Then it would return the sub-sequence from 6 to 10.
>>> 
>>> Probably Dr Osborne had made a mistake when writing the use-guide
>>> HOWTO:Beginners.
>>> 
>>> 
>>> -- 
>>> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
>>> 100875, China
>>> email: tzhu at mail.bnu.edu.cn
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 
> 
> 



From Seidl-Michael at t-online.de  Wed Oct 27 04:58:03 2010
From: Seidl-Michael at t-online.de (seidl-michael)
Date: Wed, 27 Oct 2010 10:58:03 +0200
Subject: [Bioperl-l] Tiling of hsps using Bioperl
Message-ID: <041D7AC1-99F2-4760-B709-29FE138E05FA@web.de>

Hi everyone,

I have a question about the Bio::Search::Tiling::MapTiling  package. I  
want to get the range of my tilled hsps using the "range" function.  
The reported range is, unfortunately, not what I would expect while  
looking at my data:

 >A
          Length = 1967

Score = 70.1 bits (170), Expect = 1e-11,   Method: Compositional  
matrix adjust.
Identities = 47/110 (42%), Positives = 66/110 (60%), Gaps = 29/110 (26%)

Query: 358   
EAARQEEVARELEVKSSMATKIQSHWRGMAARSEVSTLRAEAAAAEAAASEAARQEEVAR 417
            E ARQEE+AR+ E +S+MATKIQSHWRG  ARSEV+++R+ AA A+        Q +++R
Sbjct: 1344 ELARQEELARQAEAESAMATKIQSHWRGSVARSEVASMRS-AAIADV------- 
QTQLSR 1395

Query: 418  QEEDARRKEAARQEEVARELEVKSSMATKIQSHWRGTAARSEVSTLRAEA 467
                                 +++  A +IQS WRG  AR +V++LRAEA
Sbjct: 1396 ---------------------IENLTAVRIQSRWRGVLARVKVASLRAEA 1424



Score = 57.8 bits (138), Expect = 7e-08,   Method: Compositional  
matrix adjust.
Identities = 28/39 (71%), Positives = 33/39 (84%)

Query: 358  EAARQEEVARELEVKSSMATKIQSHWRGMAARSEVSTLR 396
            E ARQEE+AR+ E +S+MATKIQSHWRG  ARSEV+ LR
Sbjct: 1222 ELARQEELARQAEAESAMATKIQSHWRGSVARSEVAVLR 1260



Score = 47.4 bits (111), Expect = 1e-04,   Method: Compositional  
matrix adjust.
Identities = 43/115 (37%), Positives = 58/115 (50%), Gaps = 29/115 (25%)

Query: 299  
RELEVKSSMATKIQSHWRGMAARSEVSTLRAEAAAAEAAASEAARQEEVARQEEDARRKE 358
           +E + K+ MAT+IQS  RG+ AR        EA + + AASE        R + + RR++
Sbjct: 433 KETQRKNDMATQIQSGVRGVIAR--------EAYSEKLAASERI---- 
AIRIQTEFRRRQ 480

Query: 359 AARQEEVARE-----------------LEVKSSMATKIQSHWRGMAARSEVSTLR 396
           A +Q E  R+                  +   S ATKIQSHWRG  ARSEV+ LR
Sbjct: 481 AQKQLEALRQQLQREQTCAVVIQKILSSDSNESAATKIQSHWRGSVARSEVAVLR 535

I would expect to get [433,1424] when using:

my $tiling = Bio::Search::Tiling::MapTiling->new($hit);
my @range = $tiling->range('subject');

Instead my array includes [1344,535]. Do I have a conceptional problem  
with the function of "range" or is there something wired happening?

Thanks a lot for any help and suggestions,

Michael

From tzhu at mail.bnu.edu.cn  Thu Oct 28 03:38:55 2010
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Thu, 28 Oct 2010 15:38:55 +0800
Subject: [Bioperl-l] A problem on BioPerl module Bio::DB::Fasta
In-Reply-To: <25CA46EE-B73B-4C27-9CA6-28BED05C7AEB@illinois.edu>
References: <1288141691.2377.1.camel@ubuntu>
	<25CA46EE-B73B-4C27-9CA6-28BED05C7AEB@illinois.edu>
Message-ID: <1288251535.4408.18.camel@ubuntu>

Dear Chris,

Thank you for correcting the HOWTO, but in fact it hasn't been
completely correct yet. I've made some changes to the passage again like
this,

************************
use Bio::DB::Fasta; 
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
$db = Bio::DB::Fasta->new($file);
$seq = $db->seq($id,$start,$end);
print $seq,"\n";
************************

The original passage is like this,
************************
use Bio::DB::Fasta;
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
$db = Bio::DB::Fasta->new($file);
$seqobj = $db->seq($id,$start,$end); 
print $seqobj->seq;
************************

We should notice that if method '$db->seq()' is called, then it would
return a simple string, not a Bio::Seq object.



? 2010-10-27?? 13:40 -0500?Chris Fields???
> Tao,
> 
> I've made that correction to the HOWTO.  In the future, if you see an error on the wiki you are free to make changes to correct them.  
> 
> Thanks!
> 
> chris
> 
> On Oct 26, 2010, at 8:08 PM, Tao Zhu wrote:
> 
> > Hello, everyone!
> > 
> > I hope it isn't true, but I really find a problem on BioPerl module
> > Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
> > Osborne wrote that we could catch sub-sequences like this,
> > 
> > 
> > use Bio::DB::Fasta;
> > ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> > $db = Bio::DB::Fasta->new($file);
> > $seqobj = $db->get_Seq_by_id($id,$start,$end);
> > print $seqobj->seq,"\n";
> > 
> > 
> > In fact it didn't work. I only got the whole sequence after running the
> > script. Therefore I referred to the Pdoc documentation and realized it
> > should be written as follows,
> > 
> > 
> > use Bio::DB::Fasta;
> > ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> > $db = Bio::DB::Fasta->new($file);
> > $seq = $db->seq($id,$start,$end);
> > print $seq,"\n";
> > 
> > 
> > Then it would return the sub-sequence from 6 to 10.
> > 
> > Probably Dr Osborne had made a mistake when writing the use-guide
> > HOWTO:Beginners.
> > 
> > 
> > -- 
> > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> > 100875, China
> > email: tzhu at mail.bnu.edu.cn
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 




From edwardsa at cs.man.ac.uk  Thu Oct 28 16:52:58 2010
From: edwardsa at cs.man.ac.uk (Andrea Edwards)
Date: Thu, 28 Oct 2010 21:52:58 +0100
Subject: [Bioperl-l] Installation of bioperl on Ubuntu
Message-ID: <4CC9E2AA.6020302@cs.man.ac.uk>

Hi

I'm new to Perl and linux and I think I may have messed up my 
installation of Bioperl.

I followed the instructions on this page verbatim
http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server

However the

./Build test


command failed and I noticed a lot of modules were missing from the 
output of the test. I then used CPAN to install these modules. One of 
them was Bio::FeatureIO. When I installed this it seemed to be 
installing lots of BioPerl 1.6.1 files. However when i downloaded the 
bioperl as instructed here

wget -N http://bioperl.org/DIST/current_core_unstable.tar.bz2

the version that I got was 1.5.2_102

I am confused by the presence of 2 different version numbers and don't 
know how to proceed. It looks as if I have installed a lot of BioPerl 
1.6.1 and if i carry on with the make test/install instructions from the 
website I will then install version 1.5.

When i looked at the files installed in the Bio folder in my perl 
libraries there were 88 files and the only files missing compared to my 
other BioPerl installations were:
ANSI directory
BioEntry.pm
ConfigData.pm

I looked at some of the modules to try and see which version they were 
but they all had different version numbers. I think I have inadvertently 
used CPAN to install 1.6.1. What do you think?

many thanks

From buiduyminh at gmail.com  Thu Oct 28 17:07:06 2010
From: buiduyminh at gmail.com (Minh Bui)
Date: Thu, 28 Oct 2010 17:07:06 -0400
Subject: [Bioperl-l] Installation of bioperl on Ubuntu
In-Reply-To: <4CC9E2AA.6020302@cs.man.ac.uk>
References: <4CC9E2AA.6020302@cs.man.ac.uk>
Message-ID: <AANLkTi=Vr3zYRdtUaDptrxexkDmo_wj-2f5BiLvAAzfr@mail.gmail.com>

Hi Andrea,

You don't have to install Bioperl manually on Ubuntu.

You can go to *System* > *Administration* > "*Synaptic Package Manager*" ,
search for "Bioperl" and install it. I believe it has the latest version.

Minh.


On Thu, Oct 28, 2010 at 4:52 PM, Andrea Edwards <edwardsa at cs.man.ac.uk>wrote:

> Hi
>
> I'm new to Perl and linux and I think I may have messed up my installation
> of Bioperl.
>
> I followed the instructions on this page verbatim
> http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server
>
> However the
>
> ./Build test
>
>
> command failed and I noticed a lot of modules were missing from the output
> of the test. I then used CPAN to install these modules. One of them was
> Bio::FeatureIO. When I installed this it seemed to be installing lots of
> BioPerl 1.6.1 files. However when i downloaded the bioperl as instructed
> here
>
> wget -N http://bioperl.org/DIST/current_core_unstable.tar.bz2
>
> the version that I got was 1.5.2_102
>
> I am confused by the presence of 2 different version numbers and don't know
> how to proceed. It looks as if I have installed a lot of BioPerl 1.6.1 and
> if i carry on with the make test/install instructions from the website I
> will then install version 1.5.
>
> When i looked at the files installed in the Bio folder in my perl libraries
> there were 88 files and the only files missing compared to my other BioPerl
> installations were:
> ANSI directory
> BioEntry.pm
> ConfigData.pm
>
> I looked at some of the modules to try and see which version they were but
> they all had different version numbers. I think I have inadvertently used
> CPAN to install 1.6.1. What do you think?
>
> many thanks
> _______________________________________________
> 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 Oct 28 17:28:17 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 28 Oct 2010 16:28:17 -0500
Subject: [Bioperl-l] Installation of bioperl on Ubuntu
In-Reply-To: <4CC9E2AA.6020302@cs.man.ac.uk>
References: <4CC9E2AA.6020302@cs.man.ac.uk>
Message-ID: <22C0CD13-6081-4FC4-97B7-939696D85A74@illinois.edu>

On Oct 28, 2010, at 3:52 PM, Andrea Edwards wrote:

> Hi
> 
> I'm new to Perl and linux and I think I may have messed up my installation of Bioperl.
> 
> I followed the instructions on this page verbatim
> http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server
> 
> However the
> 
> ./Build test
> 
> 
> command failed and I noticed a lot of modules were missing from the output of the test. I then used CPAN to install these modules. One of them was Bio::FeatureIO. When I installed this it seemed to be installing lots of BioPerl 1.6.1 files. However when i downloaded the bioperl as instructed here
> 
> wget -N http://bioperl.org/DIST/current_core_unstable.tar.bz2
> 
> the version that I got was 1.5.2_102

Ugh, that's not good; that should be removed (we're now at v 1.6.1 stable, but about 10 months past that release now and sorely due for another).  For the latest 'unstable' code, you can go to github:

http://github.com/bioperl/bioperl-live

Click on the 'Downloads' button.

Just a warning, but FeatureIO will likely disappear from the github bioperl-live repo master branch.  We're breaking out chunks of code that can be released independently, FeatureIO being one.

> I am confused by the presence of 2 different version numbers and don't know how to proceed. It looks as if I have installed a lot of BioPerl 1.6.1 and if i carry on with the make test/install instructions from the website I will then install version 1.5.
> 
> When i looked at the files installed in the Bio folder in my perl libraries there were 88 files and the only files missing compared to my other BioPerl installations were:
> ANSI directory
> BioEntry.pm
> ConfigData.pm

ConfigData is only for the installation.  Not sure about the others.

> I looked at some of the modules to try and see which version they were but they all had different version numbers. I think I have inadvertently used CPAN to install 1.6.1. What do you think?
> 
> many thanks

Since we moved to github this past May we no longer have different revision numbers per module (git doesn't support them, but so far we haven't seen many actually missing them).  

chris

From daniel.standage at gmail.com  Thu Oct 28 22:45:24 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Thu, 28 Oct 2010 19:45:24 -0700 (PDT)
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
Message-ID: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>

I am using the Bio::Tools::GFF parser to process and store GFF3 data
in an application. Calls to next_feature() return
Bio::SeqFeature::Generic objects. I have written a class that extends
the Bio::SeqFeature::Generic class, but I still want to use the
Bio::Tools::GFF class to do the initial parsing of the data.

Is there a way for me to tell the Bio::Tools::GFF parser that I want
it to give me objects from my custom class? Or should I just re-bless
the objects it gives me? Will I run into garbage collection problems
if I re-bless the Bio::SeqFeature::Generic objects to my custom class
(that extends the Bio::SeqFeature::Generic class)?

Thanks!

Daniel

From scott at scottcain.net  Thu Oct 28 23:41:09 2010
From: scott at scottcain.net (Scott Cain)
Date: Thu, 28 Oct 2010 23:41:09 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
In-Reply-To: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
References: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
Message-ID: <AANLkTika2Nkx5T-Gf_y74NhEij9udqF6V3DFibzMf90G@mail.gmail.com>

Hi Daniel,

It seems like the easiest thing to do would be to subclass
Bio::Tools::GFF.  BSFGeneric is only mentioned explicitly a few times
(maybe only once), so subclassing and having it use your class instead
would probably be the easiest thing to do.

Also, about having it produce GFF3: make sure you're actually getting
valid GFF3.  Bio::Tools::GFF is fairly old, and I am sure you could
give it valid SeqFeature objects and get invalid GFF3 out in some
circumstances.

Scott


On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> I am using the Bio::Tools::GFF parser to process and store GFF3 data
> in an application. Calls to next_feature() return
> Bio::SeqFeature::Generic objects. I have written a class that extends
> the Bio::SeqFeature::Generic class, but I still want to use the
> Bio::Tools::GFF class to do the initial parsing of the data.
>
> Is there a way for me to tell the Bio::Tools::GFF parser that I want
> it to give me objects from my custom class? Or should I just re-bless
> the objects it gives me? Will I run into garbage collection problems
> if I re-bless the Bio::SeqFeature::Generic objects to my custom class
> (that extends the Bio::SeqFeature::Generic class)?
>
> Thanks!
>
> Daniel
> _______________________________________________
> 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 dimitark at bii.a-star.edu.sg  Fri Oct 29 04:29:53 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Fri, 29 Oct 2010 16:29:53 +0800
Subject: [Bioperl-l] about git and perl5lib
Message-ID: <4CCA8601.6020607@bii.a-star.edu.sg>

Hi guys,
i am sorry if this sounds stupid but i have problem with the PERL5LIB 
and the GIT version of BioPerl(BP). I downloaded the BP-live and BP-run 
from git. I use Slackware so I added the following line in bashrc:

  export 
PERL5LIB=$HOME/Bioperl_git/bioperl-live:$HOME/Bioperl_git/bioperl-run:$PERL5LIB

But when i start a script using StandAloneBlastPlus i see perl cant find it:

Can't locate Bio/Tools/Run/StandAloneBlastPlus.pm in @INC (@INC 
contains: /home/domine/Bioperl_git/bioperl-live 
/home/domine/Bioperl_git/bioperl-run 
/usr/lib64/perl5/5.10.1/x86_64-linux-thread-multi 
/usr/lib64/perl5/5.10.1 
/usr/lib64/perl5/site_perl/5.10.1/x86_64-linux-thread-multi 
/usr/lib64/perl5/site_perl/5.10.1 /usr/lib64/perl5/site_perl 
/usr/lib64/perl5/vendor_perl/5.10.1/x86_64-linux-thread-multi 
/usr/lib64/perl5/vendor_perl/5.10.1 /usr/lib64/perl5/vendor_perl

It seems Perl should find the module but it doesnt. Any idea where i 
could have made a mistake?

Btw with:  perl -MBio::Perl -le 'print Bio::Perl->VERSION;' i get 1.0069

Thank you
Dimitar




From David.Messina at sbc.su.se  Fri Oct 29 08:18:40 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 29 Oct 2010 08:18:40 -0400
Subject: [Bioperl-l] about git and perl5lib
In-Reply-To: <4CCA8601.6020607@bii.a-star.edu.sg>
References: <4CCA8601.6020607@bii.a-star.edu.sg>
Message-ID: <DACCDE9C-B82D-4D71-84BC-4119B6E242FD@sbc.su.se>

There's a minor inconsistency on our part: the path to the bioperl-run modules is actually bioperl-run/lib


Note that bioperl-live will I believe also be switching to this at some point; having the modules in a lib subdir is standard Perl practice.


Dave






On Oct 29, 2010, at 4:29, Dimitar Kenanov <dimitark at bii.a-star.edu.sg> wrote:

> Hi guys,
> i am sorry if this sounds stupid but i have problem with the PERL5LIB and the GIT version of BioPerl(BP). I downloaded the BP-live and BP-run from git. I use Slackware so I added the following line in bashrc:
> 
> export PERL5LIB=$HOME/Bioperl_git/bioperl-live:$HOME/Bioperl_git/bioperl-run:$PERL5LIB
> 
> But when i start a script using StandAloneBlastPlus i see perl cant find it:
> 
> Can't locate Bio/Tools/Run/StandAloneBlastPlus.pm in @INC (@INC contains: /home/domine/Bioperl_git/bioperl-live /home/domine/Bioperl_git/bioperl-run /usr/lib64/perl5/5.10.1/x86_64-linux-thread-multi /usr/lib64/perl5/5.10.1 /usr/lib64/perl5/site_perl/5.10.1/x86_64-linux-thread-multi /usr/lib64/perl5/site_perl/5.10.1 /usr/lib64/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.10.1/x86_64-linux-thread-multi /usr/lib64/perl5/vendor_perl/5.10.1 /usr/lib64/perl5/vendor_perl
> 
> It seems Perl should find the module but it doesnt. Any idea where i could have made a mistake?
> 
> Btw with:  perl -MBio::Perl -le 'print Bio::Perl->VERSION;' i get 1.0069
> 
> Thank you
> Dimitar
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From scott at scottcain.net  Fri Oct 29 10:03:54 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 29 Oct 2010 10:03:54 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
In-Reply-To: <AANLkTimVseFgymk+MaumosOkh=jP3bR9LwGVLxmB26Xf@mail.gmail.com>
References: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
	<AANLkTika2Nkx5T-Gf_y74NhEij9udqF6V3DFibzMf90G@mail.gmail.com>
	<AANLkTimVseFgymk+MaumosOkh=jP3bR9LwGVLxmB26Xf@mail.gmail.com>
Message-ID: <AANLkTinKbEtuWetY7avw6uH8w_GcXvrTxD1t7R8t9jc3@mail.gmail.com>

Hi Daniel,

I cc'ed the bioperl mailing list back in and attached your tarball.  I
don't really know what it is you want to do, and you already know that
your code compiles and runs, so I'm not sure what advice you're
looking for.

Scott

On Fri, Oct 29, 2010 at 9:28 AM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> I don't see how to attach files to the mailing list, so I'm just going to
> reply to you. Sorry if that is against the protocol.
>
> I have attached a working implementation of what I think you were
> suggesting. I have a parser class that subclasses Bio::Tools::GFF, and it
> has a method that will return objects of my class that subclasses
> Bio::SeqFeature::Generic. This is a rough test and I still need to clean
> things up and add the rest of the functionality that I originally needed, I
> just wanted to make sure that there aren't going to be any problems with the
> approach I'm taking.
>
> If you unpack and run './temptest' it should print out 7 valid features and
> 1 invalid feature.
>
> Thanks for your suggestions!
>
> Daniel
>
> On Thu, Oct 28, 2010 at 10:41 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Daniel,
>>
>> It seems like the easiest thing to do would be to subclass
>> Bio::Tools::GFF. ?BSFGeneric is only mentioned explicitly a few times
>> (maybe only once), so subclassing and having it use your class instead
>> would probably be the easiest thing to do.
>>
>> Also, about having it produce GFF3: make sure you're actually getting
>> valid GFF3. ?Bio::Tools::GFF is fairly old, and I am sure you could
>> give it valid SeqFeature objects and get invalid GFF3 out in some
>> circumstances.
>>
>> Scott
>>
>>
>> On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
>> <daniel.standage at gmail.com> wrote:
>> > I am using the Bio::Tools::GFF parser to process and store GFF3 data
>> > in an application. Calls to next_feature() return
>> > Bio::SeqFeature::Generic objects. I have written a class that extends
>> > the Bio::SeqFeature::Generic class, but I still want to use the
>> > Bio::Tools::GFF class to do the initial parsing of the data.
>> >
>> > Is there a way for me to tell the Bio::Tools::GFF parser that I want
>> > it to give me objects from my custom class? Or should I just re-bless
>> > the objects it gives me? Will I run into garbage collection problems
>> > if I re-bless the Bio::SeqFeature::Generic objects to my custom class
>> > (that extends the Bio::SeqFeature::Generic class)?
>> >
>> > Thanks!
>> >
>> > Daniel
>> > _______________________________________________
>> > 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
>
>
>
> --
> Daniel S. Standage
> Graduate Research Assistant
> Bioinformatics and Computational Biology Program
> Iowa State University
>
>



-- 
------------------------------------------------------------------------
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 scott at scottcain.net  Fri Oct 29 10:21:51 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 29 Oct 2010 10:21:51 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
In-Reply-To: <AANLkTinKbEtuWetY7avw6uH8w_GcXvrTxD1t7R8t9jc3@mail.gmail.com>
References: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
	<AANLkTika2Nkx5T-Gf_y74NhEij9udqF6V3DFibzMf90G@mail.gmail.com>
	<AANLkTimVseFgymk+MaumosOkh=jP3bR9LwGVLxmB26Xf@mail.gmail.com>
	<AANLkTinKbEtuWetY7avw6uH8w_GcXvrTxD1t7R8t9jc3@mail.gmail.com>
Message-ID: <AANLkTikoPX7ep5QfOd-EDxoGqYU43kJZtwv5MaBHawXC@mail.gmail.com>

Hi all,

I'm resending this because it seems that some mail clients don't like
having executable files hidden inside of a tarball, so I removed the
executable bit.

Scott


On Fri, Oct 29, 2010 at 10:03 AM, Scott Cain <scott at scottcain.net> wrote:
> Hi Daniel,
>
> I cc'ed the bioperl mailing list back in and attached your tarball. ?I
> don't really know what it is you want to do, and you already know that
> your code compiles and runs, so I'm not sure what advice you're
> looking for.
>
> Scott
>
> On Fri, Oct 29, 2010 at 9:28 AM, Daniel Standage
> <daniel.standage at gmail.com> wrote:
>> I don't see how to attach files to the mailing list, so I'm just going to
>> reply to you. Sorry if that is against the protocol.
>>
>> I have attached a working implementation of what I think you were
>> suggesting. I have a parser class that subclasses Bio::Tools::GFF, and it
>> has a method that will return objects of my class that subclasses
>> Bio::SeqFeature::Generic. This is a rough test and I still need to clean
>> things up and add the rest of the functionality that I originally needed, I
>> just wanted to make sure that there aren't going to be any problems with the
>> approach I'm taking.
>>
>> If you unpack and run './temptest' it should print out 7 valid features and
>> 1 invalid feature.
>>
>> Thanks for your suggestions!
>>
>> Daniel
>>
>> On Thu, Oct 28, 2010 at 10:41 PM, Scott Cain <scott at scottcain.net> wrote:
>>>
>>> Hi Daniel,
>>>
>>> It seems like the easiest thing to do would be to subclass
>>> Bio::Tools::GFF. ?BSFGeneric is only mentioned explicitly a few times
>>> (maybe only once), so subclassing and having it use your class instead
>>> would probably be the easiest thing to do.
>>>
>>> Also, about having it produce GFF3: make sure you're actually getting
>>> valid GFF3. ?Bio::Tools::GFF is fairly old, and I am sure you could
>>> give it valid SeqFeature objects and get invalid GFF3 out in some
>>> circumstances.
>>>
>>> Scott
>>>
>>>
>>> On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
>>> <daniel.standage at gmail.com> wrote:
>>> > I am using the Bio::Tools::GFF parser to process and store GFF3 data
>>> > in an application. Calls to next_feature() return
>>> > Bio::SeqFeature::Generic objects. I have written a class that extends
>>> > the Bio::SeqFeature::Generic class, but I still want to use the
>>> > Bio::Tools::GFF class to do the initial parsing of the data.
>>> >
>>> > Is there a way for me to tell the Bio::Tools::GFF parser that I want
>>> > it to give me objects from my custom class? Or should I just re-bless
>>> > the objects it gives me? Will I run into garbage collection problems
>>> > if I re-bless the Bio::SeqFeature::Generic objects to my custom class
>>> > (that extends the Bio::SeqFeature::Generic class)?
>>> >
>>> > Thanks!
>>> >
>>> > Daniel
>>> > _______________________________________________
>>> > 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
>>
>>
>>
>> --
>> Daniel S. Standage
>> Graduate Research Assistant
>> Bioinformatics and Computational Biology Program
>> Iowa State University
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> 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
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From daniel.standage at gmail.com  Fri Oct 29 10:34:41 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Fri, 29 Oct 2010 09:34:41 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
In-Reply-To: <AANLkTikoPX7ep5QfOd-EDxoGqYU43kJZtwv5MaBHawXC@mail.gmail.com>
References: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
	<AANLkTika2Nkx5T-Gf_y74NhEij9udqF6V3DFibzMf90G@mail.gmail.com>
	<AANLkTimVseFgymk+MaumosOkh=jP3bR9LwGVLxmB26Xf@mail.gmail.com>
	<AANLkTinKbEtuWetY7avw6uH8w_GcXvrTxD1t7R8t9jc3@mail.gmail.com>
	<AANLkTikoPX7ep5QfOd-EDxoGqYU43kJZtwv5MaBHawXC@mail.gmail.com>
Message-ID: <AANLkTikwhSvoEHJECSGV9GzKdXk7Yu7O6nwkk=-Mccba@mail.gmail.com>

I guess my concern is that I haven't used inheritance much in Perl and I'm
unclear about the possible consequences of the approach I've taken. I've
seen people warning against re-blessing objects, and I just wanted to make
sure that the approach that I seem to have working now isn't going to cause
any problems down the line.

Sorry I wasn't clear. Thanks for your help.

Daniel

On Fri, Oct 29, 2010 at 9:21 AM, Scott Cain <scott at scottcain.net> wrote:

> Hi all,
>
> I'm resending this because it seems that some mail clients don't like
> having executable files hidden inside of a tarball, so I removed the
> executable bit.
>
> Scott
>
>
> On Fri, Oct 29, 2010 at 10:03 AM, Scott Cain <scott at scottcain.net> wrote:
> > Hi Daniel,
> >
> > I cc'ed the bioperl mailing list back in and attached your tarball.  I
> > don't really know what it is you want to do, and you already know that
> > your code compiles and runs, so I'm not sure what advice you're
> > looking for.
> >
> > Scott
> >
> > On Fri, Oct 29, 2010 at 9:28 AM, Daniel Standage
> > <daniel.standage at gmail.com> wrote:
> >> I don't see how to attach files to the mailing list, so I'm just going
> to
> >> reply to you. Sorry if that is against the protocol.
> >>
> >> I have attached a working implementation of what I think you were
> >> suggesting. I have a parser class that subclasses Bio::Tools::GFF, and
> it
> >> has a method that will return objects of my class that subclasses
> >> Bio::SeqFeature::Generic. This is a rough test and I still need to clean
> >> things up and add the rest of the functionality that I originally
> needed, I
> >> just wanted to make sure that there aren't going to be any problems with
> the
> >> approach I'm taking.
> >>
> >> If you unpack and run './temptest' it should print out 7 valid features
> and
> >> 1 invalid feature.
> >>
> >> Thanks for your suggestions!
> >>
> >> Daniel
> >>
> >> On Thu, Oct 28, 2010 at 10:41 PM, Scott Cain <scott at scottcain.net>
> wrote:
> >>>
> >>> Hi Daniel,
> >>>
> >>> It seems like the easiest thing to do would be to subclass
> >>> Bio::Tools::GFF.  BSFGeneric is only mentioned explicitly a few times
> >>> (maybe only once), so subclassing and having it use your class instead
> >>> would probably be the easiest thing to do.
> >>>
> >>> Also, about having it produce GFF3: make sure you're actually getting
> >>> valid GFF3.  Bio::Tools::GFF is fairly old, and I am sure you could
> >>> give it valid SeqFeature objects and get invalid GFF3 out in some
> >>> circumstances.
> >>>
> >>> Scott
> >>>
> >>>
> >>> On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
> >>> <daniel.standage at gmail.com> wrote:
> >>> > I am using the Bio::Tools::GFF parser to process and store GFF3 data
> >>> > in an application. Calls to next_feature() return
> >>> > Bio::SeqFeature::Generic objects. I have written a class that extends
> >>> > the Bio::SeqFeature::Generic class, but I still want to use the
> >>> > Bio::Tools::GFF class to do the initial parsing of the data.
> >>> >
> >>> > Is there a way for me to tell the Bio::Tools::GFF parser that I want
> >>> > it to give me objects from my custom class? Or should I just re-bless
> >>> > the objects it gives me? Will I run into garbage collection problems
> >>> > if I re-bless the Bio::SeqFeature::Generic objects to my custom class
> >>> > (that extends the Bio::SeqFeature::Generic class)?
> >>> >
> >>> > Thanks!
> >>> >
> >>> > Daniel
> >>> > _______________________________________________
> >>> > 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
> >>
> >>
> >>
> >> --
> >> Daniel S. Standage
> >> Graduate Research Assistant
> >> Bioinformatics and Computational Biology Program
> >> Iowa State University
> >>
> >>
> >
> >
> >
> > --
> > ------------------------------------------------------------------------
> > 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
>



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

From scott at scottcain.net  Fri Oct  1 11:45:35 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 1 Oct 2010 11:45:35 -0400
Subject: [Bioperl-l] [Gmod-gbrowse] bp_seqfeature_delete.PL - where
	should I submit a patch?
In-Reply-To: <87782334-E5F5-4DFE-AEBD-64565D5C2F9F@sanger.ac.uk>
References: <87782334-E5F5-4DFE-AEBD-64565D5C2F9F@sanger.ac.uk>
Message-ID: <AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>

Hi Keiran,

Well, I've been told that it is easy for non-bioperl developers to use
git to commit patches, and as if to prove it, there is a very long
wiki page on the bioperl wiki describing how to use git:

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

I'm not sure what the right thing is to do; I'm cc'ing the bioperl
list to get their input.

Scott


On Fri, Oct 1, 2010 at 8:46 AM, Keiran Raine <kr2 at sanger.ac.uk> wrote:
> Hi all,
>
> Does anyone know how I should best get push a patch (new functionality) out
> for this script which is part of the BioPerl package.
>
> I've added a 'fast' option which is useful for when you want to delete a
> whole dataset. ?The problem I was having is I loaded a large set of data
> which had errors. ?To delete it I tried to use the '-t' option but this
> continually fails after several hours (eventually runs out of memory). ?To
> get round this I've added the '-f' flag which tells the script to perform
> the delete/commit on each individual feature (and associated sub-features)
> rather than attempt to do them all in a single commit.
>
> I've attached the modified version (unfortunately the formatting was kind of
> knackered so a patch file will be a bit iffy).
>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a
> charity registered in England with number 1021457 and acompany registered in
> England with number 2742969, whose registeredoffice is 215 Euston Road,
> London, NW1 2BE.
>
>
> Keiran Raine
> Senior Computer Biologist
> The Cancer Genome Project
> Ext: 7703
> kr2 at sanger.ac.uk
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



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



From dan.bolser at gmail.com  Fri Oct  1 15:14:34 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Fri, 1 Oct 2010 20:14:34 +0100
Subject: [Bioperl-l] Spam on the wiki: best way to report it?
Message-ID: <AANLkTik1panWOrmZ_hE3dnXYMCBeOTn=LGg=YSjqB2aa@mail.gmail.com>

Is there something like a spam category to report spam on the wiki?

I'm talking about this:

http://www.bioperl.org/wiki/Special:Contributions/Xiangniant


I figure this list isn't really the best place to report it all, but I
couldn't find any advice on what else to do.

Cheers,
Dan.


From cjfields at illinois.edu  Fri Oct  1 15:53:55 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 1 Oct 2010 14:53:55 -0500
Subject: [Bioperl-l] Spam on the wiki: best way to report it?
In-Reply-To: <AANLkTik1panWOrmZ_hE3dnXYMCBeOTn=LGg=YSjqB2aa@mail.gmail.com>
References: <AANLkTik1panWOrmZ_hE3dnXYMCBeOTn=LGg=YSjqB2aa@mail.gmail.com>
Message-ID: <4EC133B7-60D0-4DF3-B0F7-D1628E431397@illinois.edu>

We can delete spam and block users (I just did for that example and one other).  I'll make you a wiki admin; more hands the better!

chris

On Oct 1, 2010, at 2:14 PM, Dan Bolser wrote:

> Is there something like a spam category to report spam on the wiki?
> 
> I'm talking about this:
> 
> http://www.bioperl.org/wiki/Special:Contributions/Xiangniant
> 
> 
> I figure this list isn't really the best place to report it all, but I
> couldn't find any advice on what else to do.
> 
> 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  Fri Oct  1 15:47:31 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 1 Oct 2010 14:47:31 -0500
Subject: [Bioperl-l] [Gmod-gbrowse] bp_seqfeature_delete.PL - where
	should I submit a patch?
In-Reply-To: <AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>
References: <87782334-E5F5-4DFE-AEBD-64565D5C2F9F@sanger.ac.uk>
	<AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>
Message-ID: <1D851E84-1664-4E72-82F5-D8C75ABA3789@illinois.edu>

Keiran,

We gladly accept patches if this is easier for you.  Using git/github is one way of getting more users involved and opening up the code more; the actual barrier to submit code changes is lowered to the point where one can fork our code and hack away, then submit pull requests for those changes to be merged (all via github, using one's account).  

We are generally doing more code review these days (asking for tests, requiring passing tests for inclusion, etc), but in this case that's probably not a problem.

chris

On Oct 1, 2010, at 10:45 AM, Scott Cain wrote:

> Hi Keiran,
> 
> Well, I've been told that it is easy for non-bioperl developers to use
> git to commit patches, and as if to prove it, there is a very long
> wiki page on the bioperl wiki describing how to use git:
> 
>  http://www.bioperl.org/wiki/Using_Git
> 
> I'm not sure what the right thing is to do; I'm cc'ing the bioperl
> list to get their input.
> 
> Scott
> 
> 
> On Fri, Oct 1, 2010 at 8:46 AM, Keiran Raine <kr2 at sanger.ac.uk> wrote:
>> Hi all,
>> 
>> Does anyone know how I should best get push a patch (new functionality) out
>> for this script which is part of the BioPerl package.
>> 
>> I've added a 'fast' option which is useful for when you want to delete a
>> whole dataset.  The problem I was having is I loaded a large set of data
>> which had errors.  To delete it I tried to use the '-t' option but this
>> continually fails after several hours (eventually runs out of memory).  To
>> get round this I've added the '-f' flag which tells the script to perform
>> the delete/commit on each individual feature (and associated sub-features)
>> rather than attempt to do them all in a single commit.
>> 
>> I've attached the modified version (unfortunately the formatting was kind of
>> knackered so a patch file will be a bit iffy).
>> 
>> 
>> 
>> 
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a
>> charity registered in England with number 1021457 and acompany registered in
>> England with number 2742969, whose registeredoffice is 215 Euston Road,
>> London, NW1 2BE.
>> 
>> 
>> Keiran Raine
>> Senior Computer Biologist
>> The Cancer Genome Project
>> Ext: 7703
>> kr2 at sanger.ac.uk
>> 
>> 
>> 
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> Start uncovering the many advantages of virtual appliances
>> and start using them to simplify application deployment and
>> accelerate your shift to cloud computing.
>> http://p.sf.net/sfu/novell-sfdev2dev
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> 
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> 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 jason at bioperl.org  Fri Oct  1 17:17:36 2010
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 01 Oct 2010 14:17:36 -0700
Subject: [Bioperl-l] Bioperl sim4 parse
In-Reply-To: <A475AF196964604CAEE109F1CA0275AB1578AF1378@SJMEMXMBS10.stjude.sjcrh.local>
References: <A475AF196964604CAEE109F1CA0275AB1578AF1378@SJMEMXMBS10.stjude.sjcrh.local>
Message-ID: <4CA64FF0.2010201@bioperl.org>

Jianmin -

Your question is better addressed to the mailing list bioperl-l at bioperl.org

Please attach an example file that is attached and sample perl code you 
are using so someone can test that your problem exists with the latest code.

-jason

Wang, Jianmin wrote, On 10/1/10 1:59 PM:
> Hi, Jason and Steve,
>
> I checked the code of the sim4.pm and used it in my program.  Unforturnately, it does not work well.  When there is a single hit with a single hsp, the code does not generate the hsp correctly and many of the information are lost.  Could you help me to check the code.  For following is the sim4 output file:
>
> Warning: lowercase letter in d.fa data. Convert sequence to uppercase.
>
> seq1 = d.fa, 203 bp
> seq2 = q.fa (HWI-EAS90_614M9:2:106:16121:11311#0), 12 bp
>
>> chr18:60413870-60414073
>> HWI-EAS90_614M9:2:106:16121:11311#0
>
> 111-122  (1-12)   100%
>
>        0     .    :
>      111 CTCATATAGCTC
>          ||||||||||||
>        1 CTCATATAGCTC
>
> Warning: lowercase letter in q.fa data. Convert sequence to uppercase.
>
> seq1 = d.fa, 203 bp
> seq2 = q.fa (teat), 15 bp
>
>> chr18:60413870-60414073
>> teat
>
> 126-140  (1-15)   100%
>
>        0     .    :    .
>      126 GTGGTATACAGAGTT
>          |||||||||||||||
>        1 GTGGTATACAGAGTT
>
>
>
> I found it's impossible to get the strand and mapping position from the data.
>
> Best.
> Jianmin Wang
>
>
>
>    ________________________________
> Email Disclaimer: www.stjude.org/emaildisclaimer

-- 
Jason Stajich
jason at bioperl.org



From avilella at gmail.com  Tue Oct  5 06:00:28 2010
From: avilella at gmail.com (Albert Vilella)
Date: Tue, 5 Oct 2010 11:00:28 +0100
Subject: [Bioperl-l] bioperl version for ensembl Was: Retrieve Sequence from
	Ensembl gene id
Message-ID: <AANLkTim9rEkgWtyF-E+4pvo1G3YS9qr5fw42uFQGwEMq@mail.gmail.com>

I also tested bioperl 1.6.1 for some scripting with the Ensembl API, and it
produces a few warnings here and there, but it doesn't break anything
obvious...

On Thu, Sep 30, 2010 at 4:16 PM, Chris Fields <cjfields at illinois.edu> wrote:

> On Sep 30, 2010, at 8:36 AM, Jun Yin wrote:
>
> > Hi, Chirag,
> >
> > BioPerl does not have any module to retrieve data from Ensembl. But
> Ensembl
> > provides a BioPerl-like interface on that function.
>
> Actually, BioPerl does have Bio::Tools::Run::Ensembl, which was submitted
> by Sendu Bala a few years back.  I think it stills works rather well, at
> least tests pass.  You might get more out of using the Ensembl API directly
> as Jun states though, YMMV.
>
> BTW, the ensembl API also works with the latest bioperl code, regardless
> what the Ensembl website says (e.g. they only support v1.2.3).  Haven't
> heard more about whether this discrepancy was supposed to be addressed at
> some point.
>
> chris
>
> > You can visit Ensembl's website on how to use that module:
> > http://www.ensembl.org/info/data/api.html
> >
> > Cheers,
> > Jun Yin
> > Ph.D. student in U.C.D.
> >
> > Bioinformatics Laboratory
> > Conway Institute
> > University College Dublin
> >
> >
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org
> > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of chirag matkar
> > Sent: Thursday, September 30, 2010 1:21 PM
> > To: bioperl-l at lists.open-bio.org
> > Subject: [Bioperl-l] Retrieve Sequence from Ensembl gene id
> >
> > Hello all,
> > Is there any module to fetch dna sequence data from ensemble gene id?
> >
> > --
> > Regards,
> > Chirag Matkar
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > __________ Information from ESET Smart Security, version of virus
> signature
> > database 5377 (20100818) __________
> >
> > The message was checked by ESET Smart Security.
> >
> > http://www.eset.com
> >
> >
> >
> >
> > __________ Information from ESET Smart Security, version of virus
> signature
> > database 5377 (20100818) __________
> >
> > The message was checked by ESET Smart Security.
> >
> > http://www.eset.com
> >
> >
> >
> > __________ Information from ESET Smart Security, version of virus
> signature
> > database 5377 (20100818) __________
> >
> > The message was checked by ESET Smart Security.
> >
> > http://www.eset.com
> >
> >
> >
> > _______________________________________________
> > 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  Tue Oct  5 06:07:36 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 5 Oct 2010 11:07:36 +0100
Subject: [Bioperl-l] [Gmod-gbrowse] bp_seqfeature_delete.PL - where
	should I submit a patch?
In-Reply-To: <AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>
References: <87782334-E5F5-4DFE-AEBD-64565D5C2F9F@sanger.ac.uk>
	<AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>
Message-ID: <AANLkTinDK93L8KJZbvL-TVriEw4sNT4uJP45BzZiL9W1@mail.gmail.com>

Here is a nice SVN to GIT conversion course:

http://git.or.cz/course/svn.html


On 1 October 2010 16:45, Scott Cain <scott at scottcain.net> wrote:
> Hi Keiran,
>
> Well, I've been told that it is easy for non-bioperl developers to use
> git to commit patches, and as if to prove it, there is a very long
> wiki page on the bioperl wiki describing how to use git:
>
> ?http://www.bioperl.org/wiki/Using_Git
>
> I'm not sure what the right thing is to do; I'm cc'ing the bioperl
> list to get their input.
>
> Scott
>
>
> On Fri, Oct 1, 2010 at 8:46 AM, Keiran Raine <kr2 at sanger.ac.uk> wrote:
>> Hi all,
>>
>> Does anyone know how I should best get push a patch (new functionality) out
>> for this script which is part of the BioPerl package.
>>
>> I've added a 'fast' option which is useful for when you want to delete a
>> whole dataset. ?The problem I was having is I loaded a large set of data
>> which had errors. ?To delete it I tried to use the '-t' option but this
>> continually fails after several hours (eventually runs out of memory). ?To
>> get round this I've added the '-f' flag which tells the script to perform
>> the delete/commit on each individual feature (and associated sub-features)
>> rather than attempt to do them all in a single commit.
>>
>> I've attached the modified version (unfortunately the formatting was kind of
>> knackered so a patch file will be a bit iffy).
>>
>>
>>
>>
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a
>> charity registered in England with number 1021457 and acompany registered in
>> England with number 2742969, whose registeredoffice is 215 Euston Road,
>> London, NW1 2BE.
>>
>>
>> Keiran Raine
>> Senior Computer Biologist
>> The Cancer Genome Project
>> Ext: 7703
>> kr2 at sanger.ac.uk
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Start uncovering the many advantages of virtual appliances
>> and start using them to simplify application deployment and
>> accelerate your shift to cloud computing.
>> http://p.sf.net/sfu/novell-sfdev2dev
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



From dan.bolser at gmail.com  Tue Oct  5 06:36:49 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 5 Oct 2010 11:36:49 +0100
Subject: [Bioperl-l] Question about Bio::Coordinate::Pair
Message-ID: <AANLkTi=fmjWt95GWw=Fe+-WVkhQYcuHPDCNxE6iLpN0w@mail.gmail.com>

Hi,

Can someone describe in a bit more detail the purpose of the Gap
sublocations that are sometimes returned by Bio::Coordinate::Pair [1]?

I found that, according to Bio::Location::Split, if the Match and Gap
sublocations have a different strand, the strand method (called via
Bio::Coordinate::Result) returns undef. This is inconsistent with the
way Bio::Coordinate::Result tends to behave. See the test script and
results below, also pasted here [2].

The question is, can I just toggle the strand of the Gap sublocation
to match that of the Match sublocation? Or does the strand of the Gap
sublocation encode some important but as yet undocumented information?
If the strand of the Gap and Match sublocations are made to match
(within Bio::Coordinate::Pair) this will simplify code that uses
Bio::Coordinate::Pair, making it more consistent, and perhaps help
with some other bugs [3].


Cheers,
Dan.

[1] http://www.bioperl.org/wiki/Module:Bio::Coordinate::Pair
[2] http://www.bioperl.org/wiki/Module_Discussion:Bio::Coordinate::Pair
[3] http://tinyurl.com/36na2cp


#!/usr/bin/perl -w

## Stress test Bio::Coordinate::Pair

use strict;
use Data::Dumper;

use Bio::Location::Simple;
use Bio::Coordinate::Pair;

## A contig
my $ctg = Bio::Location::Simple->
  new( -seq_id => 'ctg',
       -start  =>    1,
       -end    => 1001,
       -strand =>   +1,
     );

## The contigs position on a chromosome (forward)
my $ctg_on_chr_f = Bio::Location::Simple->
  new( -seq_id => 'ctg on chr r',
       -start  =>           5001,
       -end    =>           6001,
       -strand =>             +1,
     );

## The contigs position on a chromosome (reverse)
my $ctg_on_chr_r = Bio::Location::Simple->
  new( -seq_id => 'ctg on chr r',
       -start  =>           5001,
       -end    =>           6001,
       -strand =>             -1,
     );

## Coordinate mapping (forward)
my $agp_f = Bio::Coordinate::Pair->
  new( -in  => $ctg,
       -out => $ctg_on_chr_f
     );

## Coordinate mapping (reverse)
my $agp_r = Bio::Coordinate::Pair->
  new( -in  => $ctg,
       -out => $ctg_on_chr_r
     );



## A match, in contig coordinates...
my $match_on_ctg_4 = Bio::Location::Simple->
  new( -seq_id => 'hit 4',
       -start  =>     925,
       -end    =>    1125,
       -strand =>      -1,
     );

## Map it into chromosome coordinates (forward)
my $match_on_chr_4_f =
  $agp_f->map( $match_on_ctg_4 );

print Dumper $match_on_chr_4_f, "\n";

## Map it into chromosome coordinates (reverse)
my $match_on_chr_4_r =
  $agp_r->map( $match_on_ctg_4 );

print Dumper $match_on_chr_4_r, "\n";

__END__

$VAR1 = bless( {
                 '_sublocations' => [
                                      bless( {
                                               '_strand' => -1,
                                               '_seqid' => 'ctg on chr r',
                                               '_start' => 5925,
                                               '_location_type' => 'EXACT',
                                               '_end' => 6001
                                             },
'Bio::Coordinate::Result::Match' ),
                                      bless( {
                                               '_strand' => -1,
                                               '_seqid' => 'ctg',
                                               '_location_type' => 'EXACT',
                                               '_start' => 1002,
                                               '_end' => 1125
                                             }, 'Bio::Coordinate::Result::Gap' )
                                    ],
                 '_gap' => $VAR1->{'_sublocations'}[1],
                 'strand' => -1,
                 '_match' => $VAR1->{'_sublocations'}[0],
                 '_splittype' => 'JOIN'
               }, 'Bio::Coordinate::Result' );
$VAR2 = '
';
$VAR1 = bless( {
                 '_sublocations' => [
                                      bless( {
                                               '_strand' => 1,
                                               '_seqid' => 'ctg on chr r',
                                               '_start' => 5001,
                                               '_location_type' => 'EXACT',
                                               '_end' => 5077
                                             },
'Bio::Coordinate::Result::Match' ),
                                      bless( {
                                               '_strand' => -1,
                                               '_seqid' => 'ctg',
                                               '_location_type' => 'EXACT',
                                               '_start' => 1002,
                                               '_end' => 1125
                                             }, 'Bio::Coordinate::Result::Gap' )
                                    ],
                 '_gap' => $VAR1->{'_sublocations'}[1],
                 'strand' => 1,
                 '_match' => $VAR1->{'_sublocations'}[0],
                 '_splittype' => 'JOIN'
               }, 'Bio::Coordinate::Result' );
$VAR2 = '
';


From gandipalem at gmail.com  Wed Oct  6 01:35:31 2010
From: gandipalem at gmail.com (gandipalem)
Date: Tue, 5 Oct 2010 22:35:31 -0700 (PDT)
Subject: [Bioperl-l] how to identify least degeneracy for a conserved region
 among all conserved regions in an amino acid alignment?
Message-ID: <29893643.post@talk.nabble.com>


Hi,

I am new to this.

I am working on designing primers for a set of highly diverged  proteins.
I designed degenerate primers for all those proteins manually starting from
multiple sequence alignment to reverse translation of conserved regions. But
this process is very time taking and robust. I would like automate this work
PERL. But I am getting a problem were I am unable to getting the logic "how
to measure/find out the least degeneracy for a conserved region among all
conserved regions of a multiple sequence alignment?".

So can anybody tell about how to find out least degenerated conserved region
in PERL?

Thanking you

Suresh
NBPGR

-- 
View this message in context: http://old.nabble.com/how-to-identify-least-degeneracy-for-a-conserved-region-among-all-conserved-regions-in-an-amino-acid-alignment--tp29893643p29893643.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From dan.bolser at gmail.com  Thu Oct  7 10:22:04 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 7 Oct 2010 15:22:04 +0100
Subject: [Bioperl-l] Installing Bio::DB::BigWig ?
In-Reply-To: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
References: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
Message-ID: <AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>

Trying to run make in .../src/kent/src (also CC'ing BP)

Dan.

# fun for everyone!
irc://irc.perl.org/#gmod

#also good!
irc://irc.freenode.net/#bioperl

On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
> Hi,
>
> I'm having trouble installing Bio::DB::BigWig.
>
> I grabbed the jkucsc code as described here [1] and built it
> successfully after setting 'export MACHTYPE=x86_64'.
>
> I then set 'export KENT_SRC=.../src/kent/src' and called:
> cpan[1]> install Bio::DB::BigWig
>
> The error comes:
> ...
> 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: comparison is always false due to
> limited range of data type
> 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: comparison is always false due to
> limited range of data type
> 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 -m64 -mtune=generic -o
> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> .../src/kent/src/lib/x86_64/jkweb.a -lz
> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
> relocation R_X86_64_32S against `a local symbol' can not be used when
> making a shared object; recompile with -fPIC
> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
> lib/Bio/DB/BigFile.o at
> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
> ?LDS/Bio-BigFile-1.03.tar.gz
> ?./Build -- NOT OK
> ...
>
>
> I tried to 'recompile with -fPIC', but saw further errors about
> missing symbols that I can't fix.
>
> Are there some specific applications of the jkucsc package that I
> should build and install first?
>
>
> Thanks for any help,
> Dan.
>
>
> [1] http://genome.ucsc.edu/admin/git.html
>



From dan.bolser at gmail.com  Thu Oct  7 11:01:50 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 7 Oct 2010 16:01:50 +0100
Subject: [Bioperl-l] Installing Bio::DB::BigWig ?
In-Reply-To: <AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>
References: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
	<AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>
Message-ID: <AANLkTikPF=qo8dv-PXEaU71tU8UtDYXjJ6cC9DB8ranV@mail.gmail.com>

I finally found the solution to this install problem. The error
message 'recompile with -fPIC' isn't referring to the Perl code, but
rather the jkucsc code...

In the directory .../src/kent/src/inc I changed the file common.mk to
add the -fPIC option to the CFLAGS...

[me at box inc]$ diff common.mk~ common.mk
6c6
< CFLAGS=
---
> CFLAGS=-fPIC


I then went back to .../src/kent/src/lib and hit 'make clean && make'.
Finally, going back to cpan, and re-installing Bio::DB::BigWig,
everything worked.


Sorry for the confusion, but it's been a long time since I needed to
install anything 'manually' ;-)

Dan.

# fun for everyone!
irc://irc.perl.org/#gmod

#also good!
irc://irc.freenode.net/#bioperl


On 7 October 2010 15:22, Dan Bolser <dan.bolser at gmail.com> wrote:
> Trying to run make in .../src/kent/src (also CC'ing BP)
>
> Dan.
>
> # fun for everyone!
> irc://irc.perl.org/#gmod
>
> #also good!
> irc://irc.freenode.net/#bioperl
>
> On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
>> Hi,
>>
>> I'm having trouble installing Bio::DB::BigWig.
>>
>> I grabbed the jkucsc code as described here [1] and built it
>> successfully after setting 'export MACHTYPE=x86_64'.
>>
>> I then set 'export KENT_SRC=.../src/kent/src' and called:
>> cpan[1]> install Bio::DB::BigWig
>>
>> The error comes:
>> ...
>> 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: comparison is always false due to
>> limited range of data type
>> 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: comparison is always false due to
>> limited range of data type
>> 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 -m64 -mtune=generic -o
>> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
>> .../src/kent/src/lib/x86_64/jkweb.a -lz
>> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
>> relocation R_X86_64_32S against `a local symbol' can not be used when
>> making a shared object; recompile with -fPIC
>> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
>> collect2: ld returned 1 exit status
>> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
>> lib/Bio/DB/BigFile.o at
>> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
>> ?LDS/Bio-BigFile-1.03.tar.gz
>> ?./Build -- NOT OK
>> ...
>>
>>
>> I tried to 'recompile with -fPIC', but saw further errors about
>> missing symbols that I can't fix.
>>
>> Are there some specific applications of the jkucsc package that I
>> should build and install first?
>>
>>
>> Thanks for any help,
>> Dan.
>>
>>
>> [1] http://genome.ucsc.edu/admin/git.html
>>
>



From lincoln.stein at gmail.com  Thu Oct  7 14:52:09 2010
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Thu, 7 Oct 2010 14:52:09 -0400
Subject: [Bioperl-l] [Gmod-gbrowse] Installing Bio::DB::BigWig ?
In-Reply-To: <AANLkTikPF=qo8dv-PXEaU71tU8UtDYXjJ6cC9DB8ranV@mail.gmail.com>
References: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
	<AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>
	<AANLkTikPF=qo8dv-PXEaU71tU8UtDYXjJ6cC9DB8ranV@mail.gmail.com>
Message-ID: <AANLkTinXx94t-RhyYF8_f4=pdj3YZwF_1Bqfe7oJMAh8@mail.gmail.com>

Sorry, I'll fix the installation documentation to warn people about -fPIC.
This seems to be needed on some platforms and not others.

Lincoln

On Thu, Oct 7, 2010 at 11:01 AM, Dan Bolser <dan.bolser at gmail.com> wrote:

> I finally found the solution to this install problem. The error
> message 'recompile with -fPIC' isn't referring to the Perl code, but
> rather the jkucsc code...
>
> In the directory .../src/kent/src/inc I changed the file common.mk to
> add the -fPIC option to the CFLAGS...
>
> [me at box inc]$ diff common.mk~ common.mk
> 6c6
> < CFLAGS=
> ---
> > CFLAGS=-fPIC
>
>
> I then went back to .../src/kent/src/lib and hit 'make clean && make'.
> Finally, going back to cpan, and re-installing Bio::DB::BigWig,
> everything worked.
>
>
> Sorry for the confusion, but it's been a long time since I needed to
> install anything 'manually' ;-)
>
> Dan.
>
> # fun for everyone!
> irc://irc.perl.org/#gmod
>
> #also good!
> irc://irc.freenode.net/#bioperl
>
>
> On 7 October 2010 15:22, Dan Bolser <dan.bolser at gmail.com> wrote:
> > Trying to run make in .../src/kent/src (also CC'ing BP)
> >
> > Dan.
> >
> > # fun for everyone!
> > irc://irc.perl.org/#gmod
> >
> > #also good!
> > irc://irc.freenode.net/#bioperl
> >
> > On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
> >> Hi,
> >>
> >> I'm having trouble installing Bio::DB::BigWig.
> >>
> >> I grabbed the jkucsc code as described here [1] and built it
> >> successfully after setting 'export MACHTYPE=x86_64'.
> >>
> >> I then set 'export KENT_SRC=.../src/kent/src' and called:
> >> cpan[1]> install Bio::DB::BigWig
> >>
> >> The error comes:
> >> ...
> >> 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: comparison is always false due to
> >> limited range of data type
> >> 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: comparison is always false due to
> >> limited range of data type
> >> 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 -m64 -mtune=generic -o
> >> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> >> .../src/kent/src/lib/x86_64/jkweb.a -lz
> >> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
> >> relocation R_X86_64_32S against `a local symbol' can not be used when
> >> making a shared object; recompile with -fPIC
> >> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
> >> collect2: ld returned 1 exit status
> >> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
> >> lib/Bio/DB/BigFile.o at
> >> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
> >>  LDS/Bio-BigFile-1.03.tar.gz
> >>  ./Build -- NOT OK
> >> ...
> >>
> >>
> >> I tried to 'recompile with -fPIC', but saw further errors about
> >> missing symbols that I can't fix.
> >>
> >> Are there some specific applications of the jkucsc package that I
> >> should build and install first?
> >>
> >>
> >> Thanks for any help,
> >> Dan.
> >>
> >>
> >> [1] http://genome.ucsc.edu/admin/git.html
> >>
> >
>
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



-- 
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  Thu Oct  7 15:58:40 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 7 Oct 2010 20:58:40 +0100
Subject: [Bioperl-l] [Gmod-gbrowse] Installing Bio::DB::BigWig ?
In-Reply-To: <AANLkTinXx94t-RhyYF8_f4=pdj3YZwF_1Bqfe7oJMAh8@mail.gmail.com>
References: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
	<AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>
	<AANLkTikPF=qo8dv-PXEaU71tU8UtDYXjJ6cC9DB8ranV@mail.gmail.com>
	<AANLkTinXx94t-RhyYF8_f4=pdj3YZwF_1Bqfe7oJMAh8@mail.gmail.com>
Message-ID: <AANLkTi=1pnkXFf4XE6K1BgQikf40AnTfbRwzV7CAvnrz@mail.gmail.com>

On 7 October 2010 19:52, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Sorry, I'll fix the installation documentation to warn people about -fPIC.
> This seems to be needed on some platforms and not others.

No problem, thanks for the update. Perhaps it should also be added to
the jkucsc code? any harm in adding -fPIC there anyway?

Here are the details of my box:

ge-002 2.6.18-92.1.22.el5 #1 SMP Tue Dec 16 11:57:43 EST 2008 x86_64
x86_64 x86_64 GNU/Linux

gcc --version
gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)
Copyright (C) 2006 Free Software Foundation, Inc.

perl --version
This is perl, v5.8.8 built for x86_64-linux-thread-multi

jkucsc ... git rev-parse HEAD
cb419933fdc44246e6bac605e65ddc27e7683559


I made some other minor changes to the jkucsc code in an attempt to
get the whole lot to compile:

diff --git a/src/inc/common.mk b/src/inc/common.mk
index 65c9f3c..b7b5389 100644
--- a/src/inc/common.mk
+++ b/src/inc/common.mk
@@ -3,7 +3,7 @@ CC=gcc
 ifeq (${COPT},)
     COPT=-O -g
 endif
-CFLAGS=
+CFLAGS=-fPIC
 HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${M
 HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../i

diff --git a/src/oneShot/smoothWindow/smoothWindow.c b/src/oneShot/smoothWindow/
index b062c91..f0d9c49 100644
--- a/src/oneShot/smoothWindow/smoothWindow.c
+++ b/src/oneShot/smoothWindow/smoothWindow.c
@@ -80,9 +80,9 @@ while (lineFileNext(lf, &line, NULL))
     val = words[1];
     dataValue = strtod(val, &valEnd);
     if ((*val == '\0') || (*valEnd != '\0'))
-       errAbort("Not a valid float at line %d: %s\n", lineCount, words[1]);
+       errAbort("Not a valid float at line %llu: %s\n", lineCount, words[1]);
     if (Offset < 1)
-       errAbort("Illegal offset: %llu at line %d, dataValue: %g", Offset,
+       errAbort("Illegal offset: %llu at line %llu, dataValue: %g", Offset,
            lineCount, dataValue);
     verbose(3, "#\tline: %llu, offset: %llu, data: %g\n",
        lineCount, Offset, dataValue);
diff --git a/src/utils/wigAsciiCrunch/wigAsciiCrunch.c b/src/utils/wigAsciiCrunc
index 04f7692..fc86036 100644
--- a/src/utils/wigAsciiCrunch/wigAsciiCrunch.c
+++ b/src/utils/wigAsciiCrunch/wigAsciiCrunch.c
@@ -103,7 +103,7 @@ while ((wordCount = lineFileChop(lf, words)) != 0)
        if (clFixOverlap)
            {
            minPos = lastOffset;
-           verbose(1, "Removing overlap %d-%d line %d of %s\n",
+           verbose(1, "Removing overlap %ld-%ld line %d of %s\n",
                    lastOffset, offset, lf->lineIx, lf->fileName);
            }
        else


Thanks again,
Dan.

# fun for everyone!
irc://irc.perl.org/#gmod

#also good!
irc://irc.freenode.net/#bioperl


> Lincoln
>
> On Thu, Oct 7, 2010 at 11:01 AM, Dan Bolser <dan.bolser at gmail.com> wrote:
>>
>> I finally found the solution to this install problem. The error
>> message 'recompile with -fPIC' isn't referring to the Perl code, but
>> rather the jkucsc code...
>>
>> In the directory .../src/kent/src/inc I changed the file common.mk to
>> add the -fPIC option to the CFLAGS...
>>
>> [me at box inc]$ diff common.mk~ common.mk
>> 6c6
>> < CFLAGS=
>> ---
>> > CFLAGS=-fPIC
>>
>>
>> I then went back to .../src/kent/src/lib and hit 'make clean && make'.
>> Finally, going back to cpan, and re-installing Bio::DB::BigWig,
>> everything worked.
>>
>>
>> Sorry for the confusion, but it's been a long time since I needed to
>> install anything 'manually' ;-)
>>
>> Dan.
>>
>> # fun for everyone!
>> irc://irc.perl.org/#gmod
>>
>> #also good!
>> irc://irc.freenode.net/#bioperl
>>
>>
>> On 7 October 2010 15:22, Dan Bolser <dan.bolser at gmail.com> wrote:
>> > Trying to run make in .../src/kent/src (also CC'ing BP)
>> >
>> > Dan.
>> >
>> > # fun for everyone!
>> > irc://irc.perl.org/#gmod
>> >
>> > #also good!
>> > irc://irc.freenode.net/#bioperl
>> >
>> > On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
>> >> Hi,
>> >>
>> >> I'm having trouble installing Bio::DB::BigWig.
>> >>
>> >> I grabbed the jkucsc code as described here [1] and built it
>> >> successfully after setting 'export MACHTYPE=x86_64'.
>> >>
>> >> I then set 'export KENT_SRC=.../src/kent/src' and called:
>> >> cpan[1]> install Bio::DB::BigWig
>> >>
>> >> The error comes:
>> >> ...
>> >> 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: comparison is always false due to
>> >> limited range of data type
>> >> 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: comparison is always false due to
>> >> limited range of data type
>> >> 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 -m64 -mtune=generic -o
>> >> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
>> >> .../src/kent/src/lib/x86_64/jkweb.a -lz
>> >> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
>> >> relocation R_X86_64_32S against `a local symbol' can not be used when
>> >> making a shared object; recompile with -fPIC
>> >> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
>> >> collect2: ld returned 1 exit status
>> >> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
>> >> lib/Bio/DB/BigFile.o at
>> >> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
>> >> ?LDS/Bio-BigFile-1.03.tar.gz
>> >> ?./Build -- NOT OK
>> >> ...
>> >>
>> >>
>> >> I tried to 'recompile with -fPIC', but saw further errors about
>> >> missing symbols that I can't fix.
>> >>
>> >> Are there some specific applications of the jkucsc package that I
>> >> should build and install first?
>> >>
>> >>
>> >> Thanks for any help,
>> >> Dan.
>> >>
>> >>
>> >> [1] http://genome.ucsc.edu/admin/git.html
>> >>
>> >
>>
>>
>> ------------------------------------------------------------------------------
>> Beautiful is writing same markup. Internet Explorer 9 supports
>> standards for HTML5, CSS3, SVG 1.1, ?ECMAScript5, and DOM L2 & L3.
>> Spend less time writing and ?rewriting code and more time creating great
>> experiences on the web. Be a part of the beta today.
>> http://p.sf.net/sfu/beautyoftheweb
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> 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 timmcilveen at talktalk.net  Fri Oct  8 05:16:48 2010
From: timmcilveen at talktalk.net (tim)
Date: Fri, 8 Oct 2010 10:16:48 +0100
Subject: [Bioperl-l] Getting BioPerl from Github
Message-ID: <201010081016.48460.timmcilveen@talktalk.net>

Hi,
I'm not an experienced Linux user but have been trying to download Bioperl via 
GitHub as I was getting lots of errors using the package installer. It was 
suggested by a list user that I use GitHub instead.

I installed Git using Yast.

I visited this page:
http://www.bioperl.org/wiki/Using_Git 

and used the installation instructions:
$ git clone git://github.com/bioperl/bioperl-live.git
bash: $ export PERL5LIB="$HOME/src/bioperl-live:$PERL5LIB"

I tested the code:
$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;' 
but the install didn't work.
Here is the ouput from my terminal.
tim at linux-oxgy:~> su
Password: 
linux-oxgy:/home/tim # git clone git://github.com/bioperl/bioperl-live.git
Initialized empty Git repository in /home/tim/bioperl-live/.git/
remote: Counting objects: 88288, done.
remote: Compressing objects: 100% (23829/23829), done.
remote: Total 88288 (delta 66885), reused 85264 (delta 63993)
Receiving objects: 100% (88288/88288), 138.20 MiB | 1.19 MiB/s, done.
Resolving deltas: 100% (66885/66885), done.
linux-oxgy:/home/tim # bash
linux-oxgy:/home/tim # export PERL5LIB="$HOME/src/biooperl-live:$PERL5LIB"
linux-oxgy:/home/tim # perl -MBIO::Perl -le 'print Bio::Perl->VERSION;'
Can't locate BIO/Perl.pm in @INC (@INC contains: /root/src/biooperl-live 
/usr/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi 
/usr/lib/perl5/site_perl/5.12.1 /usr/lib/perl5/vendor_perl/5.12.1/x86_64-
linux-thread-multi /usr/lib/perl5/vendor_perl/5.12.1 
/usr/lib/perl5/5.12.1/x86_64-linux-thread-multi /usr/lib/perl5/5.12.1 .).
BEGIN failed--compilation aborted.
linux-oxgy:/home/tim # 

I assume that something has went wrong at this step:
To use this 'live' version of BioPerl, you need to install it (simply tell 
Perl where to find it). Assuming you checked out the code above into 
$HOME/src; set this in your .bash_profile, .profile, or .cshrc: 

How do I set things up so that the code is in $HOME/src? Where is it likely to 
be if I carried out the installation as root?

Any help would be appreciated.

Thanks,
Tim




From scott at scottcain.net  Fri Oct  8 09:14:24 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 8 Oct 2010 09:14:24 -0400
Subject: [Bioperl-l] Getting BioPerl from Github
In-Reply-To: <201010081016.48460.timmcilveen@talktalk.net>
References: <201010081016.48460.timmcilveen@talktalk.net>
Message-ID: <AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>

Hi Tim,

Could it just be that you misspelled "bioperl-live" (as biooperl-live)
in your export statement?

Scott


On Fri, Oct 8, 2010 at 5:16 AM, tim <timmcilveen at talktalk.net> wrote:
> Hi,
> I'm not an experienced Linux user but have been trying to download Bioperl via
> GitHub as I was getting lots of errors using the package installer. It was
> suggested by a list user that I use GitHub instead.
>
> I installed Git using Yast.
>
> I visited this page:
> http://www.bioperl.org/wiki/Using_Git
>
> and used the installation instructions:
> $ git clone git://github.com/bioperl/bioperl-live.git
> bash: $ export PERL5LIB="$HOME/src/bioperl-live:$PERL5LIB"
>
> I tested the code:
> $ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
> but the install didn't work.
> Here is the ouput from my terminal.
> tim at linux-oxgy:~> su
> Password:
> linux-oxgy:/home/tim # git clone git://github.com/bioperl/bioperl-live.git
> Initialized empty Git repository in /home/tim/bioperl-live/.git/
> remote: Counting objects: 88288, done.
> remote: Compressing objects: 100% (23829/23829), done.
> remote: Total 88288 (delta 66885), reused 85264 (delta 63993)
> Receiving objects: 100% (88288/88288), 138.20 MiB | 1.19 MiB/s, done.
> Resolving deltas: 100% (66885/66885), done.
> linux-oxgy:/home/tim # bash
> linux-oxgy:/home/tim # export PERL5LIB="$HOME/src/biooperl-live:$PERL5LIB"
> linux-oxgy:/home/tim # perl -MBIO::Perl -le 'print Bio::Perl->VERSION;'
> Can't locate BIO/Perl.pm in @INC (@INC contains: /root/src/biooperl-live
> /usr/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi
> /usr/lib/perl5/site_perl/5.12.1 /usr/lib/perl5/vendor_perl/5.12.1/x86_64-
> linux-thread-multi /usr/lib/perl5/vendor_perl/5.12.1
> /usr/lib/perl5/5.12.1/x86_64-linux-thread-multi /usr/lib/perl5/5.12.1 .).
> BEGIN failed--compilation aborted.
> linux-oxgy:/home/tim #
>
> I assume that something has went wrong at this step:
> To use this 'live' version of BioPerl, you need to install it (simply tell
> Perl where to find it). Assuming you checked out the code above into
> $HOME/src; set this in your .bash_profile, .profile, or .cshrc:
>
> How do I set things up so that the code is in $HOME/src? Where is it likely to
> be if I carried out the installation as root?
>
> Any help would be appreciated.
>
> Thanks,
> Tim
>
>
> _______________________________________________
> 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 pjayaraman at mcw.edu  Thu Oct  7 16:46:19 2010
From: pjayaraman at mcw.edu (Jayaraman, Pushkala)
Date: Thu, 7 Oct 2010 15:46:19 -0500
Subject: [Bioperl-l] FW: bp_genbank2gff3- Unflattening error
Message-ID: <1448A38A42714048B9C53E473E13CCF00379E83D@davis.hmgc.mcw.edu>

I apologize, 

I should have sent it to the forum first.. 

 

 

FYI.. 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala 
Sent: Thursday, October 07, 2010 3:07 PM
To: 'cjm at fruitfly.org'
Subject: bp_genbank2gff3- Unflattening error

 

Hi Chris, 

I saw your response in a  post about Unflattener.pm here;

http://generic-model-organism-system-database.450254.n5.nabble.com/genba
nk-to-gff3-conversion-problem-td460065.html

 

hence decided to fwd this to you.. 

I have no clue what is going on.. 

 

NT_010799 Unflattening error:

Details: 

------------- EXCEPTION -------------

MSG: PROBLEM, SEVERITY==1

Container feature does not spatially contain subfeature. Perhaps this is
a dicistronic gene? I am expanding the parent feature

SF [Bio::SeqFeature::Generic=HASH(0x149297a0)]: gene; CCL14

 

SF [Bio::SeqFeature::Generic=HASH(0x1492d860)]: mRNA; CCL14; chemokine
(C-C motif) ligand 14 (CCL14), transcript variant 1

 

STACK Bio::SeqFeature::Tools::Unflattener::problem
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:952

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_group
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:2170

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_groups
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1798

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1503

STACK (eval) /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:915

STACK main::unflatten_seq
/usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:914

STACK toplevel /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:411

 

 

 

 

 

I even get another error under Unflattener.pm in another region.. this
is how it is described:

 

PROBLEM:

NT_024524 Unflattening error:

Details: 

------------- EXCEPTION -------------

MSG: 1 there is a conflict with exons; there was an explicitly stated
exon with location 22748456..22748502, yet I cannot generate this exon
from the supplied mRNA locations

 

1 There are some inferred exons that are not in the explicit exon list;
they are the exons at locations:

10982777..10983033

9516278..9517506

1225346..1225429

33491613..33491816

58797942..58798087

7323184..7323367

21253638..21253755

59172140..59172196

54309290..54310329

8988942..8989171

26569087..26569218

6479986..6480032

32266760..32267377

.....

 

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1631

STACK (eval) /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:915

STACK main::unflatten_seq
/usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:914

STACK toplevel /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:411

-------------------------------------

 

 

I do not know what is going on.. is it something that the data has or
something that I am doing wrong? 

the section of the genbank file that gives out this error is pasted
below.. 

 

 

 

 

Please help,

 

 

 

 

 

gene            complement(9047672..9065992)

                     /gene="CCL14-CCL15"

                     /note="chemokine ligand 14, chemokine ligand 15

                     transcription unit"

                     /db_xref="GeneID:348249"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004166.3"

                     /db_xref="GI:34335177"

                     /db_xref="GeneID:6358"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032964.2"

                     /db_xref="GI:34335178"

                     /db_xref="GeneID:6359"

                     /db_xref="MIM:601393"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032962.2"

                     /db_xref="GI:34335175"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004167.3"

                     /db_xref="GI:34335181"

                     /db_xref="GeneID:6359"

                     /db_xref="HGNC:10613"

                     /db_xref="MIM:601393"

     gene            complement(9047672..9050719)

                     /gene="CCL14"

                     /note="chemokine (C-C motif) ligand 14; synonyms:
CC-1,

                     CC-3, CKb1, MCIF, NCC2, SY14, HCC-1, HCC-3, NCC-2,
SCYL2,

                     SCYA14"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050719))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 3"

                     /transcript_id="NM_032963.2"

                     /db_xref="GI:34335176"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     STS             9047707..9047892

                     /standard_name="STS-H22017"

                     /db_xref="UniSTS:13833"

     STS             9047767..9047885

                     /standard_name="GDB:607751"

                     /db_xref="UniSTS:158278"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_116739.1"

                     /db_xref="GI:14589961"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_004157.1"

                     /db_xref="GI:4759070"

                     /db_xref="CCDS:CCDS32624.1"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 2

                     precursor"

                     /protein_id="NP_116738.1"

                     /db_xref="GI:14589959"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

 

 

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala [mailto:pjayaraman at mcw.edu] 
Sent: Thursday, October 07, 2010 2:56 PM
To: gmod-devel at lists.sourceforge.net
Cc: gmod-gbrowse at lists.sourceforge.net
Subject: [Gmod-gbrowse] FW: bp_genbank2gff3- Unflattening error

 

I am providing the section of the genbank file here as I am not able to
attach the entire genbank file here(duh!):

 

     gene            complement(9047672..9065992)

                     /gene="CCL14-CCL15"

                     /note="chemokine ligand 14, chemokine ligand 15

                     transcription unit"

                     /db_xref="GeneID:348249"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004166.3"

                     /db_xref="GI:34335177"

                     /db_xref="GeneID:6358"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032964.2"

                     /db_xref="GI:34335178"

                     /db_xref="GeneID:6359"

                     /db_xref="MIM:601393"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032962.2"

                     /db_xref="GI:34335175"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004167.3"

                     /db_xref="GI:34335181"

                     /db_xref="GeneID:6359"

                     /db_xref="HGNC:10613"

                     /db_xref="MIM:601393"

     gene            complement(9047672..9050719)

                     /gene="CCL14"

                     /note="chemokine (C-C motif) ligand 14; synonyms:
CC-1,

                     CC-3, CKb1, MCIF, NCC2, SY14, HCC-1, HCC-3, NCC-2,
SCYL2,

                     SCYA14"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050719))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 3"

                     /transcript_id="NM_032963.2"

                     /db_xref="GI:34335176"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     STS             9047707..9047892

                     /standard_name="STS-H22017"

                     /db_xref="UniSTS:13833"

     STS             9047767..9047885

                     /standard_name="GDB:607751"

                     /db_xref="UniSTS:158278"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_116739.1"

                     /db_xref="GI:14589961"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_004157.1"

                     /db_xref="GI:4759070"

                     /db_xref="CCDS:CCDS32624.1"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 2

                     precursor"

                     /protein_id="NP_116738.1"

                     /db_xref="GI:14589959"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

 

 

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala 
Sent: Thursday, October 07, 2010 2:43 PM
To: gmod-gbrowse at lists.sourceforge.net
Subject: bp_genbank2gff3- Unflattening error

 

Hello, 

Running the bp_genbank2gff3.pm gives me:

 

NT_010799 Unflattening error:

Details: 

------------- EXCEPTION -------------

MSG: PROBLEM, SEVERITY==1

Container feature does not spatially contain subfeature. Perhaps this is
a dicistronic gene? I am expanding the parent feature

SF [Bio::SeqFeature::Generic=HASH(0x149297a0)]: gene; CCL14

 

SF [Bio::SeqFeature::Generic=HASH(0x1492d860)]: mRNA; CCL14; chemokine
(C-C motif) ligand 14 (CCL14), transcript variant 1

 

STACK Bio::SeqFeature::Tools::Unflattener::problem
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:952

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_group
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:2170

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_groups
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1798

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1503

STACK (eval) /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:915

STACK main::unflatten_seq
/usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:914

STACK toplevel /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:411

 

 

 

Ive never seen this error before and have no clue how to resolve this as
the input is a .gbk file and the script is a BIOPerl script.  Because we
seem to be losing a  lot of gene information in a particular contig. 

Am I doing anything wrong?

 

Thanks,

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

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From kai.blin at biotech.uni-tuebingen.de  Fri Oct  8 09:35:02 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Fri, 08 Oct 2010 15:35:02 +0200
Subject: [Bioperl-l] Getting BioPerl from Github
In-Reply-To: <AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>
References: <201010081016.48460.timmcilveen@talktalk.net>
	<AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>
Message-ID: <4CAF1E06.2090206@biotech.uni-tuebingen.de>

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

On 2010-10-08 15:14, Scott Cain wrote:

> Could it just be that you misspelled "bioperl-live" (as biooperl-live)
> in your export statement?

Looks mighty suspicious, indeed. Good Catch.

Also, if you install into your home directory, there's no reason at all
to do this as root, and you probably never want to do the git clone as
root. There more stuff you do as root, the more likely you're going to
shoot yourself into the foot. :)

Cheers,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universit?t T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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usoRUwv/eHjEFciz4xp/t+CWkmlQ1YyPNA329FKTBgl1QxTuUxGQnXI+dksMmbra
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From David.Messina at sbc.su.se  Fri Oct  8 10:24:12 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 8 Oct 2010 16:24:12 +0200
Subject: [Bioperl-l] Getting BioPerl from Github
In-Reply-To: <AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>
References: <201010081016.48460.timmcilveen@talktalk.net>
	<AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>
Message-ID: <65D590FA-9102-4406-AA86-462CF7EFFD0C@sbc.su.se>


> Could it just be that you misspelled "bioperl-live" (as biooperl-live)
> in your export statement?


I think also the capitalization in the following statement is important. That is, -MBio::Perl not -MBIO::Perl

>> linux-oxgy:/home/tim # perl -MBIO::Perl -le 'print Bio::Perl->VERSION;'



Dave




From David.Messina at sbc.su.se  Fri Oct  8 10:37:27 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 8 Oct 2010 16:37:27 +0200
Subject: [Bioperl-l] Bio::Matrix::MatrixI
In-Reply-To: <35D95AF6C5D146479C328BBBA554FB76028C367E@mailf.lumcnet.prod.intern>
References: <35D95AF6C5D146479C328BBBA554FB76028C367E@mailf.lumcnet.prod.intern>
Message-ID: <9826175D-4FD0-44CD-9E29-348176A2C117@sbc.su.se>

Hi Anna,

You will want to use Bio::Matrix::IO to read in a Phylip matrix.

Something like:

use Bio::Matrix::IO;
my $parser = Bio::Matrix::IO->new(-format   => 'phylip',
                                  -file     => 'phylipdist.out');
my $matrix = $parser->next_matrix;


Dave


On Sep 29, 2010, at 15:28 , <A.Vakhrusheva at lumc.nl> wrote:

> Bio::Matrix::MatrixI
> 
> I have a question concerning this interface.
> 
> I want to calculate p distances matrix, but what format is acceptable
> for input? Phylip doesn't work
> 
> Anna 



From dan.bolser at gmail.com  Fri Oct  8 11:04:44 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Fri, 8 Oct 2010 16:04:44 +0100
Subject: [Bioperl-l] Question about Bio::Coordinate::Pair
In-Reply-To: <AANLkTi=fmjWt95GWw=Fe+-WVkhQYcuHPDCNxE6iLpN0w@mail.gmail.com>
References: <AANLkTi=fmjWt95GWw=Fe+-WVkhQYcuHPDCNxE6iLpN0w@mail.gmail.com>
Message-ID: <AANLkTim3fvNkvaXftcvRb0SnhATOdugtr3Z=2v8HTxrU@mail.gmail.com>

Well... I tried to toggle the strand of the gap sublocation to match
that of the match sublocation, and overall I ended up failing one test
within t/Coordinate/CoordinateMapper.t, test number 55 (line 119)...

This test actually tests for the strandedness of the gap sublocation
that I'm specifically changing because it leads to the 'unexpected'
(or at least, 'inconsistent') behaviour that I'm calling a bug (test
55 is at the end, with enough preceding context to reproduce it):

# propepide
my $match1 = Bio::Location::Simple->new
    (-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
# peptide
my $match2 = Bio::Location::Simple->new
    (-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );

ok my $pair = Bio::Coordinate::Pair->new(-in => $match1,
					 -out => $match2,
					 -negative => 0, # false, default
					);

...

#
# partial match = gap & match
#
$pos2 = Bio::Location::Simple->new
    (-start => 20, -end => 22, -strand=> -1 );

ok $res = $pair->map($pos2);

...

is $res->gap->strand, -1; # TEST 55.  Fails when I 'fix' Bio::Coordinate::Pair



In the absence of any other information, can I take this to mean that
the strand of the gap sublocations are not used for anything
significant?


Cheers,
Dan.



On 5 October 2010 11:36, Dan Bolser <dan.bolser at gmail.com> wrote:
> Hi,
>
> Can someone describe in a bit more detail the purpose of the Gap
> sublocations that are sometimes returned by Bio::Coordinate::Pair [1]?
>
> I found that, according to Bio::Location::Split, if the Match and Gap
> sublocations have a different strand, the strand method (called via
> Bio::Coordinate::Result) returns undef. This is inconsistent with the
> way Bio::Coordinate::Result tends to behave. See the test script and
> results below, also pasted here [2].
>
> The question is, can I just toggle the strand of the Gap sublocation
> to match that of the Match sublocation? Or does the strand of the Gap
> sublocation encode some important but as yet undocumented information?
> If the strand of the Gap and Match sublocations are made to match
> (within Bio::Coordinate::Pair) this will simplify code that uses
> Bio::Coordinate::Pair, making it more consistent, and perhaps help
> with some other bugs [3].
>
>
> Cheers,
> Dan.
>
> [1] http://www.bioperl.org/wiki/Module:Bio::Coordinate::Pair
> [2] http://www.bioperl.org/wiki/Module_Discussion:Bio::Coordinate::Pair
> [3] http://tinyurl.com/36na2cp
>
>
> #!/usr/bin/perl -w
>
> ## Stress test Bio::Coordinate::Pair
>
> use strict;
> use Data::Dumper;
>
> use Bio::Location::Simple;
> use Bio::Coordinate::Pair;
>
> ## A contig
> my $ctg = Bio::Location::Simple->
> ?new( -seq_id => 'ctg',
> ? ? ? -start ?=> ? ?1,
> ? ? ? -end ? ?=> 1001,
> ? ? ? -strand => ? +1,
> ? ? );
>
> ## The contigs position on a chromosome (forward)
> my $ctg_on_chr_f = Bio::Location::Simple->
> ?new( -seq_id => 'ctg on chr r',
> ? ? ? -start ?=> ? ? ? ? ? 5001,
> ? ? ? -end ? ?=> ? ? ? ? ? 6001,
> ? ? ? -strand => ? ? ? ? ? ? +1,
> ? ? );
>
> ## The contigs position on a chromosome (reverse)
> my $ctg_on_chr_r = Bio::Location::Simple->
> ?new( -seq_id => 'ctg on chr r',
> ? ? ? -start ?=> ? ? ? ? ? 5001,
> ? ? ? -end ? ?=> ? ? ? ? ? 6001,
> ? ? ? -strand => ? ? ? ? ? ? -1,
> ? ? );
>
> ## Coordinate mapping (forward)
> my $agp_f = Bio::Coordinate::Pair->
> ?new( -in ?=> $ctg,
> ? ? ? -out => $ctg_on_chr_f
> ? ? );
>
> ## Coordinate mapping (reverse)
> my $agp_r = Bio::Coordinate::Pair->
> ?new( -in ?=> $ctg,
> ? ? ? -out => $ctg_on_chr_r
> ? ? );
>
>
>
> ## A match, in contig coordinates...
> my $match_on_ctg_4 = Bio::Location::Simple->
> ?new( -seq_id => 'hit 4',
> ? ? ? -start ?=> ? ? 925,
> ? ? ? -end ? ?=> ? ?1125,
> ? ? ? -strand => ? ? ?-1,
> ? ? );
>
> ## Map it into chromosome coordinates (forward)
> my $match_on_chr_4_f =
> ?$agp_f->map( $match_on_ctg_4 );
>
> print Dumper $match_on_chr_4_f, "\n";
>
> ## Map it into chromosome coordinates (reverse)
> my $match_on_chr_4_r =
> ?$agp_r->map( $match_on_ctg_4 );
>
> print Dumper $match_on_chr_4_r, "\n";
>
> __END__
>
> $VAR1 = bless( {
> ? ? ? ? ? ? ? ? '_sublocations' => [
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg on chr r',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 5925,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 6001
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? },
> 'Bio::Coordinate::Result::Match' ),
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 1002,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 1125
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result::Gap' )
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?],
> ? ? ? ? ? ? ? ? '_gap' => $VAR1->{'_sublocations'}[1],
> ? ? ? ? ? ? ? ? 'strand' => -1,
> ? ? ? ? ? ? ? ? '_match' => $VAR1->{'_sublocations'}[0],
> ? ? ? ? ? ? ? ? '_splittype' => 'JOIN'
> ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result' );
> $VAR2 = '
> ';
> $VAR1 = bless( {
> ? ? ? ? ? ? ? ? '_sublocations' => [
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => 1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg on chr r',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 5001,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 5077
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? },
> 'Bio::Coordinate::Result::Match' ),
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 1002,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 1125
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result::Gap' )
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?],
> ? ? ? ? ? ? ? ? '_gap' => $VAR1->{'_sublocations'}[1],
> ? ? ? ? ? ? ? ? 'strand' => 1,
> ? ? ? ? ? ? ? ? '_match' => $VAR1->{'_sublocations'}[0],
> ? ? ? ? ? ? ? ? '_splittype' => 'JOIN'
> ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result' );
> $VAR2 = '
> ';
>



From cjfields at illinois.edu  Fri Oct  8 11:16:21 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 8 Oct 2010 10:16:21 -0500
Subject: [Bioperl-l] Bio::Matrix::MatrixI
In-Reply-To: <9826175D-4FD0-44CD-9E29-348176A2C117@sbc.su.se>
References: <35D95AF6C5D146479C328BBBA554FB76028C367E@mailf.lumcnet.prod.intern>
	<9826175D-4FD0-44CD-9E29-348176A2C117@sbc.su.se>
Message-ID: <D4BC1FC6-2A66-4F26-ABF3-EB6D6CD65FE9@illinois.edu>

Correct, MatrixI (and pretty much any other module 'FooI') are interfaces for API consistency.

chris

On Oct 8, 2010, at 9:37 AM, Dave Messina wrote:

> Hi Anna,
> 
> You will want to use Bio::Matrix::IO to read in a Phylip matrix.
> 
> Something like:
> 
> use Bio::Matrix::IO;
> my $parser = Bio::Matrix::IO->new(-format   => 'phylip',
>                                  -file     => 'phylipdist.out');
> my $matrix = $parser->next_matrix;
> 
> 
> Dave
> 
> 
> On Sep 29, 2010, at 15:28 , <A.Vakhrusheva at lumc.nl> wrote:
> 
>> Bio::Matrix::MatrixI
>> 
>> I have a question concerning this interface.
>> 
>> I want to calculate p distances matrix, but what format is acceptable
>> for input? Phylip doesn't work
>> 
>> Anna 
> 
> _______________________________________________
> 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  Fri Oct  8 11:57:38 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Fri, 8 Oct 2010 16:57:38 +0100
Subject: [Bioperl-l] Question about Bio::Coordinate::Pair
In-Reply-To: <AANLkTim3fvNkvaXftcvRb0SnhATOdugtr3Z=2v8HTxrU@mail.gmail.com>
References: <AANLkTi=fmjWt95GWw=Fe+-WVkhQYcuHPDCNxE6iLpN0w@mail.gmail.com>
	<AANLkTim3fvNkvaXftcvRb0SnhATOdugtr3Z=2v8HTxrU@mail.gmail.com>
Message-ID: <AANLkTimFqsJbpZ802GzKPUAnhKHUgyjRvyg3bJNPEQNL@mail.gmail.com>

Actually, I changed the Strand of the gap in a few more places [1],
and now there are a total of 4 failed tests, however, they all appear
to be of the same form as the one reported below:


not ok 84
#   Failed test at t/Coordinate/CoordinateMapper.t line 229.
#          got: '1'
#     expected: '-1'

not ok 93
#   Failed test at t/Coordinate/CoordinateMapper.t line 246.
#          got: '1'
#     expected: '-1'

not ok 99
#   Failed test at t/Coordinate/CoordinateMapper.t line 262.
#          got: '1'
#     expected: '-1'

not ok 102
#   Failed test at t/Coordinate/CoordinateMapper.t line 265.
#          got: '1'
#     expected: '-1'


So now you know.


Dan.

[1] http://github.com/dbolser/bioperl-live/tree/dbolser_bio_coordinate_pair_tests

On 8 October 2010 16:04, Dan Bolser <dan.bolser at gmail.com> wrote:
> Well... I tried to toggle the strand of the gap sublocation to match
> that of the match sublocation, and overall I ended up failing one test
> within t/Coordinate/CoordinateMapper.t, test number 55 (line 119)...
>
> This test actually tests for the strandedness of the gap sublocation
> that I'm specifically changing because it leads to the 'unexpected'
> (or at least, 'inconsistent') behaviour that I'm calling a bug (test
> 55 is at the end, with enough preceding context to reproduce it):
>
> # propepide
> my $match1 = Bio::Location::Simple->new
> ? ?(-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
> # peptide
> my $match2 = Bio::Location::Simple->new
> ? ?(-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );
>
> ok my $pair = Bio::Coordinate::Pair->new(-in => $match1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -out => $match2,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -negative => 0, # false, default
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?);
>
> ...
>
> #
> # partial match = gap & match
> #
> $pos2 = Bio::Location::Simple->new
> ? ?(-start => 20, -end => 22, -strand=> -1 );
>
> ok $res = $pair->map($pos2);
>
> ...
>
> is $res->gap->strand, -1; # TEST 55. ?Fails when I 'fix' Bio::Coordinate::Pair
>
>
>
> In the absence of any other information, can I take this to mean that
> the strand of the gap sublocations are not used for anything
> significant?
>
>
> Cheers,
> Dan.
>
>
>
> On 5 October 2010 11:36, Dan Bolser <dan.bolser at gmail.com> wrote:
>> Hi,
>>
>> Can someone describe in a bit more detail the purpose of the Gap
>> sublocations that are sometimes returned by Bio::Coordinate::Pair [1]?
>>
>> I found that, according to Bio::Location::Split, if the Match and Gap
>> sublocations have a different strand, the strand method (called via
>> Bio::Coordinate::Result) returns undef. This is inconsistent with the
>> way Bio::Coordinate::Result tends to behave. See the test script and
>> results below, also pasted here [2].
>>
>> The question is, can I just toggle the strand of the Gap sublocation
>> to match that of the Match sublocation? Or does the strand of the Gap
>> sublocation encode some important but as yet undocumented information?
>> If the strand of the Gap and Match sublocations are made to match
>> (within Bio::Coordinate::Pair) this will simplify code that uses
>> Bio::Coordinate::Pair, making it more consistent, and perhaps help
>> with some other bugs [3].
>>
>>
>> Cheers,
>> Dan.
>>
>> [1] http://www.bioperl.org/wiki/Module:Bio::Coordinate::Pair
>> [2] http://www.bioperl.org/wiki/Module_Discussion:Bio::Coordinate::Pair
>> [3] http://tinyurl.com/36na2cp
>>
>>
>> #!/usr/bin/perl -w
>>
>> ## Stress test Bio::Coordinate::Pair
>>
>> use strict;
>> use Data::Dumper;
>>
>> use Bio::Location::Simple;
>> use Bio::Coordinate::Pair;
>>
>> ## A contig
>> my $ctg = Bio::Location::Simple->
>> ?new( -seq_id => 'ctg',
>> ? ? ? -start ?=> ? ?1,
>> ? ? ? -end ? ?=> 1001,
>> ? ? ? -strand => ? +1,
>> ? ? );
>>
>> ## The contigs position on a chromosome (forward)
>> my $ctg_on_chr_f = Bio::Location::Simple->
>> ?new( -seq_id => 'ctg on chr r',
>> ? ? ? -start ?=> ? ? ? ? ? 5001,
>> ? ? ? -end ? ?=> ? ? ? ? ? 6001,
>> ? ? ? -strand => ? ? ? ? ? ? +1,
>> ? ? );
>>
>> ## The contigs position on a chromosome (reverse)
>> my $ctg_on_chr_r = Bio::Location::Simple->
>> ?new( -seq_id => 'ctg on chr r',
>> ? ? ? -start ?=> ? ? ? ? ? 5001,
>> ? ? ? -end ? ?=> ? ? ? ? ? 6001,
>> ? ? ? -strand => ? ? ? ? ? ? -1,
>> ? ? );
>>
>> ## Coordinate mapping (forward)
>> my $agp_f = Bio::Coordinate::Pair->
>> ?new( -in ?=> $ctg,
>> ? ? ? -out => $ctg_on_chr_f
>> ? ? );
>>
>> ## Coordinate mapping (reverse)
>> my $agp_r = Bio::Coordinate::Pair->
>> ?new( -in ?=> $ctg,
>> ? ? ? -out => $ctg_on_chr_r
>> ? ? );
>>
>>
>>
>> ## A match, in contig coordinates...
>> my $match_on_ctg_4 = Bio::Location::Simple->
>> ?new( -seq_id => 'hit 4',
>> ? ? ? -start ?=> ? ? 925,
>> ? ? ? -end ? ?=> ? ?1125,
>> ? ? ? -strand => ? ? ?-1,
>> ? ? );
>>
>> ## Map it into chromosome coordinates (forward)
>> my $match_on_chr_4_f =
>> ?$agp_f->map( $match_on_ctg_4 );
>>
>> print Dumper $match_on_chr_4_f, "\n";
>>
>> ## Map it into chromosome coordinates (reverse)
>> my $match_on_chr_4_r =
>> ?$agp_r->map( $match_on_ctg_4 );
>>
>> print Dumper $match_on_chr_4_r, "\n";
>>
>> __END__
>>
>> $VAR1 = bless( {
>> ? ? ? ? ? ? ? ? '_sublocations' => [
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg on chr r',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 5925,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 6001
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? },
>> 'Bio::Coordinate::Result::Match' ),
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 1002,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 1125
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result::Gap' )
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?],
>> ? ? ? ? ? ? ? ? '_gap' => $VAR1->{'_sublocations'}[1],
>> ? ? ? ? ? ? ? ? 'strand' => -1,
>> ? ? ? ? ? ? ? ? '_match' => $VAR1->{'_sublocations'}[0],
>> ? ? ? ? ? ? ? ? '_splittype' => 'JOIN'
>> ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result' );
>> $VAR2 = '
>> ';
>> $VAR1 = bless( {
>> ? ? ? ? ? ? ? ? '_sublocations' => [
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => 1,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg on chr r',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 5001,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 5077
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? },
>> 'Bio::Coordinate::Result::Match' ),
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 1002,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 1125
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result::Gap' )
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?],
>> ? ? ? ? ? ? ? ? '_gap' => $VAR1->{'_sublocations'}[1],
>> ? ? ? ? ? ? ? ? 'strand' => 1,
>> ? ? ? ? ? ? ? ? '_match' => $VAR1->{'_sublocations'}[0],
>> ? ? ? ? ? ? ? ? '_splittype' => 'JOIN'
>> ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result' );
>> $VAR2 = '
>> ';
>>
>



From mauricio at open-bio.org  Fri Oct  8 12:47:56 2010
From: mauricio at open-bio.org (Mauricio Herrera Cuadra)
Date: Fri, 08 Oct 2010 11:47:56 -0500
Subject: [Bioperl-l] Pdoc documentation & test coverage updated
Message-ID: <4CAF4B3C.1060001@open-bio.org>

The cron scripts that generate the live code Pdoc documentation and the 
test coverage reports are now updated to pull from the GitHub 
repository. Please let me know if you notice anything wonky.

Mauricio.


From cjfields at illinois.edu  Fri Oct  8 16:13:08 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 8 Oct 2010 15:13:08 -0500
Subject: [Bioperl-l] Pdoc documentation & test coverage updated
In-Reply-To: <4CAF4B3C.1060001@open-bio.org>
References: <4CAF4B3C.1060001@open-bio.org>
Message-ID: <DA23CAB1-6A1C-4EC5-9EEF-06ED68C35AE9@illinois.edu>

Thanks Mauricio!  That completely feel off my radar.

chris

On Oct 8, 2010, at 11:47 AM, Mauricio Herrera Cuadra wrote:

> The cron scripts that generate the live code Pdoc documentation and the test coverage reports are now updated to pull from the GitHub repository. Please let me know if you notice anything wonky.
> 
> Mauricio.
> _______________________________________________
> 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  Fri Oct  8 17:08:40 2010
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 08 Oct 2010 14:08:40 -0700
Subject: [Bioperl-l] Pdoc documentation & test coverage updated
In-Reply-To: <DA23CAB1-6A1C-4EC5-9EEF-06ED68C35AE9@illinois.edu>
References: <4CAF4B3C.1060001@open-bio.org>
	<DA23CAB1-6A1C-4EC5-9EEF-06ED68C35AE9@illinois.edu>
Message-ID: <4CAF8858.5090302@bioperl.org>

nice -- thanks for doing that Mauricio.


Chris Fields wrote, On 10/8/10 1:13 PM:
> Thanks Mauricio!  That completely feel off my radar.
>
> chris
>
> On Oct 8, 2010, at 11:47 AM, Mauricio Herrera Cuadra wrote:
>
>> The cron scripts that generate the live code Pdoc documentation and the test coverage reports are now updated to pull from the GitHub repository. Please let me know if you notice anything wonky.
>>
>> Mauricio.
>> _______________________________________________
>> 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

-- 
Jason Stajich
jason at bioperl.org



From avilella at gmail.com  Tue Oct 12 08:34:14 2010
From: avilella at gmail.com (Albert Vilella)
Date: Tue, 12 Oct 2010 13:34:14 +0100
Subject: [Bioperl-l] possible bug in Bio::SeqIO::fastq
Message-ID: <AANLkTi=XNY9skUoTpJYJ=cp8wcpRPiskjFeuc3RquDUk@mail.gmail.com>

Hi,

I found what seems to me could be a bug in the fastq module, which is
that if the
last line of the raw_quality section is a single "0" character, a
"if($line)" isn't
returning it properly, because it should be "if(defined $line)" instead.

Find here a test case and the line in question:

----
use strict;
use Bio::SeqIO;

my $consio = Bio::SeqIO->new
  (-format => 'fastq',
   -fh => \*DATA);

my $onelineconsout = Bio::SeqIO->new
  (-format => 'fastq',
   -fh => \*STDOUT);

while (my $seq = $consio->next_seq) {
  next if ($seq->seq =~ /^n+$/);
  $seq->seq(uc($seq->seq));
  $onelineconsout->write_seq($seq);
}
$consio->close;
$onelineconsout->close;

__DATA__
@SRR031652.634472
agtgcgctgatctgtggcccgtattgcctcaacgcaagctcaatagcttgagtatattaa
a
+
01111111111111100111111--,,011111101111111110111111111111110
0
----

--- /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm
2010-10-12 13:26:06.491743000 +0100
+++ /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm~
2010-10-12 13:07:27.462833000 +0100
@@ -80,7 +80,7 @@
                 last FASTQ
             }
             chomp $line;
-            if (!defined($line)) {
+            if (!$line) {
                 delete $self->{lastline};
                 last FASTQ;
             }


From shalabh.sharma7 at gmail.com  Tue Oct 12 10:20:58 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 12 Oct 2010 10:20:58 -0400
Subject: [Bioperl-l] fastq Problem
Message-ID: <AANLkTikTASuFtDhvwZDpvn4N4k-nMR2S1y9noQ2OcY12@mail.gmail.com>

Hi,
    I have data from illumina, i can read the data by using Bio::SeqIO but
when i am writing it back its writing in fasta format.

Is there anyway i can write it back in fastq format?

Thanks
Shalabh


From avilella at gmail.com  Tue Oct 12 10:54:46 2010
From: avilella at gmail.com (Albert Vilella)
Date: Tue, 12 Oct 2010 15:54:46 +0100
Subject: [Bioperl-l] possible bug in Bio::SeqIO::fastq
In-Reply-To: <76631143-1043-4A02-BF4C-AC7F9D8A3274@illinois.edu>
References: <AANLkTi=XNY9skUoTpJYJ=cp8wcpRPiskjFeuc3RquDUk@mail.gmail.com>
	<76631143-1043-4A02-BF4C-AC7F9D8A3274@illinois.edu>
Message-ID: <AANLkTi=m3-rR4yGLRPLTVW0azSdS3AUwQQ1u1gtvzWoP@mail.gmail.com>

aah! thanks!

On Tue, Oct 12, 2010 at 3:50 PM, Chris Fields <cjfields at illinois.edu> wrote:
> Albert,
>
> Have you tried bioperl-live? ?This is already fixed there.
>
> chris
>
> On Oct 12, 2010, at 7:34 AM, Albert Vilella wrote:
>
>> Hi,
>>
>> I found what seems to me could be a bug in the fastq module, which is
>> that if the
>> last line of the raw_quality section is a single "0" character, a
>> "if($line)" isn't
>> returning it properly, because it should be "if(defined $line)" instead.
>>
>> Find here a test case and the line in question:
>>
>> ----
>> use strict;
>> use Bio::SeqIO;
>>
>> my $consio = Bio::SeqIO->new
>> ?(-format => 'fastq',
>> ? -fh => \*DATA);
>>
>> my $onelineconsout = Bio::SeqIO->new
>> ?(-format => 'fastq',
>> ? -fh => \*STDOUT);
>>
>> while (my $seq = $consio->next_seq) {
>> ?next if ($seq->seq =~ /^n+$/);
>> ?$seq->seq(uc($seq->seq));
>> ?$onelineconsout->write_seq($seq);
>> }
>> $consio->close;
>> $onelineconsout->close;
>>
>> __DATA__
>> @SRR031652.634472
>> agtgcgctgatctgtggcccgtattgcctcaacgcaagctcaatagcttgagtatattaa
>> a
>> +
>> 01111111111111100111111--,,011111101111111110111111111111110
>> 0
>> ----
>>
>> --- /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm
>> 2010-10-12 13:26:06.491743000 +0100
>> +++ /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm~
>> 2010-10-12 13:07:27.462833000 +0100
>> @@ -80,7 +80,7 @@
>> ? ? ? ? ? ? ? ? last FASTQ
>> ? ? ? ? ? ? }
>> ? ? ? ? ? ? chomp $line;
>> - ? ? ? ? ? ?if (!defined($line)) {
>> + ? ? ? ? ? ?if (!$line) {
>> ? ? ? ? ? ? ? ? delete $self->{lastline};
>> ? ? ? ? ? ? ? ? last FASTQ;
>> ? ? ? ? ? ? }
>> _______________________________________________
>> 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 Oct 12 10:50:30 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 12 Oct 2010 09:50:30 -0500
Subject: [Bioperl-l] possible bug in Bio::SeqIO::fastq
In-Reply-To: <AANLkTi=XNY9skUoTpJYJ=cp8wcpRPiskjFeuc3RquDUk@mail.gmail.com>
References: <AANLkTi=XNY9skUoTpJYJ=cp8wcpRPiskjFeuc3RquDUk@mail.gmail.com>
Message-ID: <76631143-1043-4A02-BF4C-AC7F9D8A3274@illinois.edu>

Albert, 

Have you tried bioperl-live?  This is already fixed there.

chris

On Oct 12, 2010, at 7:34 AM, Albert Vilella wrote:

> Hi,
> 
> I found what seems to me could be a bug in the fastq module, which is
> that if the
> last line of the raw_quality section is a single "0" character, a
> "if($line)" isn't
> returning it properly, because it should be "if(defined $line)" instead.
> 
> Find here a test case and the line in question:
> 
> ----
> use strict;
> use Bio::SeqIO;
> 
> my $consio = Bio::SeqIO->new
>  (-format => 'fastq',
>   -fh => \*DATA);
> 
> my $onelineconsout = Bio::SeqIO->new
>  (-format => 'fastq',
>   -fh => \*STDOUT);
> 
> while (my $seq = $consio->next_seq) {
>  next if ($seq->seq =~ /^n+$/);
>  $seq->seq(uc($seq->seq));
>  $onelineconsout->write_seq($seq);
> }
> $consio->close;
> $onelineconsout->close;
> 
> __DATA__
> @SRR031652.634472
> agtgcgctgatctgtggcccgtattgcctcaacgcaagctcaatagcttgagtatattaa
> a
> +
> 01111111111111100111111--,,011111101111111110111111111111110
> 0
> ----
> 
> --- /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm
> 2010-10-12 13:26:06.491743000 +0100
> +++ /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm~
> 2010-10-12 13:07:27.462833000 +0100
> @@ -80,7 +80,7 @@
>                 last FASTQ
>             }
>             chomp $line;
> -            if (!defined($line)) {
> +            if (!$line) {
>                 delete $self->{lastline};
>                 last FASTQ;
>             }
> _______________________________________________
> 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 Oct 12 10:51:41 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 12 Oct 2010 09:51:41 -0500
Subject: [Bioperl-l] fastq Problem
In-Reply-To: <AANLkTikTASuFtDhvwZDpvn4N4k-nMR2S1y9noQ2OcY12@mail.gmail.com>
References: <AANLkTikTASuFtDhvwZDpvn4N4k-nMR2S1y9noQ2OcY12@mail.gmail.com>
Message-ID: <03B2F4BE-4E32-4A28-BB9E-B2B59EAEFE00@illinois.edu>

Yes, but you need to use the latest CPAN release or bioperl-live; anything older than v. 1.6.1 will not convert Illumina reads correctly.

chris

On Oct 12, 2010, at 9:20 AM, shalabh sharma wrote:

> Hi,
>    I have data from illumina, i can read the data by using Bio::SeqIO but
> when i am writing it back its writing in fasta format.
> 
> Is there anyway i can write it back in fastq format?
> 
> Thanks
> Shalabh
> _______________________________________________
> 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  Tue Oct 12 11:09:50 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 12 Oct 2010 11:09:50 -0400
Subject: [Bioperl-l] fastq Problem
In-Reply-To: <03B2F4BE-4E32-4A28-BB9E-B2B59EAEFE00@illinois.edu>
References: <AANLkTikTASuFtDhvwZDpvn4N4k-nMR2S1y9noQ2OcY12@mail.gmail.com>
	<03B2F4BE-4E32-4A28-BB9E-B2B59EAEFE00@illinois.edu>
Message-ID: <AANLkTim3Hx3SLrEoQa8D9Ha_x-ECTOjCCQY4CjHBJOaV@mail.gmail.com>

Thanks Chris,
I realized that after writing that mail. Its working now.

Thanks
Shalabh


On Tue, Oct 12, 2010 at 10:51 AM, Chris Fields <cjfields at illinois.edu>wrote:

> Yes, but you need to use the latest CPAN release or bioperl-live; anything
> older than v. 1.6.1 will not convert Illumina reads correctly.
>
> chris
>
> On Oct 12, 2010, at 9:20 AM, shalabh sharma wrote:
>
> > Hi,
> >    I have data from illumina, i can read the data by using Bio::SeqIO but
> > when i am writing it back its writing in fasta format.
> >
> > Is there anyway i can write it back in fastq format?
> >
> > Thanks
> > Shalabh
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From maj at fortinbras.us  Wed Oct 13 23:52:05 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Wed, 13 Oct 2010 23:52:05 -0400
Subject: [Bioperl-l] Next-gen flu informatics
Message-ID: <81299466177D467091763FEA84CA00FD@NewLife>

Hi All, 

Sorry about the job spam, but you are the best talent pool I know. SRA
(the company now interfering with my BioPerl work) is looking for
next-gen experienced bioinformaticists for a new contract with
CDC. Please have a look at http://www.sra.com/careers/search.php,
requisition numbers 31385, 31402 and 31467.

Thanks!
MAJ



From dichmann at berkeley.edu  Thu Oct 14 21:16:29 2010
From: dichmann at berkeley.edu (Darwin Sorento Dichmann)
Date: Thu, 14 Oct 2010 18:16:29 -0700
Subject: [Bioperl-l] Extracting sequences from MySQL DB with Bio::DB::GFF
Message-ID: <36D60149-EEC5-4A45-85B9-E7FD4F3C005C@berkeley.edu>

Greetings, 

I am trying to extract sequences from a MySQL DB with Bio::DB::GFF. The database is the same as I use for my gbrowse2 and it works fine for that. Also, I can extract all sorts of features but not sequence. 

When I run this script I thought I'd get a sequence output but apparently I get the memory address instead. 

I have very little experience with perl or other programming, but I try to follow the directions in the manual. I suspect that I overlook something very basic and any help would be greatly appreciated. 

Thanks,
Darwin 



The script:
------------
#! usr/bin/perl -w
# module to test if Bio::DB::GFF can be used to extract sequences from frog2 database.

use strict;
use Bio::Seq;
use Bio::SeqIO;
use Bio::DB::GFF;

# Open database
my $db = Bio::DB::GFF->
new( 	-adaptor => 'DBI::mysql',
     	-dsn     => 'frog2',
		-user => 'darwin',
		-password => '****',
		);

# fetch scaffold_1 (1-100000)
my $segment = $db->segment('scaffold_1', 1 => 100000) or die;

# get its DNA
 my $dna = $segment->seq or die;
print $segment, "\n";
print $dna,"\n";

# get an iterator on all curated features of type 'exon' or 'intron'
# this prints all exons and intron with transcript name on screen
	my $iterator = $segment->get_seq_stream(-type     => ['mRNA']);
	while (my $s = $iterator->next_seq) {
    print $s,"\n";
}

exit;
---------------

The output:
Macintosh:perlscripts darwin$ perl frog2_parser.pl 
scaffold_1:1,100000
Bio::PrimarySeq=HASH(0x100bb4d68)
mRNA:pick(xt42f011730m)
mRNA:pick(xt42f014902m)
mRNA:pick(xt42f016160m)
mRNA:pick(xt42f017353m)
mRNA:pick(xt42f029332m)
---------------


From scott at scottcain.net  Thu Oct 14 22:01:24 2010
From: scott at scottcain.net (Scott Cain)
Date: Thu, 14 Oct 2010 22:01:24 -0400
Subject: [Bioperl-l] Extracting sequences from MySQL DB with Bio::DB::GFF
In-Reply-To: <36D60149-EEC5-4A45-85B9-E7FD4F3C005C@berkeley.edu>
References: <36D60149-EEC5-4A45-85B9-E7FD4F3C005C@berkeley.edu>
Message-ID: <AANLkTi=i1xAoyeQJGAnT9X5wEmdchJk1v4YWMSqk7fH1@mail.gmail.com>

Hi Darwin,

The "seq" method returns a Bio::PrimarySeq object (I forget why this
is--I think it's to fulfill the contract with the Bio::SeqFeatureI
interface).  To get the sequence, you can do a few things: 1) call the
seq method on the Bio::PrimarySeq object, like this:

  my $dna = $segment->seq->seq;

or 2) use the dna method:

  my $dna = $segment->dna;

The perldoc section from Bio::DB::GFF::Segment is below.

Scott

       seq

        Title   : seq
        Usage   : $s->seq
        Function: get the sequence string for this segment
        Returns : a Bio::PrimarySeq
        Args    : none
        Status  : Public

       Returns the sequence for this segment as a Bio::PrimarySeq.  (-) strand
       segments are automatically reverse complemented

       The method is called dna() return the data as a simple sequence string.

       dna

        Title   : dna
        Usage   : $s->dna
        Function: get the DNA string for this segment
        Returns : a string
        Args    : none
        Status  : Public

       Returns the sequence for this segment as a simple string. (-) strand
       segments are automatically reverse complemented

       The method is also called protein().


On Thu, Oct 14, 2010 at 9:16 PM, Darwin Sorento Dichmann
<dichmann at berkeley.edu> wrote:
> Greetings,
>
> I am trying to extract sequences from a MySQL DB with Bio::DB::GFF. The database is the same as I use for my gbrowse2 and it works fine for that. Also, I can extract all sorts of features but not sequence.
>
> When I run this script I thought I'd get a sequence output but apparently I get the memory address instead.
>
> I have very little experience with perl or other programming, but I try to follow the directions in the manual. I suspect that I overlook something very basic and any help would be greatly appreciated.
>
> Thanks,
> Darwin
>
>
>
> The script:
> ------------
> #! usr/bin/perl -w
> # module to test if Bio::DB::GFF can be used to extract sequences from frog2 database.
>
> use strict;
> use Bio::Seq;
> use Bio::SeqIO;
> use Bio::DB::GFF;
>
> # Open database
> my $db = Bio::DB::GFF->
> new(    -adaptor => 'DBI::mysql',
>        -dsn     => 'frog2',
>                -user => 'darwin',
>                -password => '****',
>                );
>
> # fetch scaffold_1 (1-100000)
> my $segment = $db->segment('scaffold_1', 1 => 100000) or die;
>
> # get its DNA
>  my $dna = $segment->seq or die;
> print $segment, "\n";
> print $dna,"\n";
>
> # get an iterator on all curated features of type 'exon' or 'intron'
> # this prints all exons and intron with transcript name on screen
>        my $iterator = $segment->get_seq_stream(-type     => ['mRNA']);
>        while (my $s = $iterator->next_seq) {
>    print $s,"\n";
> }
>
> exit;
> ---------------
>
> The output:
> Macintosh:perlscripts darwin$ perl frog2_parser.pl
> scaffold_1:1,100000
> Bio::PrimarySeq=HASH(0x100bb4d68)
> mRNA:pick(xt42f011730m)
> mRNA:pick(xt42f014902m)
> mRNA:pick(xt42f016160m)
> mRNA:pick(xt42f017353m)
> mRNA:pick(xt42f029332m)
> ---------------
> _______________________________________________
> 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 dichmann at berkeley.edu  Fri Oct 15 13:34:02 2010
From: dichmann at berkeley.edu (Darwin Sorento Dichmann)
Date: Fri, 15 Oct 2010 10:34:02 -0700
Subject: [Bioperl-l] Extracting sequences from MySQL DB with Bio::DB::GFF
In-Reply-To: <AANLkTi=i1xAoyeQJGAnT9X5wEmdchJk1v4YWMSqk7fH1@mail.gmail.com>
References: <36D60149-EEC5-4A45-85B9-E7FD4F3C005C@berkeley.edu>
	<AANLkTi=i1xAoyeQJGAnT9X5wEmdchJk1v4YWMSqk7fH1@mail.gmail.com>
Message-ID: <9E7B9E6F-9440-4BAC-AD8D-2A739A863C1B@berkeley.edu>

It's a beauty to behold!
Thanks Scott!

Best,
Darwin

On Oct 14, 2010, at 7:01 PM, Scott Cain wrote:

> Hi Darwin,
> 
> The "seq" method returns a Bio::PrimarySeq object (I forget why this
> is--I think it's to fulfill the contract with the Bio::SeqFeatureI
> interface).  To get the sequence, you can do a few things: 1) call the
> seq method on the Bio::PrimarySeq object, like this:
> 
>  my $dna = $segment->seq->seq;
> 
> or 2) use the dna method:
> 
>  my $dna = $segment->dna;
> 
> The perldoc section from Bio::DB::GFF::Segment is below.
> 
> Scott
> 
>       seq
> 
>        Title   : seq
>        Usage   : $s->seq
>        Function: get the sequence string for this segment
>        Returns : a Bio::PrimarySeq
>        Args    : none
>        Status  : Public
> 
>       Returns the sequence for this segment as a Bio::PrimarySeq.  (-) strand
>       segments are automatically reverse complemented
> 
>       The method is called dna() return the data as a simple sequence string.
> 
>       dna
> 
>        Title   : dna
>        Usage   : $s->dna
>        Function: get the DNA string for this segment
>        Returns : a string
>        Args    : none
>        Status  : Public
> 
>       Returns the sequence for this segment as a simple string. (-) strand
>       segments are automatically reverse complemented
> 
>       The method is also called protein().
> 
> 
> On Thu, Oct 14, 2010 at 9:16 PM, Darwin Sorento Dichmann
> <dichmann at berkeley.edu> wrote:
>> Greetings,
>> 
>> I am trying to extract sequences from a MySQL DB with Bio::DB::GFF. The database is the same as I use for my gbrowse2 and it works fine for that. Also, I can extract all sorts of features but not sequence.
>> 
>> When I run this script I thought I'd get a sequence output but apparently I get the memory address instead.
>> 
>> I have very little experience with perl or other programming, but I try to follow the directions in the manual. I suspect that I overlook something very basic and any help would be greatly appreciated.
>> 
>> Thanks,
>> Darwin
>> 
>> 
>> 
>> The script:
>> ------------
>> #! usr/bin/perl -w
>> # module to test if Bio::DB::GFF can be used to extract sequences from frog2 database.
>> 
>> use strict;
>> use Bio::Seq;
>> use Bio::SeqIO;
>> use Bio::DB::GFF;
>> 
>> # Open database
>> my $db = Bio::DB::GFF->
>> new(    -adaptor => 'DBI::mysql',
>>       -dsn     => 'frog2',
>>               -user => 'darwin',
>>               -password => '****',
>>               );
>> 
>> # fetch scaffold_1 (1-100000)
>> my $segment = $db->segment('scaffold_1', 1 => 100000) or die;
>> 
>> # get its DNA
>> my $dna = $segment->seq or die;
>> print $segment, "\n";
>> print $dna,"\n";
>> 
>> # get an iterator on all curated features of type 'exon' or 'intron'
>> # this prints all exons and intron with transcript name on screen
>>       my $iterator = $segment->get_seq_stream(-type     => ['mRNA']);
>>       while (my $s = $iterator->next_seq) {
>>   print $s,"\n";
>> }
>> 
>> exit;
>> ---------------
>> 
>> The output:
>> Macintosh:perlscripts darwin$ perl frog2_parser.pl
>> scaffold_1:1,100000
>> Bio::PrimarySeq=HASH(0x100bb4d68)
>> mRNA:pick(xt42f011730m)
>> mRNA:pick(xt42f014902m)
>> mRNA:pick(xt42f016160m)
>> mRNA:pick(xt42f017353m)
>> mRNA:pick(xt42f029332m)
>> ---------------
>> _______________________________________________
>> 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 mcestep at gmail.com  Fri Oct 15 16:59:57 2010
From: mcestep at gmail.com (Matt Estep)
Date: Fri, 15 Oct 2010 15:59:57 -0500
Subject: [Bioperl-l] Installing BioPerl on New mac 10.6.4
Message-ID: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>

Hi

When running the ./build install script I get an error because it can
not make a directory in /usr/local/share/man/man3  I looked around a
bit and I have a file titled /usr/share/man/man3. I am guessing the
script does not know how to skip the local bit of the first line.

Can you tell me how to run the script so that it will make the file in
the right place. I am guessing the file struture of the new mac is a
little different.

Thanks in advance for any help.

Matt


From scott at scottcain.net  Fri Oct 15 23:41:40 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 15 Oct 2010 23:41:40 -0400
Subject: [Bioperl-l] Installing BioPerl on New mac 10.6.4
In-Reply-To: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>
References: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>
Message-ID: <AANLkTimUSO7ohhN6L80tjYhsrHk+2oQx6JWcRE11g4ob@mail.gmail.com>

Hi Matt,

Usually, when ./Build install fails to create a directory or file it
is because the user that executed the script didn't have permission to
perform that action.  Did you use "sudo" when you executed the install
command?

Scott


On Fri, Oct 15, 2010 at 4:59 PM, Matt Estep <mcestep at gmail.com> wrote:
> Hi
>
> When running the ./build install script I get an error because it can
> not make a directory in /usr/local/share/man/man3 ?I looked around a
> bit and I have a file titled /usr/share/man/man3. I am guessing the
> script does not know how to skip the local bit of the first line.
>
> Can you tell me how to run the script so that it will make the file in
> the right place. I am guessing the file struture of the new mac is a
> little different.
>
> Thanks in advance for any help.
>
> Matt
> _______________________________________________
> 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 fij at elte.hu  Sat Oct 16 07:34:06 2010
From: fij at elte.hu (Farkas, Illes)
Date: Sat, 16 Oct 2010 13:34:06 +0200
Subject: [Bioperl-l] cis-regulatory elements
Message-ID: <AANLkTinCN+qFBZeGtKiYLMWg+yzitkEP497pHMgG-ULn@mail.gmail.com>

Dear All,

Which (BioPerl or other) module/algorithm would you recommend for predicting
cis-regulatory elements (mainly TFBSs) in a variety of organisms? We (= 1
colleague and I) have looked at
http://www.nature.com/nbt/journal/v23/n1/full/nbt1053.html so far.

Thanks,
Illes
--
http://hal.elte.hu/fij


From grapeguy at gmail.com  Sat Oct 16 15:46:32 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Sat, 16 Oct 2010 15:46:32 -0400
Subject: [Bioperl-l] Installing BioPerl on New mac 10.6.4
In-Reply-To: <AANLkTimUSO7ohhN6L80tjYhsrHk+2oQx6JWcRE11g4ob@mail.gmail.com>
References: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>
	<AANLkTimUSO7ohhN6L80tjYhsrHk+2oQx6JWcRE11g4ob@mail.gmail.com>
Message-ID: <AANLkTikbZnnno5oNDi1Q0HYe9QEFhp9xuF3wH5C8NhXG@mail.gmail.com>

Matt,

I just installed on OSX 10.6.3.  Definitely use sudo to perform the install.

I actually used the PPM install.  I used this command to start PPM: sudo
perl -MCPAN -e shell

http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_CPAN

Thanks,
Bill S.
Dept. of Biomedical Informatics
Ohio State University

On Fri, Oct 15, 2010 at 11:41 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Matt,
>
> Usually, when ./Build install fails to create a directory or file it
> is because the user that executed the script didn't have permission to
> perform that action.  Did you use "sudo" when you executed the install
> command?
>
> Scott
>
>
> On Fri, Oct 15, 2010 at 4:59 PM, Matt Estep <mcestep at gmail.com> wrote:
> > Hi
> >
> > When running the ./build install script I get an error because it can
> > not make a directory in /usr/local/share/man/man3  I looked around a
> > bit and I have a file titled /usr/share/man/man3. I am guessing the
> > script does not know how to skip the local bit of the first line.
> >
> > Can you tell me how to run the script so that it will make the file in
> > the right place. I am guessing the file struture of the new mac is a
> > little different.
> >
> > Thanks in advance for any help.
> >
> > Matt
> > _______________________________________________
> > 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
>


From jun.yin at ucd.ie  Sat Oct 16 16:41:37 2010
From: jun.yin at ucd.ie (Jun Yin)
Date: Sat, 16 Oct 2010 21:41:37 +0100
Subject: [Bioperl-l] cis-regulatory elements
In-Reply-To: <AANLkTinCN+qFBZeGtKiYLMWg+yzitkEP497pHMgG-ULn@mail.gmail.com>
References: <AANLkTinCN+qFBZeGtKiYLMWg+yzitkEP497pHMgG-ULn@mail.gmail.com>
Message-ID: <001501cb6d72$8771c2b0$96554810$%yin@ucd.ie>

Hi, Illes,

Sorry I don't know any package in BioPerl predicting TFBS binding motifs. As
far as I know, neither Bio::Align nor Bio::Assembly has such functions,
though Bio::SimpleAlign can be used to manipulate your promoter alignment.
For TFBS prediction, I personally use PScan and TFFind at the moment.

I am also interested in this question. I will wait for the answer in the
mail list with you :)

Cheers,
Jun Yin
Ph.D.?student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Farkas, Illes
Sent: Saturday, October 16, 2010 12:34 PM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] cis-regulatory elements

Dear All,

Which (BioPerl or other) module/algorithm would you recommend for predicting
cis-regulatory elements (mainly TFBSs) in a variety of organisms? We (= 1
colleague and I) have looked at
http://www.nature.com/nbt/journal/v23/n1/full/nbt1053.html so far.

Thanks,
Illes
--
http://hal.elte.hu/fij
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com


 

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com
 
 

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com
 




From cjfields at illinois.edu  Sat Oct 16 23:24:32 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Sat, 16 Oct 2010 22:24:32 -0500
Subject: [Bioperl-l] cis-regulatory elements
In-Reply-To: <001501cb6d72$8771c2b0$96554810$%yin@ucd.ie>
References: <AANLkTinCN+qFBZeGtKiYLMWg+yzitkEP497pHMgG-ULn@mail.gmail.com>
	<001501cb6d72$8771c2b0$96554810$%yin@ucd.ie>
Message-ID: <ECB68538-3F18-4AEB-A097-773A913935B5@illinois.edu>

Sendu Bala delved into this a bit; you can look at a few of his modules in BioPerl, specifically Bio::DB::TFBS (which is only configured for transfac_pro at the moment).

chris

On Oct 16, 2010, at 3:41 PM, Jun Yin wrote:

> Hi, Illes,
> 
> Sorry I don't know any package in BioPerl predicting TFBS binding motifs. As
> far as I know, neither Bio::Align nor Bio::Assembly has such functions,
> though Bio::SimpleAlign can be used to manipulate your promoter alignment.
> For TFBS prediction, I personally use PScan and TFFind at the moment.
> 
> I am also interested in this question. I will wait for the answer in the
> mail list with you :)
> 
> Cheers,
> Jun Yin
> Ph.D. student in U.C.D.
> 
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Farkas, Illes
> Sent: Saturday, October 16, 2010 12:34 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] cis-regulatory elements
> 
> Dear All,
> 
> Which (BioPerl or other) module/algorithm would you recommend for predicting
> cis-regulatory elements (mainly TFBSs) in a variety of organisms? We (= 1
> colleague and I) have looked at
> http://www.nature.com/nbt/journal/v23/n1/full/nbt1053.html so far.
> 
> Thanks,
> Illes
> --
> http://hal.elte.hu/fij
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
> 
> The message was checked by ESET Smart Security.
> 
> http://www.eset.com
> 
> 
> 
> 
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
> 
> The message was checked by ESET Smart Security.
> 
> http://www.eset.com
> 
> 
> 
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
> 
> The message was checked by ESET Smart Security.
> 
> http://www.eset.com
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From grapeguy at gmail.com  Mon Oct 18 09:58:24 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Mon, 18 Oct 2010 09:58:24 -0400
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal alignment
Message-ID: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>

All,

I'm in my first week with bioperl for a class project (although I've used
Perl for years). I've successfully run a clustal alignment of several DNA
sequences to produce the aln and dnd files. Now I would like to generate a
consensus sequence from the alignment.  I see that Pise Cons does this
satisfactorily on my example data (
http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1 distribution
that I installed.

Is this another module that I need to install separately?

"cpan[2]> m /Pise/
Module    Bio::Tools::Run::AnalysisFactory::Pise
(BIRNEY/bioperl-run-1.4.tar.gz)
Module    Bio::Tools::Run::PiseApplication (BIRNEY/bioperl-run-1.4.tar.gz)"

Bill S.


From cjfields at illinois.edu  Mon Oct 18 10:54:32 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 18 Oct 2010 09:54:32 -0500
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
Message-ID: <DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>

Bill,

Actually, the page you reached at Pasteur is not Pise, but Mobyle (their replacement for the older Pise tools).  The Pise modules were in BioPerl-Run, but they were deprecated a few years ago and removed from the latest BioPerl-Run releases b/c the remote service is no longer active; there is no Perl-based replacement for Mobyle interaction.  

Have you thought about just using the functionality within the Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there are methods in place to do that.

chris

On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:

> All,
> 
> I'm in my first week with bioperl for a class project (although I've used
> Perl for years). I've successfully run a clustal alignment of several DNA
> sequences to produce the aln and dnd files. Now I would like to generate a
> consensus sequence from the alignment.  I see that Pise Cons does this
> satisfactorily on my example data (
> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1 distribution
> that I installed.
> 
> Is this another module that I need to install separately?
> 
> "cpan[2]> m /Pise/
> Module    Bio::Tools::Run::AnalysisFactory::Pise
> (BIRNEY/bioperl-run-1.4.tar.gz)
> Module    Bio::Tools::Run::PiseApplication (BIRNEY/bioperl-run-1.4.tar.gz)"
> 
> Bill S.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From grapeguy at gmail.com  Mon Oct 18 11:52:03 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Mon, 18 Oct 2010 11:52:03 -0400
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
Message-ID: <AANLkTimF5N_AnTV380fT5hPAEjjSgSP37+KVaoHNwbXN@mail.gmail.com>

Chris,

Well, That explains it.

I'll take a 2 pronged approach:
1. Try SimpleAlign
2. Driving the Mobyle UI using LWP::UserAgent, HTML::Form and
HTML::TableExtract (I do this for Tm calculations);

Thanks,
Bill S.



On Mon, Oct 18, 2010 at 10:54 AM, Chris Fields <cjfields at illinois.edu>wrote:

> Bill,
>
> Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
> replacement for the older Pise tools).  The Pise modules were in
> BioPerl-Run, but they were deprecated a few years ago and removed from the
> latest BioPerl-Run releases b/c the remote service is no longer active;
> there is no Perl-based replacement for Mobyle interaction.
>
> Have you thought about just using the functionality within the
> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there are
> methods in place to do that.
>
> chris
>
> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
>
> > All,
> >
> > I'm in my first week with bioperl for a class project (although I've used
> > Perl for years). I've successfully run a clustal alignment of several DNA
> > sequences to produce the aln and dnd files. Now I would like to generate
> a
> > consensus sequence from the alignment.  I see that Pise Cons does this
> > satisfactorily on my example data (
> > http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However,
> I'm
> > not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
> distribution
> > that I installed.
> >
> > Is this another module that I need to install separately?
> >
> > "cpan[2]> m /Pise/
> > Module    Bio::Tools::Run::AnalysisFactory::Pise
> > (BIRNEY/bioperl-run-1.4.tar.gz)
> > Module    Bio::Tools::Run::PiseApplication
> (BIRNEY/bioperl-run-1.4.tar.gz)"
> >
> > Bill S.
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From jun.yin at ucd.ie  Mon Oct 18 12:09:32 2010
From: jun.yin at ucd.ie (Jun Yin)
Date: Mon, 18 Oct 2010 17:09:32 +0100
Subject: [Bioperl-l] Generating a consensus sequence from a
	Clustal	alignment
In-Reply-To: <DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
Message-ID: <001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>

Hi, Bill,

You may consider to use consensus_iupac or consensus_string methods in
Bio::SimpleAlign to generate consensus sequence.

Cheers,
Jun Yin
Ph.D.?student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Monday, October 18, 2010 3:55 PM
To: Bill Stephens
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
alignment

Bill,

Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
replacement for the older Pise tools).  The Pise modules were in
BioPerl-Run, but they were deprecated a few years ago and removed from the
latest BioPerl-Run releases b/c the remote service is no longer active;
there is no Perl-based replacement for Mobyle interaction.  

Have you thought about just using the functionality within the
Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there are
methods in place to do that.

chris

On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:

> All,
> 
> I'm in my first week with bioperl for a class project (although I've used
> Perl for years). I've successfully run a clustal alignment of several DNA
> sequences to produce the aln and dnd files. Now I would like to generate a
> consensus sequence from the alignment.  I see that Pise Cons does this
> satisfactorily on my example data (
> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
distribution
> that I installed.
> 
> Is this another module that I need to install separately?
> 
> "cpan[2]> m /Pise/
> Module    Bio::Tools::Run::AnalysisFactory::Pise
> (BIRNEY/bioperl-run-1.4.tar.gz)
> Module    Bio::Tools::Run::PiseApplication
(BIRNEY/bioperl-run-1.4.tar.gz)"
> 
> Bill S.
> _______________________________________________
> 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

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com


 

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com
 




From mcestep at gmail.com  Sat Oct 16 22:59:24 2010
From: mcestep at gmail.com (Matt Estep)
Date: Sat, 16 Oct 2010 21:59:24 -0500
Subject: [Bioperl-l] Installing BioPerl on New mac 10.6.4
In-Reply-To: <AANLkTikbZnnno5oNDi1Q0HYe9QEFhp9xuF3wH5C8NhXG@mail.gmail.com>
References: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>
	<AANLkTimUSO7ohhN6L80tjYhsrHk+2oQx6JWcRE11g4ob@mail.gmail.com>
	<AANLkTikbZnnno5oNDi1Q0HYe9QEFhp9xuF3wH5C8NhXG@mail.gmail.com>
Message-ID: <AANLkTimiPDKCFKZwDT1UM-OG=jKqxVMe2fD5hdY_jPW-@mail.gmail.com>

Thank you both. I think this has solved my troubles.

Matt

On Sat, Oct 16, 2010 at 2:46 PM, Bill Stephens <grapeguy at gmail.com> wrote:
> Matt,
>
> I just installed on OSX 10.6.3.? Definitely use sudo to perform the install.
>
> I actually used the PPM install.? I used this command to start PPM: sudo
> perl -MCPAN -e shell
>
> http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_CPAN
>
> Thanks,
> Bill S.
> Dept. of Biomedical Informatics
> Ohio State University
>
> On Fri, Oct 15, 2010 at 11:41 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Matt,
>>
>> Usually, when ./Build install fails to create a directory or file it
>> is because the user that executed the script didn't have permission to
>> perform that action. ?Did you use "sudo" when you executed the install
>> command?
>>
>> Scott
>>
>>
>> On Fri, Oct 15, 2010 at 4:59 PM, Matt Estep <mcestep at gmail.com> wrote:
>> > Hi
>> >
>> > When running the ./build install script I get an error because it can
>> > not make a directory in /usr/local/share/man/man3 ?I looked around a
>> > bit and I have a file titled /usr/share/man/man3. I am guessing the
>> > script does not know how to skip the local bit of the first line.
>> >
>> > Can you tell me how to run the script so that it will make the file in
>> > the right place. I am guessing the file struture of the new mac is a
>> > little different.
>> >
>> > Thanks in advance for any help.
>> >
>> > Matt
>> > _______________________________________________
>> > 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
>
>



From e.cristiano at Dkfz-Heidelberg.de  Mon Oct 18 10:33:05 2010
From: e.cristiano at Dkfz-Heidelberg.de (Cristiano Elena)
Date: Mon, 18 Oct 2010 16:33:05 +0200
Subject: [Bioperl-l] bioperl easy way installation using cpan
Message-ID: <FC756E55-13EF-449F-B324-3BB76032A22B@Dkfz-Heidelberg.de>

Hi,
I am a beginner and i am trying to install bioperl via CPAN following the instructions on wiki.
i have a leopard mac 10.6 and perl version 5.10 i have X11 and i also installed fink (but the installation of bioperl wasn't successful trough fink either).

the error that i got at the end of the installation via CPAN is the following:

 SHAWNPW/PostScript-0.06.tar.gz
  /usr/bin/make install  -- OK
Warning (usually harmless): 'YAML' not installed, will not store persistent state
Running Build for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
  Has already been unwrapped into directory /Users/ecristiano/.cpan/build/BioPerl-1.6.1-66fecx
Could not make: cannot resolve circular dependency
Warning (usually harmless): 'YAML' not installed, will not store persistent state
Running Build test
  Can't test without successful make
Running Build install
  Make had returned bad status, install seems impossible
Could not read '/Users/ecristiano/.cpan/build/GraphViz-2.04-f7G5nl/META.yml'. Falling back to other methods to determine prerequisites
Failed during this command:
 MINGYILIU/Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz: make NO cannot resolve circular dependency
 CJFIELDS/BioPerl-1.6.1.tar.gz                : make NO cannot resolve circular dependency
 LBROCARD/GraphViz-2.04.tar.gz                : writemakefile NO '/usr/bin/perl Makefile.PL' returned status 512


thanks in advance



Elena




From sarahdoom at gmail.com  Mon Oct 18 11:20:25 2010
From: sarahdoom at gmail.com (Sarah Kingan)
Date: Mon, 18 Oct 2010 08:20:25 -0700 (PDT)
Subject: [Bioperl-l] DNAStatistics
Message-ID: <780929ef-4b06-43ae-9d9c-78a62e84a4d7@g18g2000yqk.googlegroups.com>

Hello,
I am trying to calculate Ka/Ks statistics using the
Align:DNAStatistics module. When I use the function, calc_KaKs_pair, I
get a long list of errors. The calculation is performed but I don't
understand the source of the errors. They include:

Use of uninitialized value in addition (+) at /usr/lib/perl5/site_perl/
5.8.8/Bio/Align/DNAStatistics.pm line 1673, <GEN0> line 25.

Use of uninitialized value in addition (+) at /usr/lib/perl5/site_perl/
5.8.8/Bio/Align/DNAStatistics.pm line 1505, <GEN0> line 25.

Use of uninitialized value in subtraction (-) at /usr/lib/perl5/
site_perl/5.8.8/Bio/Align/DNAStatistics.pm line 1506, <GEN0> line 25.

My alignment object has gaps, but I believe this module handles gaps.
The data I am analyzing comes from recently diverged species, so I
wonder if the errors could originate from a lack of substitutions.

Any help would be much appreciated.

Thanks!
Sarah.Kingan at rochester.edu


From scott at scottcain.net  Mon Oct 18 13:26:53 2010
From: scott at scottcain.net (Scott Cain)
Date: Mon, 18 Oct 2010 13:26:53 -0400
Subject: [Bioperl-l] bioperl easy way installation using cpan
In-Reply-To: <FC756E55-13EF-449F-B324-3BB76032A22B@Dkfz-Heidelberg.de>
References: <FC756E55-13EF-449F-B324-3BB76032A22B@Dkfz-Heidelberg.de>
Message-ID: <AANLkTim6NxZx2-MCNJQ190-za6TkCYF_m9WZvPfO+LhC@mail.gmail.com>

Hi Elena,

I would suggest that you answer the question about installing optional
prerequisites with a "no"; I think that will eliminate the circular
dependency problem.  Of course the only problem is if you need
Bio-ASN1-EntrezGene, but even if you do, you can probably install it
after the BioPerl install completes.

Scott


On Mon, Oct 18, 2010 at 10:33 AM, Cristiano Elena
<e.cristiano at dkfz-heidelberg.de> wrote:
> Hi,
> I am a beginner and i am trying to install bioperl via CPAN following the instructions on wiki.
> i have a leopard mac 10.6 and perl version 5.10 i have X11 and i also installed fink (but the installation of bioperl wasn't successful trough fink either).
>
> the error that i got at the end of the installation via CPAN is the following:
>
> ?SHAWNPW/PostScript-0.06.tar.gz
> ?/usr/bin/make install ?-- OK
> Warning (usually harmless): 'YAML' not installed, will not store persistent state
> Running Build for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
> ?Has already been unwrapped into directory /Users/ecristiano/.cpan/build/BioPerl-1.6.1-66fecx
> Could not make: cannot resolve circular dependency
> Warning (usually harmless): 'YAML' not installed, will not store persistent state
> Running Build test
> ?Can't test without successful make
> Running Build install
> ?Make had returned bad status, install seems impossible
> Could not read '/Users/ecristiano/.cpan/build/GraphViz-2.04-f7G5nl/META.yml'. Falling back to other methods to determine prerequisites
> Failed during this command:
> ?MINGYILIU/Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz: make NO cannot resolve circular dependency
> ?CJFIELDS/BioPerl-1.6.1.tar.gz ? ? ? ? ? ? ? ?: make NO cannot resolve circular dependency
> ?LBROCARD/GraphViz-2.04.tar.gz ? ? ? ? ? ? ? ?: writemakefile NO '/usr/bin/perl Makefile.PL' returned status 512
>
>
> thanks in advance
>
>
>
> Elena
>
>
> _______________________________________________
> 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 Oct 18 13:37:02 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 18 Oct 2010 12:37:02 -0500
Subject: [Bioperl-l] bioperl easy way installation using cpan
In-Reply-To: <AANLkTim6NxZx2-MCNJQ190-za6TkCYF_m9WZvPfO+LhC@mail.gmail.com>
References: <FC756E55-13EF-449F-B324-3BB76032A22B@Dkfz-Heidelberg.de>
	<AANLkTim6NxZx2-MCNJQ190-za6TkCYF_m9WZvPfO+LhC@mail.gmail.com>
Message-ID: <6081844C-D4CB-4926-968D-9CACAE017E57@illinois.edu>

Agreed.  Unfortunately, this is an issue that has repeatedly popped up.  The best way I can think of to solve it is to remove Bio::ASN1::EntrezGene 'recommends' from Build.PL file, manually check for it's presence, and indicate the procedure for installing (basically post-bioperl install).

chris

On Oct 18, 2010, at 12:26 PM, Scott Cain wrote:

> Hi Elena,
> 
> I would suggest that you answer the question about installing optional
> prerequisites with a "no"; I think that will eliminate the circular
> dependency problem.  Of course the only problem is if you need
> Bio-ASN1-EntrezGene, but even if you do, you can probably install it
> after the BioPerl install completes.
> 
> Scott
> 
> 
> On Mon, Oct 18, 2010 at 10:33 AM, Cristiano Elena
> <e.cristiano at dkfz-heidelberg.de> wrote:
>> Hi,
>> I am a beginner and i am trying to install bioperl via CPAN following the instructions on wiki.
>> i have a leopard mac 10.6 and perl version 5.10 i have X11 and i also installed fink (but the installation of bioperl wasn't successful trough fink either).
>> 
>> the error that i got at the end of the installation via CPAN is the following:
>> 
>>  SHAWNPW/PostScript-0.06.tar.gz
>>  /usr/bin/make install  -- OK
>> Warning (usually harmless): 'YAML' not installed, will not store persistent state
>> Running Build for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
>>  Has already been unwrapped into directory /Users/ecristiano/.cpan/build/BioPerl-1.6.1-66fecx
>> Could not make: cannot resolve circular dependency
>> Warning (usually harmless): 'YAML' not installed, will not store persistent state
>> Running Build test
>>  Can't test without successful make
>> Running Build install
>>  Make had returned bad status, install seems impossible
>> Could not read '/Users/ecristiano/.cpan/build/GraphViz-2.04-f7G5nl/META.yml'. Falling back to other methods to determine prerequisites
>> Failed during this command:
>>  MINGYILIU/Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz: make NO cannot resolve circular dependency
>>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make NO cannot resolve circular dependency
>>  LBROCARD/GraphViz-2.04.tar.gz                : writemakefile NO '/usr/bin/perl Makefile.PL' returned status 512
>> 
>> 
>> thanks in advance
>> 
>> 
>> 
>> Elena
>> 
>> 
>> _______________________________________________
>> 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




From David.Messina at sbc.su.se  Mon Oct 18 14:23:18 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 18 Oct 2010 14:23:18 -0400
Subject: [Bioperl-l] DNAStatistics
In-Reply-To: <780929ef-4b06-43ae-9d9c-78a62e84a4d7@g18g2000yqk.googlegroups.com>
References: <780929ef-4b06-43ae-9d9c-78a62e84a4d7@g18g2000yqk.googlegroups.com>
Message-ID: <B1ABB50A-0B78-44D9-85C3-4A316B52278F@sbc.su.se>

Hi Sarah,

Usually "unintialized value" errors mean you're not trying to read from an empty variable.

I would check that all of the data you're passing to calc_KaKs_pair does contain a value.


> My alignment object has gaps, but I believe this module handles gaps.

I'm not sure about that; I'd have to check. Did you try handing it some ungapped data to see if the errors go away?



Dave




From grapeguy at gmail.com  Mon Oct 18 20:02:47 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Mon, 18 Oct 2010 20:02:47 -0400
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
Message-ID: <AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>

So, I've got the SimpleAlign running. It looks like it's running the
alignment based upon the input sequence location only (first residue from
each sequence).  This is not what I need.

I'm back to to clustal, tcoffee or dalign.

Bill

On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:

> Hi, Bill,
>
> You may consider to use consensus_iupac or consensus_string methods in
> Bio::SimpleAlign to generate consensus sequence.
>
> Cheers,
> Jun Yin
> Ph.D. student in U.C.D.
>
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Monday, October 18, 2010 3:55 PM
> To: Bill Stephens
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
> alignment
>
> Bill,
>
> Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
> replacement for the older Pise tools).  The Pise modules were in
> BioPerl-Run, but they were deprecated a few years ago and removed from the
> latest BioPerl-Run releases b/c the remote service is no longer active;
> there is no Perl-based replacement for Mobyle interaction.
>
> Have you thought about just using the functionality within the
> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there
> are
> methods in place to do that.
>
> chris
>
> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
>
> > All,
> >
> > I'm in my first week with bioperl for a class project (although I've used
> > Perl for years). I've successfully run a clustal alignment of several DNA
> > sequences to produce the aln and dnd files. Now I would like to generate
> a
> > consensus sequence from the alignment.  I see that Pise Cons does this
> > satisfactorily on my example data (
> > http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However,
> I'm
> > not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
> distribution
> > that I installed.
> >
> > Is this another module that I need to install separately?
> >
> > "cpan[2]> m /Pise/
> > Module    Bio::Tools::Run::AnalysisFactory::Pise
> > (BIRNEY/bioperl-run-1.4.tar.gz)
> > Module    Bio::Tools::Run::PiseApplication
> (BIRNEY/bioperl-run-1.4.tar.gz)"
> >
> > Bill S.
> > _______________________________________________
> > 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
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>


From thomas.sharpton at gmail.com  Mon Oct 18 22:30:40 2010
From: thomas.sharpton at gmail.com (Thomas Sharpton)
Date: Mon, 18 Oct 2010 19:30:40 -0700
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
	<AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
Message-ID: <16917B57-A1EE-495C-A541-D5C666701C31@gmail.com>

While the tools you mention are sufficient, you might be interested to  
know that HMMER can also generate consensus sequences. Briefly, you  
would use the alignment you generated with clustal (or any other  
multiple sequence alignment tool) to build an HMM via the hmmbuild  
function. You can then emit a consensus sequence from the HMM file  
using the hmmemit function:

hmmemit -c HMM_file.hmm

Just FYI.

T

On Oct 18, 2010, at 5:02 PM, Bill Stephens wrote:

> So, I've got the SimpleAlign running. It looks like it's running the
> alignment based upon the input sequence location only (first residue  
> from
> each sequence).  This is not what I need.
>
> I'm back to to clustal, tcoffee or dalign.
>
> Bill
>
> On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:
>
>> Hi, Bill,
>>
>> You may consider to use consensus_iupac or consensus_string methods  
>> in
>> Bio::SimpleAlign to generate consensus sequence.
>>
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>>
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris  
>> Fields
>> Sent: Monday, October 18, 2010 3:55 PM
>> To: Bill Stephens
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] Generating a consensus sequence from a  
>> Clustal
>> alignment
>>
>> Bill,
>>
>> Actually, the page you reached at Pasteur is not Pise, but Mobyle  
>> (their
>> replacement for the older Pise tools).  The Pise modules were in
>> BioPerl-Run, but they were deprecated a few years ago and removed  
>> from the
>> latest BioPerl-Run releases b/c the remote service is no longer  
>> active;
>> there is no Perl-based replacement for Mobyle interaction.
>>
>> Have you thought about just using the functionality within the
>> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure  
>> there
>> are
>> methods in place to do that.
>>
>> chris
>>
>> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
>>
>>> All,
>>>
>>> I'm in my first week with bioperl for a class project (although  
>>> I've used
>>> Perl for years). I've successfully run a clustal alignment of  
>>> several DNA
>>> sequences to produce the aln and dnd files. Now I would like to  
>>> generate
>> a
>>> consensus sequence from the alignment.  I see that Pise Cons does  
>>> this
>>> satisfactorily on my example data (
>>> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) .  
>>> However,
>> I'm
>>> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
>> distribution
>>> that I installed.
>>>
>>> Is this another module that I need to install separately?
>>>
>>> "cpan[2]> m /Pise/
>>> Module    Bio::Tools::Run::AnalysisFactory::Pise
>>> (BIRNEY/bioperl-run-1.4.tar.gz)
>>> Module    Bio::Tools::Run::PiseApplication
>> (BIRNEY/bioperl-run-1.4.tar.gz)"
>>>
>>> Bill S.
>>> _______________________________________________
>>> 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
>>
>> __________ Information from ESET Smart Security, version of virus  
>> signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus  
>> signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jun.yin at ucd.ie  Tue Oct 19 04:17:58 2010
From: jun.yin at ucd.ie (Jun Yin)
Date: Tue, 19 Oct 2010 09:17:58 +0100
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
 alignment
In-Reply-To: <AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
	<AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
Message-ID: <003501cb6f66$23c37330$6b4a5990$%yin@ucd.ie>

Hi, Bill,

 

There are several methods you can choose from Bio::SimpleAlign to build
subalignment. For example, you can use $aln->slice  to get part of your
alignment, and then you can calculate concensus sequence from subalignment.
Another method $aln->remove_gaps, which can remove gap containing columns.

 

Cheers,

Jun Yin

Ph.D. student in U.C.D.

 

Bioinformatics Laboratory

Conway Institute

University College Dublin

 

From: Bill Stephens [mailto:grapeguy at gmail.com] 
Sent: Tuesday, October 19, 2010 1:03 AM
To: Jun Yin
Cc: Chris Fields; bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
alignment

 

So, I've got the SimpleAlign running. It looks like it's running the
alignment based upon the input sequence location only (first residue from
each sequence).  This is not what I need. 

I'm back to to clustal, tcoffee or dalign.

Bill

On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:

Hi, Bill,

You may consider to use consensus_iupac or consensus_string methods in
Bio::SimpleAlign to generate consensus sequence.

Cheers,
Jun Yin
Ph.D. student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Monday, October 18, 2010 3:55 PM
To: Bill Stephens
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
alignment

Bill,

Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
replacement for the older Pise tools).  The Pise modules were in
BioPerl-Run, but they were deprecated a few years ago and removed from the
latest BioPerl-Run releases b/c the remote service is no longer active;
there is no Perl-based replacement for Mobyle interaction.

Have you thought about just using the functionality within the
Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there are
methods in place to do that.

chris

On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:

> All,
>
> I'm in my first week with bioperl for a class project (although I've used
> Perl for years). I've successfully run a clustal alignment of several DNA
> sequences to produce the aln and dnd files. Now I would like to generate a
> consensus sequence from the alignment.  I see that Pise Cons does this
> satisfactorily on my example data (
> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
distribution
> that I installed.
>
> Is this another module that I need to install separately?
>
> "cpan[2]> m /Pise/
> Module    Bio::Tools::Run::AnalysisFactory::Pise
> (BIRNEY/bioperl-run-1.4.tar.gz)
> Module    Bio::Tools::Run::PiseApplication
(BIRNEY/bioperl-run-1.4.tar.gz)"
>
> Bill S.
> _______________________________________________
> 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

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com




__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com



 



From joseramonblas at gmail.com  Tue Oct 19 05:34:12 2010
From: joseramonblas at gmail.com (=?ISO-8859-1?Q?Jos=E9_Ram=F3n_Blas_Pastor?=)
Date: Tue, 19 Oct 2010 11:34:12 +0200
Subject: [Bioperl-l] correlated mutations analysis
Message-ID: <AANLkTimtudsQqppZtVz2+cCxKZ7gxEKXuHYPg85TC87M@mail.gmail.com>

Hi,

I have 2 protein sequences (or more). I want...
-to perform an analysis of correlated mutations in these proteins
(considering variations across 10 or 20 sps)
-obtain an statistical parameter on the significance of these mutations to
predict/hint interacting residues

Can you help me in this issue?. (Bioperl or not bioperl-based solutions are
welcome)

Thank you very much.

JR

-- 
Jos? Ram?n Blas - PhD
Dept. Biochemistry - Medicine School
University of Castilla-La Mancha

C Almansa, 14
02006 Albacete (Spain)



From cjfields at illinois.edu  Tue Oct 19 11:47:16 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 19 Oct 2010 10:47:16 -0500
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
	<AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
Message-ID: <16EDEBED-BAD4-4D57-B51B-C3234D1E8C39@illinois.edu>

Bio::SimpleAlign is the class that contains the alignment data; it does not generate the alignment for you.  You can use modules from BioPerl-Run that run ClustalW, MUSCLE, T-Coffee, etc to get a Bio::SimpleAlign instance, or parse the already-generated alignment output via Bio::AlignIO.

>From the Bio::Tools::Run::Alignment::ClustalW docs:

=================================================================

  #  Build a clustalw alignment factory
  @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
  $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);

  #  Pass the factory a list of sequences to be aligned.	
  $inputfilename = 't/data/cysprot.fa';
  $aln = $factory->align($inputfilename); # $aln is a SimpleAlign object.

  # ...or
  $seq_array_ref = \@seq_array;

  # where @seq_array is an array of Bio::Seq objects
  $aln = $factory->align($seq_array_ref);

=================================================================

$aln is a Bio::SimpleAlign derived from ClustalW output.  

>From Bio::SimpleAlign (note the use of Bio::AlignIO):

=================================================================

  # Use Bio::AlignIO to read in the alignment
  $str = Bio::AlignIO->new(-file => 't/data/testaln.pfam');
  $aln = $str->next_aln();

  # Describe
  print $aln->length;
  print $aln->num_residues;
  print $aln->is_flush;
  print $aln->num_sequences;
  print $aln->score;
  print $aln->percentage_identity;
  print $aln->consensus_string(50);

=================================================================

Note the consensus_string() method:

 Title     : consensus_string
 Usage     : $str = $ali->consensus_string($threshold_percent)
 Function  : Makes a strict consensus
 Returns   : Consensus string
 Argument  : Optional treshold ranging from 0 to 100.
             The consensus residue has to appear at least threshold %
             of the sequences at a given location, otherwise a '?'
             character will be placed at that location.
             (Default value = 0%)

chris

On Oct 18, 2010, at 7:02 PM, Bill Stephens wrote:

> So, I've got the SimpleAlign running. It looks like it's running the
> alignment based upon the input sequence location only (first residue from
> each sequence).  This is not what I need.
> 
> I'm back to to clustal, tcoffee or dalign.
> 
> Bill
> 
> On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:
> 
>> Hi, Bill,
>> 
>> You may consider to use consensus_iupac or consensus_string methods in
>> Bio::SimpleAlign to generate consensus sequence.
>> 
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>> 
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>> 
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
>> Sent: Monday, October 18, 2010 3:55 PM
>> To: Bill Stephens
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
>> alignment
>> 
>> Bill,
>> 
>> Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
>> replacement for the older Pise tools).  The Pise modules were in
>> BioPerl-Run, but they were deprecated a few years ago and removed from the
>> latest BioPerl-Run releases b/c the remote service is no longer active;
>> there is no Perl-based replacement for Mobyle interaction.
>> 
>> Have you thought about just using the functionality within the
>> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there
>> are
>> methods in place to do that.
>> 
>> chris
>> 
>> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
>> 
>>> All,
>>> 
>>> I'm in my first week with bioperl for a class project (although I've used
>>> Perl for years). I've successfully run a clustal alignment of several DNA
>>> sequences to produce the aln and dnd files. Now I would like to generate
>> a
>>> consensus sequence from the alignment.  I see that Pise Cons does this
>>> satisfactorily on my example data (
>>> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However,
>> I'm
>>> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
>> distribution
>>> that I installed.
>>> 
>>> Is this another module that I need to install separately?
>>> 
>>> "cpan[2]> m /Pise/
>>> Module    Bio::Tools::Run::AnalysisFactory::Pise
>>> (BIRNEY/bioperl-run-1.4.tar.gz)
>>> Module    Bio::Tools::Run::PiseApplication
>> (BIRNEY/bioperl-run-1.4.tar.gz)"
>>> 
>>> Bill S.
>>> _______________________________________________
>>> 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
>> 
>> __________ Information from ESET Smart Security, version of virus signature
>> database 5377 (20100818) __________
>> 
>> The message was checked by ESET Smart Security.
>> 
>> http://www.eset.com
>> 
>> 
>> 
>> 
>> __________ Information from ESET Smart Security, version of virus signature
>> database 5377 (20100818) __________
>> 
>> The message was checked by ESET Smart Security.
>> 
>> http://www.eset.com
>> 
>> 
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From td8pub at gmail.com  Tue Oct 19 13:28:07 2010
From: td8pub at gmail.com (T D)
Date: Tue, 19 Oct 2010 13:28:07 -0400
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
Message-ID: <AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>

Hi,

I'm new to BioPerl and Perl in general, and I'm trying to get
StandAloneBlastPlus to run. I got the latest versions using git and
downloaded bioperl-live  and bioperl-run.  I am having issues with Perl not
finding modules. Here is my error:

Can't locate IPC/Run.pm in @INC

Where is this module located? I am running Windows 7. I did a search for the
Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
Run.pm the older version? I have Perl v5.12.1 installed.

Thanks in advance!
Tracey


From cjfields at illinois.edu  Tue Oct 19 13:33:19 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 19 Oct 2010 12:33:19 -0500
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
	<AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>
Message-ID: <9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>

No, IPC::Run is different than IPC::Run3:

http://search.cpan.org/dist/IPC-Run/
http://search.cpan.org/dist/IPC-Run3/

Both should work under Windows, not sure about Windows7 but I can't see why they wouldn't work.

chris

On Oct 19, 2010, at 12:28 PM, T D wrote:

> Hi,
> 
> I'm new to BioPerl and Perl in general, and I'm trying to get
> StandAloneBlastPlus to run. I got the latest versions using git and
> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl not
> finding modules. Here is my error:
> 
> Can't locate IPC/Run.pm in @INC
> 
> Where is this module located? I am running Windows 7. I did a search for the
> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
> Run.pm the older version? I have Perl v5.12.1 installed.
> 
> Thanks in advance!
> Tracey
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From td8pub at gmail.com  Tue Oct 19 09:27:20 2010
From: td8pub at gmail.com (T D)
Date: Tue, 19 Oct 2010 09:27:20 -0400
Subject: [Bioperl-l] IPC/Run.pm?
Message-ID: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>

Hi,

I'm new to BioPerl and I'm trying to get StandAloneBlastPlus to run. I got
the latest versions using git and downloaded bioperl-live and and
bioperl-run.  I am having issues with Perl not finding modules. Here is my
error:

Can't locate IPC/Run.pm in @INC

Where is this module located? I am running Windows 7. I did a search for the
Run.pm and could only find IPC/*Run3.pm* under my Perl installation.

Thanks in advance!
Tracey


From anjan.purkayastha at gmail.com  Tue Oct 19 13:49:11 2010
From: anjan.purkayastha at gmail.com (ANJAN PURKAYASTHA)
Date: Tue, 19 Oct 2010 13:49:11 -0400
Subject: [Bioperl-l] Help in retrieving the DEFINITION line
Message-ID: <AANLkTimC=1mD3YBys8mOe9AUVZgo3QeNiWSydRRrfrNu@mail.gmail.com>

Hi,
I need to retrieve the DEFINITION line of a GenBank file, given the GenBank
accession ID.
The following code does not seem to do it:

use strict;
use warnings;
use Bio::Perl;
use Bio::DB::GenBank;
my $gb= new Bio::DB::GenBank;

open(F, "test_id");

while(<F>){
chomp;
my $id= $_;
my $seq= $gb->get_Seq_by_acc("$id");
my $anno_collection = $seq->annotation;
my @annotations = $anno_collection->get_Annotations('definition');
print ("@annotations\n");
}

Any thoughts on how to get this done will be deeply appreciated.
Thanks,
Anjan

-- 
===================================
anjan purkayastha, phd.
research associate
fas center for systems biology,
harvard university
52 oxford street
cambridge ma 02138
phone-703.740.6939
===================================


From David.Messina at sbc.su.se  Tue Oct 19 16:03:08 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 19 Oct 2010 16:03:08 -0400
Subject: [Bioperl-l] Help in retrieving the DEFINITION line
In-Reply-To: <AANLkTimC=1mD3YBys8mOe9AUVZgo3QeNiWSydRRrfrNu@mail.gmail.com>
References: <AANLkTimC=1mD3YBys8mOe9AUVZgo3QeNiWSydRRrfrNu@mail.gmail.com>
Message-ID: <0E6779A3-BD3E-469F-8C23-8BFA92135915@sbc.su.se>

Hi Anjan,

You can get to the definition directly, via the desc() method.

So, this works:

use strict;
use warnings;
use Bio::Perl;
use Bio::DB::GenBank;
my $gb= new Bio::DB::GenBank;

open(F, "test_id");

while(<F>){
	chomp;
	my $id= $_;
	my $seq= $gb->get_Seq_by_acc("$id");

	# I added these lines:
	my $definition      = $seq->desc;
        print $definition, "\n";}
}



Dave



From td8pub at gmail.com  Tue Oct 19 16:38:32 2010
From: td8pub at gmail.com (T D)
Date: Tue, 19 Oct 2010 16:38:32 -0400
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
	<AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>
	<9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>
Message-ID: <AANLkTi=LKy-UMPkQkDXN=83sjRFdJMgOn7Du9vVdh6x7@mail.gmail.com>

Thank you. I downloaded IPC::Run and the code seems to be working now. Is
Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?


On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:

> No, IPC::Run is different than IPC::Run3:
>
> http://search.cpan.org/dist/IPC-Run/
> http://search.cpan.org/dist/IPC-Run3/
>
> Both should work under Windows, not sure about Windows7 but I can't see why
> they wouldn't work.
>
> chris
>
> On Oct 19, 2010, at 12:28 PM, T D wrote:
>
> > Hi,
> >
> > I'm new to BioPerl and Perl in general, and I'm trying to get
> > StandAloneBlastPlus to run. I got the latest versions using git and
> > downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
> not
> > finding modules. Here is my error:
> >
> > Can't locate IPC/Run.pm in @INC
> >
> > Where is this module located? I am running Windows 7. I did a search for
> the
> > Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
> > Run.pm the older version? I have Perl v5.12.1 installed.
> >
> > Thanks in advance!
> > Tracey
> > _______________________________________________
> > 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 Oct 19 16:45:55 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 19 Oct 2010 15:45:55 -0500
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <AANLkTi=LKy-UMPkQkDXN=83sjRFdJMgOn7Du9vVdh6x7@mail.gmail.com>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
	<AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>
	<9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>
	<AANLkTi=LKy-UMPkQkDXN=83sjRFdJMgOn7Du9vVdh6x7@mail.gmail.com>
Message-ID: <840CF652-BAE0-4DD6-A375-30A817F20351@illinois.edu>

If you mean IPC::Run, I'm not sure.  I don't think BioPerl-Run was ever a part of Strawberry Perl Pro.

I do know there are some warnings that will pop up with BioPerl when using perl 5.12; these have been fixed in the github repo but haven't made their way into a release yet.

chris

On Oct 19, 2010, at 3:38 PM, T D wrote:

> Thank you. I downloaded IPC::Run and the code seems to be working now. Is
> Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?
> 
> 
> On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> No, IPC::Run is different than IPC::Run3:
>> 
>> http://search.cpan.org/dist/IPC-Run/
>> http://search.cpan.org/dist/IPC-Run3/
>> 
>> Both should work under Windows, not sure about Windows7 but I can't see why
>> they wouldn't work.
>> 
>> chris
>> 
>> On Oct 19, 2010, at 12:28 PM, T D wrote:
>> 
>>> Hi,
>>> 
>>> I'm new to BioPerl and Perl in general, and I'm trying to get
>>> StandAloneBlastPlus to run. I got the latest versions using git and
>>> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
>> not
>>> finding modules. Here is my error:
>>> 
>>> Can't locate IPC/Run.pm in @INC
>>> 
>>> Where is this module located? I am running Windows 7. I did a search for
>> the
>>> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
>>> Run.pm the older version? I have Perl v5.12.1 installed.
>>> 
>>> Thanks in advance!
>>> Tracey
>>> _______________________________________________
>>> 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 shalabh.sharma7 at gmail.com  Wed Oct 20 11:00:26 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 20 Oct 2010 11:00:26 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
Message-ID: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>

Hi All,
        Is there any module for mummer in Bioperl?

Also i need some suggestions and ideas (i think this is the best place to
ask).
I am working with huge data (around 200 million illumina reads), earlier i
was using blastx and other similar approaches to annotate but now i think
thats not possible, i would be very grateful if anyone can give me some idea
regarding this.

Thanks
Shalabh


From David.Messina at sbc.su.se  Wed Oct 20 11:25:02 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Wed, 20 Oct 2010 11:25:02 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
Message-ID: <C3E45590-33DD-4A27-87FF-533D8E8C9C09@sbc.su.se>


> Is there any module for mummer in Bioperl?

Did you try searching for mummer on the bioperl website?




From shalabh.sharma7 at gmail.com  Wed Oct 20 11:31:09 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 20 Oct 2010 11:31:09 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <C3E45590-33DD-4A27-87FF-533D8E8C9C09@sbc.su.se>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
	<C3E45590-33DD-4A27-87FF-533D8E8C9C09@sbc.su.se>
Message-ID: <AANLkTim3ig2Aa+=TUqb0Cr5HsH0f-eHoi+aZCX-pctEp@mail.gmail.com>

Yes , i did but its saying there aren't any modules available so i jsu
wanted to make sure.

-Shalabh


On Wed, Oct 20, 2010 at 11:25 AM, Dave Messina <David.Messina at sbc.su.se>wrote:

>
> > Is there any module for mummer in Bioperl?
>
> Did you try searching for mummer on the bioperl website?
>
>
>


From jimhu at tamu.edu  Wed Oct 20 11:27:08 2010
From: jimhu at tamu.edu (Jim Hu)
Date: Wed, 20 Oct 2010 10:27:08 -0500
Subject: [Bioperl-l] treeio->write_tree problem
Message-ID: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>

Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.

Jim

use Data::Dumper;
use Bio::TreeIO;
my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
                            -format => "newick");
while( my $tree = $treeio->next_tree ) {
	$treeio->write_tree($tree);
	print Dumper($tree);

}

=====================================
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 Oct 20 11:45:45 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 10:45:45 -0500
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
Message-ID: <572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>

On Oct 20, 2010, at 10:00 AM, shalabh sharma wrote:

> Hi All,
>        Is there any module for mummer in Bioperl?
> 
> Also i need some suggestions and ideas (i think this is the best place to
> ask).
> I am working with huge data (around 200 million illumina reads), earlier i
> was using blastx and other similar approaches to annotate but now i think
> thats not possible, i would be very grateful if anyone can give me some idea
> regarding this.
> 
> Thanks
> Shalabh

Hard to say unless we know a little more about what you are attempting to do.  Not sure why you are using mummer here, but...

This is something fairly well-covered in the literature for most use cases, and on places like seqanswers.  If you are doing something like aligning reads to reference genome(s) or set of gene models, you should be using something like bowtie/tophat, bwa, etc., with the output in SAM (BioPerl has perl wrappers for most of these modules).  

You can also do the same for metagenome analyses, but you may need to run BLAST and convert to SAM (maybe that's what you are doing?).  The samtools package comes with perl scripts to do that and can be further used to sort the matches, convert/index a BAM file for fast accession, etc.  From there you can then use tools like Bio::DB::SAM, R/BioConductor/RSamtools, or similar to access the sequences, find coverage statistics, run SNP calls, etc.

And, for the record, we do have an experimental mummer parser, but I believe it lies in a branch at the moment (don't think it has been merged yet):

http://github.com/bioperl/bioperl-live/tree/topic/bug-2701

chris


From cjfields at illinois.edu  Wed Oct 20 11:46:42 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 10:46:42 -0500
Subject: [Bioperl-l] treeio->write_tree problem
In-Reply-To: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
References: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
Message-ID: <112B35F0-77B6-4B46-9E3A-AAB840E7D349@illinois.edu>

Try '-format => "nhx"'.

chris

On Oct 20, 2010, at 10:27 AM, Jim Hu wrote:

> Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.
> 
> Jim
> 
> use Data::Dumper;
> use Bio::TreeIO;
> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>                            -format => "newick");
> while( my $tree = $treeio->next_tree ) {
> 	$treeio->write_tree($tree);
> 	print Dumper($tree);
> 
> }
> 
> =====================================
> Jim Hu
> Associate Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jimhu at tamu.edu  Wed Oct 20 12:16:52 2010
From: jimhu at tamu.edu (Jim Hu)
Date: Wed, 20 Oct 2010 11:16:52 -0500
Subject: [Bioperl-l] treeio->write_tree problem
In-Reply-To: <534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>
References: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
	<534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>
Message-ID: <BADE3FC8-A40F-4832-8C63-B20CB7C40631@tamu.edu>

Doh!  I suspected it was something brain-dead that I was doing.

Thanks very much.  That worked.

Jim

On Oct 20, 2010, at 11:01 AM, Adam Witney wrote:

> 
> you are writing to your input stream. I think you need to create a separate output stream. Maybe something like this (untested):
> 
> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>                           -format => "newick");
> 
> my $treeio_out = new Bio::TreeIO(-fh   => \*STDOUT,
>                           -format => "newick");
> 
> while( my $tree = $treeio->next_tree ) {
> 	$treeio_out->write_tree($tree);
> 	print Dumper($tree);
> }
> 
> 
> 
> On 20 Oct 2010, at 16:27, Jim Hu wrote:
> 
>> Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.
>> 
>> Jim
>> 
>> use Data::Dumper;
>> use Bio::TreeIO;
>> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>>                           -format => "newick");
>> while( my $tree = $treeio->next_tree ) {
>> 	$treeio->write_tree($tree);
>> 	print Dumper($tree);
>> 
>> }
>> 
>> =====================================
>> Jim Hu
>> Associate Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>> 
>> 
>> 
>> _______________________________________________
>> 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 awitney at sgul.ac.uk  Wed Oct 20 12:01:45 2010
From: awitney at sgul.ac.uk (Adam Witney)
Date: Wed, 20 Oct 2010 17:01:45 +0100
Subject: [Bioperl-l] treeio->write_tree problem
In-Reply-To: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
References: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
Message-ID: <534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>


you are writing to your input stream. I think you need to create a separate output stream. Maybe something like this (untested):

my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
                           -format => "newick");

my $treeio_out = new Bio::TreeIO(-fh   => \*STDOUT,
                           -format => "newick");

while( my $tree = $treeio->next_tree ) {
	$treeio_out->write_tree($tree);
	print Dumper($tree);
}



On 20 Oct 2010, at 16:27, Jim Hu wrote:

> Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.
> 
> Jim
> 
> use Data::Dumper;
> use Bio::TreeIO;
> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>                            -format => "newick");
> while( my $tree = $treeio->next_tree ) {
> 	$treeio->write_tree($tree);
> 	print Dumper($tree);
> 
> }
> 
> =====================================
> Jim Hu
> Associate Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
> 
> 
> 
> _______________________________________________
> 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 Oct 20 12:35:40 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 20 Oct 2010 12:35:40 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
	<572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>
Message-ID: <AANLkTimfSXRn1u-wvqSGM+B=j0Ohhnu5SGDcO413pSBm@mail.gmail.com>

Hey Chris,
             Thanks for the reply , it was really useful.
Actually you are right, it is metagenomics sample. The thing is i've never
worked with that huge amount of data, so i am trying to test some alignment
programs (i am just trying to see if i can avoid blastx) so i am trying all
the available programs.

Blasting 200 million reads doesn't seems a right option (may be i will go
with assembly then blasting it).

Thanks
Shalabh


On Wed, Oct 20, 2010 at 11:45 AM, Chris Fields <cjfields at illinois.edu>wrote:

> On Oct 20, 2010, at 10:00 AM, shalabh sharma wrote:
>
> > Hi All,
> >        Is there any module for mummer in Bioperl?
> >
> > Also i need some suggestions and ideas (i think this is the best place to
> > ask).
> > I am working with huge data (around 200 million illumina reads), earlier
> i
> > was using blastx and other similar approaches to annotate but now i think
> > thats not possible, i would be very grateful if anyone can give me some
> idea
> > regarding this.
> >
> > Thanks
> > Shalabh
>
> Hard to say unless we know a little more about what you are attempting to
> do.  Not sure why you are using mummer here, but...
>
> This is something fairly well-covered in the literature for most use cases,
> and on places like seqanswers.  If you are doing something like aligning
> reads to reference genome(s) or set of gene models, you should be using
> something like bowtie/tophat, bwa, etc., with the output in SAM (BioPerl has
> perl wrappers for most of these modules).
>
> You can also do the same for metagenome analyses, but you may need to run
> BLAST and convert to SAM (maybe that's what you are doing?).  The samtools
> package comes with perl scripts to do that and can be further used to sort
> the matches, convert/index a BAM file for fast accession, etc.  From there
> you can then use tools like Bio::DB::SAM, R/BioConductor/RSamtools, or
> similar to access the sequences, find coverage statistics, run SNP calls,
> etc.
>
> And, for the record, we do have an experimental mummer parser, but I
> believe it lies in a branch at the moment (don't think it has been merged
> yet):
>
> http://github.com/bioperl/bioperl-live/tree/topic/bug-2701
>
> chris


From cjfields at illinois.edu  Wed Oct 20 14:15:09 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 13:15:09 -0500
Subject: [Bioperl-l] treeio->write_tree problem
In-Reply-To: <534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>
References: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
	<534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>
Message-ID: <8A7F4396-D88F-438E-B045-F2CD58293DD1@illinois.edu>

Nice catch!  Completely missed that.

chris

On Oct 20, 2010, at 11:01 AM, Adam Witney wrote:

> 
> you are writing to your input stream. I think you need to create a separate output stream. Maybe something like this (untested):
> 
> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>                           -format => "newick");
> 
> my $treeio_out = new Bio::TreeIO(-fh   => \*STDOUT,
>                           -format => "newick");
> 
> while( my $tree = $treeio->next_tree ) {
> 	$treeio_out->write_tree($tree);
> 	print Dumper($tree);
> }
> 
> 
> 
> On 20 Oct 2010, at 16:27, Jim Hu wrote:
> 
>> Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.
>> 
>> Jim
>> 
>> use Data::Dumper;
>> use Bio::TreeIO;
>> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>>                           -format => "newick");
>> while( my $tree = $treeio->next_tree ) {
>> 	$treeio->write_tree($tree);
>> 	print Dumper($tree);
>> 
>> }
>> 
>> =====================================
>> Jim Hu
>> Associate Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>> 
>> 
>> 
>> _______________________________________________
>> 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  Wed Oct 20 14:25:09 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 13:25:09 -0500
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <AANLkTimfSXRn1u-wvqSGM+B=j0Ohhnu5SGDcO413pSBm@mail.gmail.com>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
	<572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>
	<AANLkTimfSXRn1u-wvqSGM+B=j0Ohhnu5SGDcO413pSBm@mail.gmail.com>
Message-ID: <8B2DB10D-0E81-4426-8678-893669DFD0F9@illinois.edu>

I recall there being a lot of tools available for these.  In particular, one of my colleagues has used MEGAN with some success:

http://www-ab.informatik.uni-tuebingen.de/software/megan

If the sample is from a specific host (i.e. gut microbiome, etc), you can set up initial short read runs that act to filter out sequences you might not be interested in (namely those that belong to the host), then run alignments against more focused databases (rRNA, for instance, if one is doing meta-transcriptomic analyses).  Beyond that, I agree that assembly should be included early in the analysis, if it isn't already the initial step.

chris

On Oct 20, 2010, at 11:35 AM, shalabh sharma wrote:

> Hey Chris,
>              Thanks for the reply , it was really useful.
> Actually you are right, it is metagenomics sample. The thing is i've never worked with that huge amount of data, so i am trying to test some alignment programs (i am just trying to see if i can avoid blastx) so i am trying all the available programs.
> 
> Blasting 200 million reads doesn't seems a right option (may be i will go with assembly then blasting it).
> 
> Thanks
> Shalabh
> 
> 
> On Wed, Oct 20, 2010 at 11:45 AM, Chris Fields <cjfields at illinois.edu> wrote:
> On Oct 20, 2010, at 10:00 AM, shalabh sharma wrote:
> 
> > Hi All,
> >        Is there any module for mummer in Bioperl?
> >
> > Also i need some suggestions and ideas (i think this is the best place to
> > ask).
> > I am working with huge data (around 200 million illumina reads), earlier i
> > was using blastx and other similar approaches to annotate but now i think
> > thats not possible, i would be very grateful if anyone can give me some idea
> > regarding this.
> >
> > Thanks
> > Shalabh
> 
> Hard to say unless we know a little more about what you are attempting to do.  Not sure why you are using mummer here, but...
> 
> This is something fairly well-covered in the literature for most use cases, and on places like seqanswers.  If you are doing something like aligning reads to reference genome(s) or set of gene models, you should be using something like bowtie/tophat, bwa, etc., with the output in SAM (BioPerl has perl wrappers for most of these modules).
> 
> You can also do the same for metagenome analyses, but you may need to run BLAST and convert to SAM (maybe that's what you are doing?).  The samtools package comes with perl scripts to do that and can be further used to sort the matches, convert/index a BAM file for fast accession, etc.  From there you can then use tools like Bio::DB::SAM, R/BioConductor/RSamtools, or similar to access the sequences, find coverage statistics, run SNP calls, etc.
> 
> And, for the record, we do have an experimental mummer parser, but I believe it lies in a branch at the moment (don't think it has been merged yet):
> 
> http://github.com/bioperl/bioperl-live/tree/topic/bug-2701
> 
> chris
> 




From shalabh.sharma7 at gmail.com  Wed Oct 20 14:35:54 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 20 Oct 2010 14:35:54 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <8B2DB10D-0E81-4426-8678-893669DFD0F9@illinois.edu>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
	<572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>
	<AANLkTimfSXRn1u-wvqSGM+B=j0Ohhnu5SGDcO413pSBm@mail.gmail.com>
	<8B2DB10D-0E81-4426-8678-893669DFD0F9@illinois.edu>
Message-ID: <AANLkTinxFKdMkOaejxpFDN-qf0pF=Lg7brHHvqYuXk4s@mail.gmail.com>

I have used MEGAN a lot in past, but again it takes blast files as input and
here i just want to avoid blast.
The problem is its environmental sample so i cant throw any of the data.

I know its not a bioperl question but i was just wondering is there any
program that can align my reads against a huge database at amino acid level
(like with refseq or subset of refseq).
or even alignment is a good option?

I really appreciate your input.

Thanks
Shalabh


On Wed, Oct 20, 2010 at 2:25 PM, Chris Fields <cjfields at illinois.edu> wrote:

> I recall there being a lot of tools available for these.  In particular,
> one of my colleagues has used MEGAN with some success:
>
> http://www-ab.informatik.uni-tuebingen.de/software/megan
>
> If the sample is from a specific host (i.e. gut microbiome, etc), you can
> set up initial short read runs that act to filter out sequences you might
> not be interested in (namely those that belong to the host), then run
> alignments against more focused databases (rRNA, for instance, if one is
> doing meta-transcriptomic analyses).  Beyond that, I agree that assembly
> should be included early in the analysis, if it isn't already the initial
> step.
>
> chris
>
> On Oct 20, 2010, at 11:35 AM, shalabh sharma wrote:
>
> > Hey Chris,
> >              Thanks for the reply , it was really useful.
> > Actually you are right, it is metagenomics sample. The thing is i've
> never worked with that huge amount of data, so i am trying to test some
> alignment programs (i am just trying to see if i can avoid blastx) so i am
> trying all the available programs.
> >
> > Blasting 200 million reads doesn't seems a right option (may be i will go
> with assembly then blasting it).
> >
> > Thanks
> > Shalabh
> >
> >
> > On Wed, Oct 20, 2010 at 11:45 AM, Chris Fields <cjfields at illinois.edu>
> wrote:
> > On Oct 20, 2010, at 10:00 AM, shalabh sharma wrote:
> >
> > > Hi All,
> > >        Is there any module for mummer in Bioperl?
> > >
> > > Also i need some suggestions and ideas (i think this is the best place
> to
> > > ask).
> > > I am working with huge data (around 200 million illumina reads),
> earlier i
> > > was using blastx and other similar approaches to annotate but now i
> think
> > > thats not possible, i would be very grateful if anyone can give me some
> idea
> > > regarding this.
> > >
> > > Thanks
> > > Shalabh
> >
> > Hard to say unless we know a little more about what you are attempting to
> do.  Not sure why you are using mummer here, but...
> >
> > This is something fairly well-covered in the literature for most use
> cases, and on places like seqanswers.  If you are doing something like
> aligning reads to reference genome(s) or set of gene models, you should be
> using something like bowtie/tophat, bwa, etc., with the output in SAM
> (BioPerl has perl wrappers for most of these modules).
> >
> > You can also do the same for metagenome analyses, but you may need to run
> BLAST and convert to SAM (maybe that's what you are doing?).  The samtools
> package comes with perl scripts to do that and can be further used to sort
> the matches, convert/index a BAM file for fast accession, etc.  From there
> you can then use tools like Bio::DB::SAM, R/BioConductor/RSamtools, or
> similar to access the sequences, find coverage statistics, run SNP calls,
> etc.
> >
> > And, for the record, we do have an experimental mummer parser, but I
> believe it lies in a branch at the moment (don't think it has been merged
> yet):
> >
> > http://github.com/bioperl/bioperl-live/tree/topic/bug-2701
> >
> > chris
> >
>
>


From rmb32 at cornell.edu  Wed Oct 20 20:27:36 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Wed, 20 Oct 2010 17:27:36 -0700
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <840CF652-BAE0-4DD6-A375-30A817F20351@illinois.edu>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>	<AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>	<9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>	<AANLkTi=LKy-UMPkQkDXN=83sjRFdJMgOn7Du9vVdh6x7@mail.gmail.com>
	<840CF652-BAE0-4DD6-A375-30A817F20351@illinois.edu>
Message-ID: <4CBF88F8.2030601@cornell.edu>

Ah, the joys of optional deps.

You know, bioperl-run does not have that many deps right now.  Why don't 
we just make those optional ones required?

R


Chris Fields wrote:
> If you mean IPC::Run, I'm not sure.  I don't think BioPerl-Run was ever a part of Strawberry Perl Pro.
> 
> I do know there are some warnings that will pop up with BioPerl when using perl 5.12; these have been fixed in the github repo but haven't made their way into a release yet.
> 
> chris
> 
> On Oct 19, 2010, at 3:38 PM, T D wrote:
> 
>> Thank you. I downloaded IPC::Run and the code seems to be working now. Is
>> Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?
>>
>>
>> On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>
>>> No, IPC::Run is different than IPC::Run3:
>>>
>>> http://search.cpan.org/dist/IPC-Run/
>>> http://search.cpan.org/dist/IPC-Run3/
>>>
>>> Both should work under Windows, not sure about Windows7 but I can't see why
>>> they wouldn't work.
>>>
>>> chris
>>>
>>> On Oct 19, 2010, at 12:28 PM, T D wrote:
>>>
>>>> Hi,
>>>>
>>>> I'm new to BioPerl and Perl in general, and I'm trying to get
>>>> StandAloneBlastPlus to run. I got the latest versions using git and
>>>> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
>>> not
>>>> finding modules. Here is my error:
>>>>
>>>> Can't locate IPC/Run.pm in @INC
>>>>
>>>> Where is this module located? I am running Windows 7. I did a search for
>>> the
>>>> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
>>>> Run.pm the older version? I have Perl v5.12.1 installed.
>>>>
>>>> Thanks in advance!
>>>> Tracey
>>>> _______________________________________________
>>>> 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 maj at fortinbras.us  Wed Oct 20 21:21:56 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Thu, 21 Oct 2010 01:21:56 +0000
Subject: [Bioperl-l] IPC/Run.pm?
Message-ID: <W2403825015265021287624116@webmail11>

I would +1 making IPC::Run required. It's got some nice features and it much safer than system(). Might even want to make it a dev recommendation for all system calls. MAJ

>-----Original Message-----
>From: Robert Buels [mailto:rmb32 at cornell.edu]
>Sent: Wednesday, October 20, 2010 08:27 PM
>To: 'Chris Fields'
>Cc: bioperl-l at lists.open-bio.org
>Subject: Re: [Bioperl-l] IPC/Run.pm?
>
>Ah, the joys of optional deps.
>
>You know, bioperl-run does not have that many deps right now.  Why don't 
>we just make those optional ones required?
>
>R
>
>
>Chris Fields wrote:
>> If you mean IPC::Run, I'm not sure.  I don't think BioPerl-Run was ever a part of Strawberry Perl Pro.
>> 
>> I do know there are some warnings that will pop up with BioPerl when using perl 5.12; these have been fixed in the github repo but haven't made their way into a release yet.
>> 
>> chris
>> 
>> On Oct 19, 2010, at 3:38 PM, T D wrote:
>> 
>>> Thank you. I downloaded IPC::Run and the code seems to be working now. Is
>>> Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?
>>>
>>>
>>> On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>
>>>> No, IPC::Run is different than IPC::Run3:
>>>>
>>>> http://search.cpan.org/dist/IPC-Run/
>>>> http://search.cpan.org/dist/IPC-Run3/
>>>>
>>>> Both should work under Windows, not sure about Windows7 but I can't see why
>>>> they wouldn't work.
>>>>
>>>> chris
>>>>
>>>> On Oct 19, 2010, at 12:28 PM, T D wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I'm new to BioPerl and Perl in general, and I'm trying to get
>>>>> StandAloneBlastPlus to run. I got the latest versions using git and
>>>>> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
>>>> not
>>>>> finding modules. Here is my error:
>>>>>
>>>>> Can't locate IPC/Run.pm in @INC
>>>>>
>>>>> Where is this module located? I am running Windows 7. I did a search for
>>>> the
>>>>> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
>>>>> Run.pm the older version? I have Perl v5.12.1 installed.
>>>>>
>>>>> Thanks in advance!
>>>>> Tracey
>>>>> _______________________________________________
>>>>> 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 cjfields at illinois.edu  Wed Oct 20 21:54:48 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 20:54:48 -0500
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <W2403825015265021287624116@webmail11>
References: <W2403825015265021287624116@webmail11>
Message-ID: <697C7C00-5ED9-4A69-9F55-6C8C6F349DF4@illinois.edu>

+1.  Quite a few modules there use it.

chris

On Oct 20, 2010, at 8:21 PM, Mark A. Jensen wrote:

> I would +1 making IPC::Run required. It's got some nice features and it much safer than system(). Might even want to make it a dev recommendation for all system calls. MAJ
> 
>> -----Original Message-----
>> From: Robert Buels [mailto:rmb32 at cornell.edu]
>> Sent: Wednesday, October 20, 2010 08:27 PM
>> To: 'Chris Fields'
>> Cc: bioperl-l at lists.open-bio.org
>> Subject: Re: [Bioperl-l] IPC/Run.pm?
>> 
>> Ah, the joys of optional deps.
>> 
>> You know, bioperl-run does not have that many deps right now.  Why don't 
>> we just make those optional ones required?
>> 
>> R
>> 
>> 
>> Chris Fields wrote:
>>> If you mean IPC::Run, I'm not sure.  I don't think BioPerl-Run was ever a part of Strawberry Perl Pro.
>>> 
>>> I do know there are some warnings that will pop up with BioPerl when using perl 5.12; these have been fixed in the github repo but haven't made their way into a release yet.
>>> 
>>> chris
>>> 
>>> On Oct 19, 2010, at 3:38 PM, T D wrote:
>>> 
>>>> Thank you. I downloaded IPC::Run and the code seems to be working now. Is
>>>> Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?
>>>> 
>>>> 
>>>> On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>> 
>>>>> No, IPC::Run is different than IPC::Run3:
>>>>> 
>>>>> http://search.cpan.org/dist/IPC-Run/
>>>>> http://search.cpan.org/dist/IPC-Run3/
>>>>> 
>>>>> Both should work under Windows, not sure about Windows7 but I can't see why
>>>>> they wouldn't work.
>>>>> 
>>>>> chris
>>>>> 
>>>>> On Oct 19, 2010, at 12:28 PM, T D wrote:
>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I'm new to BioPerl and Perl in general, and I'm trying to get
>>>>>> StandAloneBlastPlus to run. I got the latest versions using git and
>>>>>> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
>>>>> not
>>>>>> finding modules. Here is my error:
>>>>>> 
>>>>>> Can't locate IPC/Run.pm in @INC
>>>>>> 
>>>>>> Where is this module located? I am running Windows 7. I did a search for
>>>>> the
>>>>>> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
>>>>>> Run.pm the older version? I have Perl v5.12.1 installed.
>>>>>> 
>>>>>> Thanks in advance!
>>>>>> Tracey
>>>>>> _______________________________________________
>>>>>> 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 ashwani.iiit at gmail.com  Thu Oct 21 04:39:22 2010
From: ashwani.iiit at gmail.com (ashwani sharma)
Date: Thu, 21 Oct 2010 14:09:22 +0530
Subject: [Bioperl-l] how to download PDB files using Bioperl script
Message-ID: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>

Hi All,


I have around 150 pdb file names and I need to download them from Protein
Data Bank. I wonder if someone could tell me how to do it by using Bioperl.

Thanks in advance.

Regards,
Ashwani


From hanbobio at 126.com  Tue Oct 19 07:50:07 2010
From: hanbobio at 126.com (yusheng liao)
Date: Tue, 19 Oct 2010 11:50:07 +0000 (UTC)
Subject: [Bioperl-l] Can't locate Bio/seqIO.pm in @INC
Message-ID: <loom.20101019T134347-528@post.gmane.org>

Can't locate Bio/seqIO.pm in @INC 
I try to run a .pl file to get multi sequences for t
he GenBank using the
Bioperl. The following were the error message:
linux:/home/liaoy # perl hsv-1.pl
Can't locate Bio/seqIO.pm in @INC (@INC contains:
/usr/lib/perl5/5.8.7/i586-linux-thread-multi /usr/lib/perl5/5.8.7
/usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.7 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .)
 at hsv-1.pl line 4.
BEGIN failed--compilation aborted at hsv-1.pl line 4.

what is the problem? And how to corret it? 



From cgzheng86 at gmail.com  Thu Oct 21 04:45:40 2010
From: cgzheng86 at gmail.com (Chaogu Zheng)
Date: Thu, 21 Oct 2010 01:45:40 -0700 (PDT)
Subject: [Bioperl-l] Failed to load module Bio::SeqIO::swiss
Message-ID: <63e01ab5-99f2-46a0-8901-3bdb24562c5f@g13g2000yqj.googlegroups.com>

I am extremely new to Bioperl and got a problem immediately after I
installed it.

I installed Bioperl-pm5100 and Bioperl-run-pm5100 using fink.
Everything seems to be fine. However, when I tried to retrieve some
sequences from swissprot, I found the following errors.

It seems the module Bio::SeqIO::swiss can not be loaded, though I
indeed found it under the correct directory. By the way, if I change
'swiss' to 'genbank' I can successfully run the program.

I don't know how to fix it. Anyone can help me?


Ryan

>>>>>>>>>>>>>>
Bio::SeqIO: swiss cannot be found
Exception
------------- EXCEPTION -------------
MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/
Stag.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-
multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-
multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/
5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/
Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/
5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/
5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /
Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/
Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/
5.10.0 .) at /sw/lib/perl5/5.10.0/Bio/Annotation/TagTree.pm line 123.
BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/
Annotation/TagTree.pm line 123.
Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/SeqIO/
swiss.pm line 208.
BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/SeqIO/
swiss.pm line 208.
Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/Root/Root.pm
line 439.

STACK Bio::Root::Root::_load_module /sw/lib/perl5/5.10.0/Bio/Root/
Root.pm:441
STACK (eval) /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:570
STACK Bio::SeqIO::_load_format_module /sw/lib/perl5/5.10.0/Bio/
SeqIO.pm:569
STACK Bio::SeqIO::new /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:389
STACK Bio::DB::WebDBSeqI::get_seq_stream /sw/lib/perl5/5.10.0/Bio/DB/
WebDBSeqI.pm:472
STACK Bio::DB::WebDBSeqI::get_Stream_by_acc /sw/lib/perl5/5.10.0/Bio/
DB/WebDBSeqI.pm:314
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
WebDBSeqI.pm:186
STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
STACK toplevel ./Documents/perl-programs/perl_test:8
-------------------------------------


For more information about the SeqIO system please see the SeqIO docs.
This includes ways of checking for formats at compile time, not run
time

------------- EXCEPTION -------------
MSG: acc P11217 does not exist
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
WebDBSeqI.pm:187
STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
STACK toplevel ./Documents/perl-programs/perl_test:8
-------------------------------------


From cjfields at illinois.edu  Thu Oct 21 11:02:35 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 21 Oct 2010 10:02:35 -0500
Subject: [Bioperl-l] Can't locate Bio/seqIO.pm in @INC
In-Reply-To: <loom.20101019T134347-528@post.gmane.org>
References: <loom.20101019T134347-528@post.gmane.org>
Message-ID: <9E5A48C0-4509-429B-8F16-9A1D1A440CC8@illinois.edu>

Check your spelling (note the caps below):

use Bio::SeqIO;

chris

On Oct 19, 2010, at 6:50 AM, yusheng liao wrote:

> Can't locate Bio/seqIO.pm in @INC 
> I try to run a .pl file to get multi sequences for t
> he GenBank using the
> Bioperl. The following were the error message:
> linux:/home/liaoy # perl hsv-1.pl
> Can't locate Bio/seqIO.pm in @INC (@INC contains:
> /usr/lib/perl5/5.8.7/i586-linux-thread-multi /usr/lib/perl5/5.8.7
> /usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.7 /usr/lib/perl5/site_perl
> /usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .)
> at hsv-1.pl line 4.
> BEGIN failed--compilation aborted at hsv-1.pl line 4.
> 
> what is the problem? And how to corret it? 
> 
> _______________________________________________
> 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 Oct 21 11:05:17 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 21 Oct 2010 10:05:17 -0500
Subject: [Bioperl-l] Failed to load module Bio::SeqIO::swiss
In-Reply-To: <63e01ab5-99f2-46a0-8901-3bdb24562c5f@g13g2000yqj.googlegroups.com>
References: <63e01ab5-99f2-46a0-8901-3bdb24562c5f@g13g2000yqj.googlegroups.com>
Message-ID: <23FDD4AF-3E56-4E05-AFD7-21A54DECD1C6@illinois.edu>

Like the error message says, you need to install Data::Stag (so, for some reason, this way left off).  However, I'm not sure why you are using fink as the version in stable is still 1.5.1; bioperl 1.6.1 is in fink-unstable.

chris

On Oct 21, 2010, at 3:45 AM, Chaogu Zheng wrote:

> I am extremely new to Bioperl and got a problem immediately after I
> installed it.
> 
> I installed Bioperl-pm5100 and Bioperl-run-pm5100 using fink.
> Everything seems to be fine. However, when I tried to retrieve some
> sequences from swissprot, I found the following errors.
> 
> It seems the module Bio::SeqIO::swiss can not be loaded, though I
> indeed found it under the correct directory. By the way, if I change
> 'swiss' to 'genbank' I can successfully run the program.
> 
> I don't know how to fix it. Anyone can help me?
> 
> 
> Ryan
> 
>>>>>>>>>>>>>>> 
> Bio::SeqIO: swiss cannot be found
> Exception
> ------------- EXCEPTION -------------
> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/
> Stag.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-
> multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-
> multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/
> 5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/
> Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/
> 5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/
> 5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /
> Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/
> Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/
> 5.10.0 .) at /sw/lib/perl5/5.10.0/Bio/Annotation/TagTree.pm line 123.
> BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/
> Annotation/TagTree.pm line 123.
> Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> swiss.pm line 208.
> BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> swiss.pm line 208.
> Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/Root/Root.pm
> line 439.
> 
> STACK Bio::Root::Root::_load_module /sw/lib/perl5/5.10.0/Bio/Root/
> Root.pm:441
> STACK (eval) /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:570
> STACK Bio::SeqIO::_load_format_module /sw/lib/perl5/5.10.0/Bio/
> SeqIO.pm:569
> STACK Bio::SeqIO::new /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:389
> STACK Bio::DB::WebDBSeqI::get_seq_stream /sw/lib/perl5/5.10.0/Bio/DB/
> WebDBSeqI.pm:472
> STACK Bio::DB::WebDBSeqI::get_Stream_by_acc /sw/lib/perl5/5.10.0/Bio/
> DB/WebDBSeqI.pm:314
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> WebDBSeqI.pm:186
> STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> STACK toplevel ./Documents/perl-programs/perl_test:8
> -------------------------------------
> 
> 
> For more information about the SeqIO system please see the SeqIO docs.
> This includes ways of checking for formats at compile time, not run
> time
> 
> ------------- EXCEPTION -------------
> MSG: acc P11217 does not exist
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> WebDBSeqI.pm:187
> STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> STACK toplevel ./Documents/perl-programs/perl_test:8
> -------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jimhu at tamu.edu  Thu Oct 21 13:52:32 2010
From: jimhu at tamu.edu (Jim Hu)
Date: Thu, 21 Oct 2010 12:52:32 -0500
Subject: [Bioperl-l] Does $tree->remove_Node prune or splice?
Message-ID: <927BEE54-ABC2-428A-AF42-DDEBDEABB878@tamu.edu>

I'm trying to take an unreadable tree from PFAM and prune it down to just show the paralogs from E. coli.

When you run remove_Node on an internal node, is it supposed to reconnect the ancestors to the descendants?  This seems to be way to aggressive in what it's removing.

while( my $tree = $treeio->next_tree ) {
	for my $node ( $tree->get_nodes ) {
		if ($node->id =~ m/_ECOLI/){
			#	leave this node alone
			#	print $node->id."\n";
		}else{
			if ($node->is_Leaf){
				$tree->remove_Node($node);
			}else{
				my $num_children = scalar($node->each_Descendent);
				if ($num_children == 1){ 
					print "removing ".$node->id."\n";
					$tree->remove_Node($node);
				}	
			}	
		}
	}
	$treeio_out->write_tree($tree);
}

The idea is that when I've pruned the non-ECOLI leaves, some internal nodes will not be branches anymore.  But at the end, all the ECOLI nodes are gone, presumably because an ancestor got removed and the whole branch was lost.  Is there a way to remove just a node and graft the tree back together?  My plan, once I get that working is to repeat the traversal until the output stops changing.

Jim


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





From cgzheng86 at gmail.com  Thu Oct 21 13:57:06 2010
From: cgzheng86 at gmail.com (Chaogu Zheng)
Date: Thu, 21 Oct 2010 10:57:06 -0700 (PDT)
Subject: [Bioperl-l] Failed to load module Bio::SeqIO::swiss
In-Reply-To: <23FDD4AF-3E56-4E05-AFD7-21A54DECD1C6@illinois.edu>
References: <63e01ab5-99f2-46a0-8901-3bdb24562c5f@g13g2000yqj.googlegroups.com>
	<23FDD4AF-3E56-4E05-AFD7-21A54DECD1C6@illinois.edu>
Message-ID: <974a993b-fbdf-4ca6-a59b-a7f247669eff@j18g2000yqd.googlegroups.com>

Maybe my reason for this is silly. I am using the Mac OS X 10.6, which
has the pre-installed perl 5.10.0. Fink only has the unstable bioperl
1.6.1 for Mac OS X 10.6. If I want to install bioperl-pm588 that is
the fink-stable 1.5.1 version, I guess I have to install an earlier
version of perl 5.8.8. I did not bother to do that.

So, do you think I really need to uninstall bioperl-pm5100 and get
perl 5.8.8 to try the fink-stable one?

Ryan

On Oct 21, 11:05?am, Chris Fields <cjfie... at illinois.edu> wrote:
> Like the error message says, you need to install Data::Stag (so, for some reason, this way left off). ?However, I'm not sure why you are using fink as the version in stable is still 1.5.1; bioperl 1.6.1 is in fink-unstable.
>
> chris
>
> On Oct 21, 2010, at 3:45 AM, Chaogu Zheng wrote:
>
>
>
>
>
> > I am extremely new to Bioperl and got a problem immediately after I
> > installed it.
>
> > I installed Bioperl-pm5100 and Bioperl-run-pm5100 using fink.
> > Everything seems to be fine. However, when I tried to retrieve some
> > sequences from swissprot, I found the following errors.
>
> > It seems the module Bio::SeqIO::swiss can not be loaded, though I
> > indeed found it under the correct directory. By the way, if I change
> > 'swiss' to 'genbank' I can successfully run the program.
>
> > I don't know how to fix it. Anyone can help me?
>
> > Ryan
>
> > Bio::SeqIO: swiss cannot be found
> > Exception
> > ------------- EXCEPTION -------------
> > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/
> > Stag.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-
> > multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-
> > multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/
> > 5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/
> > Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/
> > 5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/
> > 5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /
> > Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/
> > Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/
> > 5.10.0 .) at /sw/lib/perl5/5.10.0/Bio/Annotation/TagTree.pm line 123.
> > BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/
> > Annotation/TagTree.pm line 123.
> > Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> > swiss.pm line 208.
> > BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> > swiss.pm line 208.
> > Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/Root/Root.pm
> > line 439.
>
> > STACK Bio::Root::Root::_load_module /sw/lib/perl5/5.10.0/Bio/Root/
> > Root.pm:441
> > STACK (eval) /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:570
> > STACK Bio::SeqIO::_load_format_module /sw/lib/perl5/5.10.0/Bio/
> > SeqIO.pm:569
> > STACK Bio::SeqIO::new /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:389
> > STACK Bio::DB::WebDBSeqI::get_seq_stream /sw/lib/perl5/5.10.0/Bio/DB/
> > WebDBSeqI.pm:472
> > STACK Bio::DB::WebDBSeqI::get_Stream_by_acc /sw/lib/perl5/5.10.0/Bio/
> > DB/WebDBSeqI.pm:314
> > STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> > WebDBSeqI.pm:186
> > STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> > STACK toplevel ./Documents/perl-programs/perl_test:8
> > -------------------------------------
>
> > For more information about the SeqIO system please see the SeqIO docs.
> > This includes ways of checking for formats at compile time, not run
> > time
>
> > ------------- EXCEPTION -------------
> > MSG: acc P11217 does not exist
> > STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> > WebDBSeqI.pm:187
> > STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> > STACK toplevel ./Documents/perl-programs/perl_test:8
> > -------------------------------------
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioper... at lists.open-bio.org
> >http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l



From izlowe at ucdavis.edu  Thu Oct 21 22:00:24 2010
From: izlowe at ucdavis.edu (Iago Lowe)
Date: Thu, 21 Oct 2010 22:00:24 -0400
Subject: [Bioperl-l] Specifying the search set in NCBI BLAST
Message-ID: <AANLkTi=s_RstcyKyoGws0ykcK8VAb7DVcLtMrRyt2O4X@mail.gmail.com>

In the "Choose Search Set" tab on the NCBI BLAST webpage, there are some
convenient ways to restrict the size of the database for queries.  In there
a way to apply these restrictions in a remote search via Bioperl?

For example, in our research, we want to search only the "Non-human,
non-mouse ESTs" for the organism "Triticum" rather than the entire NCBI
database.

Thanks very much for any guidance.
Iago Lowe


From David.Messina at sbc.su.se  Fri Oct 22 11:29:36 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 22 Oct 2010 11:29:36 -0400
Subject: [Bioperl-l] Specifying the search set in NCBI BLAST
In-Reply-To: <AANLkTi=s_RstcyKyoGws0ykcK8VAb7DVcLtMrRyt2O4X@mail.gmail.com>
References: <AANLkTi=s_RstcyKyoGws0ykcK8VAb7DVcLtMrRyt2O4X@mail.gmail.com>
Message-ID: <C7922411-92DE-46D0-B4AA-E32A606C7415@sbc.su.se>

Hi Iago,

It is possible to do this with BioPerl, but I would recommend simply downloading Blast+ (note the +) and using the -entrez_query and -remote options.

Dave




From MEC at stowers.org  Fri Oct 22 11:40:24 2010
From: MEC at stowers.org (Cook, Malcolm)
Date: Fri, 22 Oct 2010 10:40:24 -0500
Subject: [Bioperl-l] Specifying the search set in NCBI BLAST
In-Reply-To: <C7922411-92DE-46D0-B4AA-E32A606C7415@sbc.su.se>
References: <AANLkTi=s_RstcyKyoGws0ykcK8VAb7DVcLtMrRyt2O4X@mail.gmail.com>
	<C7922411-92DE-46D0-B4AA-E32A606C7415@sbc.su.se>
Message-ID: <BD62CBAC4395B94096109020651BE2EC138AFB720D@EXCHMB-02.stowers-institute.org>

I agree with Dave.

But, if you must use BioPerl, see http://doc.bioperl.org/releases/bioperl-1.4/Bio/Tools/Run/RemoteBlast.html where it shows this code:

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

You'll probably want to set your database to  est_others (c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html#2 )

--Malcolm
 

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dave Messina
Sent: Friday, October 22, 2010 10:30 AM
To: Iago Lowe
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Specifying the search set in NCBI BLAST

Hi Iago,

It is possible to do this with BioPerl, but I would recommend simply downloading Blast+ (note the +) and using the -entrez_query and -remote options.

Dave


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



From jun.yin at ucd.ie  Fri Oct 22 12:12:45 2010
From: jun.yin at ucd.ie (Jun Yin)
Date: Fri, 22 Oct 2010 17:12:45 +0100
Subject: [Bioperl-l] how to download PDB files using Bioperl script
In-Reply-To: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
Message-ID: <01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>

Hi, Ashwani,

I havenot found any module in BioPerl for downloading PDB files, though
Bio::Structure::IO::pdb can parse PDB files.

However, PDB provides RESTful service
(http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
batch downloading the proteins.

Cheers,
Jun Yin
Ph.D.?student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
Sent: Thursday, October 21, 2010 9:39 AM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] how to download PDB files using Bioperl script

Hi All,


I have around 150 pdb file names and I need to download them from Protein
Data Bank. I wonder if someone could tell me how to do it by using Bioperl.

Thanks in advance.

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

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__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

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database 5377 (20100818) __________

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From jason at bioperl.org  Sat Oct 23 11:33:49 2010
From: jason at bioperl.org (Jason Stajich)
Date: Sat, 23 Oct 2010 08:33:49 -0700
Subject: [Bioperl-l] Question on BioPerl modules
In-Reply-To: <1287838391.5784.19.camel@ubuntu>
References: <1287838391.5784.19.camel@ubuntu>
Message-ID: <4CC3005D.1070708@bioperl.org>

Lincoln overloaded the "" method for the objects that are returned from 
Bio::DB::Fasta so that attempts to print them directly will instead 
print out the display_id field.

If you want to know what kind of object you getting back you use 'ref', 
as in:
print ref($seq),"\n";

Tao Zhu wrote, On 10/23/10 5:53 AM:
> Dear Professor Stajich,
>
> Recently I was puzzled when using two BioPerl modules, Bio::Index::Fasta
> and Bio::DB::Fasta;
>
> For example, I have a fasta file: sequence.fa, on my computer. That is:
>
>> ORFN:87
> ATGGAAGCCCCTTCAGAAATTACCGATTCCAA
>
> I hope to make a local index, then I use Bio::Index::Fasta and write:
>
> use Bio::Index::Fasta;
> $file_name = "sequence.fa";
> $id = "ORFN:87";
> $inx = Bio::Index::Fasta->new (-filename =>  $file_name . ".idx", -write_flag =>  1);
> $inx->make_index($file_name);
> $seq_obj = $inx->fetch($id);
> print "$seq_obj\n";
>
> Running the perl script, it prints "Bio::Seq=HASH(0x66590a0)" on screen.
> That means the scalar "$seq_obj" is a Bio::Seq object.
>
> However, I try another method, using Bio::DB::Fasta,
>
> use Bio::DB::Fasta;
> ($file,$id) = ("sequence.fa","ORFN:87");
> $db = Bio::DB::Fasta->new($file);
> $seq_obj = $db->get_Seq_by_id($id);
> print "$seq_obj\n";
>
> I expect it should also print "Bio::Seq=HASH(sth)",because I also get a
> Bio::Seq object. Surprisingly it prints "ORFN:87"
>
> How it comes to be?
>

-- 
Jason Stajich
jason at bioperl.org



From yifangt at hotmail.com  Sat Oct 23 02:21:40 2010
From: yifangt at hotmail.com (yifangt)
Date: Fri, 22 Oct 2010 23:21:40 -0700 (PDT)
Subject: [Bioperl-l] Can't locate Bio/seqIO.pm in @INC
In-Reply-To: <loom.20101019T134347-528@post.gmane.org>
References: <loom.20101019T134347-528@post.gmane.org>
Message-ID: <30034148.post@talk.nabble.com>


Probably your Bioperl installation is not correct. Re-install your bioperl
and try again!

Good luck!




yusheng liao wrote:
> 
> Can't locate Bio/seqIO.pm in @INC 
> I try to run a .pl file to get multi sequences for t
> he GenBank using the
> Bioperl. The following were the error message:
> linux:/home/liaoy # perl hsv-1.pl
> Can't locate Bio/seqIO.pm in @INC (@INC contains:
> /usr/lib/perl5/5.8.7/i586-linux-thread-multi /usr/lib/perl5/5.8.7
> /usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.7 /usr/lib/perl5/site_perl
> /usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .)
>  at hsv-1.pl line 4.
> BEGIN failed--compilation aborted at hsv-1.pl line 4.
> 
> what is the problem? And how to corret it? 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
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From timmcilveen at talktalk.net  Sun Oct 24 20:45:15 2010
From: timmcilveen at talktalk.net (Tim)
Date: Mon, 25 Oct 2010 01:45:15 +0100
Subject: [Bioperl-l] Installing Bioperl  from Git Hub
Message-ID: <4CC4D31B.1080905@talktalk.net>

Hi everyone,
A couple of weeks ago, I posted a query about installing Bioperl from 
GitHub. I was getting installation errors and someone on the list had 
picked up on  a typo I had made while trying to install it.
Bioperl is now installed and working properly. I forgot to acknowledge 
your help. Thanks for your advice.

Tim



From edwardsa at cs.man.ac.uk  Mon Oct 25 12:33:21 2010
From: edwardsa at cs.man.ac.uk (Andrea Edwards)
Date: Mon, 25 Oct 2010 17:33:21 +0100
Subject: [Bioperl-l] can't install bioperl 1.6.1
Message-ID: <4CC5B151.8030606@cs.man.ac.uk>

  Hi

I can't install Bioperl 1.6.1 on windows using Active Perl 5.8.8.822

I have added the repositories as mentioned in the user guide but get 
this error message

?ERROR: File conflict for 'C:/Perl/html/bin/bp_aacomp.html'.The package 
BioPerl has already installed a file that package bioperl wants to install.?

I have seen a forum thread which says the problem is due to the 
trouchelle repository.

http://www.perlmonks.org/?node_id=817531

I did remove the trouchelle repository as suggested and bioperl 1.6.1 
does seem to have installed but I don't know enough about Perl to know 
if it will have installed correctly by removing this repository.

I installed BioPerl 1.6 successfully on a different PC running 
ActivePerl 5.8.9.827 without needing to remove the trouchelle so I 'm 
not sure what to think.

Many thanks




From sahasangi at gmail.com  Tue Oct 26 07:41:01 2010
From: sahasangi at gmail.com (sangita saha)
Date: Tue, 26 Oct 2010 17:11:01 +0530
Subject: [Bioperl-l] Fwd: Need Help regarding reciprocal BLAST using BioPerl
In-Reply-To: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>
References: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>
Message-ID: <AANLkTimidEhyj=nJ4U9vwp1He45fgUg-d1LOs+dEYoq=@mail.gmail.com>

---------- Forwarded message ----------
From: sangita saha <sahasangi at gmail.com>
Date: Tue, Oct 26, 2010 at 4:32 PM
Subject: Need Help regarding reciprocal BLAST using BioPerl
To: bioperl-l at lists.open-bio.org


Hello Sir,
I have installed BioPerl and standalone BLAST in my PC.I faced problem in
doing the Reciprocal BLAST.Will anyone kindly tell me how to link between
BioPerl and Standalone BLAST ?How to use Bioperl itself to identify the
ortholog?What is the command to be used for reciprocal Blast?Since I am the
new user of it and need help to your concerned.If anybody have any
experience regarding reciprocal blast please give me a suggestion.

I will be happy to hear you from.

Thank you

With Regards,
Sangita Saha


From shalabh.sharma7 at gmail.com  Tue Oct 26 10:04:31 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 26 Oct 2010 10:04:31 -0400
Subject: [Bioperl-l] Fwd: Need Help regarding reciprocal BLAST using
	BioPerl
In-Reply-To: <AANLkTimidEhyj=nJ4U9vwp1He45fgUg-d1LOs+dEYoq=@mail.gmail.com>
References: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>
	<AANLkTimidEhyj=nJ4U9vwp1He45fgUg-d1LOs+dEYoq=@mail.gmail.com>
Message-ID: <AANLkTinhKE_KTzr3_Xftu96dyhyC4fc0QYm_2FhQ6HPU@mail.gmail.com>

Hey Sangita,
               I am not sure if bioperl has any direct command for
reciprocal blast.
But it is fairly simple, you can use all vs all blast then post process your
results in finding orthologs according to your cutoff parameters.

Other way is to use OrthoMCL :
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403725/?tool=pubmed

Also read this:
http://bioperl.org/wiki/HOWTO:PhylogeneticAnalysisPipeline
 Since you are a beginner it will help you a lot.

Hope this helps.

Shalabh
-----------------------------------
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636
On Tue, Oct 26, 2010 at 7:41 AM, sangita saha <sahasangi at gmail.com> wrote:

> ---------- Forwarded message ----------
> From: sangita saha <sahasangi at gmail.com>
> Date: Tue, Oct 26, 2010 at 4:32 PM
> Subject: Need Help regarding reciprocal BLAST using BioPerl
> To: bioperl-l at lists.open-bio.org
>
>
> Hello Sir,
> I have installed BioPerl and standalone BLAST in my PC.I faced problem in
> doing the Reciprocal BLAST.Will anyone kindly tell me how to link between
> BioPerl and Standalone BLAST ?How to use Bioperl itself to identify the
> ortholog?What is the command to be used for reciprocal Blast?Since I am the
> new user of it and need help to your concerned.If anybody have any
> experience regarding reciprocal blast please give me a suggestion.
>
> I will be happy to hear you from.
>
> Thank you
>
> With Regards,
> Sangita Saha
> _______________________________________________
> 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  Tue Oct 26 10:09:48 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 26 Oct 2010 10:09:48 -0400
Subject: [Bioperl-l] Genome Information
Message-ID: <AANLkTikLfZa-FSFXiriqPGHf63kcTgkY0+rT2Mq=7hCu@mail.gmail.com>

Hi All,
       I have thousands of taxaIds and i need to find out the following
information regarding genomes:
1) Taxonomy information
2) GC%
3) total coding genes %

I can easily find the taxonomy info by using Bio::DB::Taxonomy but for the
other two i am stuck.
Is there any way i can find this info?
I would really appreciate your help.

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


From cjfields at illinois.edu  Tue Oct 26 11:40:02 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 26 Oct 2010 10:40:02 -0500
Subject: [Bioperl-l] Fwd: Need Help regarding reciprocal BLAST using
	BioPerl
In-Reply-To: <AANLkTinhKE_KTzr3_Xftu96dyhyC4fc0QYm_2FhQ6HPU@mail.gmail.com>
References: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>
	<AANLkTimidEhyj=nJ4U9vwp1He45fgUg-d1LOs+dEYoq=@mail.gmail.com>
	<AANLkTinhKE_KTzr3_Xftu96dyhyC4fc0QYm_2FhQ6HPU@mail.gmail.com>
Message-ID: <02B10B6A-5E4A-4889-AACA-A47D8FA39E88@illinois.edu>

BioPerl does have Bio::Tools::Run::TribeMCL in BioPerl-Run, but I don't suggest using that.  mcl has a few tools in-place already within the distribition, but I personally have been using the latest version of OrthoMCL (v2), and have also started setting up a pipeline using InParanoid.

chris

On Oct 26, 2010, at 9:04 AM, shalabh sharma wrote:

> Hey Sangita,
>               I am not sure if bioperl has any direct command for
> reciprocal blast.
> But it is fairly simple, you can use all vs all blast then post process your
> results in finding orthologs according to your cutoff parameters.
> 
> Other way is to use OrthoMCL :
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403725/?tool=pubmed
> 
> Also read this:
> http://bioperl.org/wiki/HOWTO:PhylogeneticAnalysisPipeline
> Since you are a beginner it will help you a lot.
> 
> Hope this helps.
> 
> Shalabh
> -----------------------------------
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
> On Tue, Oct 26, 2010 at 7:41 AM, sangita saha <sahasangi at gmail.com> wrote:
> 
>> ---------- Forwarded message ----------
>> From: sangita saha <sahasangi at gmail.com>
>> Date: Tue, Oct 26, 2010 at 4:32 PM
>> Subject: Need Help regarding reciprocal BLAST using BioPerl
>> To: bioperl-l at lists.open-bio.org
>> 
>> 
>> Hello Sir,
>> I have installed BioPerl and standalone BLAST in my PC.I faced problem in
>> doing the Reciprocal BLAST.Will anyone kindly tell me how to link between
>> BioPerl and Standalone BLAST ?How to use Bioperl itself to identify the
>> ortholog?What is the command to be used for reciprocal Blast?Since I am the
>> new user of it and need help to your concerned.If anybody have any
>> experience regarding reciprocal blast please give me a suggestion.
>> 
>> I will be happy to hear you from.
>> 
>> Thank you
>> 
>> With Regards,
>> Sangita Saha
>> _______________________________________________
>> 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 Oct 26 12:11:05 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 26 Oct 2010 11:11:05 -0500
Subject: [Bioperl-l] Genome Information
In-Reply-To: <AANLkTikLfZa-FSFXiriqPGHf63kcTgkY0+rT2Mq=7hCu@mail.gmail.com>
References: <AANLkTikLfZa-FSFXiriqPGHf63kcTgkY0+rT2Mq=7hCu@mail.gmail.com>
Message-ID: <7A662ADB-506C-439E-9C0C-44F8DE540428@illinois.edu>

Shalabh,

I don't know if there is a quick one-step way of getting this information via NCBI w/o wrangling with query term limit magic, and even then you will be bound to whatever version of the genome is present within the database of interest.  

For instance, via eutils you can get summary information for various taxa, genomes, and genome projects using the following example code (prints the first 10 archaeal genome project summaries; set the '-db' parameter to one of 'genomeprj', 'taxonomy', 'genome'):

=================================

use Bio::DB::EUtilities;

my $term = "Archaea[ORGN]";

my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                     -db    => 'genome',
                                     -email => 'cjfields at bioperl.org',
                                     -usehistory => 'y',
                                     -term  => $term);

my $hist = $eutil->next_History || die "No history returned";

$eutil->set_parameters(-eutil   => 'esummary',
                       -history => $hist,
                       -retmax  => 10);

$eutil->print_all; # print summary info to STDOUT

=================================

GC and coding % don't appear to be stored in any of the above databases, but they are displayed via the genome overview.  You could probably use something like WWW::Mechanize to grab the summary table information displayed using the Genome UID:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=ShowDetailView&TermToSearch=25024

Just don't spam the server with a billion requests (use a timeout!) or you'll find yourself blocked.  I may pop an email to NCBI to see if this information is programmatically accessible.

chris

On Oct 26, 2010, at 9:09 AM, shalabh sharma wrote:

> Hi All,
>       I have thousands of taxaIds and i need to find out the following
> information regarding genomes:
> 1) Taxonomy information
> 2) GC%
> 3) total coding genes %
> 
> I can easily find the taxonomy info by using Bio::DB::Taxonomy but for the
> other two i am stuck.
> Is there any way i can find this info?
> I would really appreciate your help.
> 
> Thanks
> Shalabh
> -------------------------------
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
> _______________________________________________
> 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  Tue Oct 26 12:23:02 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 26 Oct 2010 12:23:02 -0400
Subject: [Bioperl-l] Genome Information
In-Reply-To: <7A662ADB-506C-439E-9C0C-44F8DE540428@illinois.edu>
References: <AANLkTikLfZa-FSFXiriqPGHf63kcTgkY0+rT2Mq=7hCu@mail.gmail.com>
	<7A662ADB-506C-439E-9C0C-44F8DE540428@illinois.edu>
Message-ID: <AANLkTin_JuaAi9Op_T9N9YVzjpOtN1hnXV=X02kPutBA@mail.gmail.com>

Hey Chris,
            This information is really useful.
Actually i was using Bio::DB::Taxonomy for taxonomy information
and Bio::DB::EUtilities to get the genome size (i didn't know that i can
just use Bio::DB::EUtilities for all the information).
I was very confused about getting GC% and coding% info but i
think WWW::Mechanize might help me out.
I really appreciate your help.

-Shalabh


On Tue, Oct 26, 2010 at 12:11 PM, Chris Fields <cjfields at illinois.edu>wrote:

> Shalabh,
>
> I don't know if there is a quick one-step way of getting this information
> via NCBI w/o wrangling with query term limit magic, and even then you will
> be bound to whatever version of the genome is present within the database of
> interest.
>
> For instance, via eutils you can get summary information for various taxa,
> genomes, and genome projects using the following example code (prints the
> first 10 archaeal genome project summaries; set the '-db' parameter to one
> of 'genomeprj', 'taxonomy', 'genome'):
>
> =================================
>
> use Bio::DB::EUtilities;
>
> my $term = "Archaea[ORGN]";
>
> my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
>                                     -db    => 'genome',
>                                     -email => 'cjfields at bioperl.org',
>                                     -usehistory => 'y',
>                                     -term  => $term);
>
> my $hist = $eutil->next_History || die "No history returned";
>
> $eutil->set_parameters(-eutil   => 'esummary',
>                       -history => $hist,
>                       -retmax  => 10);
>
> $eutil->print_all; # print summary info to STDOUT
>
> =================================
>
> GC and coding % don't appear to be stored in any of the above databases,
> but they are displayed via the genome overview.  You could probably use
> something like WWW::Mechanize to grab the summary table information
> displayed using the Genome UID:
>
>
> http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=ShowDetailView&TermToSearch=25024
>
> Just don't spam the server with a billion requests (use a timeout!) or
> you'll find yourself blocked.  I may pop an email to NCBI to see if this
> information is programmatically accessible.
>
> chris
>
> On Oct 26, 2010, at 9:09 AM, shalabh sharma wrote:
>
> > Hi All,
> >       I have thousands of taxaIds and i need to find out the following
> > information regarding genomes:
> > 1) Taxonomy information
> > 2) GC%
> > 3) total coding genes %
> >
> > I can easily find the taxonomy info by using Bio::DB::Taxonomy but for
> the
> > other two i am stuck.
> > Is there any way i can find this info?
> > I would really appreciate your help.
> >
> > Thanks
> > Shalabh
> > -------------------------------
> > Shalabh Sharma
> > Scientific Computing Professional Associate (Bioinformatics Specialist)
> > Department of Marine Sciences
> > University of Georgia
> > Athens, GA 30602-3636
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From mconte at umd.edu  Tue Oct 26 14:25:28 2010
From: mconte at umd.edu (Matthew Conte)
Date: Tue, 26 Oct 2010 14:25:28 -0400
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
Message-ID: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>

Hello,

I have a custom script for parsing out UniProt accessions from a GFF3 file
and fetching the description of the UniProt entry using Bio::DB::SwissProt
and *get_Seq_by_acc*.  This script has been working for months without any
problems until now.  The script and the format of the input files has not
changed at all.

I now get an error like this:

*------------- EXCEPTION: Bio::Root::Exception -------------*
*MSG: acc O95342 does not exist*
*STACK: Error::throw*
*STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
*STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
/Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
*STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
*-----------------------------------------------------------*

The relevant portion of my original code looks something like this:

*#!/usr/bin/perl*
*use strict;*
*use Bio::DB::SwissProt;*
*#parse out accession number*
*..*
*my $acc_num = "**O95342";*
*my $db_obj = Bio::DB::SwissProt->new;*
*my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
*
*
Looking at the documentation for Bio::DB::SwissProt, I noticed you can
specify -servertype and -hostlocation.  So I changed my code to look
something like this:

*
#!/usr/bin/perl
use strict;
use Bio::DB::SwissProt;
#parse out accession number
..
my $acc_num = "O95342";
my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
                                                           '-hostlocation'
=> 'us');
my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
*

This fixes my problem and my script works again.

The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
  Both of these urls work in a browser, though the default throws the error
in my script. Interestingly, the 'us' url has a notice that says
"*Notice:* This
page will be replaced with www.uniprot.org. Please send us your
feedback<http://www.uniprot.org/contact>
!", so hopefully it doesn't break soon as well.  Perhaps the default ebi url
was recently changed in some way?  Anyway, I figured I'd post here in case
anyone else ran into this problem.

cheers,
Matt


From grapeguy at gmail.com  Tue Oct 26 15:15:09 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Tue, 26 Oct 2010 15:15:09 -0400
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <16EDEBED-BAD4-4D57-B51B-C3234D1E8C39@illinois.edu>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
	<AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
	<16EDEBED-BAD4-4D57-B51B-C3234D1E8C39@illinois.edu>
Message-ID: <AANLkTim5_UF-AQd8HRD9v4_5SF8T5z+awWN8KAORoUGs@mail.gmail.com>

I've got my script running.

In order to support the identification of degenerate primers I had to create
a new method that would alter the IUPAC consensus. We're interested in
15-30bp sections of the consensus with high, but not 100%, conservation. We
would like to have a couple of "slices" with 2-3 mismatches to allow for the
ordering of a variety of primers.

To be completed:

   - I would *love* to hide the Clustal output that is being printed to the
   screen
   - Primer candidate identification (min_primerlength to max_primerlength)
   based on our scoring matrix
   - Primer melting temperature calculation
   - 3' Clamping identification
   - Self complementary primers

This has been a nice change from Java.

Bill


*Code*

assume: I have already read fasta input, performed Clustal align and
obtained the IUPAC consensus

sub getDegenerateConsensusIupac {
    my ($aln, $maxGapPercent, $iupacConsensus, $numSequences) = @_;

  # convert consensus into array
  my @cons = split(//, $iupacConsensus);

  # loop over the alignment "columns"
  foreach my $position ( 1 .. $aln->length() ) {
      my $consCode = $cons[$position-1];
      my %slice = getSliceHash($aln, $position);

      my $out = _applyGapPercentToConsensus ($maxGapPercent, $consCode,
$numSequences, %slice);

      # Convert consensus value new value
      if ($out ne $consCode) {
          $cons[$position-1] = $out;
      }
  }

  #rebuild consensus
  my $degenerateConsensus = join '', @cons;

  return $degenerateConsensus;
}

sub _applyGapPercentToConsensus {
    my ($maxGapPercent, $consCode, $numSequences, %slice) = @_;

        my $gapCount = $slice{'.'};

        # no gaps!
        if ($gapCount !~ /\d/) {
            return $consCode;
        }

        my $pctGap = ($gapCount / $numSequences) * 100;

        if ($pctGap > $maxGapPercent) {
            if ($consCode =~ /[A-Z]/) {
                return lc $consCode;
            }
            if ($consCode =~ /[a-z]/) {
                return '.';
            }
        }

    return $consCode;
}

sub getSliceHash{
    my ($aln, $position) = @_;

    my %sliceHash;
    foreach my $seq ($aln->each_seq) {
        my $res = $seq->subseq($position, $position);
        $sliceHash{$res}++;
    }

    return %sliceHash;
}


On Tue, Oct 19, 2010 at 11:47 AM, Chris Fields <cjfields at illinois.edu>wrote:

> Bio::SimpleAlign is the class that contains the alignment data; it does not
> generate the alignment for you.  You can use modules from BioPerl-Run that
> run ClustalW, MUSCLE, T-Coffee, etc to get a Bio::SimpleAlign instance, or
> parse the already-generated alignment output via Bio::AlignIO.
>
> From the Bio::Tools::Run::Alignment::ClustalW docs:
>
> =================================================================
>
>  #  Build a clustalw alignment factory
>  @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
>  $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
>
>  #  Pass the factory a list of sequences to be aligned.
>  $inputfilename = 't/data/cysprot.fa';
>  $aln = $factory->align($inputfilename); # $aln is a SimpleAlign object.
>
>  # ...or
>  $seq_array_ref = \@seq_array;
>
>  # where @seq_array is an array of Bio::Seq objects
>  $aln = $factory->align($seq_array_ref);
>
> =================================================================
>
> $aln is a Bio::SimpleAlign derived from ClustalW output.
>
> From Bio::SimpleAlign (note the use of Bio::AlignIO):
>
> =================================================================
>
>  # Use Bio::AlignIO to read in the alignment
>  $str = Bio::AlignIO->new(-file => 't/data/testaln.pfam');
>  $aln = $str->next_aln();
>
>  # Describe
>  print $aln->length;
>  print $aln->num_residues;
>  print $aln->is_flush;
>  print $aln->num_sequences;
>  print $aln->score;
>  print $aln->percentage_identity;
>  print $aln->consensus_string(50);
>
> =================================================================
>
> Note the consensus_string() method:
>
>  Title     : consensus_string
>  Usage     : $str = $ali->consensus_string($threshold_percent)
>  Function  : Makes a strict consensus
>  Returns   : Consensus string
>  Argument  : Optional treshold ranging from 0 to 100.
>             The consensus residue has to appear at least threshold %
>             of the sequences at a given location, otherwise a '?'
>             character will be placed at that location.
>             (Default value = 0%)
>
> chris
>
> On Oct 18, 2010, at 7:02 PM, Bill Stephens wrote:
>
> > So, I've got the SimpleAlign running. It looks like it's running the
> > alignment based upon the input sequence location only (first residue from
> > each sequence).  This is not what I need.
> >
> > I'm back to to clustal, tcoffee or dalign.
> >
> > Bill
> >
> > On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:
> >
> >> Hi, Bill,
> >>
> >> You may consider to use consensus_iupac or consensus_string methods in
> >> Bio::SimpleAlign to generate consensus sequence.
> >>
> >> Cheers,
> >> Jun Yin
> >> Ph.D. student in U.C.D.
> >>
> >> Bioinformatics Laboratory
> >> Conway Institute
> >> University College Dublin
> >>
> >> -----Original Message-----
> >> From: bioperl-l-bounces at lists.open-bio.org
> >> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
> >> Sent: Monday, October 18, 2010 3:55 PM
> >> To: Bill Stephens
> >> Cc: bioperl-l at bioperl.org
> >> Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
> >> alignment
> >>
> >> Bill,
> >>
> >> Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
> >> replacement for the older Pise tools).  The Pise modules were in
> >> BioPerl-Run, but they were deprecated a few years ago and removed from
> the
> >> latest BioPerl-Run releases b/c the remote service is no longer active;
> >> there is no Perl-based replacement for Mobyle interaction.
> >>
> >> Have you thought about just using the functionality within the
> >> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there
> >> are
> >> methods in place to do that.
> >>
> >> chris
> >>
> >> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
> >>
> >>> All,
> >>>
> >>> I'm in my first week with bioperl for a class project (although I've
> used
> >>> Perl for years). I've successfully run a clustal alignment of several
> DNA
> >>> sequences to produce the aln and dnd files. Now I would like to
> generate
> >> a
> >>> consensus sequence from the alignment.  I see that Pise Cons does this
> >>> satisfactorily on my example data (
> >>> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However,
> >> I'm
> >>> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
> >> distribution
> >>> that I installed.
> >>>
> >>> Is this another module that I need to install separately?
> >>>
> >>> "cpan[2]> m /Pise/
> >>> Module    Bio::Tools::Run::AnalysisFactory::Pise
> >>> (BIRNEY/bioperl-run-1.4.tar.gz)
> >>> Module    Bio::Tools::Run::PiseApplication
> >> (BIRNEY/bioperl-run-1.4.tar.gz)"
> >>>
> >>> Bill S.
> >>> _______________________________________________
> >>> 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
> >>
> >> __________ Information from ESET Smart Security, version of virus
> signature
> >> database 5377 (20100818) __________
> >>
> >> The message was checked by ESET Smart Security.
> >>
> >> http://www.eset.com
> >>
> >>
> >>
> >>
> >> __________ Information from ESET Smart Security, version of virus
> signature
> >> database 5377 (20100818) __________
> >>
> >> The message was checked by ESET Smart Security.
> >>
> >> http://www.eset.com
> >>
> >>
> >>
> > _______________________________________________
> > 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 Oct 26 18:02:03 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 26 Oct 2010 17:02:03 -0500
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
Message-ID: <FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>

The default was changed recently in github to 'expasy'.  My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.

chris

On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:

> Hello,
> 
> I have a custom script for parsing out UniProt accessions from a GFF3 file
> and fetching the description of the UniProt entry using Bio::DB::SwissProt
> and *get_Seq_by_acc*.  This script has been working for months without any
> problems until now.  The script and the format of the input files has not
> changed at all.
> 
> I now get an error like this:
> 
> *------------- EXCEPTION: Bio::Root::Exception -------------*
> *MSG: acc O95342 does not exist*
> *STACK: Error::throw*
> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
> *-----------------------------------------------------------*
> 
> The relevant portion of my original code looks something like this:
> 
> *#!/usr/bin/perl*
> *use strict;*
> *use Bio::DB::SwissProt;*
> *#parse out accession number*
> *..*
> *my $acc_num = "**O95342";*
> *my $db_obj = Bio::DB::SwissProt->new;*
> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
> *
> *
> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
> specify -servertype and -hostlocation.  So I changed my code to look
> something like this:
> 
> *
> #!/usr/bin/perl
> use strict;
> use Bio::DB::SwissProt;
> #parse out accession number
> ..
> my $acc_num = "O95342";
> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>                                                           '-hostlocation'
> => 'us');
> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
> *
> 
> This fixes my problem and my script works again.
> 
> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>  Both of these urls work in a browser, though the default throws the error
> in my script. Interestingly, the 'us' url has a notice that says
> "*Notice:* This
> page will be replaced with www.uniprot.org. Please send us your
> feedback<http://www.uniprot.org/contact>
> !", so hopefully it doesn't break soon as well.  Perhaps the default ebi url
> was recently changed in some way?  Anyway, I figured I'd post here in case
> anyone else ran into this problem.
> 
> cheers,
> Matt
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From sahasangi at gmail.com  Tue Oct 26 07:02:04 2010
From: sahasangi at gmail.com (sangita saha)
Date: Tue, 26 Oct 2010 16:32:04 +0530
Subject: [Bioperl-l] Need Help regarding reciprocal BLAST using BioPerl
Message-ID: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>

Hello Sir,
I have installed BioPerl and standalone BLAST in my PC.I faced problem in
doing the Reciprocal BLAST.Will anyone kindly tell me how to link between
BioPerl and Standalone BLAST ?How to use Bioperl itself to identify the
ortholog?What is the command to be used for reciprocal Blast?Since I am the
new user of it and need help to your concerned.If anybody have any
experience regarding reciprocal blast please give me a suggestion.

I will be happy to hear you from.

Thank you

With Regards,
Sangita Saha


From ameet at eecs.berkeley.edu  Tue Oct 26 19:51:17 2010
From: ameet at eecs.berkeley.edu (Ameet Talwalkar)
Date: Tue, 26 Oct 2010 16:51:17 -0700
Subject: [Bioperl-l] TreeIO for NHX format
Message-ID: <AANLkTim2hsO=rRCfa5H4Uu7waF7iVbJo9NDfTq2q8yrN@mail.gmail.com>

Hi,

I would like to use BIOPerl to convert a tree in PhyloXML format to NHX
format, and I have tried the following code:

*use Bio::TreeIO;

my $input = new Bio::TreeIO(-file   => "reconciled_test.xml",
                            -format => "phyloxml");
my $treeout = new Bio::TreeIO(-fh => \*STDOUT,
                              -format => 'nhx');

while (my $tree = $input->next_tree) {
  $treeout->write_tree($tree);
}
*

The output is indeed in NHX format, but the tags (in particular I have a
duplication / speciation tag) does not appear in the output.  Am I doing
something wrong?

Thanks.

-Ameet


From bill_zt at sina.com  Tue Oct 26 21:08:11 2010
From: bill_zt at sina.com (Tao Zhu)
Date: Wed, 27 Oct 2010 09:08:11 +0800
Subject: [Bioperl-l] A problem on BioPerl module Bio::DB::Fasta
Message-ID: <1288141691.2377.1.camel@ubuntu>

Hello, everyone!

I hope it isn't true, but I really find a problem on BioPerl module
Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
Osborne wrote that we could catch sub-sequences like this,


use Bio::DB::Fasta;
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
$db = Bio::DB::Fasta->new($file);
$seqobj = $db->get_Seq_by_id($id,$start,$end);
print $seqobj->seq,"\n";


In fact it didn't work. I only got the whole sequence after running the
script. Therefore I referred to the Pdoc documentation and realized it
should be written as follows,


use Bio::DB::Fasta;
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
$db = Bio::DB::Fasta->new($file);
$seq = $db->seq($id,$start,$end);
print $seq,"\n";


Then it would return the sub-sequence from 6 to 10.

Probably Dr Osborne had made a mistake when writing the use-guide
HOWTO:Beginners.


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
email: tzhu at mail.bnu.edu.cn



From cjfields at illinois.edu  Tue Oct 26 23:41:40 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 26 Oct 2010 22:41:40 -0500
Subject: [Bioperl-l] TreeIO for NHX format
In-Reply-To: <AANLkTim2hsO=rRCfa5H4Uu7waF7iVbJo9NDfTq2q8yrN@mail.gmail.com>
References: <AANLkTim2hsO=rRCfa5H4Uu7waF7iVbJo9NDfTq2q8yrN@mail.gmail.com>
Message-ID: <55546218-9878-421F-B4A7-FADA7760C374@illinois.edu>

Ameet,

You should file this as a bug, along with example code and data (http://bugzilla.open-bio.org/).  It's possible the tags are parsed but the NHX writer is not finding the data somehow.

chris

On Oct 26, 2010, at 6:51 PM, Ameet Talwalkar wrote:

> Hi,
> 
> I would like to use BIOPerl to convert a tree in PhyloXML format to NHX
> format, and I have tried the following code:
> 
> *use Bio::TreeIO;
> 
> my $input = new Bio::TreeIO(-file   => "reconciled_test.xml",
>                            -format => "phyloxml");
> my $treeout = new Bio::TreeIO(-fh => \*STDOUT,
>                              -format => 'nhx');
> 
> while (my $tree = $input->next_tree) {
>  $treeout->write_tree($tree);
> }
> *
> 
> The output is indeed in NHX format, but the tags (in particular I have a
> duplication / speciation tag) does not appear in the output.  Am I doing
> something wrong?
> 
> Thanks.
> 
> -Ameet
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hamish.mcwilliam at bioinfo-user.org.uk  Wed Oct 27 06:32:22 2010
From: hamish.mcwilliam at bioinfo-user.org.uk (Hamish McWilliam)
Date: Wed, 27 Oct 2010 11:32:22 +0100
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
	<FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
Message-ID: <AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>

Hi Chris,

The dbfetch service at EBI has changed, see
http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010. On
of the effects of this is the main endpoint used for dbfetch has
changed from http://www.ebi.ac.uk/cgi-bin/dbfetch to
http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. With the old endpoints
being supported via a HTTP redirect. It looks like the
Bio::DB::SwissProt module does not support redirects and is thus
getting an empty document back from the service. Looks like the URL
used in the code needs to be updated.

All the best,

Hamish

On 26 October 2010 23:02, Chris Fields <cjfields at illinois.edu> wrote:
> The default was changed recently in github to 'expasy'. ?My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.
>
> chris
>
> On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:
>
>> Hello,
>>
>> I have a custom script for parsing out UniProt accessions from a GFF3 file
>> and fetching the description of the UniProt entry using Bio::DB::SwissProt
>> and *get_Seq_by_acc*. ?This script has been working for months without any
>> problems until now. ?The script and the format of the input files has not
>> changed at all.
>>
>> I now get an error like this:
>>
>> *------------- EXCEPTION: Bio::Root::Exception -------------*
>> *MSG: acc O95342 does not exist*
>> *STACK: Error::throw*
>> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
>> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
>> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
>> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
>> *-----------------------------------------------------------*
>>
>> The relevant portion of my original code looks something like this:
>>
>> *#!/usr/bin/perl*
>> *use strict;*
>> *use Bio::DB::SwissProt;*
>> *#parse out accession number*
>> *..*
>> *my $acc_num = "**O95342";*
>> *my $db_obj = Bio::DB::SwissProt->new;*
>> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
>> *
>> *
>> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
>> specify -servertype and -hostlocation. ?So I changed my code to look
>> something like this:
>>
>> *
>> #!/usr/bin/perl
>> use strict;
>> use Bio::DB::SwissProt;
>> #parse out accession number
>> ..
>> my $acc_num = "O95342";
>> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '-hostlocation'
>> => 'us');
>> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
>> *
>>
>> This fixes my problem and my script works again.
>>
>> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
>> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>> ?Both of these urls work in a browser, though the default throws the error
>> in my script. Interestingly, the 'us' url has a notice that says
>> "*Notice:* This
>> page will be replaced with www.uniprot.org. Please send us your
>> feedback<http://www.uniprot.org/contact>
>> !", so hopefully it doesn't break soon as well. ?Perhaps the default ebi url
>> was recently changed in some way? ?Anyway, I figured I'd post here in case
>> anyone else ran into this problem.
>>
>> cheers,
>> Matt
>> _______________________________________________
>> 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
>



-- 
----
"Saying the internet has changed dramatically over the last five years
is clich? ? the internet is always changing dramatically" - Craig
Labovitz, Arbor Networks.



From cjfields at illinois.edu  Wed Oct 27 10:51:22 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 27 Oct 2010 09:51:22 -0500
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
	<FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
	<AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>
Message-ID: <FAB70AF7-B56C-4DEA-BF4D-AA9F001D6E9F@illinois.edu>

Hamish,

Thanks, but I already caught that and fixed it in main trunk where appropriate yesterday (specifically, both Bio::DB::SwissProt and Bio::DB::BioFetch).  

chris

On Oct 27, 2010, at 5:32 AM, Hamish McWilliam wrote:

> Hi Chris,
> 
> The dbfetch service at EBI has changed, see
> http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010. On
> of the effects of this is the main endpoint used for dbfetch has
> changed from http://www.ebi.ac.uk/cgi-bin/dbfetch to
> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. With the old endpoints
> being supported via a HTTP redirect. It looks like the
> Bio::DB::SwissProt module does not support redirects and is thus
> getting an empty document back from the service. Looks like the URL
> used in the code needs to be updated.
> 
> All the best,
> 
> Hamish
> 
> On 26 October 2010 23:02, Chris Fields <cjfields at illinois.edu> wrote:
>> The default was changed recently in github to 'expasy'.  My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.
>> 
>> chris
>> 
>> On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:
>> 
>>> Hello,
>>> 
>>> I have a custom script for parsing out UniProt accessions from a GFF3 file
>>> and fetching the description of the UniProt entry using Bio::DB::SwissProt
>>> and *get_Seq_by_acc*.  This script has been working for months without any
>>> problems until now.  The script and the format of the input files has not
>>> changed at all.
>>> 
>>> I now get an error like this:
>>> 
>>> *------------- EXCEPTION: Bio::Root::Exception -------------*
>>> *MSG: acc O95342 does not exist*
>>> *STACK: Error::throw*
>>> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
>>> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
>>> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
>>> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
>>> *-----------------------------------------------------------*
>>> 
>>> The relevant portion of my original code looks something like this:
>>> 
>>> *#!/usr/bin/perl*
>>> *use strict;*
>>> *use Bio::DB::SwissProt;*
>>> *#parse out accession number*
>>> *..*
>>> *my $acc_num = "**O95342";*
>>> *my $db_obj = Bio::DB::SwissProt->new;*
>>> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
>>> *
>>> *
>>> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
>>> specify -servertype and -hostlocation.  So I changed my code to look
>>> something like this:
>>> 
>>> *
>>> #!/usr/bin/perl
>>> use strict;
>>> use Bio::DB::SwissProt;
>>> #parse out accession number
>>> ..
>>> my $acc_num = "O95342";
>>> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>>>                                                           '-hostlocation'
>>> => 'us');
>>> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
>>> *
>>> 
>>> This fixes my problem and my script works again.
>>> 
>>> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
>>> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>>>  Both of these urls work in a browser, though the default throws the error
>>> in my script. Interestingly, the 'us' url has a notice that says
>>> "*Notice:* This
>>> page will be replaced with www.uniprot.org. Please send us your
>>> feedback<http://www.uniprot.org/contact>
>>> !", so hopefully it doesn't break soon as well.  Perhaps the default ebi url
>>> was recently changed in some way?  Anyway, I figured I'd post here in case
>>> anyone else ran into this problem.
>>> 
>>> cheers,
>>> Matt
>>> _______________________________________________
>>> 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
>> 
> 
> 
> 
> -- 
> ----
> "Saying the internet has changed dramatically over the last five years
> is clich? ? the internet is always changing dramatically" - Craig
> Labovitz, Arbor Networks.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hamish.mcwilliam at bioinfo-user.org.uk  Wed Oct 27 11:34:09 2010
From: hamish.mcwilliam at bioinfo-user.org.uk (Hamish McWilliam)
Date: Wed, 27 Oct 2010 16:34:09 +0100
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <FAB70AF7-B56C-4DEA-BF4D-AA9F001D6E9F@illinois.edu>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
	<FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
	<AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>
	<FAB70AF7-B56C-4DEA-BF4D-AA9F001D6E9F@illinois.edu>
Message-ID: <AANLkTik0tKy2B1W8Avd7ap=Fg4prR3p0w9OXpka5PXHP@mail.gmail.com>

Hi Chris,

Although they handle the redirect, the other modules which use dbfetch
should probably have the URLs updated too:

Bio::DB::Biblio::biofetch
Bio::DB::EMBL
Bio::DB::RefSeq

Hamish

On 27 October 2010 15:51, Chris Fields <cjfields at illinois.edu> wrote:
> Hamish,
>
> Thanks, but I already caught that and fixed it in main trunk where appropriate yesterday (specifically, both Bio::DB::SwissProt and Bio::DB::BioFetch).
>
> chris
>
> On Oct 27, 2010, at 5:32 AM, Hamish McWilliam wrote:
>
>> Hi Chris,
>>
>> The dbfetch service at EBI has changed, see
>> http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010. On
>> of the effects of this is the main endpoint used for dbfetch has
>> changed from http://www.ebi.ac.uk/cgi-bin/dbfetch to
>> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. With the old endpoints
>> being supported via a HTTP redirect. It looks like the
>> Bio::DB::SwissProt module does not support redirects and is thus
>> getting an empty document back from the service. Looks like the URL
>> used in the code needs to be updated.
>>
>> All the best,
>>
>> Hamish
>>
>> On 26 October 2010 23:02, Chris Fields <cjfields at illinois.edu> wrote:
>>> The default was changed recently in github to 'expasy'. ?My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.
>>>
>>> chris
>>>
>>> On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:
>>>
>>>> Hello,
>>>>
>>>> I have a custom script for parsing out UniProt accessions from a GFF3 file
>>>> and fetching the description of the UniProt entry using Bio::DB::SwissProt
>>>> and *get_Seq_by_acc*. ?This script has been working for months without any
>>>> problems until now. ?The script and the format of the input files has not
>>>> changed at all.
>>>>
>>>> I now get an error like this:
>>>>
>>>> *------------- EXCEPTION: Bio::Root::Exception -------------*
>>>> *MSG: acc O95342 does not exist*
>>>> *STACK: Error::throw*
>>>> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
>>>> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
>>>> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
>>>> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
>>>> *-----------------------------------------------------------*
>>>>
>>>> The relevant portion of my original code looks something like this:
>>>>
>>>> *#!/usr/bin/perl*
>>>> *use strict;*
>>>> *use Bio::DB::SwissProt;*
>>>> *#parse out accession number*
>>>> *..*
>>>> *my $acc_num = "**O95342";*
>>>> *my $db_obj = Bio::DB::SwissProt->new;*
>>>> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
>>>> *
>>>> *
>>>> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
>>>> specify -servertype and -hostlocation. ?So I changed my code to look
>>>> something like this:
>>>>
>>>> *
>>>> #!/usr/bin/perl
>>>> use strict;
>>>> use Bio::DB::SwissProt;
>>>> #parse out accession number
>>>> ..
>>>> my $acc_num = "O95342";
>>>> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '-hostlocation'
>>>> => 'us');
>>>> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
>>>> *
>>>>
>>>> This fixes my problem and my script works again.
>>>>
>>>> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
>>>> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>>>> ?Both of these urls work in a browser, though the default throws the error
>>>> in my script. Interestingly, the 'us' url has a notice that says
>>>> "*Notice:* This
>>>> page will be replaced with www.uniprot.org. Please send us your
>>>> feedback<http://www.uniprot.org/contact>
>>>> !", so hopefully it doesn't break soon as well. ?Perhaps the default ebi url
>>>> was recently changed in some way? ?Anyway, I figured I'd post here in case
>>>> anyone else ran into this problem.
>>>>
>>>> cheers,
>>>> Matt
>>>> _______________________________________________
>>>> 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
>>>
>>
>>
>>
>> --
>> ----
>> "Saying the internet has changed dramatically over the last five years
>> is clich? ? the internet is always changing dramatically" - Craig
>> Labovitz, Arbor Networks.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
----
"Saying the internet has changed dramatically over the last five years
is clich? ? the internet is always changing dramatically" - Craig
Labovitz, Arbor Networks.



From cjfields at illinois.edu  Wed Oct 27 12:20:48 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 27 Oct 2010 11:20:48 -0500
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <AANLkTik0tKy2B1W8Avd7ap=Fg4prR3p0w9OXpka5PXHP@mail.gmail.com>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
	<FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
	<AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>
	<FAB70AF7-B56C-4DEA-BF4D-AA9F001D6E9F@illinois.edu>
	<AANLkTik0tKy2B1W8Avd7ap=Fg4prR3p0w9OXpka5PXHP@mail.gmail.com>
Message-ID: <BC746329-82A8-4215-BE8D-4CCDE6911FDB@illinois.edu>

Hamish,

Ah, missed those!  That's what I get for relying on tests alone.  Thanks for pointing them out; I'll double-check the various distributions for more, just in case.

chris

On Oct 27, 2010, at 10:34 AM, Hamish McWilliam wrote:

> Hi Chris,
> 
> Although they handle the redirect, the other modules which use dbfetch
> should probably have the URLs updated too:
> 
> Bio::DB::Biblio::biofetch
> Bio::DB::EMBL
> Bio::DB::RefSeq
> 
> Hamish
> 
> On 27 October 2010 15:51, Chris Fields <cjfields at illinois.edu> wrote:
>> Hamish,
>> 
>> Thanks, but I already caught that and fixed it in main trunk where appropriate yesterday (specifically, both Bio::DB::SwissProt and Bio::DB::BioFetch).
>> 
>> chris
>> 
>> On Oct 27, 2010, at 5:32 AM, Hamish McWilliam wrote:
>> 
>>> Hi Chris,
>>> 
>>> The dbfetch service at EBI has changed, see
>>> http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010. On
>>> of the effects of this is the main endpoint used for dbfetch has
>>> changed from http://www.ebi.ac.uk/cgi-bin/dbfetch to
>>> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. With the old endpoints
>>> being supported via a HTTP redirect. It looks like the
>>> Bio::DB::SwissProt module does not support redirects and is thus
>>> getting an empty document back from the service. Looks like the URL
>>> used in the code needs to be updated.
>>> 
>>> All the best,
>>> 
>>> Hamish
>>> 
>>> On 26 October 2010 23:02, Chris Fields <cjfields at illinois.edu> wrote:
>>>> The default was changed recently in github to 'expasy'.  My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.
>>>> 
>>>> chris
>>>> 
>>>> On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:
>>>> 
>>>>> Hello,
>>>>> 
>>>>> I have a custom script for parsing out UniProt accessions from a GFF3 file
>>>>> and fetching the description of the UniProt entry using Bio::DB::SwissProt
>>>>> and *get_Seq_by_acc*.  This script has been working for months without any
>>>>> problems until now.  The script and the format of the input files has not
>>>>> changed at all.
>>>>> 
>>>>> I now get an error like this:
>>>>> 
>>>>> *------------- EXCEPTION: Bio::Root::Exception -------------*
>>>>> *MSG: acc O95342 does not exist*
>>>>> *STACK: Error::throw*
>>>>> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
>>>>> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
>>>>> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
>>>>> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
>>>>> *-----------------------------------------------------------*
>>>>> 
>>>>> The relevant portion of my original code looks something like this:
>>>>> 
>>>>> *#!/usr/bin/perl*
>>>>> *use strict;*
>>>>> *use Bio::DB::SwissProt;*
>>>>> *#parse out accession number*
>>>>> *..*
>>>>> *my $acc_num = "**O95342";*
>>>>> *my $db_obj = Bio::DB::SwissProt->new;*
>>>>> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
>>>>> *
>>>>> *
>>>>> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
>>>>> specify -servertype and -hostlocation.  So I changed my code to look
>>>>> something like this:
>>>>> 
>>>>> *
>>>>> #!/usr/bin/perl
>>>>> use strict;
>>>>> use Bio::DB::SwissProt;
>>>>> #parse out accession number
>>>>> ..
>>>>> my $acc_num = "O95342";
>>>>> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>>>>>                                                           '-hostlocation'
>>>>> => 'us');
>>>>> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
>>>>> *
>>>>> 
>>>>> This fixes my problem and my script works again.
>>>>> 
>>>>> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
>>>>> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>>>>>  Both of these urls work in a browser, though the default throws the error
>>>>> in my script. Interestingly, the 'us' url has a notice that says
>>>>> "*Notice:* This
>>>>> page will be replaced with www.uniprot.org. Please send us your
>>>>> feedback<http://www.uniprot.org/contact>
>>>>> !", so hopefully it doesn't break soon as well.  Perhaps the default ebi url
>>>>> was recently changed in some way?  Anyway, I figured I'd post here in case
>>>>> anyone else ran into this problem.
>>>>> 
>>>>> cheers,
>>>>> Matt
>>>>> _______________________________________________
>>>>> 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
>>>> 
>>> 
>>> 
>>> 
>>> --
>>> ----
>>> "Saying the internet has changed dramatically over the last five years
>>> is clich? ? the internet is always changing dramatically" - Craig
>>> Labovitz, Arbor Networks.
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> ----
> "Saying the internet has changed dramatically over the last five years
> is clich? ? the internet is always changing dramatically" - Craig
> Labovitz, Arbor Networks.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From maizemu at gmail.com  Wed Oct 27 12:53:26 2010
From: maizemu at gmail.com (Christopher Bottoms)
Date: Wed, 27 Oct 2010 11:53:26 -0500
Subject: [Bioperl-l] how to download PDB files using Bioperl script
In-Reply-To: <01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
Message-ID: <AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>

Ashwani,

Do you need to download the files once or does this need to be automated?

If you just need to do it once, check out
http://www.rcsb.org/pdb/download/download.do for downloading multiple
files.

If you need to automate the process, let me know and I'll help you
figure it out. The easiest way I can think of, which I used to do, is
downloading them from the ftp site.

Sincerely,

Christopher Bottoms

On Fri, Oct 22, 2010 at 11:12 AM, Jun Yin <jun.yin at ucd.ie> wrote:
> Hi, Ashwani,
>
> I havenot found any module in BioPerl for downloading PDB files, though
> Bio::Structure::IO::pdb can parse PDB files.
>
> However, PDB provides RESTful service
> (http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
> batch downloading the proteins.
>
> Cheers,
> Jun Yin
> Ph.D.?student in U.C.D.
>
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
> Sent: Thursday, October 21, 2010 9:39 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] how to download PDB files using Bioperl script
>
> Hi All,
>
>
> I have around 150 pdb file names and I need to download them from Protein
> Data Bank. I wonder if someone could tell me how to do it by using Bioperl.
>
> Thanks in advance.
>
> Regards,
> Ashwani
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>
> _______________________________________________
> 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 Oct 27 14:40:02 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 27 Oct 2010 13:40:02 -0500
Subject: [Bioperl-l] A problem on BioPerl module Bio::DB::Fasta
In-Reply-To: <1288141691.2377.1.camel@ubuntu>
References: <1288141691.2377.1.camel@ubuntu>
Message-ID: <25CA46EE-B73B-4C27-9CA6-28BED05C7AEB@illinois.edu>

Tao,

I've made that correction to the HOWTO.  In the future, if you see an error on the wiki you are free to make changes to correct them.  

Thanks!

chris

On Oct 26, 2010, at 8:08 PM, Tao Zhu wrote:

> Hello, everyone!
> 
> I hope it isn't true, but I really find a problem on BioPerl module
> Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
> Osborne wrote that we could catch sub-sequences like this,
> 
> 
> use Bio::DB::Fasta;
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> $db = Bio::DB::Fasta->new($file);
> $seqobj = $db->get_Seq_by_id($id,$start,$end);
> print $seqobj->seq,"\n";
> 
> 
> In fact it didn't work. I only got the whole sequence after running the
> script. Therefore I referred to the Pdoc documentation and realized it
> should be written as follows,
> 
> 
> use Bio::DB::Fasta;
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> $db = Bio::DB::Fasta->new($file);
> $seq = $db->seq($id,$start,$end);
> print $seq,"\n";
> 
> 
> Then it would return the sub-sequence from 6 to 10.
> 
> Probably Dr Osborne had made a mistake when writing the use-guide
> HOWTO:Beginners.
> 
> 
> -- 
> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> 100875, China
> email: tzhu at mail.bnu.edu.cn
> 
> _______________________________________________
> 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 Oct 28 11:10:25 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 28 Oct 2010 10:10:25 -0500
Subject: [Bioperl-l] A problem on BioPerl module Bio::DB::Fasta
In-Reply-To: <1288251535.4408.18.camel@ubuntu>
References: <1288141691.2377.1.camel@ubuntu>
	<25CA46EE-B73B-4C27-9CA6-28BED05C7AEB@illinois.edu>
	<1288251535.4408.18.camel@ubuntu>
Message-ID: <C3335F92-724B-48C7-A05F-17AF27B244D9@illinois.edu>

Very true, didn't catch that; I was just making the correction you mentioned.  That's what happens when I don't have enough coffee!

chris

On Oct 28, 2010, at 2:38 AM, Tao Zhu wrote:

> Dear Chris,
> 
> Thank you for correcting the HOWTO, but in fact it hasn't been
> completely correct yet. I've made some changes to the passage again like
> this,
> 
> ************************
> use Bio::DB::Fasta; 
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
> $db = Bio::DB::Fasta->new($file);
> $seq = $db->seq($id,$start,$end);
> print $seq,"\n";
> ************************
> 
> The original passage is like this,
> ************************
> use Bio::DB::Fasta;
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
> $db = Bio::DB::Fasta->new($file);
> $seqobj = $db->seq($id,$start,$end); 
> print $seqobj->seq;
> ************************
> 
> We should notice that if method '$db->seq()' is called, then it would
> return a simple string, not a Bio::Seq object.
> 
> 
> 
> ? 2010-10-27?? 13:40 -0500?Chris Fields???
>> Tao,
>> 
>> I've made that correction to the HOWTO.  In the future, if you see an error on the wiki you are free to make changes to correct them.  
>> 
>> Thanks!
>> 
>> chris
>> 
>> On Oct 26, 2010, at 8:08 PM, Tao Zhu wrote:
>> 
>>> Hello, everyone!
>>> 
>>> I hope it isn't true, but I really find a problem on BioPerl module
>>> Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
>>> Osborne wrote that we could catch sub-sequences like this,
>>> 
>>> 
>>> use Bio::DB::Fasta;
>>> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
>>> $db = Bio::DB::Fasta->new($file);
>>> $seqobj = $db->get_Seq_by_id($id,$start,$end);
>>> print $seqobj->seq,"\n";
>>> 
>>> 
>>> In fact it didn't work. I only got the whole sequence after running the
>>> script. Therefore I referred to the Pdoc documentation and realized it
>>> should be written as follows,
>>> 
>>> 
>>> use Bio::DB::Fasta;
>>> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
>>> $db = Bio::DB::Fasta->new($file);
>>> $seq = $db->seq($id,$start,$end);
>>> print $seq,"\n";
>>> 
>>> 
>>> Then it would return the sub-sequence from 6 to 10.
>>> 
>>> Probably Dr Osborne had made a mistake when writing the use-guide
>>> HOWTO:Beginners.
>>> 
>>> 
>>> -- 
>>> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
>>> 100875, China
>>> email: tzhu at mail.bnu.edu.cn
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 
> 
> 




From Seidl-Michael at t-online.de  Wed Oct 27 04:58:03 2010
From: Seidl-Michael at t-online.de (seidl-michael)
Date: Wed, 27 Oct 2010 10:58:03 +0200
Subject: [Bioperl-l] Tiling of hsps using Bioperl
Message-ID: <041D7AC1-99F2-4760-B709-29FE138E05FA@web.de>

Hi everyone,

I have a question about the Bio::Search::Tiling::MapTiling  package. I  
want to get the range of my tilled hsps using the "range" function.  
The reported range is, unfortunately, not what I would expect while  
looking at my data:

 >A
          Length = 1967

Score = 70.1 bits (170), Expect = 1e-11,   Method: Compositional  
matrix adjust.
Identities = 47/110 (42%), Positives = 66/110 (60%), Gaps = 29/110 (26%)

Query: 358   
EAARQEEVARELEVKSSMATKIQSHWRGMAARSEVSTLRAEAAAAEAAASEAARQEEVAR 417
            E ARQEE+AR+ E +S+MATKIQSHWRG  ARSEV+++R+ AA A+        Q +++R
Sbjct: 1344 ELARQEELARQAEAESAMATKIQSHWRGSVARSEVASMRS-AAIADV------- 
QTQLSR 1395

Query: 418  QEEDARRKEAARQEEVARELEVKSSMATKIQSHWRGTAARSEVSTLRAEA 467
                                 +++  A +IQS WRG  AR +V++LRAEA
Sbjct: 1396 ---------------------IENLTAVRIQSRWRGVLARVKVASLRAEA 1424



Score = 57.8 bits (138), Expect = 7e-08,   Method: Compositional  
matrix adjust.
Identities = 28/39 (71%), Positives = 33/39 (84%)

Query: 358  EAARQEEVARELEVKSSMATKIQSHWRGMAARSEVSTLR 396
            E ARQEE+AR+ E +S+MATKIQSHWRG  ARSEV+ LR
Sbjct: 1222 ELARQEELARQAEAESAMATKIQSHWRGSVARSEVAVLR 1260



Score = 47.4 bits (111), Expect = 1e-04,   Method: Compositional  
matrix adjust.
Identities = 43/115 (37%), Positives = 58/115 (50%), Gaps = 29/115 (25%)

Query: 299  
RELEVKSSMATKIQSHWRGMAARSEVSTLRAEAAAAEAAASEAARQEEVARQEEDARRKE 358
           +E + K+ MAT+IQS  RG+ AR        EA + + AASE        R + + RR++
Sbjct: 433 KETQRKNDMATQIQSGVRGVIAR--------EAYSEKLAASERI---- 
AIRIQTEFRRRQ 480

Query: 359 AARQEEVARE-----------------LEVKSSMATKIQSHWRGMAARSEVSTLR 396
           A +Q E  R+                  +   S ATKIQSHWRG  ARSEV+ LR
Sbjct: 481 AQKQLEALRQQLQREQTCAVVIQKILSSDSNESAATKIQSHWRGSVARSEVAVLR 535

I would expect to get [433,1424] when using:

my $tiling = Bio::Search::Tiling::MapTiling->new($hit);
my @range = $tiling->range('subject');

Instead my array includes [1344,535]. Do I have a conceptional problem  
with the function of "range" or is there something wired happening?

Thanks a lot for any help and suggestions,

Michael


From tzhu at mail.bnu.edu.cn  Thu Oct 28 03:38:55 2010
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Thu, 28 Oct 2010 15:38:55 +0800
Subject: [Bioperl-l] A problem on BioPerl module Bio::DB::Fasta
In-Reply-To: <25CA46EE-B73B-4C27-9CA6-28BED05C7AEB@illinois.edu>
References: <1288141691.2377.1.camel@ubuntu>
	<25CA46EE-B73B-4C27-9CA6-28BED05C7AEB@illinois.edu>
Message-ID: <1288251535.4408.18.camel@ubuntu>

Dear Chris,

Thank you for correcting the HOWTO, but in fact it hasn't been
completely correct yet. I've made some changes to the passage again like
this,

************************
use Bio::DB::Fasta; 
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
$db = Bio::DB::Fasta->new($file);
$seq = $db->seq($id,$start,$end);
print $seq,"\n";
************************

The original passage is like this,
************************
use Bio::DB::Fasta;
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
$db = Bio::DB::Fasta->new($file);
$seqobj = $db->seq($id,$start,$end); 
print $seqobj->seq;
************************

We should notice that if method '$db->seq()' is called, then it would
return a simple string, not a Bio::Seq object.



? 2010-10-27?? 13:40 -0500?Chris Fields???
> Tao,
> 
> I've made that correction to the HOWTO.  In the future, if you see an error on the wiki you are free to make changes to correct them.  
> 
> Thanks!
> 
> chris
> 
> On Oct 26, 2010, at 8:08 PM, Tao Zhu wrote:
> 
> > Hello, everyone!
> > 
> > I hope it isn't true, but I really find a problem on BioPerl module
> > Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
> > Osborne wrote that we could catch sub-sequences like this,
> > 
> > 
> > use Bio::DB::Fasta;
> > ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> > $db = Bio::DB::Fasta->new($file);
> > $seqobj = $db->get_Seq_by_id($id,$start,$end);
> > print $seqobj->seq,"\n";
> > 
> > 
> > In fact it didn't work. I only got the whole sequence after running the
> > script. Therefore I referred to the Pdoc documentation and realized it
> > should be written as follows,
> > 
> > 
> > use Bio::DB::Fasta;
> > ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> > $db = Bio::DB::Fasta->new($file);
> > $seq = $db->seq($id,$start,$end);
> > print $seq,"\n";
> > 
> > 
> > Then it would return the sub-sequence from 6 to 10.
> > 
> > Probably Dr Osborne had made a mistake when writing the use-guide
> > HOWTO:Beginners.
> > 
> > 
> > -- 
> > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> > 100875, China
> > email: tzhu at mail.bnu.edu.cn
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 





From edwardsa at cs.man.ac.uk  Thu Oct 28 16:52:58 2010
From: edwardsa at cs.man.ac.uk (Andrea Edwards)
Date: Thu, 28 Oct 2010 21:52:58 +0100
Subject: [Bioperl-l] Installation of bioperl on Ubuntu
Message-ID: <4CC9E2AA.6020302@cs.man.ac.uk>

Hi

I'm new to Perl and linux and I think I may have messed up my 
installation of Bioperl.

I followed the instructions on this page verbatim
http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server

However the

./Build test


command failed and I noticed a lot of modules were missing from the 
output of the test. I then used CPAN to install these modules. One of 
them was Bio::FeatureIO. When I installed this it seemed to be 
installing lots of BioPerl 1.6.1 files. However when i downloaded the 
bioperl as instructed here

wget -N http://bioperl.org/DIST/current_core_unstable.tar.bz2

the version that I got was 1.5.2_102

I am confused by the presence of 2 different version numbers and don't 
know how to proceed. It looks as if I have installed a lot of BioPerl 
1.6.1 and if i carry on with the make test/install instructions from the 
website I will then install version 1.5.

When i looked at the files installed in the Bio folder in my perl 
libraries there were 88 files and the only files missing compared to my 
other BioPerl installations were:
ANSI directory
BioEntry.pm
ConfigData.pm

I looked at some of the modules to try and see which version they were 
but they all had different version numbers. I think I have inadvertently 
used CPAN to install 1.6.1. What do you think?

many thanks


From buiduyminh at gmail.com  Thu Oct 28 17:07:06 2010
From: buiduyminh at gmail.com (Minh Bui)
Date: Thu, 28 Oct 2010 17:07:06 -0400
Subject: [Bioperl-l] Installation of bioperl on Ubuntu
In-Reply-To: <4CC9E2AA.6020302@cs.man.ac.uk>
References: <4CC9E2AA.6020302@cs.man.ac.uk>
Message-ID: <AANLkTi=Vr3zYRdtUaDptrxexkDmo_wj-2f5BiLvAAzfr@mail.gmail.com>

Hi Andrea,

You don't have to install Bioperl manually on Ubuntu.

You can go to *System* > *Administration* > "*Synaptic Package Manager*" ,
search for "Bioperl" and install it. I believe it has the latest version.

Minh.


On Thu, Oct 28, 2010 at 4:52 PM, Andrea Edwards <edwardsa at cs.man.ac.uk>wrote:

> Hi
>
> I'm new to Perl and linux and I think I may have messed up my installation
> of Bioperl.
>
> I followed the instructions on this page verbatim
> http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server
>
> However the
>
> ./Build test
>
>
> command failed and I noticed a lot of modules were missing from the output
> of the test. I then used CPAN to install these modules. One of them was
> Bio::FeatureIO. When I installed this it seemed to be installing lots of
> BioPerl 1.6.1 files. However when i downloaded the bioperl as instructed
> here
>
> wget -N http://bioperl.org/DIST/current_core_unstable.tar.bz2
>
> the version that I got was 1.5.2_102
>
> I am confused by the presence of 2 different version numbers and don't know
> how to proceed. It looks as if I have installed a lot of BioPerl 1.6.1 and
> if i carry on with the make test/install instructions from the website I
> will then install version 1.5.
>
> When i looked at the files installed in the Bio folder in my perl libraries
> there were 88 files and the only files missing compared to my other BioPerl
> installations were:
> ANSI directory
> BioEntry.pm
> ConfigData.pm
>
> I looked at some of the modules to try and see which version they were but
> they all had different version numbers. I think I have inadvertently used
> CPAN to install 1.6.1. What do you think?
>
> many thanks
> _______________________________________________
> 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 Oct 28 17:28:17 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 28 Oct 2010 16:28:17 -0500
Subject: [Bioperl-l] Installation of bioperl on Ubuntu
In-Reply-To: <4CC9E2AA.6020302@cs.man.ac.uk>
References: <4CC9E2AA.6020302@cs.man.ac.uk>
Message-ID: <22C0CD13-6081-4FC4-97B7-939696D85A74@illinois.edu>

On Oct 28, 2010, at 3:52 PM, Andrea Edwards wrote:

> Hi
> 
> I'm new to Perl and linux and I think I may have messed up my installation of Bioperl.
> 
> I followed the instructions on this page verbatim
> http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server
> 
> However the
> 
> ./Build test
> 
> 
> command failed and I noticed a lot of modules were missing from the output of the test. I then used CPAN to install these modules. One of them was Bio::FeatureIO. When I installed this it seemed to be installing lots of BioPerl 1.6.1 files. However when i downloaded the bioperl as instructed here
> 
> wget -N http://bioperl.org/DIST/current_core_unstable.tar.bz2
> 
> the version that I got was 1.5.2_102

Ugh, that's not good; that should be removed (we're now at v 1.6.1 stable, but about 10 months past that release now and sorely due for another).  For the latest 'unstable' code, you can go to github:

http://github.com/bioperl/bioperl-live

Click on the 'Downloads' button.

Just a warning, but FeatureIO will likely disappear from the github bioperl-live repo master branch.  We're breaking out chunks of code that can be released independently, FeatureIO being one.

> I am confused by the presence of 2 different version numbers and don't know how to proceed. It looks as if I have installed a lot of BioPerl 1.6.1 and if i carry on with the make test/install instructions from the website I will then install version 1.5.
> 
> When i looked at the files installed in the Bio folder in my perl libraries there were 88 files and the only files missing compared to my other BioPerl installations were:
> ANSI directory
> BioEntry.pm
> ConfigData.pm

ConfigData is only for the installation.  Not sure about the others.

> I looked at some of the modules to try and see which version they were but they all had different version numbers. I think I have inadvertently used CPAN to install 1.6.1. What do you think?
> 
> many thanks

Since we moved to github this past May we no longer have different revision numbers per module (git doesn't support them, but so far we haven't seen many actually missing them).  

chris


From daniel.standage at gmail.com  Thu Oct 28 22:45:24 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Thu, 28 Oct 2010 19:45:24 -0700 (PDT)
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
Message-ID: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>

I am using the Bio::Tools::GFF parser to process and store GFF3 data
in an application. Calls to next_feature() return
Bio::SeqFeature::Generic objects. I have written a class that extends
the Bio::SeqFeature::Generic class, but I still want to use the
Bio::Tools::GFF class to do the initial parsing of the data.

Is there a way for me to tell the Bio::Tools::GFF parser that I want
it to give me objects from my custom class? Or should I just re-bless
the objects it gives me? Will I run into garbage collection problems
if I re-bless the Bio::SeqFeature::Generic objects to my custom class
(that extends the Bio::SeqFeature::Generic class)?

Thanks!

Daniel


From scott at scottcain.net  Thu Oct 28 23:41:09 2010
From: scott at scottcain.net (Scott Cain)
Date: Thu, 28 Oct 2010 23:41:09 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
In-Reply-To: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
References: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
Message-ID: <AANLkTika2Nkx5T-Gf_y74NhEij9udqF6V3DFibzMf90G@mail.gmail.com>

Hi Daniel,

It seems like the easiest thing to do would be to subclass
Bio::Tools::GFF.  BSFGeneric is only mentioned explicitly a few times
(maybe only once), so subclassing and having it use your class instead
would probably be the easiest thing to do.

Also, about having it produce GFF3: make sure you're actually getting
valid GFF3.  Bio::Tools::GFF is fairly old, and I am sure you could
give it valid SeqFeature objects and get invalid GFF3 out in some
circumstances.

Scott


On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> I am using the Bio::Tools::GFF parser to process and store GFF3 data
> in an application. Calls to next_feature() return
> Bio::SeqFeature::Generic objects. I have written a class that extends
> the Bio::SeqFeature::Generic class, but I still want to use the
> Bio::Tools::GFF class to do the initial parsing of the data.
>
> Is there a way for me to tell the Bio::Tools::GFF parser that I want
> it to give me objects from my custom class? Or should I just re-bless
> the objects it gives me? Will I run into garbage collection problems
> if I re-bless the Bio::SeqFeature::Generic objects to my custom class
> (that extends the Bio::SeqFeature::Generic class)?
>
> Thanks!
>
> Daniel
> _______________________________________________
> 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 dimitark at bii.a-star.edu.sg  Fri Oct 29 04:29:53 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Fri, 29 Oct 2010 16:29:53 +0800
Subject: [Bioperl-l] about git and perl5lib
Message-ID: <4CCA8601.6020607@bii.a-star.edu.sg>

Hi guys,
i am sorry if this sounds stupid but i have problem with the PERL5LIB 
and the GIT version of BioPerl(BP). I downloaded the BP-live and BP-run 
from git. I use Slackware so I added the following line in bashrc:

  export 
PERL5LIB=$HOME/Bioperl_git/bioperl-live:$HOME/Bioperl_git/bioperl-run:$PERL5LIB

But when i start a script using StandAloneBlastPlus i see perl cant find it:

Can't locate Bio/Tools/Run/StandAloneBlastPlus.pm in @INC (@INC 
contains: /home/domine/Bioperl_git/bioperl-live 
/home/domine/Bioperl_git/bioperl-run 
/usr/lib64/perl5/5.10.1/x86_64-linux-thread-multi 
/usr/lib64/perl5/5.10.1 
/usr/lib64/perl5/site_perl/5.10.1/x86_64-linux-thread-multi 
/usr/lib64/perl5/site_perl/5.10.1 /usr/lib64/perl5/site_perl 
/usr/lib64/perl5/vendor_perl/5.10.1/x86_64-linux-thread-multi 
/usr/lib64/perl5/vendor_perl/5.10.1 /usr/lib64/perl5/vendor_perl

It seems Perl should find the module but it doesnt. Any idea where i 
could have made a mistake?

Btw with:  perl -MBio::Perl -le 'print Bio::Perl->VERSION;' i get 1.0069

Thank you
Dimitar





From David.Messina at sbc.su.se  Fri Oct 29 08:18:40 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 29 Oct 2010 08:18:40 -0400
Subject: [Bioperl-l] about git and perl5lib
In-Reply-To: <4CCA8601.6020607@bii.a-star.edu.sg>
References: <4CCA8601.6020607@bii.a-star.edu.sg>
Message-ID: <DACCDE9C-B82D-4D71-84BC-4119B6E242FD@sbc.su.se>

There's a minor inconsistency on our part: the path to the bioperl-run modules is actually bioperl-run/lib


Note that bioperl-live will I believe also be switching to this at some point; having the modules in a lib subdir is standard Perl practice.


Dave






On Oct 29, 2010, at 4:29, Dimitar Kenanov <dimitark at bii.a-star.edu.sg> wrote:

> Hi guys,
> i am sorry if this sounds stupid but i have problem with the PERL5LIB and the GIT version of BioPerl(BP). I downloaded the BP-live and BP-run from git. I use Slackware so I added the following line in bashrc:
> 
> export PERL5LIB=$HOME/Bioperl_git/bioperl-live:$HOME/Bioperl_git/bioperl-run:$PERL5LIB
> 
> But when i start a script using StandAloneBlastPlus i see perl cant find it:
> 
> Can't locate Bio/Tools/Run/StandAloneBlastPlus.pm in @INC (@INC contains: /home/domine/Bioperl_git/bioperl-live /home/domine/Bioperl_git/bioperl-run /usr/lib64/perl5/5.10.1/x86_64-linux-thread-multi /usr/lib64/perl5/5.10.1 /usr/lib64/perl5/site_perl/5.10.1/x86_64-linux-thread-multi /usr/lib64/perl5/site_perl/5.10.1 /usr/lib64/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.10.1/x86_64-linux-thread-multi /usr/lib64/perl5/vendor_perl/5.10.1 /usr/lib64/perl5/vendor_perl
> 
> It seems Perl should find the module but it doesnt. Any idea where i could have made a mistake?
> 
> Btw with:  perl -MBio::Perl -le 'print Bio::Perl->VERSION;' i get 1.0069
> 
> Thank you
> Dimitar
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From scott at scottcain.net  Fri Oct 29 10:03:54 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 29 Oct 2010 10:03:54 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
In-Reply-To: <AANLkTimVseFgymk+MaumosOkh=jP3bR9LwGVLxmB26Xf@mail.gmail.com>
References: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
	<AANLkTika2Nkx5T-Gf_y74NhEij9udqF6V3DFibzMf90G@mail.gmail.com>
	<AANLkTimVseFgymk+MaumosOkh=jP3bR9LwGVLxmB26Xf@mail.gmail.com>
Message-ID: <AANLkTinKbEtuWetY7avw6uH8w_GcXvrTxD1t7R8t9jc3@mail.gmail.com>

Hi Daniel,

I cc'ed the bioperl mailing list back in and attached your tarball.  I
don't really know what it is you want to do, and you already know that
your code compiles and runs, so I'm not sure what advice you're
looking for.

Scott

On Fri, Oct 29, 2010 at 9:28 AM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> I don't see how to attach files to the mailing list, so I'm just going to
> reply to you. Sorry if that is against the protocol.
>
> I have attached a working implementation of what I think you were
> suggesting. I have a parser class that subclasses Bio::Tools::GFF, and it
> has a method that will return objects of my class that subclasses
> Bio::SeqFeature::Generic. This is a rough test and I still need to clean
> things up and add the rest of the functionality that I originally needed, I
> just wanted to make sure that there aren't going to be any problems with the
> approach I'm taking.
>
> If you unpack and run './temptest' it should print out 7 valid features and
> 1 invalid feature.
>
> Thanks for your suggestions!
>
> Daniel
>
> On Thu, Oct 28, 2010 at 10:41 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Daniel,
>>
>> It seems like the easiest thing to do would be to subclass
>> Bio::Tools::GFF. ?BSFGeneric is only mentioned explicitly a few times
>> (maybe only once), so subclassing and having it use your class instead
>> would probably be the easiest thing to do.
>>
>> Also, about having it produce GFF3: make sure you're actually getting
>> valid GFF3. ?Bio::Tools::GFF is fairly old, and I am sure you could
>> give it valid SeqFeature objects and get invalid GFF3 out in some
>> circumstances.
>>
>> Scott
>>
>>
>> On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
>> <daniel.standage at gmail.com> wrote:
>> > I am using the Bio::Tools::GFF parser to process and store GFF3 data
>> > in an application. Calls to next_feature() return
>> > Bio::SeqFeature::Generic objects. I have written a class that extends
>> > the Bio::SeqFeature::Generic class, but I still want to use the
>> > Bio::Tools::GFF class to do the initial parsing of the data.
>> >
>> > Is there a way for me to tell the Bio::Tools::GFF parser that I want
>> > it to give me objects from my custom class? Or should I just re-bless
>> > the objects it gives me? Will I run into garbage collection problems
>> > if I re-bless the Bio::SeqFeature::Generic objects to my custom class
>> > (that extends the Bio::SeqFeature::Generic class)?
>> >
>> > Thanks!
>> >
>> > Daniel
>> > _______________________________________________
>> > 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
>
>
>
> --
> Daniel S. Standage
> Graduate Research Assistant
> Bioinformatics and Computational Biology Program
> Iowa State University
>
>



-- 
------------------------------------------------------------------------
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 scott at scottcain.net  Fri Oct 29 10:21:51 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 29 Oct 2010 10:21:51 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
In-Reply-To: <AANLkTinKbEtuWetY7avw6uH8w_GcXvrTxD1t7R8t9jc3@mail.gmail.com>
References: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
	<AANLkTika2Nkx5T-Gf_y74NhEij9udqF6V3DFibzMf90G@mail.gmail.com>
	<AANLkTimVseFgymk+MaumosOkh=jP3bR9LwGVLxmB26Xf@mail.gmail.com>
	<AANLkTinKbEtuWetY7avw6uH8w_GcXvrTxD1t7R8t9jc3@mail.gmail.com>
Message-ID: <AANLkTikoPX7ep5QfOd-EDxoGqYU43kJZtwv5MaBHawXC@mail.gmail.com>

Hi all,

I'm resending this because it seems that some mail clients don't like
having executable files hidden inside of a tarball, so I removed the
executable bit.

Scott


On Fri, Oct 29, 2010 at 10:03 AM, Scott Cain <scott at scottcain.net> wrote:
> Hi Daniel,
>
> I cc'ed the bioperl mailing list back in and attached your tarball. ?I
> don't really know what it is you want to do, and you already know that
> your code compiles and runs, so I'm not sure what advice you're
> looking for.
>
> Scott
>
> On Fri, Oct 29, 2010 at 9:28 AM, Daniel Standage
> <daniel.standage at gmail.com> wrote:
>> I don't see how to attach files to the mailing list, so I'm just going to
>> reply to you. Sorry if that is against the protocol.
>>
>> I have attached a working implementation of what I think you were
>> suggesting. I have a parser class that subclasses Bio::Tools::GFF, and it
>> has a method that will return objects of my class that subclasses
>> Bio::SeqFeature::Generic. This is a rough test and I still need to clean
>> things up and add the rest of the functionality that I originally needed, I
>> just wanted to make sure that there aren't going to be any problems with the
>> approach I'm taking.
>>
>> If you unpack and run './temptest' it should print out 7 valid features and
>> 1 invalid feature.
>>
>> Thanks for your suggestions!
>>
>> Daniel
>>
>> On Thu, Oct 28, 2010 at 10:41 PM, Scott Cain <scott at scottcain.net> wrote:
>>>
>>> Hi Daniel,
>>>
>>> It seems like the easiest thing to do would be to subclass
>>> Bio::Tools::GFF. ?BSFGeneric is only mentioned explicitly a few times
>>> (maybe only once), so subclassing and having it use your class instead
>>> would probably be the easiest thing to do.
>>>
>>> Also, about having it produce GFF3: make sure you're actually getting
>>> valid GFF3. ?Bio::Tools::GFF is fairly old, and I am sure you could
>>> give it valid SeqFeature objects and get invalid GFF3 out in some
>>> circumstances.
>>>
>>> Scott
>>>
>>>
>>> On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
>>> <daniel.standage at gmail.com> wrote:
>>> > I am using the Bio::Tools::GFF parser to process and store GFF3 data
>>> > in an application. Calls to next_feature() return
>>> > Bio::SeqFeature::Generic objects. I have written a class that extends
>>> > the Bio::SeqFeature::Generic class, but I still want to use the
>>> > Bio::Tools::GFF class to do the initial parsing of the data.
>>> >
>>> > Is there a way for me to tell the Bio::Tools::GFF parser that I want
>>> > it to give me objects from my custom class? Or should I just re-bless
>>> > the objects it gives me? Will I run into garbage collection problems
>>> > if I re-bless the Bio::SeqFeature::Generic objects to my custom class
>>> > (that extends the Bio::SeqFeature::Generic class)?
>>> >
>>> > Thanks!
>>> >
>>> > Daniel
>>> > _______________________________________________
>>> > 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
>>
>>
>>
>> --
>> Daniel S. Standage
>> Graduate Research Assistant
>> Bioinformatics and Computational Biology Program
>> Iowa State University
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> 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
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From daniel.standage at gmail.com  Fri Oct 29 10:34:41 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Fri, 29 Oct 2010 09:34:41 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
In-Reply-To: <AANLkTikoPX7ep5QfOd-EDxoGqYU43kJZtwv5MaBHawXC@mail.gmail.com>
References: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
	<AANLkTika2Nkx5T-Gf_y74NhEij9udqF6V3DFibzMf90G@mail.gmail.com>
	<AANLkTimVseFgymk+MaumosOkh=jP3bR9LwGVLxmB26Xf@mail.gmail.com>
	<AANLkTinKbEtuWetY7avw6uH8w_GcXvrTxD1t7R8t9jc3@mail.gmail.com>
	<AANLkTikoPX7ep5QfOd-EDxoGqYU43kJZtwv5MaBHawXC@mail.gmail.com>
Message-ID: <AANLkTikwhSvoEHJECSGV9GzKdXk7Yu7O6nwkk=-Mccba@mail.gmail.com>

I guess my concern is that I haven't used inheritance much in Perl and I'm
unclear about the possible consequences of the approach I've taken. I've
seen people warning against re-blessing objects, and I just wanted to make
sure that the approach that I seem to have working now isn't going to cause
any problems down the line.

Sorry I wasn't clear. Thanks for your help.

Daniel

On Fri, Oct 29, 2010 at 9:21 AM, Scott Cain <scott at scottcain.net> wrote:

> Hi all,
>
> I'm resending this because it seems that some mail clients don't like
> having executable files hidden inside of a tarball, so I removed the
> executable bit.
>
> Scott
>
>
> On Fri, Oct 29, 2010 at 10:03 AM, Scott Cain <scott at scottcain.net> wrote:
> > Hi Daniel,
> >
> > I cc'ed the bioperl mailing list back in and attached your tarball.  I
> > don't really know what it is you want to do, and you already know that
> > your code compiles and runs, so I'm not sure what advice you're
> > looking for.
> >
> > Scott
> >
> > On Fri, Oct 29, 2010 at 9:28 AM, Daniel Standage
> > <daniel.standage at gmail.com> wrote:
> >> I don't see how to attach files to the mailing list, so I'm just going
> to
> >> reply to you. Sorry if that is against the protocol.
> >>
> >> I have attached a working implementation of what I think you were
> >> suggesting. I have a parser class that subclasses Bio::Tools::GFF, and
> it
> >> has a method that will return objects of my class that subclasses
> >> Bio::SeqFeature::Generic. This is a rough test and I still need to clean
> >> things up and add the rest of the functionality that I originally
> needed, I
> >> just wanted to make sure that there aren't going to be any problems with
> the
> >> approach I'm taking.
> >>
> >> If you unpack and run './temptest' it should print out 7 valid features
> and
> >> 1 invalid feature.
> >>
> >> Thanks for your suggestions!
> >>
> >> Daniel
> >>
> >> On Thu, Oct 28, 2010 at 10:41 PM, Scott Cain <scott at scottcain.net>
> wrote:
> >>>
> >>> Hi Daniel,
> >>>
> >>> It seems like the easiest thing to do would be to subclass
> >>> Bio::Tools::GFF.  BSFGeneric is only mentioned explicitly a few times
> >>> (maybe only once), so subclassing and having it use your class instead
> >>> would probably be the easiest thing to do.
> >>>
> >>> Also, about having it produce GFF3: make sure you're actually getting
> >>> valid GFF3.  Bio::Tools::GFF is fairly old, and I am sure you could
> >>> give it valid SeqFeature objects and get invalid GFF3 out in some
> >>> circumstances.
> >>>
> >>> Scott
> >>>
> >>>
> >>> On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
> >>> <daniel.standage at gmail.com> wrote:
> >>> > I am using the Bio::Tools::GFF parser to process and store GFF3 data
> >>> > in an application. Calls to next_feature() return
> >>> > Bio::SeqFeature::Generic objects. I have written a class that extends
> >>> > the Bio::SeqFeature::Generic class, but I still want to use the
> >>> > Bio::Tools::GFF class to do the initial parsing of the data.
> >>> >
> >>> > Is there a way for me to tell the Bio::Tools::GFF parser that I want
> >>> > it to give me objects from my custom class? Or should I just re-bless
> >>> > the objects it gives me? Will I run into garbage collection problems
> >>> > if I re-bless the Bio::SeqFeature::Generic objects to my custom class
> >>> > (that extends the Bio::SeqFeature::Generic class)?
> >>> >
> >>> > Thanks!
> >>> >
> >>> > Daniel
> >>> > _______________________________________________
> >>> > 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
> >>
> >>
> >>
> >> --
> >> Daniel S. Standage
> >> Graduate Research Assistant
> >> Bioinformatics and Computational Biology Program
> >> Iowa State University
> >>
> >>
> >
> >
> >
> > --
> > ------------------------------------------------------------------------
> > 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
>



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


From scott at scottcain.net  Fri Oct  1 11:45:35 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 1 Oct 2010 11:45:35 -0400
Subject: [Bioperl-l] [Gmod-gbrowse] bp_seqfeature_delete.PL - where
	should I submit a patch?
In-Reply-To: <87782334-E5F5-4DFE-AEBD-64565D5C2F9F@sanger.ac.uk>
References: <87782334-E5F5-4DFE-AEBD-64565D5C2F9F@sanger.ac.uk>
Message-ID: <AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>

Hi Keiran,

Well, I've been told that it is easy for non-bioperl developers to use
git to commit patches, and as if to prove it, there is a very long
wiki page on the bioperl wiki describing how to use git:

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

I'm not sure what the right thing is to do; I'm cc'ing the bioperl
list to get their input.

Scott


On Fri, Oct 1, 2010 at 8:46 AM, Keiran Raine <kr2 at sanger.ac.uk> wrote:
> Hi all,
>
> Does anyone know how I should best get push a patch (new functionality) out
> for this script which is part of the BioPerl package.
>
> I've added a 'fast' option which is useful for when you want to delete a
> whole dataset. ?The problem I was having is I loaded a large set of data
> which had errors. ?To delete it I tried to use the '-t' option but this
> continually fails after several hours (eventually runs out of memory). ?To
> get round this I've added the '-f' flag which tells the script to perform
> the delete/commit on each individual feature (and associated sub-features)
> rather than attempt to do them all in a single commit.
>
> I've attached the modified version (unfortunately the formatting was kind of
> knackered so a patch file will be a bit iffy).
>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a
> charity registered in England with number 1021457 and acompany registered in
> England with number 2742969, whose registeredoffice is 215 Euston Road,
> London, NW1 2BE.
>
>
> Keiran Raine
> Senior Computer Biologist
> The Cancer Genome Project
> Ext: 7703
> kr2 at sanger.ac.uk
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



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



From dan.bolser at gmail.com  Fri Oct  1 15:14:34 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Fri, 1 Oct 2010 20:14:34 +0100
Subject: [Bioperl-l] Spam on the wiki: best way to report it?
Message-ID: <AANLkTik1panWOrmZ_hE3dnXYMCBeOTn=LGg=YSjqB2aa@mail.gmail.com>

Is there something like a spam category to report spam on the wiki?

I'm talking about this:

http://www.bioperl.org/wiki/Special:Contributions/Xiangniant


I figure this list isn't really the best place to report it all, but I
couldn't find any advice on what else to do.

Cheers,
Dan.


From cjfields at illinois.edu  Fri Oct  1 15:53:55 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 1 Oct 2010 14:53:55 -0500
Subject: [Bioperl-l] Spam on the wiki: best way to report it?
In-Reply-To: <AANLkTik1panWOrmZ_hE3dnXYMCBeOTn=LGg=YSjqB2aa@mail.gmail.com>
References: <AANLkTik1panWOrmZ_hE3dnXYMCBeOTn=LGg=YSjqB2aa@mail.gmail.com>
Message-ID: <4EC133B7-60D0-4DF3-B0F7-D1628E431397@illinois.edu>

We can delete spam and block users (I just did for that example and one other).  I'll make you a wiki admin; more hands the better!

chris

On Oct 1, 2010, at 2:14 PM, Dan Bolser wrote:

> Is there something like a spam category to report spam on the wiki?
> 
> I'm talking about this:
> 
> http://www.bioperl.org/wiki/Special:Contributions/Xiangniant
> 
> 
> I figure this list isn't really the best place to report it all, but I
> couldn't find any advice on what else to do.
> 
> 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  Fri Oct  1 15:47:31 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 1 Oct 2010 14:47:31 -0500
Subject: [Bioperl-l] [Gmod-gbrowse] bp_seqfeature_delete.PL - where
	should I submit a patch?
In-Reply-To: <AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>
References: <87782334-E5F5-4DFE-AEBD-64565D5C2F9F@sanger.ac.uk>
	<AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>
Message-ID: <1D851E84-1664-4E72-82F5-D8C75ABA3789@illinois.edu>

Keiran,

We gladly accept patches if this is easier for you.  Using git/github is one way of getting more users involved and opening up the code more; the actual barrier to submit code changes is lowered to the point where one can fork our code and hack away, then submit pull requests for those changes to be merged (all via github, using one's account).  

We are generally doing more code review these days (asking for tests, requiring passing tests for inclusion, etc), but in this case that's probably not a problem.

chris

On Oct 1, 2010, at 10:45 AM, Scott Cain wrote:

> Hi Keiran,
> 
> Well, I've been told that it is easy for non-bioperl developers to use
> git to commit patches, and as if to prove it, there is a very long
> wiki page on the bioperl wiki describing how to use git:
> 
>  http://www.bioperl.org/wiki/Using_Git
> 
> I'm not sure what the right thing is to do; I'm cc'ing the bioperl
> list to get their input.
> 
> Scott
> 
> 
> On Fri, Oct 1, 2010 at 8:46 AM, Keiran Raine <kr2 at sanger.ac.uk> wrote:
>> Hi all,
>> 
>> Does anyone know how I should best get push a patch (new functionality) out
>> for this script which is part of the BioPerl package.
>> 
>> I've added a 'fast' option which is useful for when you want to delete a
>> whole dataset.  The problem I was having is I loaded a large set of data
>> which had errors.  To delete it I tried to use the '-t' option but this
>> continually fails after several hours (eventually runs out of memory).  To
>> get round this I've added the '-f' flag which tells the script to perform
>> the delete/commit on each individual feature (and associated sub-features)
>> rather than attempt to do them all in a single commit.
>> 
>> I've attached the modified version (unfortunately the formatting was kind of
>> knackered so a patch file will be a bit iffy).
>> 
>> 
>> 
>> 
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a
>> charity registered in England with number 1021457 and acompany registered in
>> England with number 2742969, whose registeredoffice is 215 Euston Road,
>> London, NW1 2BE.
>> 
>> 
>> Keiran Raine
>> Senior Computer Biologist
>> The Cancer Genome Project
>> Ext: 7703
>> kr2 at sanger.ac.uk
>> 
>> 
>> 
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> Start uncovering the many advantages of virtual appliances
>> and start using them to simplify application deployment and
>> accelerate your shift to cloud computing.
>> http://p.sf.net/sfu/novell-sfdev2dev
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> 
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> 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 jason at bioperl.org  Fri Oct  1 17:17:36 2010
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 01 Oct 2010 14:17:36 -0700
Subject: [Bioperl-l] Bioperl sim4 parse
In-Reply-To: <A475AF196964604CAEE109F1CA0275AB1578AF1378@SJMEMXMBS10.stjude.sjcrh.local>
References: <A475AF196964604CAEE109F1CA0275AB1578AF1378@SJMEMXMBS10.stjude.sjcrh.local>
Message-ID: <4CA64FF0.2010201@bioperl.org>

Jianmin -

Your question is better addressed to the mailing list bioperl-l at bioperl.org

Please attach an example file that is attached and sample perl code you 
are using so someone can test that your problem exists with the latest code.

-jason

Wang, Jianmin wrote, On 10/1/10 1:59 PM:
> Hi, Jason and Steve,
>
> I checked the code of the sim4.pm and used it in my program.  Unforturnately, it does not work well.  When there is a single hit with a single hsp, the code does not generate the hsp correctly and many of the information are lost.  Could you help me to check the code.  For following is the sim4 output file:
>
> Warning: lowercase letter in d.fa data. Convert sequence to uppercase.
>
> seq1 = d.fa, 203 bp
> seq2 = q.fa (HWI-EAS90_614M9:2:106:16121:11311#0), 12 bp
>
>> chr18:60413870-60414073
>> HWI-EAS90_614M9:2:106:16121:11311#0
>
> 111-122  (1-12)   100%
>
>        0     .    :
>      111 CTCATATAGCTC
>          ||||||||||||
>        1 CTCATATAGCTC
>
> Warning: lowercase letter in q.fa data. Convert sequence to uppercase.
>
> seq1 = d.fa, 203 bp
> seq2 = q.fa (teat), 15 bp
>
>> chr18:60413870-60414073
>> teat
>
> 126-140  (1-15)   100%
>
>        0     .    :    .
>      126 GTGGTATACAGAGTT
>          |||||||||||||||
>        1 GTGGTATACAGAGTT
>
>
>
> I found it's impossible to get the strand and mapping position from the data.
>
> Best.
> Jianmin Wang
>
>
>
>    ________________________________
> Email Disclaimer: www.stjude.org/emaildisclaimer

-- 
Jason Stajich
jason at bioperl.org



From avilella at gmail.com  Tue Oct  5 06:00:28 2010
From: avilella at gmail.com (Albert Vilella)
Date: Tue, 5 Oct 2010 11:00:28 +0100
Subject: [Bioperl-l] bioperl version for ensembl Was: Retrieve Sequence from
	Ensembl gene id
Message-ID: <AANLkTim9rEkgWtyF-E+4pvo1G3YS9qr5fw42uFQGwEMq@mail.gmail.com>

I also tested bioperl 1.6.1 for some scripting with the Ensembl API, and it
produces a few warnings here and there, but it doesn't break anything
obvious...

On Thu, Sep 30, 2010 at 4:16 PM, Chris Fields <cjfields at illinois.edu> wrote:

> On Sep 30, 2010, at 8:36 AM, Jun Yin wrote:
>
> > Hi, Chirag,
> >
> > BioPerl does not have any module to retrieve data from Ensembl. But
> Ensembl
> > provides a BioPerl-like interface on that function.
>
> Actually, BioPerl does have Bio::Tools::Run::Ensembl, which was submitted
> by Sendu Bala a few years back.  I think it stills works rather well, at
> least tests pass.  You might get more out of using the Ensembl API directly
> as Jun states though, YMMV.
>
> BTW, the ensembl API also works with the latest bioperl code, regardless
> what the Ensembl website says (e.g. they only support v1.2.3).  Haven't
> heard more about whether this discrepancy was supposed to be addressed at
> some point.
>
> chris
>
> > You can visit Ensembl's website on how to use that module:
> > http://www.ensembl.org/info/data/api.html
> >
> > Cheers,
> > Jun Yin
> > Ph.D. student in U.C.D.
> >
> > Bioinformatics Laboratory
> > Conway Institute
> > University College Dublin
> >
> >
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org
> > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of chirag matkar
> > Sent: Thursday, September 30, 2010 1:21 PM
> > To: bioperl-l at lists.open-bio.org
> > Subject: [Bioperl-l] Retrieve Sequence from Ensembl gene id
> >
> > Hello all,
> > Is there any module to fetch dna sequence data from ensemble gene id?
> >
> > --
> > Regards,
> > Chirag Matkar
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > __________ Information from ESET Smart Security, version of virus
> signature
> > database 5377 (20100818) __________
> >
> > The message was checked by ESET Smart Security.
> >
> > http://www.eset.com
> >
> >
> >
> >
> > __________ Information from ESET Smart Security, version of virus
> signature
> > database 5377 (20100818) __________
> >
> > The message was checked by ESET Smart Security.
> >
> > http://www.eset.com
> >
> >
> >
> > __________ Information from ESET Smart Security, version of virus
> signature
> > database 5377 (20100818) __________
> >
> > The message was checked by ESET Smart Security.
> >
> > http://www.eset.com
> >
> >
> >
> > _______________________________________________
> > 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  Tue Oct  5 06:07:36 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 5 Oct 2010 11:07:36 +0100
Subject: [Bioperl-l] [Gmod-gbrowse] bp_seqfeature_delete.PL - where
	should I submit a patch?
In-Reply-To: <AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>
References: <87782334-E5F5-4DFE-AEBD-64565D5C2F9F@sanger.ac.uk>
	<AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>
Message-ID: <AANLkTinDK93L8KJZbvL-TVriEw4sNT4uJP45BzZiL9W1@mail.gmail.com>

Here is a nice SVN to GIT conversion course:

http://git.or.cz/course/svn.html


On 1 October 2010 16:45, Scott Cain <scott at scottcain.net> wrote:
> Hi Keiran,
>
> Well, I've been told that it is easy for non-bioperl developers to use
> git to commit patches, and as if to prove it, there is a very long
> wiki page on the bioperl wiki describing how to use git:
>
> ?http://www.bioperl.org/wiki/Using_Git
>
> I'm not sure what the right thing is to do; I'm cc'ing the bioperl
> list to get their input.
>
> Scott
>
>
> On Fri, Oct 1, 2010 at 8:46 AM, Keiran Raine <kr2 at sanger.ac.uk> wrote:
>> Hi all,
>>
>> Does anyone know how I should best get push a patch (new functionality) out
>> for this script which is part of the BioPerl package.
>>
>> I've added a 'fast' option which is useful for when you want to delete a
>> whole dataset. ?The problem I was having is I loaded a large set of data
>> which had errors. ?To delete it I tried to use the '-t' option but this
>> continually fails after several hours (eventually runs out of memory). ?To
>> get round this I've added the '-f' flag which tells the script to perform
>> the delete/commit on each individual feature (and associated sub-features)
>> rather than attempt to do them all in a single commit.
>>
>> I've attached the modified version (unfortunately the formatting was kind of
>> knackered so a patch file will be a bit iffy).
>>
>>
>>
>>
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a
>> charity registered in England with number 1021457 and acompany registered in
>> England with number 2742969, whose registeredoffice is 215 Euston Road,
>> London, NW1 2BE.
>>
>>
>> Keiran Raine
>> Senior Computer Biologist
>> The Cancer Genome Project
>> Ext: 7703
>> kr2 at sanger.ac.uk
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Start uncovering the many advantages of virtual appliances
>> and start using them to simplify application deployment and
>> accelerate your shift to cloud computing.
>> http://p.sf.net/sfu/novell-sfdev2dev
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



From dan.bolser at gmail.com  Tue Oct  5 06:36:49 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 5 Oct 2010 11:36:49 +0100
Subject: [Bioperl-l] Question about Bio::Coordinate::Pair
Message-ID: <AANLkTi=fmjWt95GWw=Fe+-WVkhQYcuHPDCNxE6iLpN0w@mail.gmail.com>

Hi,

Can someone describe in a bit more detail the purpose of the Gap
sublocations that are sometimes returned by Bio::Coordinate::Pair [1]?

I found that, according to Bio::Location::Split, if the Match and Gap
sublocations have a different strand, the strand method (called via
Bio::Coordinate::Result) returns undef. This is inconsistent with the
way Bio::Coordinate::Result tends to behave. See the test script and
results below, also pasted here [2].

The question is, can I just toggle the strand of the Gap sublocation
to match that of the Match sublocation? Or does the strand of the Gap
sublocation encode some important but as yet undocumented information?
If the strand of the Gap and Match sublocations are made to match
(within Bio::Coordinate::Pair) this will simplify code that uses
Bio::Coordinate::Pair, making it more consistent, and perhaps help
with some other bugs [3].


Cheers,
Dan.

[1] http://www.bioperl.org/wiki/Module:Bio::Coordinate::Pair
[2] http://www.bioperl.org/wiki/Module_Discussion:Bio::Coordinate::Pair
[3] http://tinyurl.com/36na2cp


#!/usr/bin/perl -w

## Stress test Bio::Coordinate::Pair

use strict;
use Data::Dumper;

use Bio::Location::Simple;
use Bio::Coordinate::Pair;

## A contig
my $ctg = Bio::Location::Simple->
  new( -seq_id => 'ctg',
       -start  =>    1,
       -end    => 1001,
       -strand =>   +1,
     );

## The contigs position on a chromosome (forward)
my $ctg_on_chr_f = Bio::Location::Simple->
  new( -seq_id => 'ctg on chr r',
       -start  =>           5001,
       -end    =>           6001,
       -strand =>             +1,
     );

## The contigs position on a chromosome (reverse)
my $ctg_on_chr_r = Bio::Location::Simple->
  new( -seq_id => 'ctg on chr r',
       -start  =>           5001,
       -end    =>           6001,
       -strand =>             -1,
     );

## Coordinate mapping (forward)
my $agp_f = Bio::Coordinate::Pair->
  new( -in  => $ctg,
       -out => $ctg_on_chr_f
     );

## Coordinate mapping (reverse)
my $agp_r = Bio::Coordinate::Pair->
  new( -in  => $ctg,
       -out => $ctg_on_chr_r
     );



## A match, in contig coordinates...
my $match_on_ctg_4 = Bio::Location::Simple->
  new( -seq_id => 'hit 4',
       -start  =>     925,
       -end    =>    1125,
       -strand =>      -1,
     );

## Map it into chromosome coordinates (forward)
my $match_on_chr_4_f =
  $agp_f->map( $match_on_ctg_4 );

print Dumper $match_on_chr_4_f, "\n";

## Map it into chromosome coordinates (reverse)
my $match_on_chr_4_r =
  $agp_r->map( $match_on_ctg_4 );

print Dumper $match_on_chr_4_r, "\n";

__END__

$VAR1 = bless( {
                 '_sublocations' => [
                                      bless( {
                                               '_strand' => -1,
                                               '_seqid' => 'ctg on chr r',
                                               '_start' => 5925,
                                               '_location_type' => 'EXACT',
                                               '_end' => 6001
                                             },
'Bio::Coordinate::Result::Match' ),
                                      bless( {
                                               '_strand' => -1,
                                               '_seqid' => 'ctg',
                                               '_location_type' => 'EXACT',
                                               '_start' => 1002,
                                               '_end' => 1125
                                             }, 'Bio::Coordinate::Result::Gap' )
                                    ],
                 '_gap' => $VAR1->{'_sublocations'}[1],
                 'strand' => -1,
                 '_match' => $VAR1->{'_sublocations'}[0],
                 '_splittype' => 'JOIN'
               }, 'Bio::Coordinate::Result' );
$VAR2 = '
';
$VAR1 = bless( {
                 '_sublocations' => [
                                      bless( {
                                               '_strand' => 1,
                                               '_seqid' => 'ctg on chr r',
                                               '_start' => 5001,
                                               '_location_type' => 'EXACT',
                                               '_end' => 5077
                                             },
'Bio::Coordinate::Result::Match' ),
                                      bless( {
                                               '_strand' => -1,
                                               '_seqid' => 'ctg',
                                               '_location_type' => 'EXACT',
                                               '_start' => 1002,
                                               '_end' => 1125
                                             }, 'Bio::Coordinate::Result::Gap' )
                                    ],
                 '_gap' => $VAR1->{'_sublocations'}[1],
                 'strand' => 1,
                 '_match' => $VAR1->{'_sublocations'}[0],
                 '_splittype' => 'JOIN'
               }, 'Bio::Coordinate::Result' );
$VAR2 = '
';


From gandipalem at gmail.com  Wed Oct  6 01:35:31 2010
From: gandipalem at gmail.com (gandipalem)
Date: Tue, 5 Oct 2010 22:35:31 -0700 (PDT)
Subject: [Bioperl-l] how to identify least degeneracy for a conserved region
 among all conserved regions in an amino acid alignment?
Message-ID: <29893643.post@talk.nabble.com>


Hi,

I am new to this.

I am working on designing primers for a set of highly diverged  proteins.
I designed degenerate primers for all those proteins manually starting from
multiple sequence alignment to reverse translation of conserved regions. But
this process is very time taking and robust. I would like automate this work
PERL. But I am getting a problem were I am unable to getting the logic "how
to measure/find out the least degeneracy for a conserved region among all
conserved regions of a multiple sequence alignment?".

So can anybody tell about how to find out least degenerated conserved region
in PERL?

Thanking you

Suresh
NBPGR

-- 
View this message in context: http://old.nabble.com/how-to-identify-least-degeneracy-for-a-conserved-region-among-all-conserved-regions-in-an-amino-acid-alignment--tp29893643p29893643.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From dan.bolser at gmail.com  Thu Oct  7 10:22:04 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 7 Oct 2010 15:22:04 +0100
Subject: [Bioperl-l] Installing Bio::DB::BigWig ?
In-Reply-To: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
References: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
Message-ID: <AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>

Trying to run make in .../src/kent/src (also CC'ing BP)

Dan.

# fun for everyone!
irc://irc.perl.org/#gmod

#also good!
irc://irc.freenode.net/#bioperl

On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
> Hi,
>
> I'm having trouble installing Bio::DB::BigWig.
>
> I grabbed the jkucsc code as described here [1] and built it
> successfully after setting 'export MACHTYPE=x86_64'.
>
> I then set 'export KENT_SRC=.../src/kent/src' and called:
> cpan[1]> install Bio::DB::BigWig
>
> The error comes:
> ...
> 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: comparison is always false due to
> limited range of data type
> 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: comparison is always false due to
> limited range of data type
> 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 -m64 -mtune=generic -o
> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> .../src/kent/src/lib/x86_64/jkweb.a -lz
> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
> relocation R_X86_64_32S against `a local symbol' can not be used when
> making a shared object; recompile with -fPIC
> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
> lib/Bio/DB/BigFile.o at
> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
> ?LDS/Bio-BigFile-1.03.tar.gz
> ?./Build -- NOT OK
> ...
>
>
> I tried to 'recompile with -fPIC', but saw further errors about
> missing symbols that I can't fix.
>
> Are there some specific applications of the jkucsc package that I
> should build and install first?
>
>
> Thanks for any help,
> Dan.
>
>
> [1] http://genome.ucsc.edu/admin/git.html
>



From dan.bolser at gmail.com  Thu Oct  7 11:01:50 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 7 Oct 2010 16:01:50 +0100
Subject: [Bioperl-l] Installing Bio::DB::BigWig ?
In-Reply-To: <AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>
References: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
	<AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>
Message-ID: <AANLkTikPF=qo8dv-PXEaU71tU8UtDYXjJ6cC9DB8ranV@mail.gmail.com>

I finally found the solution to this install problem. The error
message 'recompile with -fPIC' isn't referring to the Perl code, but
rather the jkucsc code...

In the directory .../src/kent/src/inc I changed the file common.mk to
add the -fPIC option to the CFLAGS...

[me at box inc]$ diff common.mk~ common.mk
6c6
< CFLAGS=
---
> CFLAGS=-fPIC


I then went back to .../src/kent/src/lib and hit 'make clean && make'.
Finally, going back to cpan, and re-installing Bio::DB::BigWig,
everything worked.


Sorry for the confusion, but it's been a long time since I needed to
install anything 'manually' ;-)

Dan.

# fun for everyone!
irc://irc.perl.org/#gmod

#also good!
irc://irc.freenode.net/#bioperl


On 7 October 2010 15:22, Dan Bolser <dan.bolser at gmail.com> wrote:
> Trying to run make in .../src/kent/src (also CC'ing BP)
>
> Dan.
>
> # fun for everyone!
> irc://irc.perl.org/#gmod
>
> #also good!
> irc://irc.freenode.net/#bioperl
>
> On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
>> Hi,
>>
>> I'm having trouble installing Bio::DB::BigWig.
>>
>> I grabbed the jkucsc code as described here [1] and built it
>> successfully after setting 'export MACHTYPE=x86_64'.
>>
>> I then set 'export KENT_SRC=.../src/kent/src' and called:
>> cpan[1]> install Bio::DB::BigWig
>>
>> The error comes:
>> ...
>> 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: comparison is always false due to
>> limited range of data type
>> 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: comparison is always false due to
>> limited range of data type
>> 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 -m64 -mtune=generic -o
>> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
>> .../src/kent/src/lib/x86_64/jkweb.a -lz
>> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
>> relocation R_X86_64_32S against `a local symbol' can not be used when
>> making a shared object; recompile with -fPIC
>> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
>> collect2: ld returned 1 exit status
>> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
>> lib/Bio/DB/BigFile.o at
>> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
>> ?LDS/Bio-BigFile-1.03.tar.gz
>> ?./Build -- NOT OK
>> ...
>>
>>
>> I tried to 'recompile with -fPIC', but saw further errors about
>> missing symbols that I can't fix.
>>
>> Are there some specific applications of the jkucsc package that I
>> should build and install first?
>>
>>
>> Thanks for any help,
>> Dan.
>>
>>
>> [1] http://genome.ucsc.edu/admin/git.html
>>
>



From lincoln.stein at gmail.com  Thu Oct  7 14:52:09 2010
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Thu, 7 Oct 2010 14:52:09 -0400
Subject: [Bioperl-l] [Gmod-gbrowse] Installing Bio::DB::BigWig ?
In-Reply-To: <AANLkTikPF=qo8dv-PXEaU71tU8UtDYXjJ6cC9DB8ranV@mail.gmail.com>
References: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
	<AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>
	<AANLkTikPF=qo8dv-PXEaU71tU8UtDYXjJ6cC9DB8ranV@mail.gmail.com>
Message-ID: <AANLkTinXx94t-RhyYF8_f4=pdj3YZwF_1Bqfe7oJMAh8@mail.gmail.com>

Sorry, I'll fix the installation documentation to warn people about -fPIC.
This seems to be needed on some platforms and not others.

Lincoln

On Thu, Oct 7, 2010 at 11:01 AM, Dan Bolser <dan.bolser at gmail.com> wrote:

> I finally found the solution to this install problem. The error
> message 'recompile with -fPIC' isn't referring to the Perl code, but
> rather the jkucsc code...
>
> In the directory .../src/kent/src/inc I changed the file common.mk to
> add the -fPIC option to the CFLAGS...
>
> [me at box inc]$ diff common.mk~ common.mk
> 6c6
> < CFLAGS=
> ---
> > CFLAGS=-fPIC
>
>
> I then went back to .../src/kent/src/lib and hit 'make clean && make'.
> Finally, going back to cpan, and re-installing Bio::DB::BigWig,
> everything worked.
>
>
> Sorry for the confusion, but it's been a long time since I needed to
> install anything 'manually' ;-)
>
> Dan.
>
> # fun for everyone!
> irc://irc.perl.org/#gmod
>
> #also good!
> irc://irc.freenode.net/#bioperl
>
>
> On 7 October 2010 15:22, Dan Bolser <dan.bolser at gmail.com> wrote:
> > Trying to run make in .../src/kent/src (also CC'ing BP)
> >
> > Dan.
> >
> > # fun for everyone!
> > irc://irc.perl.org/#gmod
> >
> > #also good!
> > irc://irc.freenode.net/#bioperl
> >
> > On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
> >> Hi,
> >>
> >> I'm having trouble installing Bio::DB::BigWig.
> >>
> >> I grabbed the jkucsc code as described here [1] and built it
> >> successfully after setting 'export MACHTYPE=x86_64'.
> >>
> >> I then set 'export KENT_SRC=.../src/kent/src' and called:
> >> cpan[1]> install Bio::DB::BigWig
> >>
> >> The error comes:
> >> ...
> >> 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: comparison is always false due to
> >> limited range of data type
> >> 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: comparison is always false due to
> >> limited range of data type
> >> 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 -m64 -mtune=generic -o
> >> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> >> .../src/kent/src/lib/x86_64/jkweb.a -lz
> >> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
> >> relocation R_X86_64_32S against `a local symbol' can not be used when
> >> making a shared object; recompile with -fPIC
> >> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
> >> collect2: ld returned 1 exit status
> >> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
> >> lib/Bio/DB/BigFile.o at
> >> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
> >>  LDS/Bio-BigFile-1.03.tar.gz
> >>  ./Build -- NOT OK
> >> ...
> >>
> >>
> >> I tried to 'recompile with -fPIC', but saw further errors about
> >> missing symbols that I can't fix.
> >>
> >> Are there some specific applications of the jkucsc package that I
> >> should build and install first?
> >>
> >>
> >> Thanks for any help,
> >> Dan.
> >>
> >>
> >> [1] http://genome.ucsc.edu/admin/git.html
> >>
> >
>
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



-- 
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  Thu Oct  7 15:58:40 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 7 Oct 2010 20:58:40 +0100
Subject: [Bioperl-l] [Gmod-gbrowse] Installing Bio::DB::BigWig ?
In-Reply-To: <AANLkTinXx94t-RhyYF8_f4=pdj3YZwF_1Bqfe7oJMAh8@mail.gmail.com>
References: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
	<AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>
	<AANLkTikPF=qo8dv-PXEaU71tU8UtDYXjJ6cC9DB8ranV@mail.gmail.com>
	<AANLkTinXx94t-RhyYF8_f4=pdj3YZwF_1Bqfe7oJMAh8@mail.gmail.com>
Message-ID: <AANLkTi=1pnkXFf4XE6K1BgQikf40AnTfbRwzV7CAvnrz@mail.gmail.com>

On 7 October 2010 19:52, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Sorry, I'll fix the installation documentation to warn people about -fPIC.
> This seems to be needed on some platforms and not others.

No problem, thanks for the update. Perhaps it should also be added to
the jkucsc code? any harm in adding -fPIC there anyway?

Here are the details of my box:

ge-002 2.6.18-92.1.22.el5 #1 SMP Tue Dec 16 11:57:43 EST 2008 x86_64
x86_64 x86_64 GNU/Linux

gcc --version
gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)
Copyright (C) 2006 Free Software Foundation, Inc.

perl --version
This is perl, v5.8.8 built for x86_64-linux-thread-multi

jkucsc ... git rev-parse HEAD
cb419933fdc44246e6bac605e65ddc27e7683559


I made some other minor changes to the jkucsc code in an attempt to
get the whole lot to compile:

diff --git a/src/inc/common.mk b/src/inc/common.mk
index 65c9f3c..b7b5389 100644
--- a/src/inc/common.mk
+++ b/src/inc/common.mk
@@ -3,7 +3,7 @@ CC=gcc
 ifeq (${COPT},)
     COPT=-O -g
 endif
-CFLAGS=
+CFLAGS=-fPIC
 HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${M
 HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../i

diff --git a/src/oneShot/smoothWindow/smoothWindow.c b/src/oneShot/smoothWindow/
index b062c91..f0d9c49 100644
--- a/src/oneShot/smoothWindow/smoothWindow.c
+++ b/src/oneShot/smoothWindow/smoothWindow.c
@@ -80,9 +80,9 @@ while (lineFileNext(lf, &line, NULL))
     val = words[1];
     dataValue = strtod(val, &valEnd);
     if ((*val == '\0') || (*valEnd != '\0'))
-       errAbort("Not a valid float at line %d: %s\n", lineCount, words[1]);
+       errAbort("Not a valid float at line %llu: %s\n", lineCount, words[1]);
     if (Offset < 1)
-       errAbort("Illegal offset: %llu at line %d, dataValue: %g", Offset,
+       errAbort("Illegal offset: %llu at line %llu, dataValue: %g", Offset,
            lineCount, dataValue);
     verbose(3, "#\tline: %llu, offset: %llu, data: %g\n",
        lineCount, Offset, dataValue);
diff --git a/src/utils/wigAsciiCrunch/wigAsciiCrunch.c b/src/utils/wigAsciiCrunc
index 04f7692..fc86036 100644
--- a/src/utils/wigAsciiCrunch/wigAsciiCrunch.c
+++ b/src/utils/wigAsciiCrunch/wigAsciiCrunch.c
@@ -103,7 +103,7 @@ while ((wordCount = lineFileChop(lf, words)) != 0)
        if (clFixOverlap)
            {
            minPos = lastOffset;
-           verbose(1, "Removing overlap %d-%d line %d of %s\n",
+           verbose(1, "Removing overlap %ld-%ld line %d of %s\n",
                    lastOffset, offset, lf->lineIx, lf->fileName);
            }
        else


Thanks again,
Dan.

# fun for everyone!
irc://irc.perl.org/#gmod

#also good!
irc://irc.freenode.net/#bioperl


> Lincoln
>
> On Thu, Oct 7, 2010 at 11:01 AM, Dan Bolser <dan.bolser at gmail.com> wrote:
>>
>> I finally found the solution to this install problem. The error
>> message 'recompile with -fPIC' isn't referring to the Perl code, but
>> rather the jkucsc code...
>>
>> In the directory .../src/kent/src/inc I changed the file common.mk to
>> add the -fPIC option to the CFLAGS...
>>
>> [me at box inc]$ diff common.mk~ common.mk
>> 6c6
>> < CFLAGS=
>> ---
>> > CFLAGS=-fPIC
>>
>>
>> I then went back to .../src/kent/src/lib and hit 'make clean && make'.
>> Finally, going back to cpan, and re-installing Bio::DB::BigWig,
>> everything worked.
>>
>>
>> Sorry for the confusion, but it's been a long time since I needed to
>> install anything 'manually' ;-)
>>
>> Dan.
>>
>> # fun for everyone!
>> irc://irc.perl.org/#gmod
>>
>> #also good!
>> irc://irc.freenode.net/#bioperl
>>
>>
>> On 7 October 2010 15:22, Dan Bolser <dan.bolser at gmail.com> wrote:
>> > Trying to run make in .../src/kent/src (also CC'ing BP)
>> >
>> > Dan.
>> >
>> > # fun for everyone!
>> > irc://irc.perl.org/#gmod
>> >
>> > #also good!
>> > irc://irc.freenode.net/#bioperl
>> >
>> > On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
>> >> Hi,
>> >>
>> >> I'm having trouble installing Bio::DB::BigWig.
>> >>
>> >> I grabbed the jkucsc code as described here [1] and built it
>> >> successfully after setting 'export MACHTYPE=x86_64'.
>> >>
>> >> I then set 'export KENT_SRC=.../src/kent/src' and called:
>> >> cpan[1]> install Bio::DB::BigWig
>> >>
>> >> The error comes:
>> >> ...
>> >> 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: comparison is always false due to
>> >> limited range of data type
>> >> 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: comparison is always false due to
>> >> limited range of data type
>> >> 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 -m64 -mtune=generic -o
>> >> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
>> >> .../src/kent/src/lib/x86_64/jkweb.a -lz
>> >> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
>> >> relocation R_X86_64_32S against `a local symbol' can not be used when
>> >> making a shared object; recompile with -fPIC
>> >> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
>> >> collect2: ld returned 1 exit status
>> >> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
>> >> lib/Bio/DB/BigFile.o at
>> >> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
>> >> ?LDS/Bio-BigFile-1.03.tar.gz
>> >> ?./Build -- NOT OK
>> >> ...
>> >>
>> >>
>> >> I tried to 'recompile with -fPIC', but saw further errors about
>> >> missing symbols that I can't fix.
>> >>
>> >> Are there some specific applications of the jkucsc package that I
>> >> should build and install first?
>> >>
>> >>
>> >> Thanks for any help,
>> >> Dan.
>> >>
>> >>
>> >> [1] http://genome.ucsc.edu/admin/git.html
>> >>
>> >
>>
>>
>> ------------------------------------------------------------------------------
>> Beautiful is writing same markup. Internet Explorer 9 supports
>> standards for HTML5, CSS3, SVG 1.1, ?ECMAScript5, and DOM L2 & L3.
>> Spend less time writing and ?rewriting code and more time creating great
>> experiences on the web. Be a part of the beta today.
>> http://p.sf.net/sfu/beautyoftheweb
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> 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 timmcilveen at talktalk.net  Fri Oct  8 05:16:48 2010
From: timmcilveen at talktalk.net (tim)
Date: Fri, 8 Oct 2010 10:16:48 +0100
Subject: [Bioperl-l] Getting BioPerl from Github
Message-ID: <201010081016.48460.timmcilveen@talktalk.net>

Hi,
I'm not an experienced Linux user but have been trying to download Bioperl via 
GitHub as I was getting lots of errors using the package installer. It was 
suggested by a list user that I use GitHub instead.

I installed Git using Yast.

I visited this page:
http://www.bioperl.org/wiki/Using_Git 

and used the installation instructions:
$ git clone git://github.com/bioperl/bioperl-live.git
bash: $ export PERL5LIB="$HOME/src/bioperl-live:$PERL5LIB"

I tested the code:
$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;' 
but the install didn't work.
Here is the ouput from my terminal.
tim at linux-oxgy:~> su
Password: 
linux-oxgy:/home/tim # git clone git://github.com/bioperl/bioperl-live.git
Initialized empty Git repository in /home/tim/bioperl-live/.git/
remote: Counting objects: 88288, done.
remote: Compressing objects: 100% (23829/23829), done.
remote: Total 88288 (delta 66885), reused 85264 (delta 63993)
Receiving objects: 100% (88288/88288), 138.20 MiB | 1.19 MiB/s, done.
Resolving deltas: 100% (66885/66885), done.
linux-oxgy:/home/tim # bash
linux-oxgy:/home/tim # export PERL5LIB="$HOME/src/biooperl-live:$PERL5LIB"
linux-oxgy:/home/tim # perl -MBIO::Perl -le 'print Bio::Perl->VERSION;'
Can't locate BIO/Perl.pm in @INC (@INC contains: /root/src/biooperl-live 
/usr/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi 
/usr/lib/perl5/site_perl/5.12.1 /usr/lib/perl5/vendor_perl/5.12.1/x86_64-
linux-thread-multi /usr/lib/perl5/vendor_perl/5.12.1 
/usr/lib/perl5/5.12.1/x86_64-linux-thread-multi /usr/lib/perl5/5.12.1 .).
BEGIN failed--compilation aborted.
linux-oxgy:/home/tim # 

I assume that something has went wrong at this step:
To use this 'live' version of BioPerl, you need to install it (simply tell 
Perl where to find it). Assuming you checked out the code above into 
$HOME/src; set this in your .bash_profile, .profile, or .cshrc: 

How do I set things up so that the code is in $HOME/src? Where is it likely to 
be if I carried out the installation as root?

Any help would be appreciated.

Thanks,
Tim




From scott at scottcain.net  Fri Oct  8 09:14:24 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 8 Oct 2010 09:14:24 -0400
Subject: [Bioperl-l] Getting BioPerl from Github
In-Reply-To: <201010081016.48460.timmcilveen@talktalk.net>
References: <201010081016.48460.timmcilveen@talktalk.net>
Message-ID: <AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>

Hi Tim,

Could it just be that you misspelled "bioperl-live" (as biooperl-live)
in your export statement?

Scott


On Fri, Oct 8, 2010 at 5:16 AM, tim <timmcilveen at talktalk.net> wrote:
> Hi,
> I'm not an experienced Linux user but have been trying to download Bioperl via
> GitHub as I was getting lots of errors using the package installer. It was
> suggested by a list user that I use GitHub instead.
>
> I installed Git using Yast.
>
> I visited this page:
> http://www.bioperl.org/wiki/Using_Git
>
> and used the installation instructions:
> $ git clone git://github.com/bioperl/bioperl-live.git
> bash: $ export PERL5LIB="$HOME/src/bioperl-live:$PERL5LIB"
>
> I tested the code:
> $ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
> but the install didn't work.
> Here is the ouput from my terminal.
> tim at linux-oxgy:~> su
> Password:
> linux-oxgy:/home/tim # git clone git://github.com/bioperl/bioperl-live.git
> Initialized empty Git repository in /home/tim/bioperl-live/.git/
> remote: Counting objects: 88288, done.
> remote: Compressing objects: 100% (23829/23829), done.
> remote: Total 88288 (delta 66885), reused 85264 (delta 63993)
> Receiving objects: 100% (88288/88288), 138.20 MiB | 1.19 MiB/s, done.
> Resolving deltas: 100% (66885/66885), done.
> linux-oxgy:/home/tim # bash
> linux-oxgy:/home/tim # export PERL5LIB="$HOME/src/biooperl-live:$PERL5LIB"
> linux-oxgy:/home/tim # perl -MBIO::Perl -le 'print Bio::Perl->VERSION;'
> Can't locate BIO/Perl.pm in @INC (@INC contains: /root/src/biooperl-live
> /usr/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi
> /usr/lib/perl5/site_perl/5.12.1 /usr/lib/perl5/vendor_perl/5.12.1/x86_64-
> linux-thread-multi /usr/lib/perl5/vendor_perl/5.12.1
> /usr/lib/perl5/5.12.1/x86_64-linux-thread-multi /usr/lib/perl5/5.12.1 .).
> BEGIN failed--compilation aborted.
> linux-oxgy:/home/tim #
>
> I assume that something has went wrong at this step:
> To use this 'live' version of BioPerl, you need to install it (simply tell
> Perl where to find it). Assuming you checked out the code above into
> $HOME/src; set this in your .bash_profile, .profile, or .cshrc:
>
> How do I set things up so that the code is in $HOME/src? Where is it likely to
> be if I carried out the installation as root?
>
> Any help would be appreciated.
>
> Thanks,
> Tim
>
>
> _______________________________________________
> 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 pjayaraman at mcw.edu  Thu Oct  7 16:46:19 2010
From: pjayaraman at mcw.edu (Jayaraman, Pushkala)
Date: Thu, 7 Oct 2010 15:46:19 -0500
Subject: [Bioperl-l] FW: bp_genbank2gff3- Unflattening error
Message-ID: <1448A38A42714048B9C53E473E13CCF00379E83D@davis.hmgc.mcw.edu>

I apologize, 

I should have sent it to the forum first.. 

 

 

FYI.. 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala 
Sent: Thursday, October 07, 2010 3:07 PM
To: 'cjm at fruitfly.org'
Subject: bp_genbank2gff3- Unflattening error

 

Hi Chris, 

I saw your response in a  post about Unflattener.pm here;

http://generic-model-organism-system-database.450254.n5.nabble.com/genba
nk-to-gff3-conversion-problem-td460065.html

 

hence decided to fwd this to you.. 

I have no clue what is going on.. 

 

NT_010799 Unflattening error:

Details: 

------------- EXCEPTION -------------

MSG: PROBLEM, SEVERITY==1

Container feature does not spatially contain subfeature. Perhaps this is
a dicistronic gene? I am expanding the parent feature

SF [Bio::SeqFeature::Generic=HASH(0x149297a0)]: gene; CCL14

 

SF [Bio::SeqFeature::Generic=HASH(0x1492d860)]: mRNA; CCL14; chemokine
(C-C motif) ligand 14 (CCL14), transcript variant 1

 

STACK Bio::SeqFeature::Tools::Unflattener::problem
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:952

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_group
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:2170

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_groups
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1798

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1503

STACK (eval) /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:915

STACK main::unflatten_seq
/usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:914

STACK toplevel /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:411

 

 

 

 

 

I even get another error under Unflattener.pm in another region.. this
is how it is described:

 

PROBLEM:

NT_024524 Unflattening error:

Details: 

------------- EXCEPTION -------------

MSG: 1 there is a conflict with exons; there was an explicitly stated
exon with location 22748456..22748502, yet I cannot generate this exon
from the supplied mRNA locations

 

1 There are some inferred exons that are not in the explicit exon list;
they are the exons at locations:

10982777..10983033

9516278..9517506

1225346..1225429

33491613..33491816

58797942..58798087

7323184..7323367

21253638..21253755

59172140..59172196

54309290..54310329

8988942..8989171

26569087..26569218

6479986..6480032

32266760..32267377

.....

 

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1631

STACK (eval) /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:915

STACK main::unflatten_seq
/usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:914

STACK toplevel /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:411

-------------------------------------

 

 

I do not know what is going on.. is it something that the data has or
something that I am doing wrong? 

the section of the genbank file that gives out this error is pasted
below.. 

 

 

 

 

Please help,

 

 

 

 

 

gene            complement(9047672..9065992)

                     /gene="CCL14-CCL15"

                     /note="chemokine ligand 14, chemokine ligand 15

                     transcription unit"

                     /db_xref="GeneID:348249"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004166.3"

                     /db_xref="GI:34335177"

                     /db_xref="GeneID:6358"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032964.2"

                     /db_xref="GI:34335178"

                     /db_xref="GeneID:6359"

                     /db_xref="MIM:601393"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032962.2"

                     /db_xref="GI:34335175"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004167.3"

                     /db_xref="GI:34335181"

                     /db_xref="GeneID:6359"

                     /db_xref="HGNC:10613"

                     /db_xref="MIM:601393"

     gene            complement(9047672..9050719)

                     /gene="CCL14"

                     /note="chemokine (C-C motif) ligand 14; synonyms:
CC-1,

                     CC-3, CKb1, MCIF, NCC2, SY14, HCC-1, HCC-3, NCC-2,
SCYL2,

                     SCYA14"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050719))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 3"

                     /transcript_id="NM_032963.2"

                     /db_xref="GI:34335176"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     STS             9047707..9047892

                     /standard_name="STS-H22017"

                     /db_xref="UniSTS:13833"

     STS             9047767..9047885

                     /standard_name="GDB:607751"

                     /db_xref="UniSTS:158278"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_116739.1"

                     /db_xref="GI:14589961"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_004157.1"

                     /db_xref="GI:4759070"

                     /db_xref="CCDS:CCDS32624.1"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 2

                     precursor"

                     /protein_id="NP_116738.1"

                     /db_xref="GI:14589959"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

 

 

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala [mailto:pjayaraman at mcw.edu] 
Sent: Thursday, October 07, 2010 2:56 PM
To: gmod-devel at lists.sourceforge.net
Cc: gmod-gbrowse at lists.sourceforge.net
Subject: [Gmod-gbrowse] FW: bp_genbank2gff3- Unflattening error

 

I am providing the section of the genbank file here as I am not able to
attach the entire genbank file here(duh!):

 

     gene            complement(9047672..9065992)

                     /gene="CCL14-CCL15"

                     /note="chemokine ligand 14, chemokine ligand 15

                     transcription unit"

                     /db_xref="GeneID:348249"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004166.3"

                     /db_xref="GI:34335177"

                     /db_xref="GeneID:6358"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032964.2"

                     /db_xref="GI:34335178"

                     /db_xref="GeneID:6359"

                     /db_xref="MIM:601393"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032962.2"

                     /db_xref="GI:34335175"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004167.3"

                     /db_xref="GI:34335181"

                     /db_xref="GeneID:6359"

                     /db_xref="HGNC:10613"

                     /db_xref="MIM:601393"

     gene            complement(9047672..9050719)

                     /gene="CCL14"

                     /note="chemokine (C-C motif) ligand 14; synonyms:
CC-1,

                     CC-3, CKb1, MCIF, NCC2, SY14, HCC-1, HCC-3, NCC-2,
SCYL2,

                     SCYA14"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050719))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 3"

                     /transcript_id="NM_032963.2"

                     /db_xref="GI:34335176"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     STS             9047707..9047892

                     /standard_name="STS-H22017"

                     /db_xref="UniSTS:13833"

     STS             9047767..9047885

                     /standard_name="GDB:607751"

                     /db_xref="UniSTS:158278"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_116739.1"

                     /db_xref="GI:14589961"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_004157.1"

                     /db_xref="GI:4759070"

                     /db_xref="CCDS:CCDS32624.1"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 2

                     precursor"

                     /protein_id="NP_116738.1"

                     /db_xref="GI:14589959"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

 

 

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala 
Sent: Thursday, October 07, 2010 2:43 PM
To: gmod-gbrowse at lists.sourceforge.net
Subject: bp_genbank2gff3- Unflattening error

 

Hello, 

Running the bp_genbank2gff3.pm gives me:

 

NT_010799 Unflattening error:

Details: 

------------- EXCEPTION -------------

MSG: PROBLEM, SEVERITY==1

Container feature does not spatially contain subfeature. Perhaps this is
a dicistronic gene? I am expanding the parent feature

SF [Bio::SeqFeature::Generic=HASH(0x149297a0)]: gene; CCL14

 

SF [Bio::SeqFeature::Generic=HASH(0x1492d860)]: mRNA; CCL14; chemokine
(C-C motif) ligand 14 (CCL14), transcript variant 1

 

STACK Bio::SeqFeature::Tools::Unflattener::problem
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:952

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_group
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:2170

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_groups
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1798

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1503

STACK (eval) /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:915

STACK main::unflatten_seq
/usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:914

STACK toplevel /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:411

 

 

 

Ive never seen this error before and have no clue how to resolve this as
the input is a .gbk file and the script is a BIOPerl script.  Because we
seem to be losing a  lot of gene information in a particular contig. 

Am I doing anything wrong?

 

Thanks,

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

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From kai.blin at biotech.uni-tuebingen.de  Fri Oct  8 09:35:02 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Fri, 08 Oct 2010 15:35:02 +0200
Subject: [Bioperl-l] Getting BioPerl from Github
In-Reply-To: <AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>
References: <201010081016.48460.timmcilveen@talktalk.net>
	<AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>
Message-ID: <4CAF1E06.2090206@biotech.uni-tuebingen.de>

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

On 2010-10-08 15:14, Scott Cain wrote:

> Could it just be that you misspelled "bioperl-live" (as biooperl-live)
> in your export statement?

Looks mighty suspicious, indeed. Good Catch.

Also, if you install into your home directory, there's no reason at all
to do this as root, and you probably never want to do the git clone as
root. There more stuff you do as root, the more likely you're going to
shoot yourself into the foot. :)

Cheers,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universit?t T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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From David.Messina at sbc.su.se  Fri Oct  8 10:24:12 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 8 Oct 2010 16:24:12 +0200
Subject: [Bioperl-l] Getting BioPerl from Github
In-Reply-To: <AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>
References: <201010081016.48460.timmcilveen@talktalk.net>
	<AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>
Message-ID: <65D590FA-9102-4406-AA86-462CF7EFFD0C@sbc.su.se>


> Could it just be that you misspelled "bioperl-live" (as biooperl-live)
> in your export statement?


I think also the capitalization in the following statement is important. That is, -MBio::Perl not -MBIO::Perl

>> linux-oxgy:/home/tim # perl -MBIO::Perl -le 'print Bio::Perl->VERSION;'



Dave




From David.Messina at sbc.su.se  Fri Oct  8 10:37:27 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 8 Oct 2010 16:37:27 +0200
Subject: [Bioperl-l] Bio::Matrix::MatrixI
In-Reply-To: <35D95AF6C5D146479C328BBBA554FB76028C367E@mailf.lumcnet.prod.intern>
References: <35D95AF6C5D146479C328BBBA554FB76028C367E@mailf.lumcnet.prod.intern>
Message-ID: <9826175D-4FD0-44CD-9E29-348176A2C117@sbc.su.se>

Hi Anna,

You will want to use Bio::Matrix::IO to read in a Phylip matrix.

Something like:

use Bio::Matrix::IO;
my $parser = Bio::Matrix::IO->new(-format   => 'phylip',
                                  -file     => 'phylipdist.out');
my $matrix = $parser->next_matrix;


Dave


On Sep 29, 2010, at 15:28 , <A.Vakhrusheva at lumc.nl> wrote:

> Bio::Matrix::MatrixI
> 
> I have a question concerning this interface.
> 
> I want to calculate p distances matrix, but what format is acceptable
> for input? Phylip doesn't work
> 
> Anna 



From dan.bolser at gmail.com  Fri Oct  8 11:04:44 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Fri, 8 Oct 2010 16:04:44 +0100
Subject: [Bioperl-l] Question about Bio::Coordinate::Pair
In-Reply-To: <AANLkTi=fmjWt95GWw=Fe+-WVkhQYcuHPDCNxE6iLpN0w@mail.gmail.com>
References: <AANLkTi=fmjWt95GWw=Fe+-WVkhQYcuHPDCNxE6iLpN0w@mail.gmail.com>
Message-ID: <AANLkTim3fvNkvaXftcvRb0SnhATOdugtr3Z=2v8HTxrU@mail.gmail.com>

Well... I tried to toggle the strand of the gap sublocation to match
that of the match sublocation, and overall I ended up failing one test
within t/Coordinate/CoordinateMapper.t, test number 55 (line 119)...

This test actually tests for the strandedness of the gap sublocation
that I'm specifically changing because it leads to the 'unexpected'
(or at least, 'inconsistent') behaviour that I'm calling a bug (test
55 is at the end, with enough preceding context to reproduce it):

# propepide
my $match1 = Bio::Location::Simple->new
    (-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
# peptide
my $match2 = Bio::Location::Simple->new
    (-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );

ok my $pair = Bio::Coordinate::Pair->new(-in => $match1,
					 -out => $match2,
					 -negative => 0, # false, default
					);

...

#
# partial match = gap & match
#
$pos2 = Bio::Location::Simple->new
    (-start => 20, -end => 22, -strand=> -1 );

ok $res = $pair->map($pos2);

...

is $res->gap->strand, -1; # TEST 55.  Fails when I 'fix' Bio::Coordinate::Pair



In the absence of any other information, can I take this to mean that
the strand of the gap sublocations are not used for anything
significant?


Cheers,
Dan.



On 5 October 2010 11:36, Dan Bolser <dan.bolser at gmail.com> wrote:
> Hi,
>
> Can someone describe in a bit more detail the purpose of the Gap
> sublocations that are sometimes returned by Bio::Coordinate::Pair [1]?
>
> I found that, according to Bio::Location::Split, if the Match and Gap
> sublocations have a different strand, the strand method (called via
> Bio::Coordinate::Result) returns undef. This is inconsistent with the
> way Bio::Coordinate::Result tends to behave. See the test script and
> results below, also pasted here [2].
>
> The question is, can I just toggle the strand of the Gap sublocation
> to match that of the Match sublocation? Or does the strand of the Gap
> sublocation encode some important but as yet undocumented information?
> If the strand of the Gap and Match sublocations are made to match
> (within Bio::Coordinate::Pair) this will simplify code that uses
> Bio::Coordinate::Pair, making it more consistent, and perhaps help
> with some other bugs [3].
>
>
> Cheers,
> Dan.
>
> [1] http://www.bioperl.org/wiki/Module:Bio::Coordinate::Pair
> [2] http://www.bioperl.org/wiki/Module_Discussion:Bio::Coordinate::Pair
> [3] http://tinyurl.com/36na2cp
>
>
> #!/usr/bin/perl -w
>
> ## Stress test Bio::Coordinate::Pair
>
> use strict;
> use Data::Dumper;
>
> use Bio::Location::Simple;
> use Bio::Coordinate::Pair;
>
> ## A contig
> my $ctg = Bio::Location::Simple->
> ?new( -seq_id => 'ctg',
> ? ? ? -start ?=> ? ?1,
> ? ? ? -end ? ?=> 1001,
> ? ? ? -strand => ? +1,
> ? ? );
>
> ## The contigs position on a chromosome (forward)
> my $ctg_on_chr_f = Bio::Location::Simple->
> ?new( -seq_id => 'ctg on chr r',
> ? ? ? -start ?=> ? ? ? ? ? 5001,
> ? ? ? -end ? ?=> ? ? ? ? ? 6001,
> ? ? ? -strand => ? ? ? ? ? ? +1,
> ? ? );
>
> ## The contigs position on a chromosome (reverse)
> my $ctg_on_chr_r = Bio::Location::Simple->
> ?new( -seq_id => 'ctg on chr r',
> ? ? ? -start ?=> ? ? ? ? ? 5001,
> ? ? ? -end ? ?=> ? ? ? ? ? 6001,
> ? ? ? -strand => ? ? ? ? ? ? -1,
> ? ? );
>
> ## Coordinate mapping (forward)
> my $agp_f = Bio::Coordinate::Pair->
> ?new( -in ?=> $ctg,
> ? ? ? -out => $ctg_on_chr_f
> ? ? );
>
> ## Coordinate mapping (reverse)
> my $agp_r = Bio::Coordinate::Pair->
> ?new( -in ?=> $ctg,
> ? ? ? -out => $ctg_on_chr_r
> ? ? );
>
>
>
> ## A match, in contig coordinates...
> my $match_on_ctg_4 = Bio::Location::Simple->
> ?new( -seq_id => 'hit 4',
> ? ? ? -start ?=> ? ? 925,
> ? ? ? -end ? ?=> ? ?1125,
> ? ? ? -strand => ? ? ?-1,
> ? ? );
>
> ## Map it into chromosome coordinates (forward)
> my $match_on_chr_4_f =
> ?$agp_f->map( $match_on_ctg_4 );
>
> print Dumper $match_on_chr_4_f, "\n";
>
> ## Map it into chromosome coordinates (reverse)
> my $match_on_chr_4_r =
> ?$agp_r->map( $match_on_ctg_4 );
>
> print Dumper $match_on_chr_4_r, "\n";
>
> __END__
>
> $VAR1 = bless( {
> ? ? ? ? ? ? ? ? '_sublocations' => [
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg on chr r',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 5925,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 6001
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? },
> 'Bio::Coordinate::Result::Match' ),
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 1002,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 1125
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result::Gap' )
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?],
> ? ? ? ? ? ? ? ? '_gap' => $VAR1->{'_sublocations'}[1],
> ? ? ? ? ? ? ? ? 'strand' => -1,
> ? ? ? ? ? ? ? ? '_match' => $VAR1->{'_sublocations'}[0],
> ? ? ? ? ? ? ? ? '_splittype' => 'JOIN'
> ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result' );
> $VAR2 = '
> ';
> $VAR1 = bless( {
> ? ? ? ? ? ? ? ? '_sublocations' => [
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => 1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg on chr r',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 5001,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 5077
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? },
> 'Bio::Coordinate::Result::Match' ),
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 1002,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 1125
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result::Gap' )
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?],
> ? ? ? ? ? ? ? ? '_gap' => $VAR1->{'_sublocations'}[1],
> ? ? ? ? ? ? ? ? 'strand' => 1,
> ? ? ? ? ? ? ? ? '_match' => $VAR1->{'_sublocations'}[0],
> ? ? ? ? ? ? ? ? '_splittype' => 'JOIN'
> ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result' );
> $VAR2 = '
> ';
>



From cjfields at illinois.edu  Fri Oct  8 11:16:21 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 8 Oct 2010 10:16:21 -0500
Subject: [Bioperl-l] Bio::Matrix::MatrixI
In-Reply-To: <9826175D-4FD0-44CD-9E29-348176A2C117@sbc.su.se>
References: <35D95AF6C5D146479C328BBBA554FB76028C367E@mailf.lumcnet.prod.intern>
	<9826175D-4FD0-44CD-9E29-348176A2C117@sbc.su.se>
Message-ID: <D4BC1FC6-2A66-4F26-ABF3-EB6D6CD65FE9@illinois.edu>

Correct, MatrixI (and pretty much any other module 'FooI') are interfaces for API consistency.

chris

On Oct 8, 2010, at 9:37 AM, Dave Messina wrote:

> Hi Anna,
> 
> You will want to use Bio::Matrix::IO to read in a Phylip matrix.
> 
> Something like:
> 
> use Bio::Matrix::IO;
> my $parser = Bio::Matrix::IO->new(-format   => 'phylip',
>                                  -file     => 'phylipdist.out');
> my $matrix = $parser->next_matrix;
> 
> 
> Dave
> 
> 
> On Sep 29, 2010, at 15:28 , <A.Vakhrusheva at lumc.nl> wrote:
> 
>> Bio::Matrix::MatrixI
>> 
>> I have a question concerning this interface.
>> 
>> I want to calculate p distances matrix, but what format is acceptable
>> for input? Phylip doesn't work
>> 
>> Anna 
> 
> _______________________________________________
> 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  Fri Oct  8 11:57:38 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Fri, 8 Oct 2010 16:57:38 +0100
Subject: [Bioperl-l] Question about Bio::Coordinate::Pair
In-Reply-To: <AANLkTim3fvNkvaXftcvRb0SnhATOdugtr3Z=2v8HTxrU@mail.gmail.com>
References: <AANLkTi=fmjWt95GWw=Fe+-WVkhQYcuHPDCNxE6iLpN0w@mail.gmail.com>
	<AANLkTim3fvNkvaXftcvRb0SnhATOdugtr3Z=2v8HTxrU@mail.gmail.com>
Message-ID: <AANLkTimFqsJbpZ802GzKPUAnhKHUgyjRvyg3bJNPEQNL@mail.gmail.com>

Actually, I changed the Strand of the gap in a few more places [1],
and now there are a total of 4 failed tests, however, they all appear
to be of the same form as the one reported below:


not ok 84
#   Failed test at t/Coordinate/CoordinateMapper.t line 229.
#          got: '1'
#     expected: '-1'

not ok 93
#   Failed test at t/Coordinate/CoordinateMapper.t line 246.
#          got: '1'
#     expected: '-1'

not ok 99
#   Failed test at t/Coordinate/CoordinateMapper.t line 262.
#          got: '1'
#     expected: '-1'

not ok 102
#   Failed test at t/Coordinate/CoordinateMapper.t line 265.
#          got: '1'
#     expected: '-1'


So now you know.


Dan.

[1] http://github.com/dbolser/bioperl-live/tree/dbolser_bio_coordinate_pair_tests

On 8 October 2010 16:04, Dan Bolser <dan.bolser at gmail.com> wrote:
> Well... I tried to toggle the strand of the gap sublocation to match
> that of the match sublocation, and overall I ended up failing one test
> within t/Coordinate/CoordinateMapper.t, test number 55 (line 119)...
>
> This test actually tests for the strandedness of the gap sublocation
> that I'm specifically changing because it leads to the 'unexpected'
> (or at least, 'inconsistent') behaviour that I'm calling a bug (test
> 55 is at the end, with enough preceding context to reproduce it):
>
> # propepide
> my $match1 = Bio::Location::Simple->new
> ? ?(-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
> # peptide
> my $match2 = Bio::Location::Simple->new
> ? ?(-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );
>
> ok my $pair = Bio::Coordinate::Pair->new(-in => $match1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -out => $match2,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -negative => 0, # false, default
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?);
>
> ...
>
> #
> # partial match = gap & match
> #
> $pos2 = Bio::Location::Simple->new
> ? ?(-start => 20, -end => 22, -strand=> -1 );
>
> ok $res = $pair->map($pos2);
>
> ...
>
> is $res->gap->strand, -1; # TEST 55. ?Fails when I 'fix' Bio::Coordinate::Pair
>
>
>
> In the absence of any other information, can I take this to mean that
> the strand of the gap sublocations are not used for anything
> significant?
>
>
> Cheers,
> Dan.
>
>
>
> On 5 October 2010 11:36, Dan Bolser <dan.bolser at gmail.com> wrote:
>> Hi,
>>
>> Can someone describe in a bit more detail the purpose of the Gap
>> sublocations that are sometimes returned by Bio::Coordinate::Pair [1]?
>>
>> I found that, according to Bio::Location::Split, if the Match and Gap
>> sublocations have a different strand, the strand method (called via
>> Bio::Coordinate::Result) returns undef. This is inconsistent with the
>> way Bio::Coordinate::Result tends to behave. See the test script and
>> results below, also pasted here [2].
>>
>> The question is, can I just toggle the strand of the Gap sublocation
>> to match that of the Match sublocation? Or does the strand of the Gap
>> sublocation encode some important but as yet undocumented information?
>> If the strand of the Gap and Match sublocations are made to match
>> (within Bio::Coordinate::Pair) this will simplify code that uses
>> Bio::Coordinate::Pair, making it more consistent, and perhaps help
>> with some other bugs [3].
>>
>>
>> Cheers,
>> Dan.
>>
>> [1] http://www.bioperl.org/wiki/Module:Bio::Coordinate::Pair
>> [2] http://www.bioperl.org/wiki/Module_Discussion:Bio::Coordinate::Pair
>> [3] http://tinyurl.com/36na2cp
>>
>>
>> #!/usr/bin/perl -w
>>
>> ## Stress test Bio::Coordinate::Pair
>>
>> use strict;
>> use Data::Dumper;
>>
>> use Bio::Location::Simple;
>> use Bio::Coordinate::Pair;
>>
>> ## A contig
>> my $ctg = Bio::Location::Simple->
>> ?new( -seq_id => 'ctg',
>> ? ? ? -start ?=> ? ?1,
>> ? ? ? -end ? ?=> 1001,
>> ? ? ? -strand => ? +1,
>> ? ? );
>>
>> ## The contigs position on a chromosome (forward)
>> my $ctg_on_chr_f = Bio::Location::Simple->
>> ?new( -seq_id => 'ctg on chr r',
>> ? ? ? -start ?=> ? ? ? ? ? 5001,
>> ? ? ? -end ? ?=> ? ? ? ? ? 6001,
>> ? ? ? -strand => ? ? ? ? ? ? +1,
>> ? ? );
>>
>> ## The contigs position on a chromosome (reverse)
>> my $ctg_on_chr_r = Bio::Location::Simple->
>> ?new( -seq_id => 'ctg on chr r',
>> ? ? ? -start ?=> ? ? ? ? ? 5001,
>> ? ? ? -end ? ?=> ? ? ? ? ? 6001,
>> ? ? ? -strand => ? ? ? ? ? ? -1,
>> ? ? );
>>
>> ## Coordinate mapping (forward)
>> my $agp_f = Bio::Coordinate::Pair->
>> ?new( -in ?=> $ctg,
>> ? ? ? -out => $ctg_on_chr_f
>> ? ? );
>>
>> ## Coordinate mapping (reverse)
>> my $agp_r = Bio::Coordinate::Pair->
>> ?new( -in ?=> $ctg,
>> ? ? ? -out => $ctg_on_chr_r
>> ? ? );
>>
>>
>>
>> ## A match, in contig coordinates...
>> my $match_on_ctg_4 = Bio::Location::Simple->
>> ?new( -seq_id => 'hit 4',
>> ? ? ? -start ?=> ? ? 925,
>> ? ? ? -end ? ?=> ? ?1125,
>> ? ? ? -strand => ? ? ?-1,
>> ? ? );
>>
>> ## Map it into chromosome coordinates (forward)
>> my $match_on_chr_4_f =
>> ?$agp_f->map( $match_on_ctg_4 );
>>
>> print Dumper $match_on_chr_4_f, "\n";
>>
>> ## Map it into chromosome coordinates (reverse)
>> my $match_on_chr_4_r =
>> ?$agp_r->map( $match_on_ctg_4 );
>>
>> print Dumper $match_on_chr_4_r, "\n";
>>
>> __END__
>>
>> $VAR1 = bless( {
>> ? ? ? ? ? ? ? ? '_sublocations' => [
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg on chr r',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 5925,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 6001
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? },
>> 'Bio::Coordinate::Result::Match' ),
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 1002,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 1125
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result::Gap' )
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?],
>> ? ? ? ? ? ? ? ? '_gap' => $VAR1->{'_sublocations'}[1],
>> ? ? ? ? ? ? ? ? 'strand' => -1,
>> ? ? ? ? ? ? ? ? '_match' => $VAR1->{'_sublocations'}[0],
>> ? ? ? ? ? ? ? ? '_splittype' => 'JOIN'
>> ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result' );
>> $VAR2 = '
>> ';
>> $VAR1 = bless( {
>> ? ? ? ? ? ? ? ? '_sublocations' => [
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => 1,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg on chr r',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 5001,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 5077
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? },
>> 'Bio::Coordinate::Result::Match' ),
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 1002,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 1125
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result::Gap' )
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?],
>> ? ? ? ? ? ? ? ? '_gap' => $VAR1->{'_sublocations'}[1],
>> ? ? ? ? ? ? ? ? 'strand' => 1,
>> ? ? ? ? ? ? ? ? '_match' => $VAR1->{'_sublocations'}[0],
>> ? ? ? ? ? ? ? ? '_splittype' => 'JOIN'
>> ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result' );
>> $VAR2 = '
>> ';
>>
>



From mauricio at open-bio.org  Fri Oct  8 12:47:56 2010
From: mauricio at open-bio.org (Mauricio Herrera Cuadra)
Date: Fri, 08 Oct 2010 11:47:56 -0500
Subject: [Bioperl-l] Pdoc documentation & test coverage updated
Message-ID: <4CAF4B3C.1060001@open-bio.org>

The cron scripts that generate the live code Pdoc documentation and the 
test coverage reports are now updated to pull from the GitHub 
repository. Please let me know if you notice anything wonky.

Mauricio.


From cjfields at illinois.edu  Fri Oct  8 16:13:08 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 8 Oct 2010 15:13:08 -0500
Subject: [Bioperl-l] Pdoc documentation & test coverage updated
In-Reply-To: <4CAF4B3C.1060001@open-bio.org>
References: <4CAF4B3C.1060001@open-bio.org>
Message-ID: <DA23CAB1-6A1C-4EC5-9EEF-06ED68C35AE9@illinois.edu>

Thanks Mauricio!  That completely feel off my radar.

chris

On Oct 8, 2010, at 11:47 AM, Mauricio Herrera Cuadra wrote:

> The cron scripts that generate the live code Pdoc documentation and the test coverage reports are now updated to pull from the GitHub repository. Please let me know if you notice anything wonky.
> 
> Mauricio.
> _______________________________________________
> 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  Fri Oct  8 17:08:40 2010
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 08 Oct 2010 14:08:40 -0700
Subject: [Bioperl-l] Pdoc documentation & test coverage updated
In-Reply-To: <DA23CAB1-6A1C-4EC5-9EEF-06ED68C35AE9@illinois.edu>
References: <4CAF4B3C.1060001@open-bio.org>
	<DA23CAB1-6A1C-4EC5-9EEF-06ED68C35AE9@illinois.edu>
Message-ID: <4CAF8858.5090302@bioperl.org>

nice -- thanks for doing that Mauricio.


Chris Fields wrote, On 10/8/10 1:13 PM:
> Thanks Mauricio!  That completely feel off my radar.
>
> chris
>
> On Oct 8, 2010, at 11:47 AM, Mauricio Herrera Cuadra wrote:
>
>> The cron scripts that generate the live code Pdoc documentation and the test coverage reports are now updated to pull from the GitHub repository. Please let me know if you notice anything wonky.
>>
>> Mauricio.
>> _______________________________________________
>> 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

-- 
Jason Stajich
jason at bioperl.org



From avilella at gmail.com  Tue Oct 12 08:34:14 2010
From: avilella at gmail.com (Albert Vilella)
Date: Tue, 12 Oct 2010 13:34:14 +0100
Subject: [Bioperl-l] possible bug in Bio::SeqIO::fastq
Message-ID: <AANLkTi=XNY9skUoTpJYJ=cp8wcpRPiskjFeuc3RquDUk@mail.gmail.com>

Hi,

I found what seems to me could be a bug in the fastq module, which is
that if the
last line of the raw_quality section is a single "0" character, a
"if($line)" isn't
returning it properly, because it should be "if(defined $line)" instead.

Find here a test case and the line in question:

----
use strict;
use Bio::SeqIO;

my $consio = Bio::SeqIO->new
  (-format => 'fastq',
   -fh => \*DATA);

my $onelineconsout = Bio::SeqIO->new
  (-format => 'fastq',
   -fh => \*STDOUT);

while (my $seq = $consio->next_seq) {
  next if ($seq->seq =~ /^n+$/);
  $seq->seq(uc($seq->seq));
  $onelineconsout->write_seq($seq);
}
$consio->close;
$onelineconsout->close;

__DATA__
@SRR031652.634472
agtgcgctgatctgtggcccgtattgcctcaacgcaagctcaatagcttgagtatattaa
a
+
01111111111111100111111--,,011111101111111110111111111111110
0
----

--- /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm
2010-10-12 13:26:06.491743000 +0100
+++ /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm~
2010-10-12 13:07:27.462833000 +0100
@@ -80,7 +80,7 @@
                 last FASTQ
             }
             chomp $line;
-            if (!defined($line)) {
+            if (!$line) {
                 delete $self->{lastline};
                 last FASTQ;
             }


From shalabh.sharma7 at gmail.com  Tue Oct 12 10:20:58 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 12 Oct 2010 10:20:58 -0400
Subject: [Bioperl-l] fastq Problem
Message-ID: <AANLkTikTASuFtDhvwZDpvn4N4k-nMR2S1y9noQ2OcY12@mail.gmail.com>

Hi,
    I have data from illumina, i can read the data by using Bio::SeqIO but
when i am writing it back its writing in fasta format.

Is there anyway i can write it back in fastq format?

Thanks
Shalabh


From avilella at gmail.com  Tue Oct 12 10:54:46 2010
From: avilella at gmail.com (Albert Vilella)
Date: Tue, 12 Oct 2010 15:54:46 +0100
Subject: [Bioperl-l] possible bug in Bio::SeqIO::fastq
In-Reply-To: <76631143-1043-4A02-BF4C-AC7F9D8A3274@illinois.edu>
References: <AANLkTi=XNY9skUoTpJYJ=cp8wcpRPiskjFeuc3RquDUk@mail.gmail.com>
	<76631143-1043-4A02-BF4C-AC7F9D8A3274@illinois.edu>
Message-ID: <AANLkTi=m3-rR4yGLRPLTVW0azSdS3AUwQQ1u1gtvzWoP@mail.gmail.com>

aah! thanks!

On Tue, Oct 12, 2010 at 3:50 PM, Chris Fields <cjfields at illinois.edu> wrote:
> Albert,
>
> Have you tried bioperl-live? ?This is already fixed there.
>
> chris
>
> On Oct 12, 2010, at 7:34 AM, Albert Vilella wrote:
>
>> Hi,
>>
>> I found what seems to me could be a bug in the fastq module, which is
>> that if the
>> last line of the raw_quality section is a single "0" character, a
>> "if($line)" isn't
>> returning it properly, because it should be "if(defined $line)" instead.
>>
>> Find here a test case and the line in question:
>>
>> ----
>> use strict;
>> use Bio::SeqIO;
>>
>> my $consio = Bio::SeqIO->new
>> ?(-format => 'fastq',
>> ? -fh => \*DATA);
>>
>> my $onelineconsout = Bio::SeqIO->new
>> ?(-format => 'fastq',
>> ? -fh => \*STDOUT);
>>
>> while (my $seq = $consio->next_seq) {
>> ?next if ($seq->seq =~ /^n+$/);
>> ?$seq->seq(uc($seq->seq));
>> ?$onelineconsout->write_seq($seq);
>> }
>> $consio->close;
>> $onelineconsout->close;
>>
>> __DATA__
>> @SRR031652.634472
>> agtgcgctgatctgtggcccgtattgcctcaacgcaagctcaatagcttgagtatattaa
>> a
>> +
>> 01111111111111100111111--,,011111101111111110111111111111110
>> 0
>> ----
>>
>> --- /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm
>> 2010-10-12 13:26:06.491743000 +0100
>> +++ /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm~
>> 2010-10-12 13:07:27.462833000 +0100
>> @@ -80,7 +80,7 @@
>> ? ? ? ? ? ? ? ? last FASTQ
>> ? ? ? ? ? ? }
>> ? ? ? ? ? ? chomp $line;
>> - ? ? ? ? ? ?if (!defined($line)) {
>> + ? ? ? ? ? ?if (!$line) {
>> ? ? ? ? ? ? ? ? delete $self->{lastline};
>> ? ? ? ? ? ? ? ? last FASTQ;
>> ? ? ? ? ? ? }
>> _______________________________________________
>> 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 Oct 12 10:50:30 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 12 Oct 2010 09:50:30 -0500
Subject: [Bioperl-l] possible bug in Bio::SeqIO::fastq
In-Reply-To: <AANLkTi=XNY9skUoTpJYJ=cp8wcpRPiskjFeuc3RquDUk@mail.gmail.com>
References: <AANLkTi=XNY9skUoTpJYJ=cp8wcpRPiskjFeuc3RquDUk@mail.gmail.com>
Message-ID: <76631143-1043-4A02-BF4C-AC7F9D8A3274@illinois.edu>

Albert, 

Have you tried bioperl-live?  This is already fixed there.

chris

On Oct 12, 2010, at 7:34 AM, Albert Vilella wrote:

> Hi,
> 
> I found what seems to me could be a bug in the fastq module, which is
> that if the
> last line of the raw_quality section is a single "0" character, a
> "if($line)" isn't
> returning it properly, because it should be "if(defined $line)" instead.
> 
> Find here a test case and the line in question:
> 
> ----
> use strict;
> use Bio::SeqIO;
> 
> my $consio = Bio::SeqIO->new
>  (-format => 'fastq',
>   -fh => \*DATA);
> 
> my $onelineconsout = Bio::SeqIO->new
>  (-format => 'fastq',
>   -fh => \*STDOUT);
> 
> while (my $seq = $consio->next_seq) {
>  next if ($seq->seq =~ /^n+$/);
>  $seq->seq(uc($seq->seq));
>  $onelineconsout->write_seq($seq);
> }
> $consio->close;
> $onelineconsout->close;
> 
> __DATA__
> @SRR031652.634472
> agtgcgctgatctgtggcccgtattgcctcaacgcaagctcaatagcttgagtatattaa
> a
> +
> 01111111111111100111111--,,011111101111111110111111111111110
> 0
> ----
> 
> --- /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm
> 2010-10-12 13:26:06.491743000 +0100
> +++ /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm~
> 2010-10-12 13:07:27.462833000 +0100
> @@ -80,7 +80,7 @@
>                 last FASTQ
>             }
>             chomp $line;
> -            if (!defined($line)) {
> +            if (!$line) {
>                 delete $self->{lastline};
>                 last FASTQ;
>             }
> _______________________________________________
> 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 Oct 12 10:51:41 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 12 Oct 2010 09:51:41 -0500
Subject: [Bioperl-l] fastq Problem
In-Reply-To: <AANLkTikTASuFtDhvwZDpvn4N4k-nMR2S1y9noQ2OcY12@mail.gmail.com>
References: <AANLkTikTASuFtDhvwZDpvn4N4k-nMR2S1y9noQ2OcY12@mail.gmail.com>
Message-ID: <03B2F4BE-4E32-4A28-BB9E-B2B59EAEFE00@illinois.edu>

Yes, but you need to use the latest CPAN release or bioperl-live; anything older than v. 1.6.1 will not convert Illumina reads correctly.

chris

On Oct 12, 2010, at 9:20 AM, shalabh sharma wrote:

> Hi,
>    I have data from illumina, i can read the data by using Bio::SeqIO but
> when i am writing it back its writing in fasta format.
> 
> Is there anyway i can write it back in fastq format?
> 
> Thanks
> Shalabh
> _______________________________________________
> 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  Tue Oct 12 11:09:50 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 12 Oct 2010 11:09:50 -0400
Subject: [Bioperl-l] fastq Problem
In-Reply-To: <03B2F4BE-4E32-4A28-BB9E-B2B59EAEFE00@illinois.edu>
References: <AANLkTikTASuFtDhvwZDpvn4N4k-nMR2S1y9noQ2OcY12@mail.gmail.com>
	<03B2F4BE-4E32-4A28-BB9E-B2B59EAEFE00@illinois.edu>
Message-ID: <AANLkTim3Hx3SLrEoQa8D9Ha_x-ECTOjCCQY4CjHBJOaV@mail.gmail.com>

Thanks Chris,
I realized that after writing that mail. Its working now.

Thanks
Shalabh


On Tue, Oct 12, 2010 at 10:51 AM, Chris Fields <cjfields at illinois.edu>wrote:

> Yes, but you need to use the latest CPAN release or bioperl-live; anything
> older than v. 1.6.1 will not convert Illumina reads correctly.
>
> chris
>
> On Oct 12, 2010, at 9:20 AM, shalabh sharma wrote:
>
> > Hi,
> >    I have data from illumina, i can read the data by using Bio::SeqIO but
> > when i am writing it back its writing in fasta format.
> >
> > Is there anyway i can write it back in fastq format?
> >
> > Thanks
> > Shalabh
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From maj at fortinbras.us  Wed Oct 13 23:52:05 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Wed, 13 Oct 2010 23:52:05 -0400
Subject: [Bioperl-l] Next-gen flu informatics
Message-ID: <81299466177D467091763FEA84CA00FD@NewLife>

Hi All, 

Sorry about the job spam, but you are the best talent pool I know. SRA
(the company now interfering with my BioPerl work) is looking for
next-gen experienced bioinformaticists for a new contract with
CDC. Please have a look at http://www.sra.com/careers/search.php,
requisition numbers 31385, 31402 and 31467.

Thanks!
MAJ



From dichmann at berkeley.edu  Thu Oct 14 21:16:29 2010
From: dichmann at berkeley.edu (Darwin Sorento Dichmann)
Date: Thu, 14 Oct 2010 18:16:29 -0700
Subject: [Bioperl-l] Extracting sequences from MySQL DB with Bio::DB::GFF
Message-ID: <36D60149-EEC5-4A45-85B9-E7FD4F3C005C@berkeley.edu>

Greetings, 

I am trying to extract sequences from a MySQL DB with Bio::DB::GFF. The database is the same as I use for my gbrowse2 and it works fine for that. Also, I can extract all sorts of features but not sequence. 

When I run this script I thought I'd get a sequence output but apparently I get the memory address instead. 

I have very little experience with perl or other programming, but I try to follow the directions in the manual. I suspect that I overlook something very basic and any help would be greatly appreciated. 

Thanks,
Darwin 



The script:
------------
#! usr/bin/perl -w
# module to test if Bio::DB::GFF can be used to extract sequences from frog2 database.

use strict;
use Bio::Seq;
use Bio::SeqIO;
use Bio::DB::GFF;

# Open database
my $db = Bio::DB::GFF->
new( 	-adaptor => 'DBI::mysql',
     	-dsn     => 'frog2',
		-user => 'darwin',
		-password => '****',
		);

# fetch scaffold_1 (1-100000)
my $segment = $db->segment('scaffold_1', 1 => 100000) or die;

# get its DNA
 my $dna = $segment->seq or die;
print $segment, "\n";
print $dna,"\n";

# get an iterator on all curated features of type 'exon' or 'intron'
# this prints all exons and intron with transcript name on screen
	my $iterator = $segment->get_seq_stream(-type     => ['mRNA']);
	while (my $s = $iterator->next_seq) {
    print $s,"\n";
}

exit;
---------------

The output:
Macintosh:perlscripts darwin$ perl frog2_parser.pl 
scaffold_1:1,100000
Bio::PrimarySeq=HASH(0x100bb4d68)
mRNA:pick(xt42f011730m)
mRNA:pick(xt42f014902m)
mRNA:pick(xt42f016160m)
mRNA:pick(xt42f017353m)
mRNA:pick(xt42f029332m)
---------------


From scott at scottcain.net  Thu Oct 14 22:01:24 2010
From: scott at scottcain.net (Scott Cain)
Date: Thu, 14 Oct 2010 22:01:24 -0400
Subject: [Bioperl-l] Extracting sequences from MySQL DB with Bio::DB::GFF
In-Reply-To: <36D60149-EEC5-4A45-85B9-E7FD4F3C005C@berkeley.edu>
References: <36D60149-EEC5-4A45-85B9-E7FD4F3C005C@berkeley.edu>
Message-ID: <AANLkTi=i1xAoyeQJGAnT9X5wEmdchJk1v4YWMSqk7fH1@mail.gmail.com>

Hi Darwin,

The "seq" method returns a Bio::PrimarySeq object (I forget why this
is--I think it's to fulfill the contract with the Bio::SeqFeatureI
interface).  To get the sequence, you can do a few things: 1) call the
seq method on the Bio::PrimarySeq object, like this:

  my $dna = $segment->seq->seq;

or 2) use the dna method:

  my $dna = $segment->dna;

The perldoc section from Bio::DB::GFF::Segment is below.

Scott

       seq

        Title   : seq
        Usage   : $s->seq
        Function: get the sequence string for this segment
        Returns : a Bio::PrimarySeq
        Args    : none
        Status  : Public

       Returns the sequence for this segment as a Bio::PrimarySeq.  (-) strand
       segments are automatically reverse complemented

       The method is called dna() return the data as a simple sequence string.

       dna

        Title   : dna
        Usage   : $s->dna
        Function: get the DNA string for this segment
        Returns : a string
        Args    : none
        Status  : Public

       Returns the sequence for this segment as a simple string. (-) strand
       segments are automatically reverse complemented

       The method is also called protein().


On Thu, Oct 14, 2010 at 9:16 PM, Darwin Sorento Dichmann
<dichmann at berkeley.edu> wrote:
> Greetings,
>
> I am trying to extract sequences from a MySQL DB with Bio::DB::GFF. The database is the same as I use for my gbrowse2 and it works fine for that. Also, I can extract all sorts of features but not sequence.
>
> When I run this script I thought I'd get a sequence output but apparently I get the memory address instead.
>
> I have very little experience with perl or other programming, but I try to follow the directions in the manual. I suspect that I overlook something very basic and any help would be greatly appreciated.
>
> Thanks,
> Darwin
>
>
>
> The script:
> ------------
> #! usr/bin/perl -w
> # module to test if Bio::DB::GFF can be used to extract sequences from frog2 database.
>
> use strict;
> use Bio::Seq;
> use Bio::SeqIO;
> use Bio::DB::GFF;
>
> # Open database
> my $db = Bio::DB::GFF->
> new(    -adaptor => 'DBI::mysql',
>        -dsn     => 'frog2',
>                -user => 'darwin',
>                -password => '****',
>                );
>
> # fetch scaffold_1 (1-100000)
> my $segment = $db->segment('scaffold_1', 1 => 100000) or die;
>
> # get its DNA
>  my $dna = $segment->seq or die;
> print $segment, "\n";
> print $dna,"\n";
>
> # get an iterator on all curated features of type 'exon' or 'intron'
> # this prints all exons and intron with transcript name on screen
>        my $iterator = $segment->get_seq_stream(-type     => ['mRNA']);
>        while (my $s = $iterator->next_seq) {
>    print $s,"\n";
> }
>
> exit;
> ---------------
>
> The output:
> Macintosh:perlscripts darwin$ perl frog2_parser.pl
> scaffold_1:1,100000
> Bio::PrimarySeq=HASH(0x100bb4d68)
> mRNA:pick(xt42f011730m)
> mRNA:pick(xt42f014902m)
> mRNA:pick(xt42f016160m)
> mRNA:pick(xt42f017353m)
> mRNA:pick(xt42f029332m)
> ---------------
> _______________________________________________
> 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 dichmann at berkeley.edu  Fri Oct 15 13:34:02 2010
From: dichmann at berkeley.edu (Darwin Sorento Dichmann)
Date: Fri, 15 Oct 2010 10:34:02 -0700
Subject: [Bioperl-l] Extracting sequences from MySQL DB with Bio::DB::GFF
In-Reply-To: <AANLkTi=i1xAoyeQJGAnT9X5wEmdchJk1v4YWMSqk7fH1@mail.gmail.com>
References: <36D60149-EEC5-4A45-85B9-E7FD4F3C005C@berkeley.edu>
	<AANLkTi=i1xAoyeQJGAnT9X5wEmdchJk1v4YWMSqk7fH1@mail.gmail.com>
Message-ID: <9E7B9E6F-9440-4BAC-AD8D-2A739A863C1B@berkeley.edu>

It's a beauty to behold!
Thanks Scott!

Best,
Darwin

On Oct 14, 2010, at 7:01 PM, Scott Cain wrote:

> Hi Darwin,
> 
> The "seq" method returns a Bio::PrimarySeq object (I forget why this
> is--I think it's to fulfill the contract with the Bio::SeqFeatureI
> interface).  To get the sequence, you can do a few things: 1) call the
> seq method on the Bio::PrimarySeq object, like this:
> 
>  my $dna = $segment->seq->seq;
> 
> or 2) use the dna method:
> 
>  my $dna = $segment->dna;
> 
> The perldoc section from Bio::DB::GFF::Segment is below.
> 
> Scott
> 
>       seq
> 
>        Title   : seq
>        Usage   : $s->seq
>        Function: get the sequence string for this segment
>        Returns : a Bio::PrimarySeq
>        Args    : none
>        Status  : Public
> 
>       Returns the sequence for this segment as a Bio::PrimarySeq.  (-) strand
>       segments are automatically reverse complemented
> 
>       The method is called dna() return the data as a simple sequence string.
> 
>       dna
> 
>        Title   : dna
>        Usage   : $s->dna
>        Function: get the DNA string for this segment
>        Returns : a string
>        Args    : none
>        Status  : Public
> 
>       Returns the sequence for this segment as a simple string. (-) strand
>       segments are automatically reverse complemented
> 
>       The method is also called protein().
> 
> 
> On Thu, Oct 14, 2010 at 9:16 PM, Darwin Sorento Dichmann
> <dichmann at berkeley.edu> wrote:
>> Greetings,
>> 
>> I am trying to extract sequences from a MySQL DB with Bio::DB::GFF. The database is the same as I use for my gbrowse2 and it works fine for that. Also, I can extract all sorts of features but not sequence.
>> 
>> When I run this script I thought I'd get a sequence output but apparently I get the memory address instead.
>> 
>> I have very little experience with perl or other programming, but I try to follow the directions in the manual. I suspect that I overlook something very basic and any help would be greatly appreciated.
>> 
>> Thanks,
>> Darwin
>> 
>> 
>> 
>> The script:
>> ------------
>> #! usr/bin/perl -w
>> # module to test if Bio::DB::GFF can be used to extract sequences from frog2 database.
>> 
>> use strict;
>> use Bio::Seq;
>> use Bio::SeqIO;
>> use Bio::DB::GFF;
>> 
>> # Open database
>> my $db = Bio::DB::GFF->
>> new(    -adaptor => 'DBI::mysql',
>>       -dsn     => 'frog2',
>>               -user => 'darwin',
>>               -password => '****',
>>               );
>> 
>> # fetch scaffold_1 (1-100000)
>> my $segment = $db->segment('scaffold_1', 1 => 100000) or die;
>> 
>> # get its DNA
>> my $dna = $segment->seq or die;
>> print $segment, "\n";
>> print $dna,"\n";
>> 
>> # get an iterator on all curated features of type 'exon' or 'intron'
>> # this prints all exons and intron with transcript name on screen
>>       my $iterator = $segment->get_seq_stream(-type     => ['mRNA']);
>>       while (my $s = $iterator->next_seq) {
>>   print $s,"\n";
>> }
>> 
>> exit;
>> ---------------
>> 
>> The output:
>> Macintosh:perlscripts darwin$ perl frog2_parser.pl
>> scaffold_1:1,100000
>> Bio::PrimarySeq=HASH(0x100bb4d68)
>> mRNA:pick(xt42f011730m)
>> mRNA:pick(xt42f014902m)
>> mRNA:pick(xt42f016160m)
>> mRNA:pick(xt42f017353m)
>> mRNA:pick(xt42f029332m)
>> ---------------
>> _______________________________________________
>> 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 mcestep at gmail.com  Fri Oct 15 16:59:57 2010
From: mcestep at gmail.com (Matt Estep)
Date: Fri, 15 Oct 2010 15:59:57 -0500
Subject: [Bioperl-l] Installing BioPerl on New mac 10.6.4
Message-ID: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>

Hi

When running the ./build install script I get an error because it can
not make a directory in /usr/local/share/man/man3  I looked around a
bit and I have a file titled /usr/share/man/man3. I am guessing the
script does not know how to skip the local bit of the first line.

Can you tell me how to run the script so that it will make the file in
the right place. I am guessing the file struture of the new mac is a
little different.

Thanks in advance for any help.

Matt


From scott at scottcain.net  Fri Oct 15 23:41:40 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 15 Oct 2010 23:41:40 -0400
Subject: [Bioperl-l] Installing BioPerl on New mac 10.6.4
In-Reply-To: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>
References: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>
Message-ID: <AANLkTimUSO7ohhN6L80tjYhsrHk+2oQx6JWcRE11g4ob@mail.gmail.com>

Hi Matt,

Usually, when ./Build install fails to create a directory or file it
is because the user that executed the script didn't have permission to
perform that action.  Did you use "sudo" when you executed the install
command?

Scott


On Fri, Oct 15, 2010 at 4:59 PM, Matt Estep <mcestep at gmail.com> wrote:
> Hi
>
> When running the ./build install script I get an error because it can
> not make a directory in /usr/local/share/man/man3 ?I looked around a
> bit and I have a file titled /usr/share/man/man3. I am guessing the
> script does not know how to skip the local bit of the first line.
>
> Can you tell me how to run the script so that it will make the file in
> the right place. I am guessing the file struture of the new mac is a
> little different.
>
> Thanks in advance for any help.
>
> Matt
> _______________________________________________
> 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 fij at elte.hu  Sat Oct 16 07:34:06 2010
From: fij at elte.hu (Farkas, Illes)
Date: Sat, 16 Oct 2010 13:34:06 +0200
Subject: [Bioperl-l] cis-regulatory elements
Message-ID: <AANLkTinCN+qFBZeGtKiYLMWg+yzitkEP497pHMgG-ULn@mail.gmail.com>

Dear All,

Which (BioPerl or other) module/algorithm would you recommend for predicting
cis-regulatory elements (mainly TFBSs) in a variety of organisms? We (= 1
colleague and I) have looked at
http://www.nature.com/nbt/journal/v23/n1/full/nbt1053.html so far.

Thanks,
Illes
--
http://hal.elte.hu/fij


From grapeguy at gmail.com  Sat Oct 16 15:46:32 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Sat, 16 Oct 2010 15:46:32 -0400
Subject: [Bioperl-l] Installing BioPerl on New mac 10.6.4
In-Reply-To: <AANLkTimUSO7ohhN6L80tjYhsrHk+2oQx6JWcRE11g4ob@mail.gmail.com>
References: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>
	<AANLkTimUSO7ohhN6L80tjYhsrHk+2oQx6JWcRE11g4ob@mail.gmail.com>
Message-ID: <AANLkTikbZnnno5oNDi1Q0HYe9QEFhp9xuF3wH5C8NhXG@mail.gmail.com>

Matt,

I just installed on OSX 10.6.3.  Definitely use sudo to perform the install.

I actually used the PPM install.  I used this command to start PPM: sudo
perl -MCPAN -e shell

http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_CPAN

Thanks,
Bill S.
Dept. of Biomedical Informatics
Ohio State University

On Fri, Oct 15, 2010 at 11:41 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Matt,
>
> Usually, when ./Build install fails to create a directory or file it
> is because the user that executed the script didn't have permission to
> perform that action.  Did you use "sudo" when you executed the install
> command?
>
> Scott
>
>
> On Fri, Oct 15, 2010 at 4:59 PM, Matt Estep <mcestep at gmail.com> wrote:
> > Hi
> >
> > When running the ./build install script I get an error because it can
> > not make a directory in /usr/local/share/man/man3  I looked around a
> > bit and I have a file titled /usr/share/man/man3. I am guessing the
> > script does not know how to skip the local bit of the first line.
> >
> > Can you tell me how to run the script so that it will make the file in
> > the right place. I am guessing the file struture of the new mac is a
> > little different.
> >
> > Thanks in advance for any help.
> >
> > Matt
> > _______________________________________________
> > 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
>


From jun.yin at ucd.ie  Sat Oct 16 16:41:37 2010
From: jun.yin at ucd.ie (Jun Yin)
Date: Sat, 16 Oct 2010 21:41:37 +0100
Subject: [Bioperl-l] cis-regulatory elements
In-Reply-To: <AANLkTinCN+qFBZeGtKiYLMWg+yzitkEP497pHMgG-ULn@mail.gmail.com>
References: <AANLkTinCN+qFBZeGtKiYLMWg+yzitkEP497pHMgG-ULn@mail.gmail.com>
Message-ID: <001501cb6d72$8771c2b0$96554810$%yin@ucd.ie>

Hi, Illes,

Sorry I don't know any package in BioPerl predicting TFBS binding motifs. As
far as I know, neither Bio::Align nor Bio::Assembly has such functions,
though Bio::SimpleAlign can be used to manipulate your promoter alignment.
For TFBS prediction, I personally use PScan and TFFind at the moment.

I am also interested in this question. I will wait for the answer in the
mail list with you :)

Cheers,
Jun Yin
Ph.D.?student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Farkas, Illes
Sent: Saturday, October 16, 2010 12:34 PM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] cis-regulatory elements

Dear All,

Which (BioPerl or other) module/algorithm would you recommend for predicting
cis-regulatory elements (mainly TFBSs) in a variety of organisms? We (= 1
colleague and I) have looked at
http://www.nature.com/nbt/journal/v23/n1/full/nbt1053.html so far.

Thanks,
Illes
--
http://hal.elte.hu/fij
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com


 

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com
 
 

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com
 




From cjfields at illinois.edu  Sat Oct 16 23:24:32 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Sat, 16 Oct 2010 22:24:32 -0500
Subject: [Bioperl-l] cis-regulatory elements
In-Reply-To: <001501cb6d72$8771c2b0$96554810$%yin@ucd.ie>
References: <AANLkTinCN+qFBZeGtKiYLMWg+yzitkEP497pHMgG-ULn@mail.gmail.com>
	<001501cb6d72$8771c2b0$96554810$%yin@ucd.ie>
Message-ID: <ECB68538-3F18-4AEB-A097-773A913935B5@illinois.edu>

Sendu Bala delved into this a bit; you can look at a few of his modules in BioPerl, specifically Bio::DB::TFBS (which is only configured for transfac_pro at the moment).

chris

On Oct 16, 2010, at 3:41 PM, Jun Yin wrote:

> Hi, Illes,
> 
> Sorry I don't know any package in BioPerl predicting TFBS binding motifs. As
> far as I know, neither Bio::Align nor Bio::Assembly has such functions,
> though Bio::SimpleAlign can be used to manipulate your promoter alignment.
> For TFBS prediction, I personally use PScan and TFFind at the moment.
> 
> I am also interested in this question. I will wait for the answer in the
> mail list with you :)
> 
> Cheers,
> Jun Yin
> Ph.D. student in U.C.D.
> 
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Farkas, Illes
> Sent: Saturday, October 16, 2010 12:34 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] cis-regulatory elements
> 
> Dear All,
> 
> Which (BioPerl or other) module/algorithm would you recommend for predicting
> cis-regulatory elements (mainly TFBSs) in a variety of organisms? We (= 1
> colleague and I) have looked at
> http://www.nature.com/nbt/journal/v23/n1/full/nbt1053.html so far.
> 
> Thanks,
> Illes
> --
> http://hal.elte.hu/fij
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
> 
> The message was checked by ESET Smart Security.
> 
> http://www.eset.com
> 
> 
> 
> 
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
> 
> The message was checked by ESET Smart Security.
> 
> http://www.eset.com
> 
> 
> 
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
> 
> The message was checked by ESET Smart Security.
> 
> http://www.eset.com
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From grapeguy at gmail.com  Mon Oct 18 09:58:24 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Mon, 18 Oct 2010 09:58:24 -0400
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal alignment
Message-ID: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>

All,

I'm in my first week with bioperl for a class project (although I've used
Perl for years). I've successfully run a clustal alignment of several DNA
sequences to produce the aln and dnd files. Now I would like to generate a
consensus sequence from the alignment.  I see that Pise Cons does this
satisfactorily on my example data (
http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1 distribution
that I installed.

Is this another module that I need to install separately?

"cpan[2]> m /Pise/
Module    Bio::Tools::Run::AnalysisFactory::Pise
(BIRNEY/bioperl-run-1.4.tar.gz)
Module    Bio::Tools::Run::PiseApplication (BIRNEY/bioperl-run-1.4.tar.gz)"

Bill S.


From cjfields at illinois.edu  Mon Oct 18 10:54:32 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 18 Oct 2010 09:54:32 -0500
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
Message-ID: <DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>

Bill,

Actually, the page you reached at Pasteur is not Pise, but Mobyle (their replacement for the older Pise tools).  The Pise modules were in BioPerl-Run, but they were deprecated a few years ago and removed from the latest BioPerl-Run releases b/c the remote service is no longer active; there is no Perl-based replacement for Mobyle interaction.  

Have you thought about just using the functionality within the Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there are methods in place to do that.

chris

On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:

> All,
> 
> I'm in my first week with bioperl for a class project (although I've used
> Perl for years). I've successfully run a clustal alignment of several DNA
> sequences to produce the aln and dnd files. Now I would like to generate a
> consensus sequence from the alignment.  I see that Pise Cons does this
> satisfactorily on my example data (
> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1 distribution
> that I installed.
> 
> Is this another module that I need to install separately?
> 
> "cpan[2]> m /Pise/
> Module    Bio::Tools::Run::AnalysisFactory::Pise
> (BIRNEY/bioperl-run-1.4.tar.gz)
> Module    Bio::Tools::Run::PiseApplication (BIRNEY/bioperl-run-1.4.tar.gz)"
> 
> Bill S.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From grapeguy at gmail.com  Mon Oct 18 11:52:03 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Mon, 18 Oct 2010 11:52:03 -0400
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
Message-ID: <AANLkTimF5N_AnTV380fT5hPAEjjSgSP37+KVaoHNwbXN@mail.gmail.com>

Chris,

Well, That explains it.

I'll take a 2 pronged approach:
1. Try SimpleAlign
2. Driving the Mobyle UI using LWP::UserAgent, HTML::Form and
HTML::TableExtract (I do this for Tm calculations);

Thanks,
Bill S.



On Mon, Oct 18, 2010 at 10:54 AM, Chris Fields <cjfields at illinois.edu>wrote:

> Bill,
>
> Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
> replacement for the older Pise tools).  The Pise modules were in
> BioPerl-Run, but they were deprecated a few years ago and removed from the
> latest BioPerl-Run releases b/c the remote service is no longer active;
> there is no Perl-based replacement for Mobyle interaction.
>
> Have you thought about just using the functionality within the
> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there are
> methods in place to do that.
>
> chris
>
> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
>
> > All,
> >
> > I'm in my first week with bioperl for a class project (although I've used
> > Perl for years). I've successfully run a clustal alignment of several DNA
> > sequences to produce the aln and dnd files. Now I would like to generate
> a
> > consensus sequence from the alignment.  I see that Pise Cons does this
> > satisfactorily on my example data (
> > http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However,
> I'm
> > not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
> distribution
> > that I installed.
> >
> > Is this another module that I need to install separately?
> >
> > "cpan[2]> m /Pise/
> > Module    Bio::Tools::Run::AnalysisFactory::Pise
> > (BIRNEY/bioperl-run-1.4.tar.gz)
> > Module    Bio::Tools::Run::PiseApplication
> (BIRNEY/bioperl-run-1.4.tar.gz)"
> >
> > Bill S.
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From jun.yin at ucd.ie  Mon Oct 18 12:09:32 2010
From: jun.yin at ucd.ie (Jun Yin)
Date: Mon, 18 Oct 2010 17:09:32 +0100
Subject: [Bioperl-l] Generating a consensus sequence from a
	Clustal	alignment
In-Reply-To: <DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
Message-ID: <001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>

Hi, Bill,

You may consider to use consensus_iupac or consensus_string methods in
Bio::SimpleAlign to generate consensus sequence.

Cheers,
Jun Yin
Ph.D.?student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Monday, October 18, 2010 3:55 PM
To: Bill Stephens
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
alignment

Bill,

Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
replacement for the older Pise tools).  The Pise modules were in
BioPerl-Run, but they were deprecated a few years ago and removed from the
latest BioPerl-Run releases b/c the remote service is no longer active;
there is no Perl-based replacement for Mobyle interaction.  

Have you thought about just using the functionality within the
Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there are
methods in place to do that.

chris

On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:

> All,
> 
> I'm in my first week with bioperl for a class project (although I've used
> Perl for years). I've successfully run a clustal alignment of several DNA
> sequences to produce the aln and dnd files. Now I would like to generate a
> consensus sequence from the alignment.  I see that Pise Cons does this
> satisfactorily on my example data (
> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
distribution
> that I installed.
> 
> Is this another module that I need to install separately?
> 
> "cpan[2]> m /Pise/
> Module    Bio::Tools::Run::AnalysisFactory::Pise
> (BIRNEY/bioperl-run-1.4.tar.gz)
> Module    Bio::Tools::Run::PiseApplication
(BIRNEY/bioperl-run-1.4.tar.gz)"
> 
> Bill S.
> _______________________________________________
> 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

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com


 

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com
 




From mcestep at gmail.com  Sat Oct 16 22:59:24 2010
From: mcestep at gmail.com (Matt Estep)
Date: Sat, 16 Oct 2010 21:59:24 -0500
Subject: [Bioperl-l] Installing BioPerl on New mac 10.6.4
In-Reply-To: <AANLkTikbZnnno5oNDi1Q0HYe9QEFhp9xuF3wH5C8NhXG@mail.gmail.com>
References: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>
	<AANLkTimUSO7ohhN6L80tjYhsrHk+2oQx6JWcRE11g4ob@mail.gmail.com>
	<AANLkTikbZnnno5oNDi1Q0HYe9QEFhp9xuF3wH5C8NhXG@mail.gmail.com>
Message-ID: <AANLkTimiPDKCFKZwDT1UM-OG=jKqxVMe2fD5hdY_jPW-@mail.gmail.com>

Thank you both. I think this has solved my troubles.

Matt

On Sat, Oct 16, 2010 at 2:46 PM, Bill Stephens <grapeguy at gmail.com> wrote:
> Matt,
>
> I just installed on OSX 10.6.3.? Definitely use sudo to perform the install.
>
> I actually used the PPM install.? I used this command to start PPM: sudo
> perl -MCPAN -e shell
>
> http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_CPAN
>
> Thanks,
> Bill S.
> Dept. of Biomedical Informatics
> Ohio State University
>
> On Fri, Oct 15, 2010 at 11:41 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Matt,
>>
>> Usually, when ./Build install fails to create a directory or file it
>> is because the user that executed the script didn't have permission to
>> perform that action. ?Did you use "sudo" when you executed the install
>> command?
>>
>> Scott
>>
>>
>> On Fri, Oct 15, 2010 at 4:59 PM, Matt Estep <mcestep at gmail.com> wrote:
>> > Hi
>> >
>> > When running the ./build install script I get an error because it can
>> > not make a directory in /usr/local/share/man/man3 ?I looked around a
>> > bit and I have a file titled /usr/share/man/man3. I am guessing the
>> > script does not know how to skip the local bit of the first line.
>> >
>> > Can you tell me how to run the script so that it will make the file in
>> > the right place. I am guessing the file struture of the new mac is a
>> > little different.
>> >
>> > Thanks in advance for any help.
>> >
>> > Matt
>> > _______________________________________________
>> > 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
>
>



From e.cristiano at Dkfz-Heidelberg.de  Mon Oct 18 10:33:05 2010
From: e.cristiano at Dkfz-Heidelberg.de (Cristiano Elena)
Date: Mon, 18 Oct 2010 16:33:05 +0200
Subject: [Bioperl-l] bioperl easy way installation using cpan
Message-ID: <FC756E55-13EF-449F-B324-3BB76032A22B@Dkfz-Heidelberg.de>

Hi,
I am a beginner and i am trying to install bioperl via CPAN following the instructions on wiki.
i have a leopard mac 10.6 and perl version 5.10 i have X11 and i also installed fink (but the installation of bioperl wasn't successful trough fink either).

the error that i got at the end of the installation via CPAN is the following:

 SHAWNPW/PostScript-0.06.tar.gz
  /usr/bin/make install  -- OK
Warning (usually harmless): 'YAML' not installed, will not store persistent state
Running Build for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
  Has already been unwrapped into directory /Users/ecristiano/.cpan/build/BioPerl-1.6.1-66fecx
Could not make: cannot resolve circular dependency
Warning (usually harmless): 'YAML' not installed, will not store persistent state
Running Build test
  Can't test without successful make
Running Build install
  Make had returned bad status, install seems impossible
Could not read '/Users/ecristiano/.cpan/build/GraphViz-2.04-f7G5nl/META.yml'. Falling back to other methods to determine prerequisites
Failed during this command:
 MINGYILIU/Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz: make NO cannot resolve circular dependency
 CJFIELDS/BioPerl-1.6.1.tar.gz                : make NO cannot resolve circular dependency
 LBROCARD/GraphViz-2.04.tar.gz                : writemakefile NO '/usr/bin/perl Makefile.PL' returned status 512


thanks in advance



Elena




From sarahdoom at gmail.com  Mon Oct 18 11:20:25 2010
From: sarahdoom at gmail.com (Sarah Kingan)
Date: Mon, 18 Oct 2010 08:20:25 -0700 (PDT)
Subject: [Bioperl-l] DNAStatistics
Message-ID: <780929ef-4b06-43ae-9d9c-78a62e84a4d7@g18g2000yqk.googlegroups.com>

Hello,
I am trying to calculate Ka/Ks statistics using the
Align:DNAStatistics module. When I use the function, calc_KaKs_pair, I
get a long list of errors. The calculation is performed but I don't
understand the source of the errors. They include:

Use of uninitialized value in addition (+) at /usr/lib/perl5/site_perl/
5.8.8/Bio/Align/DNAStatistics.pm line 1673, <GEN0> line 25.

Use of uninitialized value in addition (+) at /usr/lib/perl5/site_perl/
5.8.8/Bio/Align/DNAStatistics.pm line 1505, <GEN0> line 25.

Use of uninitialized value in subtraction (-) at /usr/lib/perl5/
site_perl/5.8.8/Bio/Align/DNAStatistics.pm line 1506, <GEN0> line 25.

My alignment object has gaps, but I believe this module handles gaps.
The data I am analyzing comes from recently diverged species, so I
wonder if the errors could originate from a lack of substitutions.

Any help would be much appreciated.

Thanks!
Sarah.Kingan at rochester.edu


From scott at scottcain.net  Mon Oct 18 13:26:53 2010
From: scott at scottcain.net (Scott Cain)
Date: Mon, 18 Oct 2010 13:26:53 -0400
Subject: [Bioperl-l] bioperl easy way installation using cpan
In-Reply-To: <FC756E55-13EF-449F-B324-3BB76032A22B@Dkfz-Heidelberg.de>
References: <FC756E55-13EF-449F-B324-3BB76032A22B@Dkfz-Heidelberg.de>
Message-ID: <AANLkTim6NxZx2-MCNJQ190-za6TkCYF_m9WZvPfO+LhC@mail.gmail.com>

Hi Elena,

I would suggest that you answer the question about installing optional
prerequisites with a "no"; I think that will eliminate the circular
dependency problem.  Of course the only problem is if you need
Bio-ASN1-EntrezGene, but even if you do, you can probably install it
after the BioPerl install completes.

Scott


On Mon, Oct 18, 2010 at 10:33 AM, Cristiano Elena
<e.cristiano at dkfz-heidelberg.de> wrote:
> Hi,
> I am a beginner and i am trying to install bioperl via CPAN following the instructions on wiki.
> i have a leopard mac 10.6 and perl version 5.10 i have X11 and i also installed fink (but the installation of bioperl wasn't successful trough fink either).
>
> the error that i got at the end of the installation via CPAN is the following:
>
> ?SHAWNPW/PostScript-0.06.tar.gz
> ?/usr/bin/make install ?-- OK
> Warning (usually harmless): 'YAML' not installed, will not store persistent state
> Running Build for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
> ?Has already been unwrapped into directory /Users/ecristiano/.cpan/build/BioPerl-1.6.1-66fecx
> Could not make: cannot resolve circular dependency
> Warning (usually harmless): 'YAML' not installed, will not store persistent state
> Running Build test
> ?Can't test without successful make
> Running Build install
> ?Make had returned bad status, install seems impossible
> Could not read '/Users/ecristiano/.cpan/build/GraphViz-2.04-f7G5nl/META.yml'. Falling back to other methods to determine prerequisites
> Failed during this command:
> ?MINGYILIU/Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz: make NO cannot resolve circular dependency
> ?CJFIELDS/BioPerl-1.6.1.tar.gz ? ? ? ? ? ? ? ?: make NO cannot resolve circular dependency
> ?LBROCARD/GraphViz-2.04.tar.gz ? ? ? ? ? ? ? ?: writemakefile NO '/usr/bin/perl Makefile.PL' returned status 512
>
>
> thanks in advance
>
>
>
> Elena
>
>
> _______________________________________________
> 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 Oct 18 13:37:02 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 18 Oct 2010 12:37:02 -0500
Subject: [Bioperl-l] bioperl easy way installation using cpan
In-Reply-To: <AANLkTim6NxZx2-MCNJQ190-za6TkCYF_m9WZvPfO+LhC@mail.gmail.com>
References: <FC756E55-13EF-449F-B324-3BB76032A22B@Dkfz-Heidelberg.de>
	<AANLkTim6NxZx2-MCNJQ190-za6TkCYF_m9WZvPfO+LhC@mail.gmail.com>
Message-ID: <6081844C-D4CB-4926-968D-9CACAE017E57@illinois.edu>

Agreed.  Unfortunately, this is an issue that has repeatedly popped up.  The best way I can think of to solve it is to remove Bio::ASN1::EntrezGene 'recommends' from Build.PL file, manually check for it's presence, and indicate the procedure for installing (basically post-bioperl install).

chris

On Oct 18, 2010, at 12:26 PM, Scott Cain wrote:

> Hi Elena,
> 
> I would suggest that you answer the question about installing optional
> prerequisites with a "no"; I think that will eliminate the circular
> dependency problem.  Of course the only problem is if you need
> Bio-ASN1-EntrezGene, but even if you do, you can probably install it
> after the BioPerl install completes.
> 
> Scott
> 
> 
> On Mon, Oct 18, 2010 at 10:33 AM, Cristiano Elena
> <e.cristiano at dkfz-heidelberg.de> wrote:
>> Hi,
>> I am a beginner and i am trying to install bioperl via CPAN following the instructions on wiki.
>> i have a leopard mac 10.6 and perl version 5.10 i have X11 and i also installed fink (but the installation of bioperl wasn't successful trough fink either).
>> 
>> the error that i got at the end of the installation via CPAN is the following:
>> 
>>  SHAWNPW/PostScript-0.06.tar.gz
>>  /usr/bin/make install  -- OK
>> Warning (usually harmless): 'YAML' not installed, will not store persistent state
>> Running Build for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
>>  Has already been unwrapped into directory /Users/ecristiano/.cpan/build/BioPerl-1.6.1-66fecx
>> Could not make: cannot resolve circular dependency
>> Warning (usually harmless): 'YAML' not installed, will not store persistent state
>> Running Build test
>>  Can't test without successful make
>> Running Build install
>>  Make had returned bad status, install seems impossible
>> Could not read '/Users/ecristiano/.cpan/build/GraphViz-2.04-f7G5nl/META.yml'. Falling back to other methods to determine prerequisites
>> Failed during this command:
>>  MINGYILIU/Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz: make NO cannot resolve circular dependency
>>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make NO cannot resolve circular dependency
>>  LBROCARD/GraphViz-2.04.tar.gz                : writemakefile NO '/usr/bin/perl Makefile.PL' returned status 512
>> 
>> 
>> thanks in advance
>> 
>> 
>> 
>> Elena
>> 
>> 
>> _______________________________________________
>> 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




From David.Messina at sbc.su.se  Mon Oct 18 14:23:18 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 18 Oct 2010 14:23:18 -0400
Subject: [Bioperl-l] DNAStatistics
In-Reply-To: <780929ef-4b06-43ae-9d9c-78a62e84a4d7@g18g2000yqk.googlegroups.com>
References: <780929ef-4b06-43ae-9d9c-78a62e84a4d7@g18g2000yqk.googlegroups.com>
Message-ID: <B1ABB50A-0B78-44D9-85C3-4A316B52278F@sbc.su.se>

Hi Sarah,

Usually "unintialized value" errors mean you're not trying to read from an empty variable.

I would check that all of the data you're passing to calc_KaKs_pair does contain a value.


> My alignment object has gaps, but I believe this module handles gaps.

I'm not sure about that; I'd have to check. Did you try handing it some ungapped data to see if the errors go away?



Dave




From grapeguy at gmail.com  Mon Oct 18 20:02:47 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Mon, 18 Oct 2010 20:02:47 -0400
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
Message-ID: <AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>

So, I've got the SimpleAlign running. It looks like it's running the
alignment based upon the input sequence location only (first residue from
each sequence).  This is not what I need.

I'm back to to clustal, tcoffee or dalign.

Bill

On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:

> Hi, Bill,
>
> You may consider to use consensus_iupac or consensus_string methods in
> Bio::SimpleAlign to generate consensus sequence.
>
> Cheers,
> Jun Yin
> Ph.D. student in U.C.D.
>
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Monday, October 18, 2010 3:55 PM
> To: Bill Stephens
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
> alignment
>
> Bill,
>
> Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
> replacement for the older Pise tools).  The Pise modules were in
> BioPerl-Run, but they were deprecated a few years ago and removed from the
> latest BioPerl-Run releases b/c the remote service is no longer active;
> there is no Perl-based replacement for Mobyle interaction.
>
> Have you thought about just using the functionality within the
> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there
> are
> methods in place to do that.
>
> chris
>
> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
>
> > All,
> >
> > I'm in my first week with bioperl for a class project (although I've used
> > Perl for years). I've successfully run a clustal alignment of several DNA
> > sequences to produce the aln and dnd files. Now I would like to generate
> a
> > consensus sequence from the alignment.  I see that Pise Cons does this
> > satisfactorily on my example data (
> > http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However,
> I'm
> > not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
> distribution
> > that I installed.
> >
> > Is this another module that I need to install separately?
> >
> > "cpan[2]> m /Pise/
> > Module    Bio::Tools::Run::AnalysisFactory::Pise
> > (BIRNEY/bioperl-run-1.4.tar.gz)
> > Module    Bio::Tools::Run::PiseApplication
> (BIRNEY/bioperl-run-1.4.tar.gz)"
> >
> > Bill S.
> > _______________________________________________
> > 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
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>


From thomas.sharpton at gmail.com  Mon Oct 18 22:30:40 2010
From: thomas.sharpton at gmail.com (Thomas Sharpton)
Date: Mon, 18 Oct 2010 19:30:40 -0700
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
	<AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
Message-ID: <16917B57-A1EE-495C-A541-D5C666701C31@gmail.com>

While the tools you mention are sufficient, you might be interested to  
know that HMMER can also generate consensus sequences. Briefly, you  
would use the alignment you generated with clustal (or any other  
multiple sequence alignment tool) to build an HMM via the hmmbuild  
function. You can then emit a consensus sequence from the HMM file  
using the hmmemit function:

hmmemit -c HMM_file.hmm

Just FYI.

T

On Oct 18, 2010, at 5:02 PM, Bill Stephens wrote:

> So, I've got the SimpleAlign running. It looks like it's running the
> alignment based upon the input sequence location only (first residue  
> from
> each sequence).  This is not what I need.
>
> I'm back to to clustal, tcoffee or dalign.
>
> Bill
>
> On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:
>
>> Hi, Bill,
>>
>> You may consider to use consensus_iupac or consensus_string methods  
>> in
>> Bio::SimpleAlign to generate consensus sequence.
>>
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>>
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris  
>> Fields
>> Sent: Monday, October 18, 2010 3:55 PM
>> To: Bill Stephens
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] Generating a consensus sequence from a  
>> Clustal
>> alignment
>>
>> Bill,
>>
>> Actually, the page you reached at Pasteur is not Pise, but Mobyle  
>> (their
>> replacement for the older Pise tools).  The Pise modules were in
>> BioPerl-Run, but they were deprecated a few years ago and removed  
>> from the
>> latest BioPerl-Run releases b/c the remote service is no longer  
>> active;
>> there is no Perl-based replacement for Mobyle interaction.
>>
>> Have you thought about just using the functionality within the
>> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure  
>> there
>> are
>> methods in place to do that.
>>
>> chris
>>
>> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
>>
>>> All,
>>>
>>> I'm in my first week with bioperl for a class project (although  
>>> I've used
>>> Perl for years). I've successfully run a clustal alignment of  
>>> several DNA
>>> sequences to produce the aln and dnd files. Now I would like to  
>>> generate
>> a
>>> consensus sequence from the alignment.  I see that Pise Cons does  
>>> this
>>> satisfactorily on my example data (
>>> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) .  
>>> However,
>> I'm
>>> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
>> distribution
>>> that I installed.
>>>
>>> Is this another module that I need to install separately?
>>>
>>> "cpan[2]> m /Pise/
>>> Module    Bio::Tools::Run::AnalysisFactory::Pise
>>> (BIRNEY/bioperl-run-1.4.tar.gz)
>>> Module    Bio::Tools::Run::PiseApplication
>> (BIRNEY/bioperl-run-1.4.tar.gz)"
>>>
>>> Bill S.
>>> _______________________________________________
>>> 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
>>
>> __________ Information from ESET Smart Security, version of virus  
>> signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus  
>> signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jun.yin at ucd.ie  Tue Oct 19 04:17:58 2010
From: jun.yin at ucd.ie (Jun Yin)
Date: Tue, 19 Oct 2010 09:17:58 +0100
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
 alignment
In-Reply-To: <AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
	<AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
Message-ID: <003501cb6f66$23c37330$6b4a5990$%yin@ucd.ie>

Hi, Bill,

 

There are several methods you can choose from Bio::SimpleAlign to build
subalignment. For example, you can use $aln->slice  to get part of your
alignment, and then you can calculate concensus sequence from subalignment.
Another method $aln->remove_gaps, which can remove gap containing columns.

 

Cheers,

Jun Yin

Ph.D. student in U.C.D.

 

Bioinformatics Laboratory

Conway Institute

University College Dublin

 

From: Bill Stephens [mailto:grapeguy at gmail.com] 
Sent: Tuesday, October 19, 2010 1:03 AM
To: Jun Yin
Cc: Chris Fields; bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
alignment

 

So, I've got the SimpleAlign running. It looks like it's running the
alignment based upon the input sequence location only (first residue from
each sequence).  This is not what I need. 

I'm back to to clustal, tcoffee or dalign.

Bill

On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:

Hi, Bill,

You may consider to use consensus_iupac or consensus_string methods in
Bio::SimpleAlign to generate consensus sequence.

Cheers,
Jun Yin
Ph.D. student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Monday, October 18, 2010 3:55 PM
To: Bill Stephens
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
alignment

Bill,

Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
replacement for the older Pise tools).  The Pise modules were in
BioPerl-Run, but they were deprecated a few years ago and removed from the
latest BioPerl-Run releases b/c the remote service is no longer active;
there is no Perl-based replacement for Mobyle interaction.

Have you thought about just using the functionality within the
Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there are
methods in place to do that.

chris

On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:

> All,
>
> I'm in my first week with bioperl for a class project (although I've used
> Perl for years). I've successfully run a clustal alignment of several DNA
> sequences to produce the aln and dnd files. Now I would like to generate a
> consensus sequence from the alignment.  I see that Pise Cons does this
> satisfactorily on my example data (
> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
distribution
> that I installed.
>
> Is this another module that I need to install separately?
>
> "cpan[2]> m /Pise/
> Module    Bio::Tools::Run::AnalysisFactory::Pise
> (BIRNEY/bioperl-run-1.4.tar.gz)
> Module    Bio::Tools::Run::PiseApplication
(BIRNEY/bioperl-run-1.4.tar.gz)"
>
> Bill S.
> _______________________________________________
> 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

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com




__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com



 



From joseramonblas at gmail.com  Tue Oct 19 05:34:12 2010
From: joseramonblas at gmail.com (=?ISO-8859-1?Q?Jos=E9_Ram=F3n_Blas_Pastor?=)
Date: Tue, 19 Oct 2010 11:34:12 +0200
Subject: [Bioperl-l] correlated mutations analysis
Message-ID: <AANLkTimtudsQqppZtVz2+cCxKZ7gxEKXuHYPg85TC87M@mail.gmail.com>

Hi,

I have 2 protein sequences (or more). I want...
-to perform an analysis of correlated mutations in these proteins
(considering variations across 10 or 20 sps)
-obtain an statistical parameter on the significance of these mutations to
predict/hint interacting residues

Can you help me in this issue?. (Bioperl or not bioperl-based solutions are
welcome)

Thank you very much.

JR

-- 
Jos? Ram?n Blas - PhD
Dept. Biochemistry - Medicine School
University of Castilla-La Mancha

C Almansa, 14
02006 Albacete (Spain)



From cjfields at illinois.edu  Tue Oct 19 11:47:16 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 19 Oct 2010 10:47:16 -0500
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
	<AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
Message-ID: <16EDEBED-BAD4-4D57-B51B-C3234D1E8C39@illinois.edu>

Bio::SimpleAlign is the class that contains the alignment data; it does not generate the alignment for you.  You can use modules from BioPerl-Run that run ClustalW, MUSCLE, T-Coffee, etc to get a Bio::SimpleAlign instance, or parse the already-generated alignment output via Bio::AlignIO.

>From the Bio::Tools::Run::Alignment::ClustalW docs:

=================================================================

  #  Build a clustalw alignment factory
  @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
  $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);

  #  Pass the factory a list of sequences to be aligned.	
  $inputfilename = 't/data/cysprot.fa';
  $aln = $factory->align($inputfilename); # $aln is a SimpleAlign object.

  # ...or
  $seq_array_ref = \@seq_array;

  # where @seq_array is an array of Bio::Seq objects
  $aln = $factory->align($seq_array_ref);

=================================================================

$aln is a Bio::SimpleAlign derived from ClustalW output.  

>From Bio::SimpleAlign (note the use of Bio::AlignIO):

=================================================================

  # Use Bio::AlignIO to read in the alignment
  $str = Bio::AlignIO->new(-file => 't/data/testaln.pfam');
  $aln = $str->next_aln();

  # Describe
  print $aln->length;
  print $aln->num_residues;
  print $aln->is_flush;
  print $aln->num_sequences;
  print $aln->score;
  print $aln->percentage_identity;
  print $aln->consensus_string(50);

=================================================================

Note the consensus_string() method:

 Title     : consensus_string
 Usage     : $str = $ali->consensus_string($threshold_percent)
 Function  : Makes a strict consensus
 Returns   : Consensus string
 Argument  : Optional treshold ranging from 0 to 100.
             The consensus residue has to appear at least threshold %
             of the sequences at a given location, otherwise a '?'
             character will be placed at that location.
             (Default value = 0%)

chris

On Oct 18, 2010, at 7:02 PM, Bill Stephens wrote:

> So, I've got the SimpleAlign running. It looks like it's running the
> alignment based upon the input sequence location only (first residue from
> each sequence).  This is not what I need.
> 
> I'm back to to clustal, tcoffee or dalign.
> 
> Bill
> 
> On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:
> 
>> Hi, Bill,
>> 
>> You may consider to use consensus_iupac or consensus_string methods in
>> Bio::SimpleAlign to generate consensus sequence.
>> 
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>> 
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>> 
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
>> Sent: Monday, October 18, 2010 3:55 PM
>> To: Bill Stephens
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
>> alignment
>> 
>> Bill,
>> 
>> Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
>> replacement for the older Pise tools).  The Pise modules were in
>> BioPerl-Run, but they were deprecated a few years ago and removed from the
>> latest BioPerl-Run releases b/c the remote service is no longer active;
>> there is no Perl-based replacement for Mobyle interaction.
>> 
>> Have you thought about just using the functionality within the
>> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there
>> are
>> methods in place to do that.
>> 
>> chris
>> 
>> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
>> 
>>> All,
>>> 
>>> I'm in my first week with bioperl for a class project (although I've used
>>> Perl for years). I've successfully run a clustal alignment of several DNA
>>> sequences to produce the aln and dnd files. Now I would like to generate
>> a
>>> consensus sequence from the alignment.  I see that Pise Cons does this
>>> satisfactorily on my example data (
>>> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However,
>> I'm
>>> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
>> distribution
>>> that I installed.
>>> 
>>> Is this another module that I need to install separately?
>>> 
>>> "cpan[2]> m /Pise/
>>> Module    Bio::Tools::Run::AnalysisFactory::Pise
>>> (BIRNEY/bioperl-run-1.4.tar.gz)
>>> Module    Bio::Tools::Run::PiseApplication
>> (BIRNEY/bioperl-run-1.4.tar.gz)"
>>> 
>>> Bill S.
>>> _______________________________________________
>>> 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
>> 
>> __________ Information from ESET Smart Security, version of virus signature
>> database 5377 (20100818) __________
>> 
>> The message was checked by ESET Smart Security.
>> 
>> http://www.eset.com
>> 
>> 
>> 
>> 
>> __________ Information from ESET Smart Security, version of virus signature
>> database 5377 (20100818) __________
>> 
>> The message was checked by ESET Smart Security.
>> 
>> http://www.eset.com
>> 
>> 
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From td8pub at gmail.com  Tue Oct 19 13:28:07 2010
From: td8pub at gmail.com (T D)
Date: Tue, 19 Oct 2010 13:28:07 -0400
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
Message-ID: <AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>

Hi,

I'm new to BioPerl and Perl in general, and I'm trying to get
StandAloneBlastPlus to run. I got the latest versions using git and
downloaded bioperl-live  and bioperl-run.  I am having issues with Perl not
finding modules. Here is my error:

Can't locate IPC/Run.pm in @INC

Where is this module located? I am running Windows 7. I did a search for the
Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
Run.pm the older version? I have Perl v5.12.1 installed.

Thanks in advance!
Tracey


From cjfields at illinois.edu  Tue Oct 19 13:33:19 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 19 Oct 2010 12:33:19 -0500
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
	<AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>
Message-ID: <9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>

No, IPC::Run is different than IPC::Run3:

http://search.cpan.org/dist/IPC-Run/
http://search.cpan.org/dist/IPC-Run3/

Both should work under Windows, not sure about Windows7 but I can't see why they wouldn't work.

chris

On Oct 19, 2010, at 12:28 PM, T D wrote:

> Hi,
> 
> I'm new to BioPerl and Perl in general, and I'm trying to get
> StandAloneBlastPlus to run. I got the latest versions using git and
> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl not
> finding modules. Here is my error:
> 
> Can't locate IPC/Run.pm in @INC
> 
> Where is this module located? I am running Windows 7. I did a search for the
> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
> Run.pm the older version? I have Perl v5.12.1 installed.
> 
> Thanks in advance!
> Tracey
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From td8pub at gmail.com  Tue Oct 19 09:27:20 2010
From: td8pub at gmail.com (T D)
Date: Tue, 19 Oct 2010 09:27:20 -0400
Subject: [Bioperl-l] IPC/Run.pm?
Message-ID: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>

Hi,

I'm new to BioPerl and I'm trying to get StandAloneBlastPlus to run. I got
the latest versions using git and downloaded bioperl-live and and
bioperl-run.  I am having issues with Perl not finding modules. Here is my
error:

Can't locate IPC/Run.pm in @INC

Where is this module located? I am running Windows 7. I did a search for the
Run.pm and could only find IPC/*Run3.pm* under my Perl installation.

Thanks in advance!
Tracey


From anjan.purkayastha at gmail.com  Tue Oct 19 13:49:11 2010
From: anjan.purkayastha at gmail.com (ANJAN PURKAYASTHA)
Date: Tue, 19 Oct 2010 13:49:11 -0400
Subject: [Bioperl-l] Help in retrieving the DEFINITION line
Message-ID: <AANLkTimC=1mD3YBys8mOe9AUVZgo3QeNiWSydRRrfrNu@mail.gmail.com>

Hi,
I need to retrieve the DEFINITION line of a GenBank file, given the GenBank
accession ID.
The following code does not seem to do it:

use strict;
use warnings;
use Bio::Perl;
use Bio::DB::GenBank;
my $gb= new Bio::DB::GenBank;

open(F, "test_id");

while(<F>){
chomp;
my $id= $_;
my $seq= $gb->get_Seq_by_acc("$id");
my $anno_collection = $seq->annotation;
my @annotations = $anno_collection->get_Annotations('definition');
print ("@annotations\n");
}

Any thoughts on how to get this done will be deeply appreciated.
Thanks,
Anjan

-- 
===================================
anjan purkayastha, phd.
research associate
fas center for systems biology,
harvard university
52 oxford street
cambridge ma 02138
phone-703.740.6939
===================================


From David.Messina at sbc.su.se  Tue Oct 19 16:03:08 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 19 Oct 2010 16:03:08 -0400
Subject: [Bioperl-l] Help in retrieving the DEFINITION line
In-Reply-To: <AANLkTimC=1mD3YBys8mOe9AUVZgo3QeNiWSydRRrfrNu@mail.gmail.com>
References: <AANLkTimC=1mD3YBys8mOe9AUVZgo3QeNiWSydRRrfrNu@mail.gmail.com>
Message-ID: <0E6779A3-BD3E-469F-8C23-8BFA92135915@sbc.su.se>

Hi Anjan,

You can get to the definition directly, via the desc() method.

So, this works:

use strict;
use warnings;
use Bio::Perl;
use Bio::DB::GenBank;
my $gb= new Bio::DB::GenBank;

open(F, "test_id");

while(<F>){
	chomp;
	my $id= $_;
	my $seq= $gb->get_Seq_by_acc("$id");

	# I added these lines:
	my $definition      = $seq->desc;
        print $definition, "\n";}
}



Dave



From td8pub at gmail.com  Tue Oct 19 16:38:32 2010
From: td8pub at gmail.com (T D)
Date: Tue, 19 Oct 2010 16:38:32 -0400
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
	<AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>
	<9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>
Message-ID: <AANLkTi=LKy-UMPkQkDXN=83sjRFdJMgOn7Du9vVdh6x7@mail.gmail.com>

Thank you. I downloaded IPC::Run and the code seems to be working now. Is
Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?


On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:

> No, IPC::Run is different than IPC::Run3:
>
> http://search.cpan.org/dist/IPC-Run/
> http://search.cpan.org/dist/IPC-Run3/
>
> Both should work under Windows, not sure about Windows7 but I can't see why
> they wouldn't work.
>
> chris
>
> On Oct 19, 2010, at 12:28 PM, T D wrote:
>
> > Hi,
> >
> > I'm new to BioPerl and Perl in general, and I'm trying to get
> > StandAloneBlastPlus to run. I got the latest versions using git and
> > downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
> not
> > finding modules. Here is my error:
> >
> > Can't locate IPC/Run.pm in @INC
> >
> > Where is this module located? I am running Windows 7. I did a search for
> the
> > Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
> > Run.pm the older version? I have Perl v5.12.1 installed.
> >
> > Thanks in advance!
> > Tracey
> > _______________________________________________
> > 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 Oct 19 16:45:55 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 19 Oct 2010 15:45:55 -0500
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <AANLkTi=LKy-UMPkQkDXN=83sjRFdJMgOn7Du9vVdh6x7@mail.gmail.com>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
	<AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>
	<9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>
	<AANLkTi=LKy-UMPkQkDXN=83sjRFdJMgOn7Du9vVdh6x7@mail.gmail.com>
Message-ID: <840CF652-BAE0-4DD6-A375-30A817F20351@illinois.edu>

If you mean IPC::Run, I'm not sure.  I don't think BioPerl-Run was ever a part of Strawberry Perl Pro.

I do know there are some warnings that will pop up with BioPerl when using perl 5.12; these have been fixed in the github repo but haven't made their way into a release yet.

chris

On Oct 19, 2010, at 3:38 PM, T D wrote:

> Thank you. I downloaded IPC::Run and the code seems to be working now. Is
> Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?
> 
> 
> On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> No, IPC::Run is different than IPC::Run3:
>> 
>> http://search.cpan.org/dist/IPC-Run/
>> http://search.cpan.org/dist/IPC-Run3/
>> 
>> Both should work under Windows, not sure about Windows7 but I can't see why
>> they wouldn't work.
>> 
>> chris
>> 
>> On Oct 19, 2010, at 12:28 PM, T D wrote:
>> 
>>> Hi,
>>> 
>>> I'm new to BioPerl and Perl in general, and I'm trying to get
>>> StandAloneBlastPlus to run. I got the latest versions using git and
>>> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
>> not
>>> finding modules. Here is my error:
>>> 
>>> Can't locate IPC/Run.pm in @INC
>>> 
>>> Where is this module located? I am running Windows 7. I did a search for
>> the
>>> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
>>> Run.pm the older version? I have Perl v5.12.1 installed.
>>> 
>>> Thanks in advance!
>>> Tracey
>>> _______________________________________________
>>> 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 shalabh.sharma7 at gmail.com  Wed Oct 20 11:00:26 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 20 Oct 2010 11:00:26 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
Message-ID: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>

Hi All,
        Is there any module for mummer in Bioperl?

Also i need some suggestions and ideas (i think this is the best place to
ask).
I am working with huge data (around 200 million illumina reads), earlier i
was using blastx and other similar approaches to annotate but now i think
thats not possible, i would be very grateful if anyone can give me some idea
regarding this.

Thanks
Shalabh


From David.Messina at sbc.su.se  Wed Oct 20 11:25:02 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Wed, 20 Oct 2010 11:25:02 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
Message-ID: <C3E45590-33DD-4A27-87FF-533D8E8C9C09@sbc.su.se>


> Is there any module for mummer in Bioperl?

Did you try searching for mummer on the bioperl website?




From shalabh.sharma7 at gmail.com  Wed Oct 20 11:31:09 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 20 Oct 2010 11:31:09 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <C3E45590-33DD-4A27-87FF-533D8E8C9C09@sbc.su.se>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
	<C3E45590-33DD-4A27-87FF-533D8E8C9C09@sbc.su.se>
Message-ID: <AANLkTim3ig2Aa+=TUqb0Cr5HsH0f-eHoi+aZCX-pctEp@mail.gmail.com>

Yes , i did but its saying there aren't any modules available so i jsu
wanted to make sure.

-Shalabh


On Wed, Oct 20, 2010 at 11:25 AM, Dave Messina <David.Messina at sbc.su.se>wrote:

>
> > Is there any module for mummer in Bioperl?
>
> Did you try searching for mummer on the bioperl website?
>
>
>


From jimhu at tamu.edu  Wed Oct 20 11:27:08 2010
From: jimhu at tamu.edu (Jim Hu)
Date: Wed, 20 Oct 2010 10:27:08 -0500
Subject: [Bioperl-l] treeio->write_tree problem
Message-ID: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>

Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.

Jim

use Data::Dumper;
use Bio::TreeIO;
my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
                            -format => "newick");
while( my $tree = $treeio->next_tree ) {
	$treeio->write_tree($tree);
	print Dumper($tree);

}

=====================================
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 Oct 20 11:45:45 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 10:45:45 -0500
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
Message-ID: <572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>

On Oct 20, 2010, at 10:00 AM, shalabh sharma wrote:

> Hi All,
>        Is there any module for mummer in Bioperl?
> 
> Also i need some suggestions and ideas (i think this is the best place to
> ask).
> I am working with huge data (around 200 million illumina reads), earlier i
> was using blastx and other similar approaches to annotate but now i think
> thats not possible, i would be very grateful if anyone can give me some idea
> regarding this.
> 
> Thanks
> Shalabh

Hard to say unless we know a little more about what you are attempting to do.  Not sure why you are using mummer here, but...

This is something fairly well-covered in the literature for most use cases, and on places like seqanswers.  If you are doing something like aligning reads to reference genome(s) or set of gene models, you should be using something like bowtie/tophat, bwa, etc., with the output in SAM (BioPerl has perl wrappers for most of these modules).  

You can also do the same for metagenome analyses, but you may need to run BLAST and convert to SAM (maybe that's what you are doing?).  The samtools package comes with perl scripts to do that and can be further used to sort the matches, convert/index a BAM file for fast accession, etc.  From there you can then use tools like Bio::DB::SAM, R/BioConductor/RSamtools, or similar to access the sequences, find coverage statistics, run SNP calls, etc.

And, for the record, we do have an experimental mummer parser, but I believe it lies in a branch at the moment (don't think it has been merged yet):

http://github.com/bioperl/bioperl-live/tree/topic/bug-2701

chris


From cjfields at illinois.edu  Wed Oct 20 11:46:42 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 10:46:42 -0500
Subject: [Bioperl-l] treeio->write_tree problem
In-Reply-To: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
References: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
Message-ID: <112B35F0-77B6-4B46-9E3A-AAB840E7D349@illinois.edu>

Try '-format => "nhx"'.

chris

On Oct 20, 2010, at 10:27 AM, Jim Hu wrote:

> Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.
> 
> Jim
> 
> use Data::Dumper;
> use Bio::TreeIO;
> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>                            -format => "newick");
> while( my $tree = $treeio->next_tree ) {
> 	$treeio->write_tree($tree);
> 	print Dumper($tree);
> 
> }
> 
> =====================================
> Jim Hu
> Associate Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jimhu at tamu.edu  Wed Oct 20 12:16:52 2010
From: jimhu at tamu.edu (Jim Hu)
Date: Wed, 20 Oct 2010 11:16:52 -0500
Subject: [Bioperl-l] treeio->write_tree problem
In-Reply-To: <534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>
References: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
	<534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>
Message-ID: <BADE3FC8-A40F-4832-8C63-B20CB7C40631@tamu.edu>

Doh!  I suspected it was something brain-dead that I was doing.

Thanks very much.  That worked.

Jim

On Oct 20, 2010, at 11:01 AM, Adam Witney wrote:

> 
> you are writing to your input stream. I think you need to create a separate output stream. Maybe something like this (untested):
> 
> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>                           -format => "newick");
> 
> my $treeio_out = new Bio::TreeIO(-fh   => \*STDOUT,
>                           -format => "newick");
> 
> while( my $tree = $treeio->next_tree ) {
> 	$treeio_out->write_tree($tree);
> 	print Dumper($tree);
> }
> 
> 
> 
> On 20 Oct 2010, at 16:27, Jim Hu wrote:
> 
>> Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.
>> 
>> Jim
>> 
>> use Data::Dumper;
>> use Bio::TreeIO;
>> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>>                           -format => "newick");
>> while( my $tree = $treeio->next_tree ) {
>> 	$treeio->write_tree($tree);
>> 	print Dumper($tree);
>> 
>> }
>> 
>> =====================================
>> Jim Hu
>> Associate Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>> 
>> 
>> 
>> _______________________________________________
>> 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 awitney at sgul.ac.uk  Wed Oct 20 12:01:45 2010
From: awitney at sgul.ac.uk (Adam Witney)
Date: Wed, 20 Oct 2010 17:01:45 +0100
Subject: [Bioperl-l] treeio->write_tree problem
In-Reply-To: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
References: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
Message-ID: <534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>


you are writing to your input stream. I think you need to create a separate output stream. Maybe something like this (untested):

my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
                           -format => "newick");

my $treeio_out = new Bio::TreeIO(-fh   => \*STDOUT,
                           -format => "newick");

while( my $tree = $treeio->next_tree ) {
	$treeio_out->write_tree($tree);
	print Dumper($tree);
}



On 20 Oct 2010, at 16:27, Jim Hu wrote:

> Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.
> 
> Jim
> 
> use Data::Dumper;
> use Bio::TreeIO;
> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>                            -format => "newick");
> while( my $tree = $treeio->next_tree ) {
> 	$treeio->write_tree($tree);
> 	print Dumper($tree);
> 
> }
> 
> =====================================
> Jim Hu
> Associate Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
> 
> 
> 
> _______________________________________________
> 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 Oct 20 12:35:40 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 20 Oct 2010 12:35:40 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
	<572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>
Message-ID: <AANLkTimfSXRn1u-wvqSGM+B=j0Ohhnu5SGDcO413pSBm@mail.gmail.com>

Hey Chris,
             Thanks for the reply , it was really useful.
Actually you are right, it is metagenomics sample. The thing is i've never
worked with that huge amount of data, so i am trying to test some alignment
programs (i am just trying to see if i can avoid blastx) so i am trying all
the available programs.

Blasting 200 million reads doesn't seems a right option (may be i will go
with assembly then blasting it).

Thanks
Shalabh


On Wed, Oct 20, 2010 at 11:45 AM, Chris Fields <cjfields at illinois.edu>wrote:

> On Oct 20, 2010, at 10:00 AM, shalabh sharma wrote:
>
> > Hi All,
> >        Is there any module for mummer in Bioperl?
> >
> > Also i need some suggestions and ideas (i think this is the best place to
> > ask).
> > I am working with huge data (around 200 million illumina reads), earlier
> i
> > was using blastx and other similar approaches to annotate but now i think
> > thats not possible, i would be very grateful if anyone can give me some
> idea
> > regarding this.
> >
> > Thanks
> > Shalabh
>
> Hard to say unless we know a little more about what you are attempting to
> do.  Not sure why you are using mummer here, but...
>
> This is something fairly well-covered in the literature for most use cases,
> and on places like seqanswers.  If you are doing something like aligning
> reads to reference genome(s) or set of gene models, you should be using
> something like bowtie/tophat, bwa, etc., with the output in SAM (BioPerl has
> perl wrappers for most of these modules).
>
> You can also do the same for metagenome analyses, but you may need to run
> BLAST and convert to SAM (maybe that's what you are doing?).  The samtools
> package comes with perl scripts to do that and can be further used to sort
> the matches, convert/index a BAM file for fast accession, etc.  From there
> you can then use tools like Bio::DB::SAM, R/BioConductor/RSamtools, or
> similar to access the sequences, find coverage statistics, run SNP calls,
> etc.
>
> And, for the record, we do have an experimental mummer parser, but I
> believe it lies in a branch at the moment (don't think it has been merged
> yet):
>
> http://github.com/bioperl/bioperl-live/tree/topic/bug-2701
>
> chris


From cjfields at illinois.edu  Wed Oct 20 14:15:09 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 13:15:09 -0500
Subject: [Bioperl-l] treeio->write_tree problem
In-Reply-To: <534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>
References: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
	<534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>
Message-ID: <8A7F4396-D88F-438E-B045-F2CD58293DD1@illinois.edu>

Nice catch!  Completely missed that.

chris

On Oct 20, 2010, at 11:01 AM, Adam Witney wrote:

> 
> you are writing to your input stream. I think you need to create a separate output stream. Maybe something like this (untested):
> 
> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>                           -format => "newick");
> 
> my $treeio_out = new Bio::TreeIO(-fh   => \*STDOUT,
>                           -format => "newick");
> 
> while( my $tree = $treeio->next_tree ) {
> 	$treeio_out->write_tree($tree);
> 	print Dumper($tree);
> }
> 
> 
> 
> On 20 Oct 2010, at 16:27, Jim Hu wrote:
> 
>> Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.
>> 
>> Jim
>> 
>> use Data::Dumper;
>> use Bio::TreeIO;
>> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>>                           -format => "newick");
>> while( my $tree = $treeio->next_tree ) {
>> 	$treeio->write_tree($tree);
>> 	print Dumper($tree);
>> 
>> }
>> 
>> =====================================
>> Jim Hu
>> Associate Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>> 
>> 
>> 
>> _______________________________________________
>> 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  Wed Oct 20 14:25:09 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 13:25:09 -0500
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <AANLkTimfSXRn1u-wvqSGM+B=j0Ohhnu5SGDcO413pSBm@mail.gmail.com>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
	<572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>
	<AANLkTimfSXRn1u-wvqSGM+B=j0Ohhnu5SGDcO413pSBm@mail.gmail.com>
Message-ID: <8B2DB10D-0E81-4426-8678-893669DFD0F9@illinois.edu>

I recall there being a lot of tools available for these.  In particular, one of my colleagues has used MEGAN with some success:

http://www-ab.informatik.uni-tuebingen.de/software/megan

If the sample is from a specific host (i.e. gut microbiome, etc), you can set up initial short read runs that act to filter out sequences you might not be interested in (namely those that belong to the host), then run alignments against more focused databases (rRNA, for instance, if one is doing meta-transcriptomic analyses).  Beyond that, I agree that assembly should be included early in the analysis, if it isn't already the initial step.

chris

On Oct 20, 2010, at 11:35 AM, shalabh sharma wrote:

> Hey Chris,
>              Thanks for the reply , it was really useful.
> Actually you are right, it is metagenomics sample. The thing is i've never worked with that huge amount of data, so i am trying to test some alignment programs (i am just trying to see if i can avoid blastx) so i am trying all the available programs.
> 
> Blasting 200 million reads doesn't seems a right option (may be i will go with assembly then blasting it).
> 
> Thanks
> Shalabh
> 
> 
> On Wed, Oct 20, 2010 at 11:45 AM, Chris Fields <cjfields at illinois.edu> wrote:
> On Oct 20, 2010, at 10:00 AM, shalabh sharma wrote:
> 
> > Hi All,
> >        Is there any module for mummer in Bioperl?
> >
> > Also i need some suggestions and ideas (i think this is the best place to
> > ask).
> > I am working with huge data (around 200 million illumina reads), earlier i
> > was using blastx and other similar approaches to annotate but now i think
> > thats not possible, i would be very grateful if anyone can give me some idea
> > regarding this.
> >
> > Thanks
> > Shalabh
> 
> Hard to say unless we know a little more about what you are attempting to do.  Not sure why you are using mummer here, but...
> 
> This is something fairly well-covered in the literature for most use cases, and on places like seqanswers.  If you are doing something like aligning reads to reference genome(s) or set of gene models, you should be using something like bowtie/tophat, bwa, etc., with the output in SAM (BioPerl has perl wrappers for most of these modules).
> 
> You can also do the same for metagenome analyses, but you may need to run BLAST and convert to SAM (maybe that's what you are doing?).  The samtools package comes with perl scripts to do that and can be further used to sort the matches, convert/index a BAM file for fast accession, etc.  From there you can then use tools like Bio::DB::SAM, R/BioConductor/RSamtools, or similar to access the sequences, find coverage statistics, run SNP calls, etc.
> 
> And, for the record, we do have an experimental mummer parser, but I believe it lies in a branch at the moment (don't think it has been merged yet):
> 
> http://github.com/bioperl/bioperl-live/tree/topic/bug-2701
> 
> chris
> 




From shalabh.sharma7 at gmail.com  Wed Oct 20 14:35:54 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 20 Oct 2010 14:35:54 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <8B2DB10D-0E81-4426-8678-893669DFD0F9@illinois.edu>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
	<572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>
	<AANLkTimfSXRn1u-wvqSGM+B=j0Ohhnu5SGDcO413pSBm@mail.gmail.com>
	<8B2DB10D-0E81-4426-8678-893669DFD0F9@illinois.edu>
Message-ID: <AANLkTinxFKdMkOaejxpFDN-qf0pF=Lg7brHHvqYuXk4s@mail.gmail.com>

I have used MEGAN a lot in past, but again it takes blast files as input and
here i just want to avoid blast.
The problem is its environmental sample so i cant throw any of the data.

I know its not a bioperl question but i was just wondering is there any
program that can align my reads against a huge database at amino acid level
(like with refseq or subset of refseq).
or even alignment is a good option?

I really appreciate your input.

Thanks
Shalabh


On Wed, Oct 20, 2010 at 2:25 PM, Chris Fields <cjfields at illinois.edu> wrote:

> I recall there being a lot of tools available for these.  In particular,
> one of my colleagues has used MEGAN with some success:
>
> http://www-ab.informatik.uni-tuebingen.de/software/megan
>
> If the sample is from a specific host (i.e. gut microbiome, etc), you can
> set up initial short read runs that act to filter out sequences you might
> not be interested in (namely those that belong to the host), then run
> alignments against more focused databases (rRNA, for instance, if one is
> doing meta-transcriptomic analyses).  Beyond that, I agree that assembly
> should be included early in the analysis, if it isn't already the initial
> step.
>
> chris
>
> On Oct 20, 2010, at 11:35 AM, shalabh sharma wrote:
>
> > Hey Chris,
> >              Thanks for the reply , it was really useful.
> > Actually you are right, it is metagenomics sample. The thing is i've
> never worked with that huge amount of data, so i am trying to test some
> alignment programs (i am just trying to see if i can avoid blastx) so i am
> trying all the available programs.
> >
> > Blasting 200 million reads doesn't seems a right option (may be i will go
> with assembly then blasting it).
> >
> > Thanks
> > Shalabh
> >
> >
> > On Wed, Oct 20, 2010 at 11:45 AM, Chris Fields <cjfields at illinois.edu>
> wrote:
> > On Oct 20, 2010, at 10:00 AM, shalabh sharma wrote:
> >
> > > Hi All,
> > >        Is there any module for mummer in Bioperl?
> > >
> > > Also i need some suggestions and ideas (i think this is the best place
> to
> > > ask).
> > > I am working with huge data (around 200 million illumina reads),
> earlier i
> > > was using blastx and other similar approaches to annotate but now i
> think
> > > thats not possible, i would be very grateful if anyone can give me some
> idea
> > > regarding this.
> > >
> > > Thanks
> > > Shalabh
> >
> > Hard to say unless we know a little more about what you are attempting to
> do.  Not sure why you are using mummer here, but...
> >
> > This is something fairly well-covered in the literature for most use
> cases, and on places like seqanswers.  If you are doing something like
> aligning reads to reference genome(s) or set of gene models, you should be
> using something like bowtie/tophat, bwa, etc., with the output in SAM
> (BioPerl has perl wrappers for most of these modules).
> >
> > You can also do the same for metagenome analyses, but you may need to run
> BLAST and convert to SAM (maybe that's what you are doing?).  The samtools
> package comes with perl scripts to do that and can be further used to sort
> the matches, convert/index a BAM file for fast accession, etc.  From there
> you can then use tools like Bio::DB::SAM, R/BioConductor/RSamtools, or
> similar to access the sequences, find coverage statistics, run SNP calls,
> etc.
> >
> > And, for the record, we do have an experimental mummer parser, but I
> believe it lies in a branch at the moment (don't think it has been merged
> yet):
> >
> > http://github.com/bioperl/bioperl-live/tree/topic/bug-2701
> >
> > chris
> >
>
>


From rmb32 at cornell.edu  Wed Oct 20 20:27:36 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Wed, 20 Oct 2010 17:27:36 -0700
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <840CF652-BAE0-4DD6-A375-30A817F20351@illinois.edu>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>	<AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>	<9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>	<AANLkTi=LKy-UMPkQkDXN=83sjRFdJMgOn7Du9vVdh6x7@mail.gmail.com>
	<840CF652-BAE0-4DD6-A375-30A817F20351@illinois.edu>
Message-ID: <4CBF88F8.2030601@cornell.edu>

Ah, the joys of optional deps.

You know, bioperl-run does not have that many deps right now.  Why don't 
we just make those optional ones required?

R


Chris Fields wrote:
> If you mean IPC::Run, I'm not sure.  I don't think BioPerl-Run was ever a part of Strawberry Perl Pro.
> 
> I do know there are some warnings that will pop up with BioPerl when using perl 5.12; these have been fixed in the github repo but haven't made their way into a release yet.
> 
> chris
> 
> On Oct 19, 2010, at 3:38 PM, T D wrote:
> 
>> Thank you. I downloaded IPC::Run and the code seems to be working now. Is
>> Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?
>>
>>
>> On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>
>>> No, IPC::Run is different than IPC::Run3:
>>>
>>> http://search.cpan.org/dist/IPC-Run/
>>> http://search.cpan.org/dist/IPC-Run3/
>>>
>>> Both should work under Windows, not sure about Windows7 but I can't see why
>>> they wouldn't work.
>>>
>>> chris
>>>
>>> On Oct 19, 2010, at 12:28 PM, T D wrote:
>>>
>>>> Hi,
>>>>
>>>> I'm new to BioPerl and Perl in general, and I'm trying to get
>>>> StandAloneBlastPlus to run. I got the latest versions using git and
>>>> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
>>> not
>>>> finding modules. Here is my error:
>>>>
>>>> Can't locate IPC/Run.pm in @INC
>>>>
>>>> Where is this module located? I am running Windows 7. I did a search for
>>> the
>>>> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
>>>> Run.pm the older version? I have Perl v5.12.1 installed.
>>>>
>>>> Thanks in advance!
>>>> Tracey
>>>> _______________________________________________
>>>> 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 maj at fortinbras.us  Wed Oct 20 21:21:56 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Thu, 21 Oct 2010 01:21:56 +0000
Subject: [Bioperl-l] IPC/Run.pm?
Message-ID: <W2403825015265021287624116@webmail11>

I would +1 making IPC::Run required. It's got some nice features and it much safer than system(). Might even want to make it a dev recommendation for all system calls. MAJ

>-----Original Message-----
>From: Robert Buels [mailto:rmb32 at cornell.edu]
>Sent: Wednesday, October 20, 2010 08:27 PM
>To: 'Chris Fields'
>Cc: bioperl-l at lists.open-bio.org
>Subject: Re: [Bioperl-l] IPC/Run.pm?
>
>Ah, the joys of optional deps.
>
>You know, bioperl-run does not have that many deps right now.  Why don't 
>we just make those optional ones required?
>
>R
>
>
>Chris Fields wrote:
>> If you mean IPC::Run, I'm not sure.  I don't think BioPerl-Run was ever a part of Strawberry Perl Pro.
>> 
>> I do know there are some warnings that will pop up with BioPerl when using perl 5.12; these have been fixed in the github repo but haven't made their way into a release yet.
>> 
>> chris
>> 
>> On Oct 19, 2010, at 3:38 PM, T D wrote:
>> 
>>> Thank you. I downloaded IPC::Run and the code seems to be working now. Is
>>> Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?
>>>
>>>
>>> On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>
>>>> No, IPC::Run is different than IPC::Run3:
>>>>
>>>> http://search.cpan.org/dist/IPC-Run/
>>>> http://search.cpan.org/dist/IPC-Run3/
>>>>
>>>> Both should work under Windows, not sure about Windows7 but I can't see why
>>>> they wouldn't work.
>>>>
>>>> chris
>>>>
>>>> On Oct 19, 2010, at 12:28 PM, T D wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I'm new to BioPerl and Perl in general, and I'm trying to get
>>>>> StandAloneBlastPlus to run. I got the latest versions using git and
>>>>> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
>>>> not
>>>>> finding modules. Here is my error:
>>>>>
>>>>> Can't locate IPC/Run.pm in @INC
>>>>>
>>>>> Where is this module located? I am running Windows 7. I did a search for
>>>> the
>>>>> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
>>>>> Run.pm the older version? I have Perl v5.12.1 installed.
>>>>>
>>>>> Thanks in advance!
>>>>> Tracey
>>>>> _______________________________________________
>>>>> 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 cjfields at illinois.edu  Wed Oct 20 21:54:48 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 20:54:48 -0500
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <W2403825015265021287624116@webmail11>
References: <W2403825015265021287624116@webmail11>
Message-ID: <697C7C00-5ED9-4A69-9F55-6C8C6F349DF4@illinois.edu>

+1.  Quite a few modules there use it.

chris

On Oct 20, 2010, at 8:21 PM, Mark A. Jensen wrote:

> I would +1 making IPC::Run required. It's got some nice features and it much safer than system(). Might even want to make it a dev recommendation for all system calls. MAJ
> 
>> -----Original Message-----
>> From: Robert Buels [mailto:rmb32 at cornell.edu]
>> Sent: Wednesday, October 20, 2010 08:27 PM
>> To: 'Chris Fields'
>> Cc: bioperl-l at lists.open-bio.org
>> Subject: Re: [Bioperl-l] IPC/Run.pm?
>> 
>> Ah, the joys of optional deps.
>> 
>> You know, bioperl-run does not have that many deps right now.  Why don't 
>> we just make those optional ones required?
>> 
>> R
>> 
>> 
>> Chris Fields wrote:
>>> If you mean IPC::Run, I'm not sure.  I don't think BioPerl-Run was ever a part of Strawberry Perl Pro.
>>> 
>>> I do know there are some warnings that will pop up with BioPerl when using perl 5.12; these have been fixed in the github repo but haven't made their way into a release yet.
>>> 
>>> chris
>>> 
>>> On Oct 19, 2010, at 3:38 PM, T D wrote:
>>> 
>>>> Thank you. I downloaded IPC::Run and the code seems to be working now. Is
>>>> Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?
>>>> 
>>>> 
>>>> On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>> 
>>>>> No, IPC::Run is different than IPC::Run3:
>>>>> 
>>>>> http://search.cpan.org/dist/IPC-Run/
>>>>> http://search.cpan.org/dist/IPC-Run3/
>>>>> 
>>>>> Both should work under Windows, not sure about Windows7 but I can't see why
>>>>> they wouldn't work.
>>>>> 
>>>>> chris
>>>>> 
>>>>> On Oct 19, 2010, at 12:28 PM, T D wrote:
>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I'm new to BioPerl and Perl in general, and I'm trying to get
>>>>>> StandAloneBlastPlus to run. I got the latest versions using git and
>>>>>> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
>>>>> not
>>>>>> finding modules. Here is my error:
>>>>>> 
>>>>>> Can't locate IPC/Run.pm in @INC
>>>>>> 
>>>>>> Where is this module located? I am running Windows 7. I did a search for
>>>>> the
>>>>>> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
>>>>>> Run.pm the older version? I have Perl v5.12.1 installed.
>>>>>> 
>>>>>> Thanks in advance!
>>>>>> Tracey
>>>>>> _______________________________________________
>>>>>> 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 ashwani.iiit at gmail.com  Thu Oct 21 04:39:22 2010
From: ashwani.iiit at gmail.com (ashwani sharma)
Date: Thu, 21 Oct 2010 14:09:22 +0530
Subject: [Bioperl-l] how to download PDB files using Bioperl script
Message-ID: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>

Hi All,


I have around 150 pdb file names and I need to download them from Protein
Data Bank. I wonder if someone could tell me how to do it by using Bioperl.

Thanks in advance.

Regards,
Ashwani


From hanbobio at 126.com  Tue Oct 19 07:50:07 2010
From: hanbobio at 126.com (yusheng liao)
Date: Tue, 19 Oct 2010 11:50:07 +0000 (UTC)
Subject: [Bioperl-l] Can't locate Bio/seqIO.pm in @INC
Message-ID: <loom.20101019T134347-528@post.gmane.org>

Can't locate Bio/seqIO.pm in @INC 
I try to run a .pl file to get multi sequences for t
he GenBank using the
Bioperl. The following were the error message:
linux:/home/liaoy # perl hsv-1.pl
Can't locate Bio/seqIO.pm in @INC (@INC contains:
/usr/lib/perl5/5.8.7/i586-linux-thread-multi /usr/lib/perl5/5.8.7
/usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.7 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .)
 at hsv-1.pl line 4.
BEGIN failed--compilation aborted at hsv-1.pl line 4.

what is the problem? And how to corret it? 



From cgzheng86 at gmail.com  Thu Oct 21 04:45:40 2010
From: cgzheng86 at gmail.com (Chaogu Zheng)
Date: Thu, 21 Oct 2010 01:45:40 -0700 (PDT)
Subject: [Bioperl-l] Failed to load module Bio::SeqIO::swiss
Message-ID: <63e01ab5-99f2-46a0-8901-3bdb24562c5f@g13g2000yqj.googlegroups.com>

I am extremely new to Bioperl and got a problem immediately after I
installed it.

I installed Bioperl-pm5100 and Bioperl-run-pm5100 using fink.
Everything seems to be fine. However, when I tried to retrieve some
sequences from swissprot, I found the following errors.

It seems the module Bio::SeqIO::swiss can not be loaded, though I
indeed found it under the correct directory. By the way, if I change
'swiss' to 'genbank' I can successfully run the program.

I don't know how to fix it. Anyone can help me?


Ryan

>>>>>>>>>>>>>>
Bio::SeqIO: swiss cannot be found
Exception
------------- EXCEPTION -------------
MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/
Stag.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-
multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-
multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/
5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/
Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/
5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/
5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /
Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/
Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/
5.10.0 .) at /sw/lib/perl5/5.10.0/Bio/Annotation/TagTree.pm line 123.
BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/
Annotation/TagTree.pm line 123.
Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/SeqIO/
swiss.pm line 208.
BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/SeqIO/
swiss.pm line 208.
Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/Root/Root.pm
line 439.

STACK Bio::Root::Root::_load_module /sw/lib/perl5/5.10.0/Bio/Root/
Root.pm:441
STACK (eval) /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:570
STACK Bio::SeqIO::_load_format_module /sw/lib/perl5/5.10.0/Bio/
SeqIO.pm:569
STACK Bio::SeqIO::new /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:389
STACK Bio::DB::WebDBSeqI::get_seq_stream /sw/lib/perl5/5.10.0/Bio/DB/
WebDBSeqI.pm:472
STACK Bio::DB::WebDBSeqI::get_Stream_by_acc /sw/lib/perl5/5.10.0/Bio/
DB/WebDBSeqI.pm:314
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
WebDBSeqI.pm:186
STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
STACK toplevel ./Documents/perl-programs/perl_test:8
-------------------------------------


For more information about the SeqIO system please see the SeqIO docs.
This includes ways of checking for formats at compile time, not run
time

------------- EXCEPTION -------------
MSG: acc P11217 does not exist
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
WebDBSeqI.pm:187
STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
STACK toplevel ./Documents/perl-programs/perl_test:8
-------------------------------------


From cjfields at illinois.edu  Thu Oct 21 11:02:35 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 21 Oct 2010 10:02:35 -0500
Subject: [Bioperl-l] Can't locate Bio/seqIO.pm in @INC
In-Reply-To: <loom.20101019T134347-528@post.gmane.org>
References: <loom.20101019T134347-528@post.gmane.org>
Message-ID: <9E5A48C0-4509-429B-8F16-9A1D1A440CC8@illinois.edu>

Check your spelling (note the caps below):

use Bio::SeqIO;

chris

On Oct 19, 2010, at 6:50 AM, yusheng liao wrote:

> Can't locate Bio/seqIO.pm in @INC 
> I try to run a .pl file to get multi sequences for t
> he GenBank using the
> Bioperl. The following were the error message:
> linux:/home/liaoy # perl hsv-1.pl
> Can't locate Bio/seqIO.pm in @INC (@INC contains:
> /usr/lib/perl5/5.8.7/i586-linux-thread-multi /usr/lib/perl5/5.8.7
> /usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.7 /usr/lib/perl5/site_perl
> /usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .)
> at hsv-1.pl line 4.
> BEGIN failed--compilation aborted at hsv-1.pl line 4.
> 
> what is the problem? And how to corret it? 
> 
> _______________________________________________
> 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 Oct 21 11:05:17 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 21 Oct 2010 10:05:17 -0500
Subject: [Bioperl-l] Failed to load module Bio::SeqIO::swiss
In-Reply-To: <63e01ab5-99f2-46a0-8901-3bdb24562c5f@g13g2000yqj.googlegroups.com>
References: <63e01ab5-99f2-46a0-8901-3bdb24562c5f@g13g2000yqj.googlegroups.com>
Message-ID: <23FDD4AF-3E56-4E05-AFD7-21A54DECD1C6@illinois.edu>

Like the error message says, you need to install Data::Stag (so, for some reason, this way left off).  However, I'm not sure why you are using fink as the version in stable is still 1.5.1; bioperl 1.6.1 is in fink-unstable.

chris

On Oct 21, 2010, at 3:45 AM, Chaogu Zheng wrote:

> I am extremely new to Bioperl and got a problem immediately after I
> installed it.
> 
> I installed Bioperl-pm5100 and Bioperl-run-pm5100 using fink.
> Everything seems to be fine. However, when I tried to retrieve some
> sequences from swissprot, I found the following errors.
> 
> It seems the module Bio::SeqIO::swiss can not be loaded, though I
> indeed found it under the correct directory. By the way, if I change
> 'swiss' to 'genbank' I can successfully run the program.
> 
> I don't know how to fix it. Anyone can help me?
> 
> 
> Ryan
> 
>>>>>>>>>>>>>>> 
> Bio::SeqIO: swiss cannot be found
> Exception
> ------------- EXCEPTION -------------
> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/
> Stag.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-
> multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-
> multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/
> 5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/
> Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/
> 5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/
> 5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /
> Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/
> Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/
> 5.10.0 .) at /sw/lib/perl5/5.10.0/Bio/Annotation/TagTree.pm line 123.
> BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/
> Annotation/TagTree.pm line 123.
> Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> swiss.pm line 208.
> BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> swiss.pm line 208.
> Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/Root/Root.pm
> line 439.
> 
> STACK Bio::Root::Root::_load_module /sw/lib/perl5/5.10.0/Bio/Root/
> Root.pm:441
> STACK (eval) /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:570
> STACK Bio::SeqIO::_load_format_module /sw/lib/perl5/5.10.0/Bio/
> SeqIO.pm:569
> STACK Bio::SeqIO::new /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:389
> STACK Bio::DB::WebDBSeqI::get_seq_stream /sw/lib/perl5/5.10.0/Bio/DB/
> WebDBSeqI.pm:472
> STACK Bio::DB::WebDBSeqI::get_Stream_by_acc /sw/lib/perl5/5.10.0/Bio/
> DB/WebDBSeqI.pm:314
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> WebDBSeqI.pm:186
> STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> STACK toplevel ./Documents/perl-programs/perl_test:8
> -------------------------------------
> 
> 
> For more information about the SeqIO system please see the SeqIO docs.
> This includes ways of checking for formats at compile time, not run
> time
> 
> ------------- EXCEPTION -------------
> MSG: acc P11217 does not exist
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> WebDBSeqI.pm:187
> STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> STACK toplevel ./Documents/perl-programs/perl_test:8
> -------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jimhu at tamu.edu  Thu Oct 21 13:52:32 2010
From: jimhu at tamu.edu (Jim Hu)
Date: Thu, 21 Oct 2010 12:52:32 -0500
Subject: [Bioperl-l] Does $tree->remove_Node prune or splice?
Message-ID: <927BEE54-ABC2-428A-AF42-DDEBDEABB878@tamu.edu>

I'm trying to take an unreadable tree from PFAM and prune it down to just show the paralogs from E. coli.

When you run remove_Node on an internal node, is it supposed to reconnect the ancestors to the descendants?  This seems to be way to aggressive in what it's removing.

while( my $tree = $treeio->next_tree ) {
	for my $node ( $tree->get_nodes ) {
		if ($node->id =~ m/_ECOLI/){
			#	leave this node alone
			#	print $node->id."\n";
		}else{
			if ($node->is_Leaf){
				$tree->remove_Node($node);
			}else{
				my $num_children = scalar($node->each_Descendent);
				if ($num_children == 1){ 
					print "removing ".$node->id."\n";
					$tree->remove_Node($node);
				}	
			}	
		}
	}
	$treeio_out->write_tree($tree);
}

The idea is that when I've pruned the non-ECOLI leaves, some internal nodes will not be branches anymore.  But at the end, all the ECOLI nodes are gone, presumably because an ancestor got removed and the whole branch was lost.  Is there a way to remove just a node and graft the tree back together?  My plan, once I get that working is to repeat the traversal until the output stops changing.

Jim


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





From cgzheng86 at gmail.com  Thu Oct 21 13:57:06 2010
From: cgzheng86 at gmail.com (Chaogu Zheng)
Date: Thu, 21 Oct 2010 10:57:06 -0700 (PDT)
Subject: [Bioperl-l] Failed to load module Bio::SeqIO::swiss
In-Reply-To: <23FDD4AF-3E56-4E05-AFD7-21A54DECD1C6@illinois.edu>
References: <63e01ab5-99f2-46a0-8901-3bdb24562c5f@g13g2000yqj.googlegroups.com>
	<23FDD4AF-3E56-4E05-AFD7-21A54DECD1C6@illinois.edu>
Message-ID: <974a993b-fbdf-4ca6-a59b-a7f247669eff@j18g2000yqd.googlegroups.com>

Maybe my reason for this is silly. I am using the Mac OS X 10.6, which
has the pre-installed perl 5.10.0. Fink only has the unstable bioperl
1.6.1 for Mac OS X 10.6. If I want to install bioperl-pm588 that is
the fink-stable 1.5.1 version, I guess I have to install an earlier
version of perl 5.8.8. I did not bother to do that.

So, do you think I really need to uninstall bioperl-pm5100 and get
perl 5.8.8 to try the fink-stable one?

Ryan

On Oct 21, 11:05?am, Chris Fields <cjfie... at illinois.edu> wrote:
> Like the error message says, you need to install Data::Stag (so, for some reason, this way left off). ?However, I'm not sure why you are using fink as the version in stable is still 1.5.1; bioperl 1.6.1 is in fink-unstable.
>
> chris
>
> On Oct 21, 2010, at 3:45 AM, Chaogu Zheng wrote:
>
>
>
>
>
> > I am extremely new to Bioperl and got a problem immediately after I
> > installed it.
>
> > I installed Bioperl-pm5100 and Bioperl-run-pm5100 using fink.
> > Everything seems to be fine. However, when I tried to retrieve some
> > sequences from swissprot, I found the following errors.
>
> > It seems the module Bio::SeqIO::swiss can not be loaded, though I
> > indeed found it under the correct directory. By the way, if I change
> > 'swiss' to 'genbank' I can successfully run the program.
>
> > I don't know how to fix it. Anyone can help me?
>
> > Ryan
>
> > Bio::SeqIO: swiss cannot be found
> > Exception
> > ------------- EXCEPTION -------------
> > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/
> > Stag.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-
> > multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-
> > multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/
> > 5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/
> > Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/
> > 5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/
> > 5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /
> > Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/
> > Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/
> > 5.10.0 .) at /sw/lib/perl5/5.10.0/Bio/Annotation/TagTree.pm line 123.
> > BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/
> > Annotation/TagTree.pm line 123.
> > Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> > swiss.pm line 208.
> > BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> > swiss.pm line 208.
> > Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/Root/Root.pm
> > line 439.
>
> > STACK Bio::Root::Root::_load_module /sw/lib/perl5/5.10.0/Bio/Root/
> > Root.pm:441
> > STACK (eval) /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:570
> > STACK Bio::SeqIO::_load_format_module /sw/lib/perl5/5.10.0/Bio/
> > SeqIO.pm:569
> > STACK Bio::SeqIO::new /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:389
> > STACK Bio::DB::WebDBSeqI::get_seq_stream /sw/lib/perl5/5.10.0/Bio/DB/
> > WebDBSeqI.pm:472
> > STACK Bio::DB::WebDBSeqI::get_Stream_by_acc /sw/lib/perl5/5.10.0/Bio/
> > DB/WebDBSeqI.pm:314
> > STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> > WebDBSeqI.pm:186
> > STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> > STACK toplevel ./Documents/perl-programs/perl_test:8
> > -------------------------------------
>
> > For more information about the SeqIO system please see the SeqIO docs.
> > This includes ways of checking for formats at compile time, not run
> > time
>
> > ------------- EXCEPTION -------------
> > MSG: acc P11217 does not exist
> > STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> > WebDBSeqI.pm:187
> > STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> > STACK toplevel ./Documents/perl-programs/perl_test:8
> > -------------------------------------
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioper... at lists.open-bio.org
> >http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l



From izlowe at ucdavis.edu  Thu Oct 21 22:00:24 2010
From: izlowe at ucdavis.edu (Iago Lowe)
Date: Thu, 21 Oct 2010 22:00:24 -0400
Subject: [Bioperl-l] Specifying the search set in NCBI BLAST
Message-ID: <AANLkTi=s_RstcyKyoGws0ykcK8VAb7DVcLtMrRyt2O4X@mail.gmail.com>

In the "Choose Search Set" tab on the NCBI BLAST webpage, there are some
convenient ways to restrict the size of the database for queries.  In there
a way to apply these restrictions in a remote search via Bioperl?

For example, in our research, we want to search only the "Non-human,
non-mouse ESTs" for the organism "Triticum" rather than the entire NCBI
database.

Thanks very much for any guidance.
Iago Lowe


From David.Messina at sbc.su.se  Fri Oct 22 11:29:36 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 22 Oct 2010 11:29:36 -0400
Subject: [Bioperl-l] Specifying the search set in NCBI BLAST
In-Reply-To: <AANLkTi=s_RstcyKyoGws0ykcK8VAb7DVcLtMrRyt2O4X@mail.gmail.com>
References: <AANLkTi=s_RstcyKyoGws0ykcK8VAb7DVcLtMrRyt2O4X@mail.gmail.com>
Message-ID: <C7922411-92DE-46D0-B4AA-E32A606C7415@sbc.su.se>

Hi Iago,

It is possible to do this with BioPerl, but I would recommend simply downloading Blast+ (note the +) and using the -entrez_query and -remote options.

Dave




From MEC at stowers.org  Fri Oct 22 11:40:24 2010
From: MEC at stowers.org (Cook, Malcolm)
Date: Fri, 22 Oct 2010 10:40:24 -0500
Subject: [Bioperl-l] Specifying the search set in NCBI BLAST
In-Reply-To: <C7922411-92DE-46D0-B4AA-E32A606C7415@sbc.su.se>
References: <AANLkTi=s_RstcyKyoGws0ykcK8VAb7DVcLtMrRyt2O4X@mail.gmail.com>
	<C7922411-92DE-46D0-B4AA-E32A606C7415@sbc.su.se>
Message-ID: <BD62CBAC4395B94096109020651BE2EC138AFB720D@EXCHMB-02.stowers-institute.org>

I agree with Dave.

But, if you must use BioPerl, see http://doc.bioperl.org/releases/bioperl-1.4/Bio/Tools/Run/RemoteBlast.html where it shows this code:

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

You'll probably want to set your database to  est_others (c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html#2 )

--Malcolm
 

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dave Messina
Sent: Friday, October 22, 2010 10:30 AM
To: Iago Lowe
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Specifying the search set in NCBI BLAST

Hi Iago,

It is possible to do this with BioPerl, but I would recommend simply downloading Blast+ (note the +) and using the -entrez_query and -remote options.

Dave


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



From jun.yin at ucd.ie  Fri Oct 22 12:12:45 2010
From: jun.yin at ucd.ie (Jun Yin)
Date: Fri, 22 Oct 2010 17:12:45 +0100
Subject: [Bioperl-l] how to download PDB files using Bioperl script
In-Reply-To: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
Message-ID: <01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>

Hi, Ashwani,

I havenot found any module in BioPerl for downloading PDB files, though
Bio::Structure::IO::pdb can parse PDB files.

However, PDB provides RESTful service
(http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
batch downloading the proteins.

Cheers,
Jun Yin
Ph.D.?student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
Sent: Thursday, October 21, 2010 9:39 AM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] how to download PDB files using Bioperl script

Hi All,


I have around 150 pdb file names and I need to download them from Protein
Data Bank. I wonder if someone could tell me how to do it by using Bioperl.

Thanks in advance.

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

__________ Information from ESET Smart Security, version of virus signature
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__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

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http://www.eset.com
 
 

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com
 




From jason at bioperl.org  Sat Oct 23 11:33:49 2010
From: jason at bioperl.org (Jason Stajich)
Date: Sat, 23 Oct 2010 08:33:49 -0700
Subject: [Bioperl-l] Question on BioPerl modules
In-Reply-To: <1287838391.5784.19.camel@ubuntu>
References: <1287838391.5784.19.camel@ubuntu>
Message-ID: <4CC3005D.1070708@bioperl.org>

Lincoln overloaded the "" method for the objects that are returned from 
Bio::DB::Fasta so that attempts to print them directly will instead 
print out the display_id field.

If you want to know what kind of object you getting back you use 'ref', 
as in:
print ref($seq),"\n";

Tao Zhu wrote, On 10/23/10 5:53 AM:
> Dear Professor Stajich,
>
> Recently I was puzzled when using two BioPerl modules, Bio::Index::Fasta
> and Bio::DB::Fasta;
>
> For example, I have a fasta file: sequence.fa, on my computer. That is:
>
>> ORFN:87
> ATGGAAGCCCCTTCAGAAATTACCGATTCCAA
>
> I hope to make a local index, then I use Bio::Index::Fasta and write:
>
> use Bio::Index::Fasta;
> $file_name = "sequence.fa";
> $id = "ORFN:87";
> $inx = Bio::Index::Fasta->new (-filename =>  $file_name . ".idx", -write_flag =>  1);
> $inx->make_index($file_name);
> $seq_obj = $inx->fetch($id);
> print "$seq_obj\n";
>
> Running the perl script, it prints "Bio::Seq=HASH(0x66590a0)" on screen.
> That means the scalar "$seq_obj" is a Bio::Seq object.
>
> However, I try another method, using Bio::DB::Fasta,
>
> use Bio::DB::Fasta;
> ($file,$id) = ("sequence.fa","ORFN:87");
> $db = Bio::DB::Fasta->new($file);
> $seq_obj = $db->get_Seq_by_id($id);
> print "$seq_obj\n";
>
> I expect it should also print "Bio::Seq=HASH(sth)",because I also get a
> Bio::Seq object. Surprisingly it prints "ORFN:87"
>
> How it comes to be?
>

-- 
Jason Stajich
jason at bioperl.org



From yifangt at hotmail.com  Sat Oct 23 02:21:40 2010
From: yifangt at hotmail.com (yifangt)
Date: Fri, 22 Oct 2010 23:21:40 -0700 (PDT)
Subject: [Bioperl-l] Can't locate Bio/seqIO.pm in @INC
In-Reply-To: <loom.20101019T134347-528@post.gmane.org>
References: <loom.20101019T134347-528@post.gmane.org>
Message-ID: <30034148.post@talk.nabble.com>


Probably your Bioperl installation is not correct. Re-install your bioperl
and try again!

Good luck!




yusheng liao wrote:
> 
> Can't locate Bio/seqIO.pm in @INC 
> I try to run a .pl file to get multi sequences for t
> he GenBank using the
> Bioperl. The following were the error message:
> linux:/home/liaoy # perl hsv-1.pl
> Can't locate Bio/seqIO.pm in @INC (@INC contains:
> /usr/lib/perl5/5.8.7/i586-linux-thread-multi /usr/lib/perl5/5.8.7
> /usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.7 /usr/lib/perl5/site_perl
> /usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .)
>  at hsv-1.pl line 4.
> BEGIN failed--compilation aborted at hsv-1.pl line 4.
> 
> what is the problem? And how to corret it? 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/Can%27t-locate-Bio-seqIO.pm-in-%40INC-tp30019789p30034148.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From timmcilveen at talktalk.net  Sun Oct 24 20:45:15 2010
From: timmcilveen at talktalk.net (Tim)
Date: Mon, 25 Oct 2010 01:45:15 +0100
Subject: [Bioperl-l] Installing Bioperl  from Git Hub
Message-ID: <4CC4D31B.1080905@talktalk.net>

Hi everyone,
A couple of weeks ago, I posted a query about installing Bioperl from 
GitHub. I was getting installation errors and someone on the list had 
picked up on  a typo I had made while trying to install it.
Bioperl is now installed and working properly. I forgot to acknowledge 
your help. Thanks for your advice.

Tim



From edwardsa at cs.man.ac.uk  Mon Oct 25 12:33:21 2010
From: edwardsa at cs.man.ac.uk (Andrea Edwards)
Date: Mon, 25 Oct 2010 17:33:21 +0100
Subject: [Bioperl-l] can't install bioperl 1.6.1
Message-ID: <4CC5B151.8030606@cs.man.ac.uk>

  Hi

I can't install Bioperl 1.6.1 on windows using Active Perl 5.8.8.822

I have added the repositories as mentioned in the user guide but get 
this error message

?ERROR: File conflict for 'C:/Perl/html/bin/bp_aacomp.html'.The package 
BioPerl has already installed a file that package bioperl wants to install.?

I have seen a forum thread which says the problem is due to the 
trouchelle repository.

http://www.perlmonks.org/?node_id=817531

I did remove the trouchelle repository as suggested and bioperl 1.6.1 
does seem to have installed but I don't know enough about Perl to know 
if it will have installed correctly by removing this repository.

I installed BioPerl 1.6 successfully on a different PC running 
ActivePerl 5.8.9.827 without needing to remove the trouchelle so I 'm 
not sure what to think.

Many thanks




From sahasangi at gmail.com  Tue Oct 26 07:41:01 2010
From: sahasangi at gmail.com (sangita saha)
Date: Tue, 26 Oct 2010 17:11:01 +0530
Subject: [Bioperl-l] Fwd: Need Help regarding reciprocal BLAST using BioPerl
In-Reply-To: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>
References: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>
Message-ID: <AANLkTimidEhyj=nJ4U9vwp1He45fgUg-d1LOs+dEYoq=@mail.gmail.com>

---------- Forwarded message ----------
From: sangita saha <sahasangi at gmail.com>
Date: Tue, Oct 26, 2010 at 4:32 PM
Subject: Need Help regarding reciprocal BLAST using BioPerl
To: bioperl-l at lists.open-bio.org


Hello Sir,
I have installed BioPerl and standalone BLAST in my PC.I faced problem in
doing the Reciprocal BLAST.Will anyone kindly tell me how to link between
BioPerl and Standalone BLAST ?How to use Bioperl itself to identify the
ortholog?What is the command to be used for reciprocal Blast?Since I am the
new user of it and need help to your concerned.If anybody have any
experience regarding reciprocal blast please give me a suggestion.

I will be happy to hear you from.

Thank you

With Regards,
Sangita Saha


From shalabh.sharma7 at gmail.com  Tue Oct 26 10:04:31 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 26 Oct 2010 10:04:31 -0400
Subject: [Bioperl-l] Fwd: Need Help regarding reciprocal BLAST using
	BioPerl
In-Reply-To: <AANLkTimidEhyj=nJ4U9vwp1He45fgUg-d1LOs+dEYoq=@mail.gmail.com>
References: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>
	<AANLkTimidEhyj=nJ4U9vwp1He45fgUg-d1LOs+dEYoq=@mail.gmail.com>
Message-ID: <AANLkTinhKE_KTzr3_Xftu96dyhyC4fc0QYm_2FhQ6HPU@mail.gmail.com>

Hey Sangita,
               I am not sure if bioperl has any direct command for
reciprocal blast.
But it is fairly simple, you can use all vs all blast then post process your
results in finding orthologs according to your cutoff parameters.

Other way is to use OrthoMCL :
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403725/?tool=pubmed

Also read this:
http://bioperl.org/wiki/HOWTO:PhylogeneticAnalysisPipeline
 Since you are a beginner it will help you a lot.

Hope this helps.

Shalabh
-----------------------------------
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636
On Tue, Oct 26, 2010 at 7:41 AM, sangita saha <sahasangi at gmail.com> wrote:

> ---------- Forwarded message ----------
> From: sangita saha <sahasangi at gmail.com>
> Date: Tue, Oct 26, 2010 at 4:32 PM
> Subject: Need Help regarding reciprocal BLAST using BioPerl
> To: bioperl-l at lists.open-bio.org
>
>
> Hello Sir,
> I have installed BioPerl and standalone BLAST in my PC.I faced problem in
> doing the Reciprocal BLAST.Will anyone kindly tell me how to link between
> BioPerl and Standalone BLAST ?How to use Bioperl itself to identify the
> ortholog?What is the command to be used for reciprocal Blast?Since I am the
> new user of it and need help to your concerned.If anybody have any
> experience regarding reciprocal blast please give me a suggestion.
>
> I will be happy to hear you from.
>
> Thank you
>
> With Regards,
> Sangita Saha
> _______________________________________________
> 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  Tue Oct 26 10:09:48 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 26 Oct 2010 10:09:48 -0400
Subject: [Bioperl-l] Genome Information
Message-ID: <AANLkTikLfZa-FSFXiriqPGHf63kcTgkY0+rT2Mq=7hCu@mail.gmail.com>

Hi All,
       I have thousands of taxaIds and i need to find out the following
information regarding genomes:
1) Taxonomy information
2) GC%
3) total coding genes %

I can easily find the taxonomy info by using Bio::DB::Taxonomy but for the
other two i am stuck.
Is there any way i can find this info?
I would really appreciate your help.

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


From cjfields at illinois.edu  Tue Oct 26 11:40:02 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 26 Oct 2010 10:40:02 -0500
Subject: [Bioperl-l] Fwd: Need Help regarding reciprocal BLAST using
	BioPerl
In-Reply-To: <AANLkTinhKE_KTzr3_Xftu96dyhyC4fc0QYm_2FhQ6HPU@mail.gmail.com>
References: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>
	<AANLkTimidEhyj=nJ4U9vwp1He45fgUg-d1LOs+dEYoq=@mail.gmail.com>
	<AANLkTinhKE_KTzr3_Xftu96dyhyC4fc0QYm_2FhQ6HPU@mail.gmail.com>
Message-ID: <02B10B6A-5E4A-4889-AACA-A47D8FA39E88@illinois.edu>

BioPerl does have Bio::Tools::Run::TribeMCL in BioPerl-Run, but I don't suggest using that.  mcl has a few tools in-place already within the distribition, but I personally have been using the latest version of OrthoMCL (v2), and have also started setting up a pipeline using InParanoid.

chris

On Oct 26, 2010, at 9:04 AM, shalabh sharma wrote:

> Hey Sangita,
>               I am not sure if bioperl has any direct command for
> reciprocal blast.
> But it is fairly simple, you can use all vs all blast then post process your
> results in finding orthologs according to your cutoff parameters.
> 
> Other way is to use OrthoMCL :
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403725/?tool=pubmed
> 
> Also read this:
> http://bioperl.org/wiki/HOWTO:PhylogeneticAnalysisPipeline
> Since you are a beginner it will help you a lot.
> 
> Hope this helps.
> 
> Shalabh
> -----------------------------------
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
> On Tue, Oct 26, 2010 at 7:41 AM, sangita saha <sahasangi at gmail.com> wrote:
> 
>> ---------- Forwarded message ----------
>> From: sangita saha <sahasangi at gmail.com>
>> Date: Tue, Oct 26, 2010 at 4:32 PM
>> Subject: Need Help regarding reciprocal BLAST using BioPerl
>> To: bioperl-l at lists.open-bio.org
>> 
>> 
>> Hello Sir,
>> I have installed BioPerl and standalone BLAST in my PC.I faced problem in
>> doing the Reciprocal BLAST.Will anyone kindly tell me how to link between
>> BioPerl and Standalone BLAST ?How to use Bioperl itself to identify the
>> ortholog?What is the command to be used for reciprocal Blast?Since I am the
>> new user of it and need help to your concerned.If anybody have any
>> experience regarding reciprocal blast please give me a suggestion.
>> 
>> I will be happy to hear you from.
>> 
>> Thank you
>> 
>> With Regards,
>> Sangita Saha
>> _______________________________________________
>> 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 Oct 26 12:11:05 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 26 Oct 2010 11:11:05 -0500
Subject: [Bioperl-l] Genome Information
In-Reply-To: <AANLkTikLfZa-FSFXiriqPGHf63kcTgkY0+rT2Mq=7hCu@mail.gmail.com>
References: <AANLkTikLfZa-FSFXiriqPGHf63kcTgkY0+rT2Mq=7hCu@mail.gmail.com>
Message-ID: <7A662ADB-506C-439E-9C0C-44F8DE540428@illinois.edu>

Shalabh,

I don't know if there is a quick one-step way of getting this information via NCBI w/o wrangling with query term limit magic, and even then you will be bound to whatever version of the genome is present within the database of interest.  

For instance, via eutils you can get summary information for various taxa, genomes, and genome projects using the following example code (prints the first 10 archaeal genome project summaries; set the '-db' parameter to one of 'genomeprj', 'taxonomy', 'genome'):

=================================

use Bio::DB::EUtilities;

my $term = "Archaea[ORGN]";

my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                     -db    => 'genome',
                                     -email => 'cjfields at bioperl.org',
                                     -usehistory => 'y',
                                     -term  => $term);

my $hist = $eutil->next_History || die "No history returned";

$eutil->set_parameters(-eutil   => 'esummary',
                       -history => $hist,
                       -retmax  => 10);

$eutil->print_all; # print summary info to STDOUT

=================================

GC and coding % don't appear to be stored in any of the above databases, but they are displayed via the genome overview.  You could probably use something like WWW::Mechanize to grab the summary table information displayed using the Genome UID:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=ShowDetailView&TermToSearch=25024

Just don't spam the server with a billion requests (use a timeout!) or you'll find yourself blocked.  I may pop an email to NCBI to see if this information is programmatically accessible.

chris

On Oct 26, 2010, at 9:09 AM, shalabh sharma wrote:

> Hi All,
>       I have thousands of taxaIds and i need to find out the following
> information regarding genomes:
> 1) Taxonomy information
> 2) GC%
> 3) total coding genes %
> 
> I can easily find the taxonomy info by using Bio::DB::Taxonomy but for the
> other two i am stuck.
> Is there any way i can find this info?
> I would really appreciate your help.
> 
> Thanks
> Shalabh
> -------------------------------
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
> _______________________________________________
> 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  Tue Oct 26 12:23:02 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 26 Oct 2010 12:23:02 -0400
Subject: [Bioperl-l] Genome Information
In-Reply-To: <7A662ADB-506C-439E-9C0C-44F8DE540428@illinois.edu>
References: <AANLkTikLfZa-FSFXiriqPGHf63kcTgkY0+rT2Mq=7hCu@mail.gmail.com>
	<7A662ADB-506C-439E-9C0C-44F8DE540428@illinois.edu>
Message-ID: <AANLkTin_JuaAi9Op_T9N9YVzjpOtN1hnXV=X02kPutBA@mail.gmail.com>

Hey Chris,
            This information is really useful.
Actually i was using Bio::DB::Taxonomy for taxonomy information
and Bio::DB::EUtilities to get the genome size (i didn't know that i can
just use Bio::DB::EUtilities for all the information).
I was very confused about getting GC% and coding% info but i
think WWW::Mechanize might help me out.
I really appreciate your help.

-Shalabh


On Tue, Oct 26, 2010 at 12:11 PM, Chris Fields <cjfields at illinois.edu>wrote:

> Shalabh,
>
> I don't know if there is a quick one-step way of getting this information
> via NCBI w/o wrangling with query term limit magic, and even then you will
> be bound to whatever version of the genome is present within the database of
> interest.
>
> For instance, via eutils you can get summary information for various taxa,
> genomes, and genome projects using the following example code (prints the
> first 10 archaeal genome project summaries; set the '-db' parameter to one
> of 'genomeprj', 'taxonomy', 'genome'):
>
> =================================
>
> use Bio::DB::EUtilities;
>
> my $term = "Archaea[ORGN]";
>
> my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
>                                     -db    => 'genome',
>                                     -email => 'cjfields at bioperl.org',
>                                     -usehistory => 'y',
>                                     -term  => $term);
>
> my $hist = $eutil->next_History || die "No history returned";
>
> $eutil->set_parameters(-eutil   => 'esummary',
>                       -history => $hist,
>                       -retmax  => 10);
>
> $eutil->print_all; # print summary info to STDOUT
>
> =================================
>
> GC and coding % don't appear to be stored in any of the above databases,
> but they are displayed via the genome overview.  You could probably use
> something like WWW::Mechanize to grab the summary table information
> displayed using the Genome UID:
>
>
> http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=ShowDetailView&TermToSearch=25024
>
> Just don't spam the server with a billion requests (use a timeout!) or
> you'll find yourself blocked.  I may pop an email to NCBI to see if this
> information is programmatically accessible.
>
> chris
>
> On Oct 26, 2010, at 9:09 AM, shalabh sharma wrote:
>
> > Hi All,
> >       I have thousands of taxaIds and i need to find out the following
> > information regarding genomes:
> > 1) Taxonomy information
> > 2) GC%
> > 3) total coding genes %
> >
> > I can easily find the taxonomy info by using Bio::DB::Taxonomy but for
> the
> > other two i am stuck.
> > Is there any way i can find this info?
> > I would really appreciate your help.
> >
> > Thanks
> > Shalabh
> > -------------------------------
> > Shalabh Sharma
> > Scientific Computing Professional Associate (Bioinformatics Specialist)
> > Department of Marine Sciences
> > University of Georgia
> > Athens, GA 30602-3636
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From mconte at umd.edu  Tue Oct 26 14:25:28 2010
From: mconte at umd.edu (Matthew Conte)
Date: Tue, 26 Oct 2010 14:25:28 -0400
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
Message-ID: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>

Hello,

I have a custom script for parsing out UniProt accessions from a GFF3 file
and fetching the description of the UniProt entry using Bio::DB::SwissProt
and *get_Seq_by_acc*.  This script has been working for months without any
problems until now.  The script and the format of the input files has not
changed at all.

I now get an error like this:

*------------- EXCEPTION: Bio::Root::Exception -------------*
*MSG: acc O95342 does not exist*
*STACK: Error::throw*
*STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
*STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
/Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
*STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
*-----------------------------------------------------------*

The relevant portion of my original code looks something like this:

*#!/usr/bin/perl*
*use strict;*
*use Bio::DB::SwissProt;*
*#parse out accession number*
*..*
*my $acc_num = "**O95342";*
*my $db_obj = Bio::DB::SwissProt->new;*
*my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
*
*
Looking at the documentation for Bio::DB::SwissProt, I noticed you can
specify -servertype and -hostlocation.  So I changed my code to look
something like this:

*
#!/usr/bin/perl
use strict;
use Bio::DB::SwissProt;
#parse out accession number
..
my $acc_num = "O95342";
my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
                                                           '-hostlocation'
=> 'us');
my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
*

This fixes my problem and my script works again.

The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
  Both of these urls work in a browser, though the default throws the error
in my script. Interestingly, the 'us' url has a notice that says
"*Notice:* This
page will be replaced with www.uniprot.org. Please send us your
feedback<http://www.uniprot.org/contact>
!", so hopefully it doesn't break soon as well.  Perhaps the default ebi url
was recently changed in some way?  Anyway, I figured I'd post here in case
anyone else ran into this problem.

cheers,
Matt


From grapeguy at gmail.com  Tue Oct 26 15:15:09 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Tue, 26 Oct 2010 15:15:09 -0400
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <16EDEBED-BAD4-4D57-B51B-C3234D1E8C39@illinois.edu>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
	<AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
	<16EDEBED-BAD4-4D57-B51B-C3234D1E8C39@illinois.edu>
Message-ID: <AANLkTim5_UF-AQd8HRD9v4_5SF8T5z+awWN8KAORoUGs@mail.gmail.com>

I've got my script running.

In order to support the identification of degenerate primers I had to create
a new method that would alter the IUPAC consensus. We're interested in
15-30bp sections of the consensus with high, but not 100%, conservation. We
would like to have a couple of "slices" with 2-3 mismatches to allow for the
ordering of a variety of primers.

To be completed:

   - I would *love* to hide the Clustal output that is being printed to the
   screen
   - Primer candidate identification (min_primerlength to max_primerlength)
   based on our scoring matrix
   - Primer melting temperature calculation
   - 3' Clamping identification
   - Self complementary primers

This has been a nice change from Java.

Bill


*Code*

assume: I have already read fasta input, performed Clustal align and
obtained the IUPAC consensus

sub getDegenerateConsensusIupac {
    my ($aln, $maxGapPercent, $iupacConsensus, $numSequences) = @_;

  # convert consensus into array
  my @cons = split(//, $iupacConsensus);

  # loop over the alignment "columns"
  foreach my $position ( 1 .. $aln->length() ) {
      my $consCode = $cons[$position-1];
      my %slice = getSliceHash($aln, $position);

      my $out = _applyGapPercentToConsensus ($maxGapPercent, $consCode,
$numSequences, %slice);

      # Convert consensus value new value
      if ($out ne $consCode) {
          $cons[$position-1] = $out;
      }
  }

  #rebuild consensus
  my $degenerateConsensus = join '', @cons;

  return $degenerateConsensus;
}

sub _applyGapPercentToConsensus {
    my ($maxGapPercent, $consCode, $numSequences, %slice) = @_;

        my $gapCount = $slice{'.'};

        # no gaps!
        if ($gapCount !~ /\d/) {
            return $consCode;
        }

        my $pctGap = ($gapCount / $numSequences) * 100;

        if ($pctGap > $maxGapPercent) {
            if ($consCode =~ /[A-Z]/) {
                return lc $consCode;
            }
            if ($consCode =~ /[a-z]/) {
                return '.';
            }
        }

    return $consCode;
}

sub getSliceHash{
    my ($aln, $position) = @_;

    my %sliceHash;
    foreach my $seq ($aln->each_seq) {
        my $res = $seq->subseq($position, $position);
        $sliceHash{$res}++;
    }

    return %sliceHash;
}


On Tue, Oct 19, 2010 at 11:47 AM, Chris Fields <cjfields at illinois.edu>wrote:

> Bio::SimpleAlign is the class that contains the alignment data; it does not
> generate the alignment for you.  You can use modules from BioPerl-Run that
> run ClustalW, MUSCLE, T-Coffee, etc to get a Bio::SimpleAlign instance, or
> parse the already-generated alignment output via Bio::AlignIO.
>
> From the Bio::Tools::Run::Alignment::ClustalW docs:
>
> =================================================================
>
>  #  Build a clustalw alignment factory
>  @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
>  $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
>
>  #  Pass the factory a list of sequences to be aligned.
>  $inputfilename = 't/data/cysprot.fa';
>  $aln = $factory->align($inputfilename); # $aln is a SimpleAlign object.
>
>  # ...or
>  $seq_array_ref = \@seq_array;
>
>  # where @seq_array is an array of Bio::Seq objects
>  $aln = $factory->align($seq_array_ref);
>
> =================================================================
>
> $aln is a Bio::SimpleAlign derived from ClustalW output.
>
> From Bio::SimpleAlign (note the use of Bio::AlignIO):
>
> =================================================================
>
>  # Use Bio::AlignIO to read in the alignment
>  $str = Bio::AlignIO->new(-file => 't/data/testaln.pfam');
>  $aln = $str->next_aln();
>
>  # Describe
>  print $aln->length;
>  print $aln->num_residues;
>  print $aln->is_flush;
>  print $aln->num_sequences;
>  print $aln->score;
>  print $aln->percentage_identity;
>  print $aln->consensus_string(50);
>
> =================================================================
>
> Note the consensus_string() method:
>
>  Title     : consensus_string
>  Usage     : $str = $ali->consensus_string($threshold_percent)
>  Function  : Makes a strict consensus
>  Returns   : Consensus string
>  Argument  : Optional treshold ranging from 0 to 100.
>             The consensus residue has to appear at least threshold %
>             of the sequences at a given location, otherwise a '?'
>             character will be placed at that location.
>             (Default value = 0%)
>
> chris
>
> On Oct 18, 2010, at 7:02 PM, Bill Stephens wrote:
>
> > So, I've got the SimpleAlign running. It looks like it's running the
> > alignment based upon the input sequence location only (first residue from
> > each sequence).  This is not what I need.
> >
> > I'm back to to clustal, tcoffee or dalign.
> >
> > Bill
> >
> > On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:
> >
> >> Hi, Bill,
> >>
> >> You may consider to use consensus_iupac or consensus_string methods in
> >> Bio::SimpleAlign to generate consensus sequence.
> >>
> >> Cheers,
> >> Jun Yin
> >> Ph.D. student in U.C.D.
> >>
> >> Bioinformatics Laboratory
> >> Conway Institute
> >> University College Dublin
> >>
> >> -----Original Message-----
> >> From: bioperl-l-bounces at lists.open-bio.org
> >> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
> >> Sent: Monday, October 18, 2010 3:55 PM
> >> To: Bill Stephens
> >> Cc: bioperl-l at bioperl.org
> >> Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
> >> alignment
> >>
> >> Bill,
> >>
> >> Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
> >> replacement for the older Pise tools).  The Pise modules were in
> >> BioPerl-Run, but they were deprecated a few years ago and removed from
> the
> >> latest BioPerl-Run releases b/c the remote service is no longer active;
> >> there is no Perl-based replacement for Mobyle interaction.
> >>
> >> Have you thought about just using the functionality within the
> >> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there
> >> are
> >> methods in place to do that.
> >>
> >> chris
> >>
> >> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
> >>
> >>> All,
> >>>
> >>> I'm in my first week with bioperl for a class project (although I've
> used
> >>> Perl for years). I've successfully run a clustal alignment of several
> DNA
> >>> sequences to produce the aln and dnd files. Now I would like to
> generate
> >> a
> >>> consensus sequence from the alignment.  I see that Pise Cons does this
> >>> satisfactorily on my example data (
> >>> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However,
> >> I'm
> >>> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
> >> distribution
> >>> that I installed.
> >>>
> >>> Is this another module that I need to install separately?
> >>>
> >>> "cpan[2]> m /Pise/
> >>> Module    Bio::Tools::Run::AnalysisFactory::Pise
> >>> (BIRNEY/bioperl-run-1.4.tar.gz)
> >>> Module    Bio::Tools::Run::PiseApplication
> >> (BIRNEY/bioperl-run-1.4.tar.gz)"
> >>>
> >>> Bill S.
> >>> _______________________________________________
> >>> 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
> >>
> >> __________ Information from ESET Smart Security, version of virus
> signature
> >> database 5377 (20100818) __________
> >>
> >> The message was checked by ESET Smart Security.
> >>
> >> http://www.eset.com
> >>
> >>
> >>
> >>
> >> __________ Information from ESET Smart Security, version of virus
> signature
> >> database 5377 (20100818) __________
> >>
> >> The message was checked by ESET Smart Security.
> >>
> >> http://www.eset.com
> >>
> >>
> >>
> > _______________________________________________
> > 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 Oct 26 18:02:03 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 26 Oct 2010 17:02:03 -0500
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
Message-ID: <FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>

The default was changed recently in github to 'expasy'.  My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.

chris

On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:

> Hello,
> 
> I have a custom script for parsing out UniProt accessions from a GFF3 file
> and fetching the description of the UniProt entry using Bio::DB::SwissProt
> and *get_Seq_by_acc*.  This script has been working for months without any
> problems until now.  The script and the format of the input files has not
> changed at all.
> 
> I now get an error like this:
> 
> *------------- EXCEPTION: Bio::Root::Exception -------------*
> *MSG: acc O95342 does not exist*
> *STACK: Error::throw*
> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
> *-----------------------------------------------------------*
> 
> The relevant portion of my original code looks something like this:
> 
> *#!/usr/bin/perl*
> *use strict;*
> *use Bio::DB::SwissProt;*
> *#parse out accession number*
> *..*
> *my $acc_num = "**O95342";*
> *my $db_obj = Bio::DB::SwissProt->new;*
> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
> *
> *
> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
> specify -servertype and -hostlocation.  So I changed my code to look
> something like this:
> 
> *
> #!/usr/bin/perl
> use strict;
> use Bio::DB::SwissProt;
> #parse out accession number
> ..
> my $acc_num = "O95342";
> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>                                                           '-hostlocation'
> => 'us');
> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
> *
> 
> This fixes my problem and my script works again.
> 
> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>  Both of these urls work in a browser, though the default throws the error
> in my script. Interestingly, the 'us' url has a notice that says
> "*Notice:* This
> page will be replaced with www.uniprot.org. Please send us your
> feedback<http://www.uniprot.org/contact>
> !", so hopefully it doesn't break soon as well.  Perhaps the default ebi url
> was recently changed in some way?  Anyway, I figured I'd post here in case
> anyone else ran into this problem.
> 
> cheers,
> Matt
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From sahasangi at gmail.com  Tue Oct 26 07:02:04 2010
From: sahasangi at gmail.com (sangita saha)
Date: Tue, 26 Oct 2010 16:32:04 +0530
Subject: [Bioperl-l] Need Help regarding reciprocal BLAST using BioPerl
Message-ID: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>

Hello Sir,
I have installed BioPerl and standalone BLAST in my PC.I faced problem in
doing the Reciprocal BLAST.Will anyone kindly tell me how to link between
BioPerl and Standalone BLAST ?How to use Bioperl itself to identify the
ortholog?What is the command to be used for reciprocal Blast?Since I am the
new user of it and need help to your concerned.If anybody have any
experience regarding reciprocal blast please give me a suggestion.

I will be happy to hear you from.

Thank you

With Regards,
Sangita Saha


From ameet at eecs.berkeley.edu  Tue Oct 26 19:51:17 2010
From: ameet at eecs.berkeley.edu (Ameet Talwalkar)
Date: Tue, 26 Oct 2010 16:51:17 -0700
Subject: [Bioperl-l] TreeIO for NHX format
Message-ID: <AANLkTim2hsO=rRCfa5H4Uu7waF7iVbJo9NDfTq2q8yrN@mail.gmail.com>

Hi,

I would like to use BIOPerl to convert a tree in PhyloXML format to NHX
format, and I have tried the following code:

*use Bio::TreeIO;

my $input = new Bio::TreeIO(-file   => "reconciled_test.xml",
                            -format => "phyloxml");
my $treeout = new Bio::TreeIO(-fh => \*STDOUT,
                              -format => 'nhx');

while (my $tree = $input->next_tree) {
  $treeout->write_tree($tree);
}
*

The output is indeed in NHX format, but the tags (in particular I have a
duplication / speciation tag) does not appear in the output.  Am I doing
something wrong?

Thanks.

-Ameet


From bill_zt at sina.com  Tue Oct 26 21:08:11 2010
From: bill_zt at sina.com (Tao Zhu)
Date: Wed, 27 Oct 2010 09:08:11 +0800
Subject: [Bioperl-l] A problem on BioPerl module Bio::DB::Fasta
Message-ID: <1288141691.2377.1.camel@ubuntu>

Hello, everyone!

I hope it isn't true, but I really find a problem on BioPerl module
Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
Osborne wrote that we could catch sub-sequences like this,


use Bio::DB::Fasta;
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
$db = Bio::DB::Fasta->new($file);
$seqobj = $db->get_Seq_by_id($id,$start,$end);
print $seqobj->seq,"\n";


In fact it didn't work. I only got the whole sequence after running the
script. Therefore I referred to the Pdoc documentation and realized it
should be written as follows,


use Bio::DB::Fasta;
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
$db = Bio::DB::Fasta->new($file);
$seq = $db->seq($id,$start,$end);
print $seq,"\n";


Then it would return the sub-sequence from 6 to 10.

Probably Dr Osborne had made a mistake when writing the use-guide
HOWTO:Beginners.


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
email: tzhu at mail.bnu.edu.cn



From cjfields at illinois.edu  Tue Oct 26 23:41:40 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 26 Oct 2010 22:41:40 -0500
Subject: [Bioperl-l] TreeIO for NHX format
In-Reply-To: <AANLkTim2hsO=rRCfa5H4Uu7waF7iVbJo9NDfTq2q8yrN@mail.gmail.com>
References: <AANLkTim2hsO=rRCfa5H4Uu7waF7iVbJo9NDfTq2q8yrN@mail.gmail.com>
Message-ID: <55546218-9878-421F-B4A7-FADA7760C374@illinois.edu>

Ameet,

You should file this as a bug, along with example code and data (http://bugzilla.open-bio.org/).  It's possible the tags are parsed but the NHX writer is not finding the data somehow.

chris

On Oct 26, 2010, at 6:51 PM, Ameet Talwalkar wrote:

> Hi,
> 
> I would like to use BIOPerl to convert a tree in PhyloXML format to NHX
> format, and I have tried the following code:
> 
> *use Bio::TreeIO;
> 
> my $input = new Bio::TreeIO(-file   => "reconciled_test.xml",
>                            -format => "phyloxml");
> my $treeout = new Bio::TreeIO(-fh => \*STDOUT,
>                              -format => 'nhx');
> 
> while (my $tree = $input->next_tree) {
>  $treeout->write_tree($tree);
> }
> *
> 
> The output is indeed in NHX format, but the tags (in particular I have a
> duplication / speciation tag) does not appear in the output.  Am I doing
> something wrong?
> 
> Thanks.
> 
> -Ameet
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hamish.mcwilliam at bioinfo-user.org.uk  Wed Oct 27 06:32:22 2010
From: hamish.mcwilliam at bioinfo-user.org.uk (Hamish McWilliam)
Date: Wed, 27 Oct 2010 11:32:22 +0100
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
	<FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
Message-ID: <AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>

Hi Chris,

The dbfetch service at EBI has changed, see
http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010. On
of the effects of this is the main endpoint used for dbfetch has
changed from http://www.ebi.ac.uk/cgi-bin/dbfetch to
http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. With the old endpoints
being supported via a HTTP redirect. It looks like the
Bio::DB::SwissProt module does not support redirects and is thus
getting an empty document back from the service. Looks like the URL
used in the code needs to be updated.

All the best,

Hamish

On 26 October 2010 23:02, Chris Fields <cjfields at illinois.edu> wrote:
> The default was changed recently in github to 'expasy'. ?My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.
>
> chris
>
> On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:
>
>> Hello,
>>
>> I have a custom script for parsing out UniProt accessions from a GFF3 file
>> and fetching the description of the UniProt entry using Bio::DB::SwissProt
>> and *get_Seq_by_acc*. ?This script has been working for months without any
>> problems until now. ?The script and the format of the input files has not
>> changed at all.
>>
>> I now get an error like this:
>>
>> *------------- EXCEPTION: Bio::Root::Exception -------------*
>> *MSG: acc O95342 does not exist*
>> *STACK: Error::throw*
>> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
>> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
>> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
>> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
>> *-----------------------------------------------------------*
>>
>> The relevant portion of my original code looks something like this:
>>
>> *#!/usr/bin/perl*
>> *use strict;*
>> *use Bio::DB::SwissProt;*
>> *#parse out accession number*
>> *..*
>> *my $acc_num = "**O95342";*
>> *my $db_obj = Bio::DB::SwissProt->new;*
>> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
>> *
>> *
>> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
>> specify -servertype and -hostlocation. ?So I changed my code to look
>> something like this:
>>
>> *
>> #!/usr/bin/perl
>> use strict;
>> use Bio::DB::SwissProt;
>> #parse out accession number
>> ..
>> my $acc_num = "O95342";
>> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '-hostlocation'
>> => 'us');
>> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
>> *
>>
>> This fixes my problem and my script works again.
>>
>> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
>> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>> ?Both of these urls work in a browser, though the default throws the error
>> in my script. Interestingly, the 'us' url has a notice that says
>> "*Notice:* This
>> page will be replaced with www.uniprot.org. Please send us your
>> feedback<http://www.uniprot.org/contact>
>> !", so hopefully it doesn't break soon as well. ?Perhaps the default ebi url
>> was recently changed in some way? ?Anyway, I figured I'd post here in case
>> anyone else ran into this problem.
>>
>> cheers,
>> Matt
>> _______________________________________________
>> 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
>



-- 
----
"Saying the internet has changed dramatically over the last five years
is clich? ? the internet is always changing dramatically" - Craig
Labovitz, Arbor Networks.



From cjfields at illinois.edu  Wed Oct 27 10:51:22 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 27 Oct 2010 09:51:22 -0500
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
	<FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
	<AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>
Message-ID: <FAB70AF7-B56C-4DEA-BF4D-AA9F001D6E9F@illinois.edu>

Hamish,

Thanks, but I already caught that and fixed it in main trunk where appropriate yesterday (specifically, both Bio::DB::SwissProt and Bio::DB::BioFetch).  

chris

On Oct 27, 2010, at 5:32 AM, Hamish McWilliam wrote:

> Hi Chris,
> 
> The dbfetch service at EBI has changed, see
> http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010. On
> of the effects of this is the main endpoint used for dbfetch has
> changed from http://www.ebi.ac.uk/cgi-bin/dbfetch to
> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. With the old endpoints
> being supported via a HTTP redirect. It looks like the
> Bio::DB::SwissProt module does not support redirects and is thus
> getting an empty document back from the service. Looks like the URL
> used in the code needs to be updated.
> 
> All the best,
> 
> Hamish
> 
> On 26 October 2010 23:02, Chris Fields <cjfields at illinois.edu> wrote:
>> The default was changed recently in github to 'expasy'.  My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.
>> 
>> chris
>> 
>> On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:
>> 
>>> Hello,
>>> 
>>> I have a custom script for parsing out UniProt accessions from a GFF3 file
>>> and fetching the description of the UniProt entry using Bio::DB::SwissProt
>>> and *get_Seq_by_acc*.  This script has been working for months without any
>>> problems until now.  The script and the format of the input files has not
>>> changed at all.
>>> 
>>> I now get an error like this:
>>> 
>>> *------------- EXCEPTION: Bio::Root::Exception -------------*
>>> *MSG: acc O95342 does not exist*
>>> *STACK: Error::throw*
>>> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
>>> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
>>> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
>>> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
>>> *-----------------------------------------------------------*
>>> 
>>> The relevant portion of my original code looks something like this:
>>> 
>>> *#!/usr/bin/perl*
>>> *use strict;*
>>> *use Bio::DB::SwissProt;*
>>> *#parse out accession number*
>>> *..*
>>> *my $acc_num = "**O95342";*
>>> *my $db_obj = Bio::DB::SwissProt->new;*
>>> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
>>> *
>>> *
>>> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
>>> specify -servertype and -hostlocation.  So I changed my code to look
>>> something like this:
>>> 
>>> *
>>> #!/usr/bin/perl
>>> use strict;
>>> use Bio::DB::SwissProt;
>>> #parse out accession number
>>> ..
>>> my $acc_num = "O95342";
>>> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>>>                                                           '-hostlocation'
>>> => 'us');
>>> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
>>> *
>>> 
>>> This fixes my problem and my script works again.
>>> 
>>> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
>>> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>>>  Both of these urls work in a browser, though the default throws the error
>>> in my script. Interestingly, the 'us' url has a notice that says
>>> "*Notice:* This
>>> page will be replaced with www.uniprot.org. Please send us your
>>> feedback<http://www.uniprot.org/contact>
>>> !", so hopefully it doesn't break soon as well.  Perhaps the default ebi url
>>> was recently changed in some way?  Anyway, I figured I'd post here in case
>>> anyone else ran into this problem.
>>> 
>>> cheers,
>>> Matt
>>> _______________________________________________
>>> 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
>> 
> 
> 
> 
> -- 
> ----
> "Saying the internet has changed dramatically over the last five years
> is clich? ? the internet is always changing dramatically" - Craig
> Labovitz, Arbor Networks.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hamish.mcwilliam at bioinfo-user.org.uk  Wed Oct 27 11:34:09 2010
From: hamish.mcwilliam at bioinfo-user.org.uk (Hamish McWilliam)
Date: Wed, 27 Oct 2010 16:34:09 +0100
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <FAB70AF7-B56C-4DEA-BF4D-AA9F001D6E9F@illinois.edu>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
	<FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
	<AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>
	<FAB70AF7-B56C-4DEA-BF4D-AA9F001D6E9F@illinois.edu>
Message-ID: <AANLkTik0tKy2B1W8Avd7ap=Fg4prR3p0w9OXpka5PXHP@mail.gmail.com>

Hi Chris,

Although they handle the redirect, the other modules which use dbfetch
should probably have the URLs updated too:

Bio::DB::Biblio::biofetch
Bio::DB::EMBL
Bio::DB::RefSeq

Hamish

On 27 October 2010 15:51, Chris Fields <cjfields at illinois.edu> wrote:
> Hamish,
>
> Thanks, but I already caught that and fixed it in main trunk where appropriate yesterday (specifically, both Bio::DB::SwissProt and Bio::DB::BioFetch).
>
> chris
>
> On Oct 27, 2010, at 5:32 AM, Hamish McWilliam wrote:
>
>> Hi Chris,
>>
>> The dbfetch service at EBI has changed, see
>> http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010. On
>> of the effects of this is the main endpoint used for dbfetch has
>> changed from http://www.ebi.ac.uk/cgi-bin/dbfetch to
>> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. With the old endpoints
>> being supported via a HTTP redirect. It looks like the
>> Bio::DB::SwissProt module does not support redirects and is thus
>> getting an empty document back from the service. Looks like the URL
>> used in the code needs to be updated.
>>
>> All the best,
>>
>> Hamish
>>
>> On 26 October 2010 23:02, Chris Fields <cjfields at illinois.edu> wrote:
>>> The default was changed recently in github to 'expasy'. ?My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.
>>>
>>> chris
>>>
>>> On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:
>>>
>>>> Hello,
>>>>
>>>> I have a custom script for parsing out UniProt accessions from a GFF3 file
>>>> and fetching the description of the UniProt entry using Bio::DB::SwissProt
>>>> and *get_Seq_by_acc*. ?This script has been working for months without any
>>>> problems until now. ?The script and the format of the input files has not
>>>> changed at all.
>>>>
>>>> I now get an error like this:
>>>>
>>>> *------------- EXCEPTION: Bio::Root::Exception -------------*
>>>> *MSG: acc O95342 does not exist*
>>>> *STACK: Error::throw*
>>>> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
>>>> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
>>>> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
>>>> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
>>>> *-----------------------------------------------------------*
>>>>
>>>> The relevant portion of my original code looks something like this:
>>>>
>>>> *#!/usr/bin/perl*
>>>> *use strict;*
>>>> *use Bio::DB::SwissProt;*
>>>> *#parse out accession number*
>>>> *..*
>>>> *my $acc_num = "**O95342";*
>>>> *my $db_obj = Bio::DB::SwissProt->new;*
>>>> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
>>>> *
>>>> *
>>>> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
>>>> specify -servertype and -hostlocation. ?So I changed my code to look
>>>> something like this:
>>>>
>>>> *
>>>> #!/usr/bin/perl
>>>> use strict;
>>>> use Bio::DB::SwissProt;
>>>> #parse out accession number
>>>> ..
>>>> my $acc_num = "O95342";
>>>> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '-hostlocation'
>>>> => 'us');
>>>> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
>>>> *
>>>>
>>>> This fixes my problem and my script works again.
>>>>
>>>> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
>>>> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>>>> ?Both of these urls work in a browser, though the default throws the error
>>>> in my script. Interestingly, the 'us' url has a notice that says
>>>> "*Notice:* This
>>>> page will be replaced with www.uniprot.org. Please send us your
>>>> feedback<http://www.uniprot.org/contact>
>>>> !", so hopefully it doesn't break soon as well. ?Perhaps the default ebi url
>>>> was recently changed in some way? ?Anyway, I figured I'd post here in case
>>>> anyone else ran into this problem.
>>>>
>>>> cheers,
>>>> Matt
>>>> _______________________________________________
>>>> 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
>>>
>>
>>
>>
>> --
>> ----
>> "Saying the internet has changed dramatically over the last five years
>> is clich? ? the internet is always changing dramatically" - Craig
>> Labovitz, Arbor Networks.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
----
"Saying the internet has changed dramatically over the last five years
is clich? ? the internet is always changing dramatically" - Craig
Labovitz, Arbor Networks.



From cjfields at illinois.edu  Wed Oct 27 12:20:48 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 27 Oct 2010 11:20:48 -0500
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <AANLkTik0tKy2B1W8Avd7ap=Fg4prR3p0w9OXpka5PXHP@mail.gmail.com>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
	<FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
	<AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>
	<FAB70AF7-B56C-4DEA-BF4D-AA9F001D6E9F@illinois.edu>
	<AANLkTik0tKy2B1W8Avd7ap=Fg4prR3p0w9OXpka5PXHP@mail.gmail.com>
Message-ID: <BC746329-82A8-4215-BE8D-4CCDE6911FDB@illinois.edu>

Hamish,

Ah, missed those!  That's what I get for relying on tests alone.  Thanks for pointing them out; I'll double-check the various distributions for more, just in case.

chris

On Oct 27, 2010, at 10:34 AM, Hamish McWilliam wrote:

> Hi Chris,
> 
> Although they handle the redirect, the other modules which use dbfetch
> should probably have the URLs updated too:
> 
> Bio::DB::Biblio::biofetch
> Bio::DB::EMBL
> Bio::DB::RefSeq
> 
> Hamish
> 
> On 27 October 2010 15:51, Chris Fields <cjfields at illinois.edu> wrote:
>> Hamish,
>> 
>> Thanks, but I already caught that and fixed it in main trunk where appropriate yesterday (specifically, both Bio::DB::SwissProt and Bio::DB::BioFetch).
>> 
>> chris
>> 
>> On Oct 27, 2010, at 5:32 AM, Hamish McWilliam wrote:
>> 
>>> Hi Chris,
>>> 
>>> The dbfetch service at EBI has changed, see
>>> http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010. On
>>> of the effects of this is the main endpoint used for dbfetch has
>>> changed from http://www.ebi.ac.uk/cgi-bin/dbfetch to
>>> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. With the old endpoints
>>> being supported via a HTTP redirect. It looks like the
>>> Bio::DB::SwissProt module does not support redirects and is thus
>>> getting an empty document back from the service. Looks like the URL
>>> used in the code needs to be updated.
>>> 
>>> All the best,
>>> 
>>> Hamish
>>> 
>>> On 26 October 2010 23:02, Chris Fields <cjfields at illinois.edu> wrote:
>>>> The default was changed recently in github to 'expasy'.  My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.
>>>> 
>>>> chris
>>>> 
>>>> On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:
>>>> 
>>>>> Hello,
>>>>> 
>>>>> I have a custom script for parsing out UniProt accessions from a GFF3 file
>>>>> and fetching the description of the UniProt entry using Bio::DB::SwissProt
>>>>> and *get_Seq_by_acc*.  This script has been working for months without any
>>>>> problems until now.  The script and the format of the input files has not
>>>>> changed at all.
>>>>> 
>>>>> I now get an error like this:
>>>>> 
>>>>> *------------- EXCEPTION: Bio::Root::Exception -------------*
>>>>> *MSG: acc O95342 does not exist*
>>>>> *STACK: Error::throw*
>>>>> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
>>>>> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
>>>>> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
>>>>> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
>>>>> *-----------------------------------------------------------*
>>>>> 
>>>>> The relevant portion of my original code looks something like this:
>>>>> 
>>>>> *#!/usr/bin/perl*
>>>>> *use strict;*
>>>>> *use Bio::DB::SwissProt;*
>>>>> *#parse out accession number*
>>>>> *..*
>>>>> *my $acc_num = "**O95342";*
>>>>> *my $db_obj = Bio::DB::SwissProt->new;*
>>>>> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
>>>>> *
>>>>> *
>>>>> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
>>>>> specify -servertype and -hostlocation.  So I changed my code to look
>>>>> something like this:
>>>>> 
>>>>> *
>>>>> #!/usr/bin/perl
>>>>> use strict;
>>>>> use Bio::DB::SwissProt;
>>>>> #parse out accession number
>>>>> ..
>>>>> my $acc_num = "O95342";
>>>>> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>>>>>                                                           '-hostlocation'
>>>>> => 'us');
>>>>> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
>>>>> *
>>>>> 
>>>>> This fixes my problem and my script works again.
>>>>> 
>>>>> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
>>>>> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>>>>>  Both of these urls work in a browser, though the default throws the error
>>>>> in my script. Interestingly, the 'us' url has a notice that says
>>>>> "*Notice:* This
>>>>> page will be replaced with www.uniprot.org. Please send us your
>>>>> feedback<http://www.uniprot.org/contact>
>>>>> !", so hopefully it doesn't break soon as well.  Perhaps the default ebi url
>>>>> was recently changed in some way?  Anyway, I figured I'd post here in case
>>>>> anyone else ran into this problem.
>>>>> 
>>>>> cheers,
>>>>> Matt
>>>>> _______________________________________________
>>>>> 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
>>>> 
>>> 
>>> 
>>> 
>>> --
>>> ----
>>> "Saying the internet has changed dramatically over the last five years
>>> is clich? ? the internet is always changing dramatically" - Craig
>>> Labovitz, Arbor Networks.
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> ----
> "Saying the internet has changed dramatically over the last five years
> is clich? ? the internet is always changing dramatically" - Craig
> Labovitz, Arbor Networks.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From maizemu at gmail.com  Wed Oct 27 12:53:26 2010
From: maizemu at gmail.com (Christopher Bottoms)
Date: Wed, 27 Oct 2010 11:53:26 -0500
Subject: [Bioperl-l] how to download PDB files using Bioperl script
In-Reply-To: <01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
Message-ID: <AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>

Ashwani,

Do you need to download the files once or does this need to be automated?

If you just need to do it once, check out
http://www.rcsb.org/pdb/download/download.do for downloading multiple
files.

If you need to automate the process, let me know and I'll help you
figure it out. The easiest way I can think of, which I used to do, is
downloading them from the ftp site.

Sincerely,

Christopher Bottoms

On Fri, Oct 22, 2010 at 11:12 AM, Jun Yin <jun.yin at ucd.ie> wrote:
> Hi, Ashwani,
>
> I havenot found any module in BioPerl for downloading PDB files, though
> Bio::Structure::IO::pdb can parse PDB files.
>
> However, PDB provides RESTful service
> (http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
> batch downloading the proteins.
>
> Cheers,
> Jun Yin
> Ph.D.?student in U.C.D.
>
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
> Sent: Thursday, October 21, 2010 9:39 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] how to download PDB files using Bioperl script
>
> Hi All,
>
>
> I have around 150 pdb file names and I need to download them from Protein
> Data Bank. I wonder if someone could tell me how to do it by using Bioperl.
>
> Thanks in advance.
>
> Regards,
> Ashwani
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>
> _______________________________________________
> 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 Oct 27 14:40:02 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 27 Oct 2010 13:40:02 -0500
Subject: [Bioperl-l] A problem on BioPerl module Bio::DB::Fasta
In-Reply-To: <1288141691.2377.1.camel@ubuntu>
References: <1288141691.2377.1.camel@ubuntu>
Message-ID: <25CA46EE-B73B-4C27-9CA6-28BED05C7AEB@illinois.edu>

Tao,

I've made that correction to the HOWTO.  In the future, if you see an error on the wiki you are free to make changes to correct them.  

Thanks!

chris

On Oct 26, 2010, at 8:08 PM, Tao Zhu wrote:

> Hello, everyone!
> 
> I hope it isn't true, but I really find a problem on BioPerl module
> Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
> Osborne wrote that we could catch sub-sequences like this,
> 
> 
> use Bio::DB::Fasta;
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> $db = Bio::DB::Fasta->new($file);
> $seqobj = $db->get_Seq_by_id($id,$start,$end);
> print $seqobj->seq,"\n";
> 
> 
> In fact it didn't work. I only got the whole sequence after running the
> script. Therefore I referred to the Pdoc documentation and realized it
> should be written as follows,
> 
> 
> use Bio::DB::Fasta;
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> $db = Bio::DB::Fasta->new($file);
> $seq = $db->seq($id,$start,$end);
> print $seq,"\n";
> 
> 
> Then it would return the sub-sequence from 6 to 10.
> 
> Probably Dr Osborne had made a mistake when writing the use-guide
> HOWTO:Beginners.
> 
> 
> -- 
> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> 100875, China
> email: tzhu at mail.bnu.edu.cn
> 
> _______________________________________________
> 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 Oct 28 11:10:25 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 28 Oct 2010 10:10:25 -0500
Subject: [Bioperl-l] A problem on BioPerl module Bio::DB::Fasta
In-Reply-To: <1288251535.4408.18.camel@ubuntu>
References: <1288141691.2377.1.camel@ubuntu>
	<25CA46EE-B73B-4C27-9CA6-28BED05C7AEB@illinois.edu>
	<1288251535.4408.18.camel@ubuntu>
Message-ID: <C3335F92-724B-48C7-A05F-17AF27B244D9@illinois.edu>

Very true, didn't catch that; I was just making the correction you mentioned.  That's what happens when I don't have enough coffee!

chris

On Oct 28, 2010, at 2:38 AM, Tao Zhu wrote:

> Dear Chris,
> 
> Thank you for correcting the HOWTO, but in fact it hasn't been
> completely correct yet. I've made some changes to the passage again like
> this,
> 
> ************************
> use Bio::DB::Fasta; 
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
> $db = Bio::DB::Fasta->new($file);
> $seq = $db->seq($id,$start,$end);
> print $seq,"\n";
> ************************
> 
> The original passage is like this,
> ************************
> use Bio::DB::Fasta;
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
> $db = Bio::DB::Fasta->new($file);
> $seqobj = $db->seq($id,$start,$end); 
> print $seqobj->seq;
> ************************
> 
> We should notice that if method '$db->seq()' is called, then it would
> return a simple string, not a Bio::Seq object.
> 
> 
> 
> ? 2010-10-27?? 13:40 -0500?Chris Fields???
>> Tao,
>> 
>> I've made that correction to the HOWTO.  In the future, if you see an error on the wiki you are free to make changes to correct them.  
>> 
>> Thanks!
>> 
>> chris
>> 
>> On Oct 26, 2010, at 8:08 PM, Tao Zhu wrote:
>> 
>>> Hello, everyone!
>>> 
>>> I hope it isn't true, but I really find a problem on BioPerl module
>>> Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
>>> Osborne wrote that we could catch sub-sequences like this,
>>> 
>>> 
>>> use Bio::DB::Fasta;
>>> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
>>> $db = Bio::DB::Fasta->new($file);
>>> $seqobj = $db->get_Seq_by_id($id,$start,$end);
>>> print $seqobj->seq,"\n";
>>> 
>>> 
>>> In fact it didn't work. I only got the whole sequence after running the
>>> script. Therefore I referred to the Pdoc documentation and realized it
>>> should be written as follows,
>>> 
>>> 
>>> use Bio::DB::Fasta;
>>> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
>>> $db = Bio::DB::Fasta->new($file);
>>> $seq = $db->seq($id,$start,$end);
>>> print $seq,"\n";
>>> 
>>> 
>>> Then it would return the sub-sequence from 6 to 10.
>>> 
>>> Probably Dr Osborne had made a mistake when writing the use-guide
>>> HOWTO:Beginners.
>>> 
>>> 
>>> -- 
>>> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
>>> 100875, China
>>> email: tzhu at mail.bnu.edu.cn
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 
> 
> 




From Seidl-Michael at t-online.de  Wed Oct 27 04:58:03 2010
From: Seidl-Michael at t-online.de (seidl-michael)
Date: Wed, 27 Oct 2010 10:58:03 +0200
Subject: [Bioperl-l] Tiling of hsps using Bioperl
Message-ID: <041D7AC1-99F2-4760-B709-29FE138E05FA@web.de>

Hi everyone,

I have a question about the Bio::Search::Tiling::MapTiling  package. I  
want to get the range of my tilled hsps using the "range" function.  
The reported range is, unfortunately, not what I would expect while  
looking at my data:

 >A
          Length = 1967

Score = 70.1 bits (170), Expect = 1e-11,   Method: Compositional  
matrix adjust.
Identities = 47/110 (42%), Positives = 66/110 (60%), Gaps = 29/110 (26%)

Query: 358   
EAARQEEVARELEVKSSMATKIQSHWRGMAARSEVSTLRAEAAAAEAAASEAARQEEVAR 417
            E ARQEE+AR+ E +S+MATKIQSHWRG  ARSEV+++R+ AA A+        Q +++R
Sbjct: 1344 ELARQEELARQAEAESAMATKIQSHWRGSVARSEVASMRS-AAIADV------- 
QTQLSR 1395

Query: 418  QEEDARRKEAARQEEVARELEVKSSMATKIQSHWRGTAARSEVSTLRAEA 467
                                 +++  A +IQS WRG  AR +V++LRAEA
Sbjct: 1396 ---------------------IENLTAVRIQSRWRGVLARVKVASLRAEA 1424



Score = 57.8 bits (138), Expect = 7e-08,   Method: Compositional  
matrix adjust.
Identities = 28/39 (71%), Positives = 33/39 (84%)

Query: 358  EAARQEEVARELEVKSSMATKIQSHWRGMAARSEVSTLR 396
            E ARQEE+AR+ E +S+MATKIQSHWRG  ARSEV+ LR
Sbjct: 1222 ELARQEELARQAEAESAMATKIQSHWRGSVARSEVAVLR 1260



Score = 47.4 bits (111), Expect = 1e-04,   Method: Compositional  
matrix adjust.
Identities = 43/115 (37%), Positives = 58/115 (50%), Gaps = 29/115 (25%)

Query: 299  
RELEVKSSMATKIQSHWRGMAARSEVSTLRAEAAAAEAAASEAARQEEVARQEEDARRKE 358
           +E + K+ MAT+IQS  RG+ AR        EA + + AASE        R + + RR++
Sbjct: 433 KETQRKNDMATQIQSGVRGVIAR--------EAYSEKLAASERI---- 
AIRIQTEFRRRQ 480

Query: 359 AARQEEVARE-----------------LEVKSSMATKIQSHWRGMAARSEVSTLR 396
           A +Q E  R+                  +   S ATKIQSHWRG  ARSEV+ LR
Sbjct: 481 AQKQLEALRQQLQREQTCAVVIQKILSSDSNESAATKIQSHWRGSVARSEVAVLR 535

I would expect to get [433,1424] when using:

my $tiling = Bio::Search::Tiling::MapTiling->new($hit);
my @range = $tiling->range('subject');

Instead my array includes [1344,535]. Do I have a conceptional problem  
with the function of "range" or is there something wired happening?

Thanks a lot for any help and suggestions,

Michael


From tzhu at mail.bnu.edu.cn  Thu Oct 28 03:38:55 2010
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Thu, 28 Oct 2010 15:38:55 +0800
Subject: [Bioperl-l] A problem on BioPerl module Bio::DB::Fasta
In-Reply-To: <25CA46EE-B73B-4C27-9CA6-28BED05C7AEB@illinois.edu>
References: <1288141691.2377.1.camel@ubuntu>
	<25CA46EE-B73B-4C27-9CA6-28BED05C7AEB@illinois.edu>
Message-ID: <1288251535.4408.18.camel@ubuntu>

Dear Chris,

Thank you for correcting the HOWTO, but in fact it hasn't been
completely correct yet. I've made some changes to the passage again like
this,

************************
use Bio::DB::Fasta; 
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
$db = Bio::DB::Fasta->new($file);
$seq = $db->seq($id,$start,$end);
print $seq,"\n";
************************

The original passage is like this,
************************
use Bio::DB::Fasta;
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
$db = Bio::DB::Fasta->new($file);
$seqobj = $db->seq($id,$start,$end); 
print $seqobj->seq;
************************

We should notice that if method '$db->seq()' is called, then it would
return a simple string, not a Bio::Seq object.



? 2010-10-27?? 13:40 -0500?Chris Fields???
> Tao,
> 
> I've made that correction to the HOWTO.  In the future, if you see an error on the wiki you are free to make changes to correct them.  
> 
> Thanks!
> 
> chris
> 
> On Oct 26, 2010, at 8:08 PM, Tao Zhu wrote:
> 
> > Hello, everyone!
> > 
> > I hope it isn't true, but I really find a problem on BioPerl module
> > Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
> > Osborne wrote that we could catch sub-sequences like this,
> > 
> > 
> > use Bio::DB::Fasta;
> > ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> > $db = Bio::DB::Fasta->new($file);
> > $seqobj = $db->get_Seq_by_id($id,$start,$end);
> > print $seqobj->seq,"\n";
> > 
> > 
> > In fact it didn't work. I only got the whole sequence after running the
> > script. Therefore I referred to the Pdoc documentation and realized it
> > should be written as follows,
> > 
> > 
> > use Bio::DB::Fasta;
> > ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> > $db = Bio::DB::Fasta->new($file);
> > $seq = $db->seq($id,$start,$end);
> > print $seq,"\n";
> > 
> > 
> > Then it would return the sub-sequence from 6 to 10.
> > 
> > Probably Dr Osborne had made a mistake when writing the use-guide
> > HOWTO:Beginners.
> > 
> > 
> > -- 
> > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> > 100875, China
> > email: tzhu at mail.bnu.edu.cn
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 





From edwardsa at cs.man.ac.uk  Thu Oct 28 16:52:58 2010
From: edwardsa at cs.man.ac.uk (Andrea Edwards)
Date: Thu, 28 Oct 2010 21:52:58 +0100
Subject: [Bioperl-l] Installation of bioperl on Ubuntu
Message-ID: <4CC9E2AA.6020302@cs.man.ac.uk>

Hi

I'm new to Perl and linux and I think I may have messed up my 
installation of Bioperl.

I followed the instructions on this page verbatim
http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server

However the

./Build test


command failed and I noticed a lot of modules were missing from the 
output of the test. I then used CPAN to install these modules. One of 
them was Bio::FeatureIO. When I installed this it seemed to be 
installing lots of BioPerl 1.6.1 files. However when i downloaded the 
bioperl as instructed here

wget -N http://bioperl.org/DIST/current_core_unstable.tar.bz2

the version that I got was 1.5.2_102

I am confused by the presence of 2 different version numbers and don't 
know how to proceed. It looks as if I have installed a lot of BioPerl 
1.6.1 and if i carry on with the make test/install instructions from the 
website I will then install version 1.5.

When i looked at the files installed in the Bio folder in my perl 
libraries there were 88 files and the only files missing compared to my 
other BioPerl installations were:
ANSI directory
BioEntry.pm
ConfigData.pm

I looked at some of the modules to try and see which version they were 
but they all had different version numbers. I think I have inadvertently 
used CPAN to install 1.6.1. What do you think?

many thanks


From buiduyminh at gmail.com  Thu Oct 28 17:07:06 2010
From: buiduyminh at gmail.com (Minh Bui)
Date: Thu, 28 Oct 2010 17:07:06 -0400
Subject: [Bioperl-l] Installation of bioperl on Ubuntu
In-Reply-To: <4CC9E2AA.6020302@cs.man.ac.uk>
References: <4CC9E2AA.6020302@cs.man.ac.uk>
Message-ID: <AANLkTi=Vr3zYRdtUaDptrxexkDmo_wj-2f5BiLvAAzfr@mail.gmail.com>

Hi Andrea,

You don't have to install Bioperl manually on Ubuntu.

You can go to *System* > *Administration* > "*Synaptic Package Manager*" ,
search for "Bioperl" and install it. I believe it has the latest version.

Minh.


On Thu, Oct 28, 2010 at 4:52 PM, Andrea Edwards <edwardsa at cs.man.ac.uk>wrote:

> Hi
>
> I'm new to Perl and linux and I think I may have messed up my installation
> of Bioperl.
>
> I followed the instructions on this page verbatim
> http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server
>
> However the
>
> ./Build test
>
>
> command failed and I noticed a lot of modules were missing from the output
> of the test. I then used CPAN to install these modules. One of them was
> Bio::FeatureIO. When I installed this it seemed to be installing lots of
> BioPerl 1.6.1 files. However when i downloaded the bioperl as instructed
> here
>
> wget -N http://bioperl.org/DIST/current_core_unstable.tar.bz2
>
> the version that I got was 1.5.2_102
>
> I am confused by the presence of 2 different version numbers and don't know
> how to proceed. It looks as if I have installed a lot of BioPerl 1.6.1 and
> if i carry on with the make test/install instructions from the website I
> will then install version 1.5.
>
> When i looked at the files installed in the Bio folder in my perl libraries
> there were 88 files and the only files missing compared to my other BioPerl
> installations were:
> ANSI directory
> BioEntry.pm
> ConfigData.pm
>
> I looked at some of the modules to try and see which version they were but
> they all had different version numbers. I think I have inadvertently used
> CPAN to install 1.6.1. What do you think?
>
> many thanks
> _______________________________________________
> 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 Oct 28 17:28:17 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 28 Oct 2010 16:28:17 -0500
Subject: [Bioperl-l] Installation of bioperl on Ubuntu
In-Reply-To: <4CC9E2AA.6020302@cs.man.ac.uk>
References: <4CC9E2AA.6020302@cs.man.ac.uk>
Message-ID: <22C0CD13-6081-4FC4-97B7-939696D85A74@illinois.edu>

On Oct 28, 2010, at 3:52 PM, Andrea Edwards wrote:

> Hi
> 
> I'm new to Perl and linux and I think I may have messed up my installation of Bioperl.
> 
> I followed the instructions on this page verbatim
> http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server
> 
> However the
> 
> ./Build test
> 
> 
> command failed and I noticed a lot of modules were missing from the output of the test. I then used CPAN to install these modules. One of them was Bio::FeatureIO. When I installed this it seemed to be installing lots of BioPerl 1.6.1 files. However when i downloaded the bioperl as instructed here
> 
> wget -N http://bioperl.org/DIST/current_core_unstable.tar.bz2
> 
> the version that I got was 1.5.2_102

Ugh, that's not good; that should be removed (we're now at v 1.6.1 stable, but about 10 months past that release now and sorely due for another).  For the latest 'unstable' code, you can go to github:

http://github.com/bioperl/bioperl-live

Click on the 'Downloads' button.

Just a warning, but FeatureIO will likely disappear from the github bioperl-live repo master branch.  We're breaking out chunks of code that can be released independently, FeatureIO being one.

> I am confused by the presence of 2 different version numbers and don't know how to proceed. It looks as if I have installed a lot of BioPerl 1.6.1 and if i carry on with the make test/install instructions from the website I will then install version 1.5.
> 
> When i looked at the files installed in the Bio folder in my perl libraries there were 88 files and the only files missing compared to my other BioPerl installations were:
> ANSI directory
> BioEntry.pm
> ConfigData.pm

ConfigData is only for the installation.  Not sure about the others.

> I looked at some of the modules to try and see which version they were but they all had different version numbers. I think I have inadvertently used CPAN to install 1.6.1. What do you think?
> 
> many thanks

Since we moved to github this past May we no longer have different revision numbers per module (git doesn't support them, but so far we haven't seen many actually missing them).  

chris


From daniel.standage at gmail.com  Thu Oct 28 22:45:24 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Thu, 28 Oct 2010 19:45:24 -0700 (PDT)
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
Message-ID: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>

I am using the Bio::Tools::GFF parser to process and store GFF3 data
in an application. Calls to next_feature() return
Bio::SeqFeature::Generic objects. I have written a class that extends
the Bio::SeqFeature::Generic class, but I still want to use the
Bio::Tools::GFF class to do the initial parsing of the data.

Is there a way for me to tell the Bio::Tools::GFF parser that I want
it to give me objects from my custom class? Or should I just re-bless
the objects it gives me? Will I run into garbage collection problems
if I re-bless the Bio::SeqFeature::Generic objects to my custom class
(that extends the Bio::SeqFeature::Generic class)?

Thanks!

Daniel


From scott at scottcain.net  Thu Oct 28 23:41:09 2010
From: scott at scottcain.net (Scott Cain)
Date: Thu, 28 Oct 2010 23:41:09 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
In-Reply-To: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
References: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
Message-ID: <AANLkTika2Nkx5T-Gf_y74NhEij9udqF6V3DFibzMf90G@mail.gmail.com>

Hi Daniel,

It seems like the easiest thing to do would be to subclass
Bio::Tools::GFF.  BSFGeneric is only mentioned explicitly a few times
(maybe only once), so subclassing and having it use your class instead
would probably be the easiest thing to do.

Also, about having it produce GFF3: make sure you're actually getting
valid GFF3.  Bio::Tools::GFF is fairly old, and I am sure you could
give it valid SeqFeature objects and get invalid GFF3 out in some
circumstances.

Scott


On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> I am using the Bio::Tools::GFF parser to process and store GFF3 data
> in an application. Calls to next_feature() return
> Bio::SeqFeature::Generic objects. I have written a class that extends
> the Bio::SeqFeature::Generic class, but I still want to use the
> Bio::Tools::GFF class to do the initial parsing of the data.
>
> Is there a way for me to tell the Bio::Tools::GFF parser that I want
> it to give me objects from my custom class? Or should I just re-bless
> the objects it gives me? Will I run into garbage collection problems
> if I re-bless the Bio::SeqFeature::Generic objects to my custom class
> (that extends the Bio::SeqFeature::Generic class)?
>
> Thanks!
>
> Daniel
> _______________________________________________
> 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 dimitark at bii.a-star.edu.sg  Fri Oct 29 04:29:53 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Fri, 29 Oct 2010 16:29:53 +0800
Subject: [Bioperl-l] about git and perl5lib
Message-ID: <4CCA8601.6020607@bii.a-star.edu.sg>

Hi guys,
i am sorry if this sounds stupid but i have problem with the PERL5LIB 
and the GIT version of BioPerl(BP). I downloaded the BP-live and BP-run 
from git. I use Slackware so I added the following line in bashrc:

  export 
PERL5LIB=$HOME/Bioperl_git/bioperl-live:$HOME/Bioperl_git/bioperl-run:$PERL5LIB

But when i start a script using StandAloneBlastPlus i see perl cant find it:

Can't locate Bio/Tools/Run/StandAloneBlastPlus.pm in @INC (@INC 
contains: /home/domine/Bioperl_git/bioperl-live 
/home/domine/Bioperl_git/bioperl-run 
/usr/lib64/perl5/5.10.1/x86_64-linux-thread-multi 
/usr/lib64/perl5/5.10.1 
/usr/lib64/perl5/site_perl/5.10.1/x86_64-linux-thread-multi 
/usr/lib64/perl5/site_perl/5.10.1 /usr/lib64/perl5/site_perl 
/usr/lib64/perl5/vendor_perl/5.10.1/x86_64-linux-thread-multi 
/usr/lib64/perl5/vendor_perl/5.10.1 /usr/lib64/perl5/vendor_perl

It seems Perl should find the module but it doesnt. Any idea where i 
could have made a mistake?

Btw with:  perl -MBio::Perl -le 'print Bio::Perl->VERSION;' i get 1.0069

Thank you
Dimitar





From David.Messina at sbc.su.se  Fri Oct 29 08:18:40 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 29 Oct 2010 08:18:40 -0400
Subject: [Bioperl-l] about git and perl5lib
In-Reply-To: <4CCA8601.6020607@bii.a-star.edu.sg>
References: <4CCA8601.6020607@bii.a-star.edu.sg>
Message-ID: <DACCDE9C-B82D-4D71-84BC-4119B6E242FD@sbc.su.se>

There's a minor inconsistency on our part: the path to the bioperl-run modules is actually bioperl-run/lib


Note that bioperl-live will I believe also be switching to this at some point; having the modules in a lib subdir is standard Perl practice.


Dave






On Oct 29, 2010, at 4:29, Dimitar Kenanov <dimitark at bii.a-star.edu.sg> wrote:

> Hi guys,
> i am sorry if this sounds stupid but i have problem with the PERL5LIB and the GIT version of BioPerl(BP). I downloaded the BP-live and BP-run from git. I use Slackware so I added the following line in bashrc:
> 
> export PERL5LIB=$HOME/Bioperl_git/bioperl-live:$HOME/Bioperl_git/bioperl-run:$PERL5LIB
> 
> But when i start a script using StandAloneBlastPlus i see perl cant find it:
> 
> Can't locate Bio/Tools/Run/StandAloneBlastPlus.pm in @INC (@INC contains: /home/domine/Bioperl_git/bioperl-live /home/domine/Bioperl_git/bioperl-run /usr/lib64/perl5/5.10.1/x86_64-linux-thread-multi /usr/lib64/perl5/5.10.1 /usr/lib64/perl5/site_perl/5.10.1/x86_64-linux-thread-multi /usr/lib64/perl5/site_perl/5.10.1 /usr/lib64/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.10.1/x86_64-linux-thread-multi /usr/lib64/perl5/vendor_perl/5.10.1 /usr/lib64/perl5/vendor_perl
> 
> It seems Perl should find the module but it doesnt. Any idea where i could have made a mistake?
> 
> Btw with:  perl -MBio::Perl -le 'print Bio::Perl->VERSION;' i get 1.0069
> 
> Thank you
> Dimitar
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From scott at scottcain.net  Fri Oct 29 10:03:54 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 29 Oct 2010 10:03:54 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
In-Reply-To: <AANLkTimVseFgymk+MaumosOkh=jP3bR9LwGVLxmB26Xf@mail.gmail.com>
References: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
	<AANLkTika2Nkx5T-Gf_y74NhEij9udqF6V3DFibzMf90G@mail.gmail.com>
	<AANLkTimVseFgymk+MaumosOkh=jP3bR9LwGVLxmB26Xf@mail.gmail.com>
Message-ID: <AANLkTinKbEtuWetY7avw6uH8w_GcXvrTxD1t7R8t9jc3@mail.gmail.com>

Hi Daniel,

I cc'ed the bioperl mailing list back in and attached your tarball.  I
don't really know what it is you want to do, and you already know that
your code compiles and runs, so I'm not sure what advice you're
looking for.

Scott

On Fri, Oct 29, 2010 at 9:28 AM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> I don't see how to attach files to the mailing list, so I'm just going to
> reply to you. Sorry if that is against the protocol.
>
> I have attached a working implementation of what I think you were
> suggesting. I have a parser class that subclasses Bio::Tools::GFF, and it
> has a method that will return objects of my class that subclasses
> Bio::SeqFeature::Generic. This is a rough test and I still need to clean
> things up and add the rest of the functionality that I originally needed, I
> just wanted to make sure that there aren't going to be any problems with the
> approach I'm taking.
>
> If you unpack and run './temptest' it should print out 7 valid features and
> 1 invalid feature.
>
> Thanks for your suggestions!
>
> Daniel
>
> On Thu, Oct 28, 2010 at 10:41 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Daniel,
>>
>> It seems like the easiest thing to do would be to subclass
>> Bio::Tools::GFF. ?BSFGeneric is only mentioned explicitly a few times
>> (maybe only once), so subclassing and having it use your class instead
>> would probably be the easiest thing to do.
>>
>> Also, about having it produce GFF3: make sure you're actually getting
>> valid GFF3. ?Bio::Tools::GFF is fairly old, and I am sure you could
>> give it valid SeqFeature objects and get invalid GFF3 out in some
>> circumstances.
>>
>> Scott
>>
>>
>> On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
>> <daniel.standage at gmail.com> wrote:
>> > I am using the Bio::Tools::GFF parser to process and store GFF3 data
>> > in an application. Calls to next_feature() return
>> > Bio::SeqFeature::Generic objects. I have written a class that extends
>> > the Bio::SeqFeature::Generic class, but I still want to use the
>> > Bio::Tools::GFF class to do the initial parsing of the data.
>> >
>> > Is there a way for me to tell the Bio::Tools::GFF parser that I want
>> > it to give me objects from my custom class? Or should I just re-bless
>> > the objects it gives me? Will I run into garbage collection problems
>> > if I re-bless the Bio::SeqFeature::Generic objects to my custom class
>> > (that extends the Bio::SeqFeature::Generic class)?
>> >
>> > Thanks!
>> >
>> > Daniel
>> > _______________________________________________
>> > 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
>
>
>
> --
> Daniel S. Standage
> Graduate Research Assistant
> Bioinformatics and Computational Biology Program
> Iowa State University
>
>



-- 
------------------------------------------------------------------------
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 scott at scottcain.net  Fri Oct 29 10:21:51 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 29 Oct 2010 10:21:51 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
In-Reply-To: <AANLkTinKbEtuWetY7avw6uH8w_GcXvrTxD1t7R8t9jc3@mail.gmail.com>
References: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
	<AANLkTika2Nkx5T-Gf_y74NhEij9udqF6V3DFibzMf90G@mail.gmail.com>
	<AANLkTimVseFgymk+MaumosOkh=jP3bR9LwGVLxmB26Xf@mail.gmail.com>
	<AANLkTinKbEtuWetY7avw6uH8w_GcXvrTxD1t7R8t9jc3@mail.gmail.com>
Message-ID: <AANLkTikoPX7ep5QfOd-EDxoGqYU43kJZtwv5MaBHawXC@mail.gmail.com>

Hi all,

I'm resending this because it seems that some mail clients don't like
having executable files hidden inside of a tarball, so I removed the
executable bit.

Scott


On Fri, Oct 29, 2010 at 10:03 AM, Scott Cain <scott at scottcain.net> wrote:
> Hi Daniel,
>
> I cc'ed the bioperl mailing list back in and attached your tarball. ?I
> don't really know what it is you want to do, and you already know that
> your code compiles and runs, so I'm not sure what advice you're
> looking for.
>
> Scott
>
> On Fri, Oct 29, 2010 at 9:28 AM, Daniel Standage
> <daniel.standage at gmail.com> wrote:
>> I don't see how to attach files to the mailing list, so I'm just going to
>> reply to you. Sorry if that is against the protocol.
>>
>> I have attached a working implementation of what I think you were
>> suggesting. I have a parser class that subclasses Bio::Tools::GFF, and it
>> has a method that will return objects of my class that subclasses
>> Bio::SeqFeature::Generic. This is a rough test and I still need to clean
>> things up and add the rest of the functionality that I originally needed, I
>> just wanted to make sure that there aren't going to be any problems with the
>> approach I'm taking.
>>
>> If you unpack and run './temptest' it should print out 7 valid features and
>> 1 invalid feature.
>>
>> Thanks for your suggestions!
>>
>> Daniel
>>
>> On Thu, Oct 28, 2010 at 10:41 PM, Scott Cain <scott at scottcain.net> wrote:
>>>
>>> Hi Daniel,
>>>
>>> It seems like the easiest thing to do would be to subclass
>>> Bio::Tools::GFF. ?BSFGeneric is only mentioned explicitly a few times
>>> (maybe only once), so subclassing and having it use your class instead
>>> would probably be the easiest thing to do.
>>>
>>> Also, about having it produce GFF3: make sure you're actually getting
>>> valid GFF3. ?Bio::Tools::GFF is fairly old, and I am sure you could
>>> give it valid SeqFeature objects and get invalid GFF3 out in some
>>> circumstances.
>>>
>>> Scott
>>>
>>>
>>> On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
>>> <daniel.standage at gmail.com> wrote:
>>> > I am using the Bio::Tools::GFF parser to process and store GFF3 data
>>> > in an application. Calls to next_feature() return
>>> > Bio::SeqFeature::Generic objects. I have written a class that extends
>>> > the Bio::SeqFeature::Generic class, but I still want to use the
>>> > Bio::Tools::GFF class to do the initial parsing of the data.
>>> >
>>> > Is there a way for me to tell the Bio::Tools::GFF parser that I want
>>> > it to give me objects from my custom class? Or should I just re-bless
>>> > the objects it gives me? Will I run into garbage collection problems
>>> > if I re-bless the Bio::SeqFeature::Generic objects to my custom class
>>> > (that extends the Bio::SeqFeature::Generic class)?
>>> >
>>> > Thanks!
>>> >
>>> > Daniel
>>> > _______________________________________________
>>> > 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
>>
>>
>>
>> --
>> Daniel S. Standage
>> Graduate Research Assistant
>> Bioinformatics and Computational Biology Program
>> Iowa State University
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> 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
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From daniel.standage at gmail.com  Fri Oct 29 10:34:41 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Fri, 29 Oct 2010 09:34:41 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
In-Reply-To: <AANLkTikoPX7ep5QfOd-EDxoGqYU43kJZtwv5MaBHawXC@mail.gmail.com>
References: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
	<AANLkTika2Nkx5T-Gf_y74NhEij9udqF6V3DFibzMf90G@mail.gmail.com>
	<AANLkTimVseFgymk+MaumosOkh=jP3bR9LwGVLxmB26Xf@mail.gmail.com>
	<AANLkTinKbEtuWetY7avw6uH8w_GcXvrTxD1t7R8t9jc3@mail.gmail.com>
	<AANLkTikoPX7ep5QfOd-EDxoGqYU43kJZtwv5MaBHawXC@mail.gmail.com>
Message-ID: <AANLkTikwhSvoEHJECSGV9GzKdXk7Yu7O6nwkk=-Mccba@mail.gmail.com>

I guess my concern is that I haven't used inheritance much in Perl and I'm
unclear about the possible consequences of the approach I've taken. I've
seen people warning against re-blessing objects, and I just wanted to make
sure that the approach that I seem to have working now isn't going to cause
any problems down the line.

Sorry I wasn't clear. Thanks for your help.

Daniel

On Fri, Oct 29, 2010 at 9:21 AM, Scott Cain <scott at scottcain.net> wrote:

> Hi all,
>
> I'm resending this because it seems that some mail clients don't like
> having executable files hidden inside of a tarball, so I removed the
> executable bit.
>
> Scott
>
>
> On Fri, Oct 29, 2010 at 10:03 AM, Scott Cain <scott at scottcain.net> wrote:
> > Hi Daniel,
> >
> > I cc'ed the bioperl mailing list back in and attached your tarball.  I
> > don't really know what it is you want to do, and you already know that
> > your code compiles and runs, so I'm not sure what advice you're
> > looking for.
> >
> > Scott
> >
> > On Fri, Oct 29, 2010 at 9:28 AM, Daniel Standage
> > <daniel.standage at gmail.com> wrote:
> >> I don't see how to attach files to the mailing list, so I'm just going
> to
> >> reply to you. Sorry if that is against the protocol.
> >>
> >> I have attached a working implementation of what I think you were
> >> suggesting. I have a parser class that subclasses Bio::Tools::GFF, and
> it
> >> has a method that will return objects of my class that subclasses
> >> Bio::SeqFeature::Generic. This is a rough test and I still need to clean
> >> things up and add the rest of the functionality that I originally
> needed, I
> >> just wanted to make sure that there aren't going to be any problems with
> the
> >> approach I'm taking.
> >>
> >> If you unpack and run './temptest' it should print out 7 valid features
> and
> >> 1 invalid feature.
> >>
> >> Thanks for your suggestions!
> >>
> >> Daniel
> >>
> >> On Thu, Oct 28, 2010 at 10:41 PM, Scott Cain <scott at scottcain.net>
> wrote:
> >>>
> >>> Hi Daniel,
> >>>
> >>> It seems like the easiest thing to do would be to subclass
> >>> Bio::Tools::GFF.  BSFGeneric is only mentioned explicitly a few times
> >>> (maybe only once), so subclassing and having it use your class instead
> >>> would probably be the easiest thing to do.
> >>>
> >>> Also, about having it produce GFF3: make sure you're actually getting
> >>> valid GFF3.  Bio::Tools::GFF is fairly old, and I am sure you could
> >>> give it valid SeqFeature objects and get invalid GFF3 out in some
> >>> circumstances.
> >>>
> >>> Scott
> >>>
> >>>
> >>> On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
> >>> <daniel.standage at gmail.com> wrote:
> >>> > I am using the Bio::Tools::GFF parser to process and store GFF3 data
> >>> > in an application. Calls to next_feature() return
> >>> > Bio::SeqFeature::Generic objects. I have written a class that extends
> >>> > the Bio::SeqFeature::Generic class, but I still want to use the
> >>> > Bio::Tools::GFF class to do the initial parsing of the data.
> >>> >
> >>> > Is there a way for me to tell the Bio::Tools::GFF parser that I want
> >>> > it to give me objects from my custom class? Or should I just re-bless
> >>> > the objects it gives me? Will I run into garbage collection problems
> >>> > if I re-bless the Bio::SeqFeature::Generic objects to my custom class
> >>> > (that extends the Bio::SeqFeature::Generic class)?
> >>> >
> >>> > Thanks!
> >>> >
> >>> > Daniel
> >>> > _______________________________________________
> >>> > 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
> >>
> >>
> >>
> >> --
> >> Daniel S. Standage
> >> Graduate Research Assistant
> >> Bioinformatics and Computational Biology Program
> >> Iowa State University
> >>
> >>
> >
> >
> >
> > --
> > ------------------------------------------------------------------------
> > 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
>



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


From scott at scottcain.net  Fri Oct  1 15:45:35 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 1 Oct 2010 11:45:35 -0400
Subject: [Bioperl-l] [Gmod-gbrowse] bp_seqfeature_delete.PL - where
	should I submit a patch?
In-Reply-To: <87782334-E5F5-4DFE-AEBD-64565D5C2F9F@sanger.ac.uk>
References: <87782334-E5F5-4DFE-AEBD-64565D5C2F9F@sanger.ac.uk>
Message-ID: <AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>

Hi Keiran,

Well, I've been told that it is easy for non-bioperl developers to use
git to commit patches, and as if to prove it, there is a very long
wiki page on the bioperl wiki describing how to use git:

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

I'm not sure what the right thing is to do; I'm cc'ing the bioperl
list to get their input.

Scott


On Fri, Oct 1, 2010 at 8:46 AM, Keiran Raine <kr2 at sanger.ac.uk> wrote:
> Hi all,
>
> Does anyone know how I should best get push a patch (new functionality) out
> for this script which is part of the BioPerl package.
>
> I've added a 'fast' option which is useful for when you want to delete a
> whole dataset. ?The problem I was having is I loaded a large set of data
> which had errors. ?To delete it I tried to use the '-t' option but this
> continually fails after several hours (eventually runs out of memory). ?To
> get round this I've added the '-f' flag which tells the script to perform
> the delete/commit on each individual feature (and associated sub-features)
> rather than attempt to do them all in a single commit.
>
> I've attached the modified version (unfortunately the formatting was kind of
> knackered so a patch file will be a bit iffy).
>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a
> charity registered in England with number 1021457 and acompany registered in
> England with number 2742969, whose registeredoffice is 215 Euston Road,
> London, NW1 2BE.
>
>
> Keiran Raine
> Senior Computer Biologist
> The Cancer Genome Project
> Ext: 7703
> kr2 at sanger.ac.uk
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



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



From dan.bolser at gmail.com  Fri Oct  1 19:14:34 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Fri, 1 Oct 2010 20:14:34 +0100
Subject: [Bioperl-l] Spam on the wiki: best way to report it?
Message-ID: <AANLkTik1panWOrmZ_hE3dnXYMCBeOTn=LGg=YSjqB2aa@mail.gmail.com>

Is there something like a spam category to report spam on the wiki?

I'm talking about this:

http://www.bioperl.org/wiki/Special:Contributions/Xiangniant


I figure this list isn't really the best place to report it all, but I
couldn't find any advice on what else to do.

Cheers,
Dan.


From cjfields at illinois.edu  Fri Oct  1 19:53:55 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 1 Oct 2010 14:53:55 -0500
Subject: [Bioperl-l] Spam on the wiki: best way to report it?
In-Reply-To: <AANLkTik1panWOrmZ_hE3dnXYMCBeOTn=LGg=YSjqB2aa@mail.gmail.com>
References: <AANLkTik1panWOrmZ_hE3dnXYMCBeOTn=LGg=YSjqB2aa@mail.gmail.com>
Message-ID: <4EC133B7-60D0-4DF3-B0F7-D1628E431397@illinois.edu>

We can delete spam and block users (I just did for that example and one other).  I'll make you a wiki admin; more hands the better!

chris

On Oct 1, 2010, at 2:14 PM, Dan Bolser wrote:

> Is there something like a spam category to report spam on the wiki?
> 
> I'm talking about this:
> 
> http://www.bioperl.org/wiki/Special:Contributions/Xiangniant
> 
> 
> I figure this list isn't really the best place to report it all, but I
> couldn't find any advice on what else to do.
> 
> 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  Fri Oct  1 19:47:31 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 1 Oct 2010 14:47:31 -0500
Subject: [Bioperl-l] [Gmod-gbrowse] bp_seqfeature_delete.PL - where
	should I submit a patch?
In-Reply-To: <AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>
References: <87782334-E5F5-4DFE-AEBD-64565D5C2F9F@sanger.ac.uk>
	<AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>
Message-ID: <1D851E84-1664-4E72-82F5-D8C75ABA3789@illinois.edu>

Keiran,

We gladly accept patches if this is easier for you.  Using git/github is one way of getting more users involved and opening up the code more; the actual barrier to submit code changes is lowered to the point where one can fork our code and hack away, then submit pull requests for those changes to be merged (all via github, using one's account).  

We are generally doing more code review these days (asking for tests, requiring passing tests for inclusion, etc), but in this case that's probably not a problem.

chris

On Oct 1, 2010, at 10:45 AM, Scott Cain wrote:

> Hi Keiran,
> 
> Well, I've been told that it is easy for non-bioperl developers to use
> git to commit patches, and as if to prove it, there is a very long
> wiki page on the bioperl wiki describing how to use git:
> 
>  http://www.bioperl.org/wiki/Using_Git
> 
> I'm not sure what the right thing is to do; I'm cc'ing the bioperl
> list to get their input.
> 
> Scott
> 
> 
> On Fri, Oct 1, 2010 at 8:46 AM, Keiran Raine <kr2 at sanger.ac.uk> wrote:
>> Hi all,
>> 
>> Does anyone know how I should best get push a patch (new functionality) out
>> for this script which is part of the BioPerl package.
>> 
>> I've added a 'fast' option which is useful for when you want to delete a
>> whole dataset.  The problem I was having is I loaded a large set of data
>> which had errors.  To delete it I tried to use the '-t' option but this
>> continually fails after several hours (eventually runs out of memory).  To
>> get round this I've added the '-f' flag which tells the script to perform
>> the delete/commit on each individual feature (and associated sub-features)
>> rather than attempt to do them all in a single commit.
>> 
>> I've attached the modified version (unfortunately the formatting was kind of
>> knackered so a patch file will be a bit iffy).
>> 
>> 
>> 
>> 
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a
>> charity registered in England with number 1021457 and acompany registered in
>> England with number 2742969, whose registeredoffice is 215 Euston Road,
>> London, NW1 2BE.
>> 
>> 
>> Keiran Raine
>> Senior Computer Biologist
>> The Cancer Genome Project
>> Ext: 7703
>> kr2 at sanger.ac.uk
>> 
>> 
>> 
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> Start uncovering the many advantages of virtual appliances
>> and start using them to simplify application deployment and
>> accelerate your shift to cloud computing.
>> http://p.sf.net/sfu/novell-sfdev2dev
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> 
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> 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 jason at bioperl.org  Fri Oct  1 21:17:36 2010
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 01 Oct 2010 14:17:36 -0700
Subject: [Bioperl-l] Bioperl sim4 parse
In-Reply-To: <A475AF196964604CAEE109F1CA0275AB1578AF1378@SJMEMXMBS10.stjude.sjcrh.local>
References: <A475AF196964604CAEE109F1CA0275AB1578AF1378@SJMEMXMBS10.stjude.sjcrh.local>
Message-ID: <4CA64FF0.2010201@bioperl.org>

Jianmin -

Your question is better addressed to the mailing list bioperl-l at bioperl.org

Please attach an example file that is attached and sample perl code you 
are using so someone can test that your problem exists with the latest code.

-jason

Wang, Jianmin wrote, On 10/1/10 1:59 PM:
> Hi, Jason and Steve,
>
> I checked the code of the sim4.pm and used it in my program.  Unforturnately, it does not work well.  When there is a single hit with a single hsp, the code does not generate the hsp correctly and many of the information are lost.  Could you help me to check the code.  For following is the sim4 output file:
>
> Warning: lowercase letter in d.fa data. Convert sequence to uppercase.
>
> seq1 = d.fa, 203 bp
> seq2 = q.fa (HWI-EAS90_614M9:2:106:16121:11311#0), 12 bp
>
>> chr18:60413870-60414073
>> HWI-EAS90_614M9:2:106:16121:11311#0
>
> 111-122  (1-12)   100%
>
>        0     .    :
>      111 CTCATATAGCTC
>          ||||||||||||
>        1 CTCATATAGCTC
>
> Warning: lowercase letter in q.fa data. Convert sequence to uppercase.
>
> seq1 = d.fa, 203 bp
> seq2 = q.fa (teat), 15 bp
>
>> chr18:60413870-60414073
>> teat
>
> 126-140  (1-15)   100%
>
>        0     .    :    .
>      126 GTGGTATACAGAGTT
>          |||||||||||||||
>        1 GTGGTATACAGAGTT
>
>
>
> I found it's impossible to get the strand and mapping position from the data.
>
> Best.
> Jianmin Wang
>
>
>
>    ________________________________
> Email Disclaimer: www.stjude.org/emaildisclaimer

-- 
Jason Stajich
jason at bioperl.org



From avilella at gmail.com  Tue Oct  5 10:00:28 2010
From: avilella at gmail.com (Albert Vilella)
Date: Tue, 5 Oct 2010 11:00:28 +0100
Subject: [Bioperl-l] bioperl version for ensembl Was: Retrieve Sequence from
	Ensembl gene id
Message-ID: <AANLkTim9rEkgWtyF-E+4pvo1G3YS9qr5fw42uFQGwEMq@mail.gmail.com>

I also tested bioperl 1.6.1 for some scripting with the Ensembl API, and it
produces a few warnings here and there, but it doesn't break anything
obvious...

On Thu, Sep 30, 2010 at 4:16 PM, Chris Fields <cjfields at illinois.edu> wrote:

> On Sep 30, 2010, at 8:36 AM, Jun Yin wrote:
>
> > Hi, Chirag,
> >
> > BioPerl does not have any module to retrieve data from Ensembl. But
> Ensembl
> > provides a BioPerl-like interface on that function.
>
> Actually, BioPerl does have Bio::Tools::Run::Ensembl, which was submitted
> by Sendu Bala a few years back.  I think it stills works rather well, at
> least tests pass.  You might get more out of using the Ensembl API directly
> as Jun states though, YMMV.
>
> BTW, the ensembl API also works with the latest bioperl code, regardless
> what the Ensembl website says (e.g. they only support v1.2.3).  Haven't
> heard more about whether this discrepancy was supposed to be addressed at
> some point.
>
> chris
>
> > You can visit Ensembl's website on how to use that module:
> > http://www.ensembl.org/info/data/api.html
> >
> > Cheers,
> > Jun Yin
> > Ph.D. student in U.C.D.
> >
> > Bioinformatics Laboratory
> > Conway Institute
> > University College Dublin
> >
> >
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org
> > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of chirag matkar
> > Sent: Thursday, September 30, 2010 1:21 PM
> > To: bioperl-l at lists.open-bio.org
> > Subject: [Bioperl-l] Retrieve Sequence from Ensembl gene id
> >
> > Hello all,
> > Is there any module to fetch dna sequence data from ensemble gene id?
> >
> > --
> > Regards,
> > Chirag Matkar
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > __________ Information from ESET Smart Security, version of virus
> signature
> > database 5377 (20100818) __________
> >
> > The message was checked by ESET Smart Security.
> >
> > http://www.eset.com
> >
> >
> >
> >
> > __________ Information from ESET Smart Security, version of virus
> signature
> > database 5377 (20100818) __________
> >
> > The message was checked by ESET Smart Security.
> >
> > http://www.eset.com
> >
> >
> >
> > __________ Information from ESET Smart Security, version of virus
> signature
> > database 5377 (20100818) __________
> >
> > The message was checked by ESET Smart Security.
> >
> > http://www.eset.com
> >
> >
> >
> > _______________________________________________
> > 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  Tue Oct  5 10:07:36 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 5 Oct 2010 11:07:36 +0100
Subject: [Bioperl-l] [Gmod-gbrowse] bp_seqfeature_delete.PL - where
	should I submit a patch?
In-Reply-To: <AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>
References: <87782334-E5F5-4DFE-AEBD-64565D5C2F9F@sanger.ac.uk>
	<AANLkTinybbqP2y4AxPnKgtZb2x7CYN6q96Nvrnu+ZN=b@mail.gmail.com>
Message-ID: <AANLkTinDK93L8KJZbvL-TVriEw4sNT4uJP45BzZiL9W1@mail.gmail.com>

Here is a nice SVN to GIT conversion course:

http://git.or.cz/course/svn.html


On 1 October 2010 16:45, Scott Cain <scott at scottcain.net> wrote:
> Hi Keiran,
>
> Well, I've been told that it is easy for non-bioperl developers to use
> git to commit patches, and as if to prove it, there is a very long
> wiki page on the bioperl wiki describing how to use git:
>
> ?http://www.bioperl.org/wiki/Using_Git
>
> I'm not sure what the right thing is to do; I'm cc'ing the bioperl
> list to get their input.
>
> Scott
>
>
> On Fri, Oct 1, 2010 at 8:46 AM, Keiran Raine <kr2 at sanger.ac.uk> wrote:
>> Hi all,
>>
>> Does anyone know how I should best get push a patch (new functionality) out
>> for this script which is part of the BioPerl package.
>>
>> I've added a 'fast' option which is useful for when you want to delete a
>> whole dataset. ?The problem I was having is I loaded a large set of data
>> which had errors. ?To delete it I tried to use the '-t' option but this
>> continually fails after several hours (eventually runs out of memory). ?To
>> get round this I've added the '-f' flag which tells the script to perform
>> the delete/commit on each individual feature (and associated sub-features)
>> rather than attempt to do them all in a single commit.
>>
>> I've attached the modified version (unfortunately the formatting was kind of
>> knackered so a patch file will be a bit iffy).
>>
>>
>>
>>
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a
>> charity registered in England with number 1021457 and acompany registered in
>> England with number 2742969, whose registeredoffice is 215 Euston Road,
>> London, NW1 2BE.
>>
>>
>> Keiran Raine
>> Senior Computer Biologist
>> The Cancer Genome Project
>> Ext: 7703
>> kr2 at sanger.ac.uk
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Start uncovering the many advantages of virtual appliances
>> and start using them to simplify application deployment and
>> accelerate your shift to cloud computing.
>> http://p.sf.net/sfu/novell-sfdev2dev
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



From dan.bolser at gmail.com  Tue Oct  5 10:36:49 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 5 Oct 2010 11:36:49 +0100
Subject: [Bioperl-l] Question about Bio::Coordinate::Pair
Message-ID: <AANLkTi=fmjWt95GWw=Fe+-WVkhQYcuHPDCNxE6iLpN0w@mail.gmail.com>

Hi,

Can someone describe in a bit more detail the purpose of the Gap
sublocations that are sometimes returned by Bio::Coordinate::Pair [1]?

I found that, according to Bio::Location::Split, if the Match and Gap
sublocations have a different strand, the strand method (called via
Bio::Coordinate::Result) returns undef. This is inconsistent with the
way Bio::Coordinate::Result tends to behave. See the test script and
results below, also pasted here [2].

The question is, can I just toggle the strand of the Gap sublocation
to match that of the Match sublocation? Or does the strand of the Gap
sublocation encode some important but as yet undocumented information?
If the strand of the Gap and Match sublocations are made to match
(within Bio::Coordinate::Pair) this will simplify code that uses
Bio::Coordinate::Pair, making it more consistent, and perhaps help
with some other bugs [3].


Cheers,
Dan.

[1] http://www.bioperl.org/wiki/Module:Bio::Coordinate::Pair
[2] http://www.bioperl.org/wiki/Module_Discussion:Bio::Coordinate::Pair
[3] http://tinyurl.com/36na2cp


#!/usr/bin/perl -w

## Stress test Bio::Coordinate::Pair

use strict;
use Data::Dumper;

use Bio::Location::Simple;
use Bio::Coordinate::Pair;

## A contig
my $ctg = Bio::Location::Simple->
  new( -seq_id => 'ctg',
       -start  =>    1,
       -end    => 1001,
       -strand =>   +1,
     );

## The contigs position on a chromosome (forward)
my $ctg_on_chr_f = Bio::Location::Simple->
  new( -seq_id => 'ctg on chr r',
       -start  =>           5001,
       -end    =>           6001,
       -strand =>             +1,
     );

## The contigs position on a chromosome (reverse)
my $ctg_on_chr_r = Bio::Location::Simple->
  new( -seq_id => 'ctg on chr r',
       -start  =>           5001,
       -end    =>           6001,
       -strand =>             -1,
     );

## Coordinate mapping (forward)
my $agp_f = Bio::Coordinate::Pair->
  new( -in  => $ctg,
       -out => $ctg_on_chr_f
     );

## Coordinate mapping (reverse)
my $agp_r = Bio::Coordinate::Pair->
  new( -in  => $ctg,
       -out => $ctg_on_chr_r
     );



## A match, in contig coordinates...
my $match_on_ctg_4 = Bio::Location::Simple->
  new( -seq_id => 'hit 4',
       -start  =>     925,
       -end    =>    1125,
       -strand =>      -1,
     );

## Map it into chromosome coordinates (forward)
my $match_on_chr_4_f =
  $agp_f->map( $match_on_ctg_4 );

print Dumper $match_on_chr_4_f, "\n";

## Map it into chromosome coordinates (reverse)
my $match_on_chr_4_r =
  $agp_r->map( $match_on_ctg_4 );

print Dumper $match_on_chr_4_r, "\n";

__END__

$VAR1 = bless( {
                 '_sublocations' => [
                                      bless( {
                                               '_strand' => -1,
                                               '_seqid' => 'ctg on chr r',
                                               '_start' => 5925,
                                               '_location_type' => 'EXACT',
                                               '_end' => 6001
                                             },
'Bio::Coordinate::Result::Match' ),
                                      bless( {
                                               '_strand' => -1,
                                               '_seqid' => 'ctg',
                                               '_location_type' => 'EXACT',
                                               '_start' => 1002,
                                               '_end' => 1125
                                             }, 'Bio::Coordinate::Result::Gap' )
                                    ],
                 '_gap' => $VAR1->{'_sublocations'}[1],
                 'strand' => -1,
                 '_match' => $VAR1->{'_sublocations'}[0],
                 '_splittype' => 'JOIN'
               }, 'Bio::Coordinate::Result' );
$VAR2 = '
';
$VAR1 = bless( {
                 '_sublocations' => [
                                      bless( {
                                               '_strand' => 1,
                                               '_seqid' => 'ctg on chr r',
                                               '_start' => 5001,
                                               '_location_type' => 'EXACT',
                                               '_end' => 5077
                                             },
'Bio::Coordinate::Result::Match' ),
                                      bless( {
                                               '_strand' => -1,
                                               '_seqid' => 'ctg',
                                               '_location_type' => 'EXACT',
                                               '_start' => 1002,
                                               '_end' => 1125
                                             }, 'Bio::Coordinate::Result::Gap' )
                                    ],
                 '_gap' => $VAR1->{'_sublocations'}[1],
                 'strand' => 1,
                 '_match' => $VAR1->{'_sublocations'}[0],
                 '_splittype' => 'JOIN'
               }, 'Bio::Coordinate::Result' );
$VAR2 = '
';


From gandipalem at gmail.com  Wed Oct  6 05:35:31 2010
From: gandipalem at gmail.com (gandipalem)
Date: Tue, 5 Oct 2010 22:35:31 -0700 (PDT)
Subject: [Bioperl-l] how to identify least degeneracy for a conserved region
 among all conserved regions in an amino acid alignment?
Message-ID: <29893643.post@talk.nabble.com>


Hi,

I am new to this.

I am working on designing primers for a set of highly diverged  proteins.
I designed degenerate primers for all those proteins manually starting from
multiple sequence alignment to reverse translation of conserved regions. But
this process is very time taking and robust. I would like automate this work
PERL. But I am getting a problem were I am unable to getting the logic "how
to measure/find out the least degeneracy for a conserved region among all
conserved regions of a multiple sequence alignment?".

So can anybody tell about how to find out least degenerated conserved region
in PERL?

Thanking you

Suresh
NBPGR

-- 
View this message in context: http://old.nabble.com/how-to-identify-least-degeneracy-for-a-conserved-region-among-all-conserved-regions-in-an-amino-acid-alignment--tp29893643p29893643.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From dan.bolser at gmail.com  Thu Oct  7 14:22:04 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 7 Oct 2010 15:22:04 +0100
Subject: [Bioperl-l] Installing Bio::DB::BigWig ?
In-Reply-To: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
References: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
Message-ID: <AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>

Trying to run make in .../src/kent/src (also CC'ing BP)

Dan.

# fun for everyone!
irc://irc.perl.org/#gmod

#also good!
irc://irc.freenode.net/#bioperl

On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
> Hi,
>
> I'm having trouble installing Bio::DB::BigWig.
>
> I grabbed the jkucsc code as described here [1] and built it
> successfully after setting 'export MACHTYPE=x86_64'.
>
> I then set 'export KENT_SRC=.../src/kent/src' and called:
> cpan[1]> install Bio::DB::BigWig
>
> The error comes:
> ...
> 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: comparison is always false due to
> limited range of data type
> 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: comparison is always false due to
> limited range of data type
> 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 -m64 -mtune=generic -o
> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> .../src/kent/src/lib/x86_64/jkweb.a -lz
> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
> relocation R_X86_64_32S against `a local symbol' can not be used when
> making a shared object; recompile with -fPIC
> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
> lib/Bio/DB/BigFile.o at
> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
> ?LDS/Bio-BigFile-1.03.tar.gz
> ?./Build -- NOT OK
> ...
>
>
> I tried to 'recompile with -fPIC', but saw further errors about
> missing symbols that I can't fix.
>
> Are there some specific applications of the jkucsc package that I
> should build and install first?
>
>
> Thanks for any help,
> Dan.
>
>
> [1] http://genome.ucsc.edu/admin/git.html
>



From dan.bolser at gmail.com  Thu Oct  7 15:01:50 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 7 Oct 2010 16:01:50 +0100
Subject: [Bioperl-l] Installing Bio::DB::BigWig ?
In-Reply-To: <AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>
References: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
	<AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>
Message-ID: <AANLkTikPF=qo8dv-PXEaU71tU8UtDYXjJ6cC9DB8ranV@mail.gmail.com>

I finally found the solution to this install problem. The error
message 'recompile with -fPIC' isn't referring to the Perl code, but
rather the jkucsc code...

In the directory .../src/kent/src/inc I changed the file common.mk to
add the -fPIC option to the CFLAGS...

[me at box inc]$ diff common.mk~ common.mk
6c6
< CFLAGS=
---
> CFLAGS=-fPIC


I then went back to .../src/kent/src/lib and hit 'make clean && make'.
Finally, going back to cpan, and re-installing Bio::DB::BigWig,
everything worked.


Sorry for the confusion, but it's been a long time since I needed to
install anything 'manually' ;-)

Dan.

# fun for everyone!
irc://irc.perl.org/#gmod

#also good!
irc://irc.freenode.net/#bioperl


On 7 October 2010 15:22, Dan Bolser <dan.bolser at gmail.com> wrote:
> Trying to run make in .../src/kent/src (also CC'ing BP)
>
> Dan.
>
> # fun for everyone!
> irc://irc.perl.org/#gmod
>
> #also good!
> irc://irc.freenode.net/#bioperl
>
> On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
>> Hi,
>>
>> I'm having trouble installing Bio::DB::BigWig.
>>
>> I grabbed the jkucsc code as described here [1] and built it
>> successfully after setting 'export MACHTYPE=x86_64'.
>>
>> I then set 'export KENT_SRC=.../src/kent/src' and called:
>> cpan[1]> install Bio::DB::BigWig
>>
>> The error comes:
>> ...
>> 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: comparison is always false due to
>> limited range of data type
>> 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: comparison is always false due to
>> limited range of data type
>> 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 -m64 -mtune=generic -o
>> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
>> .../src/kent/src/lib/x86_64/jkweb.a -lz
>> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
>> relocation R_X86_64_32S against `a local symbol' can not be used when
>> making a shared object; recompile with -fPIC
>> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
>> collect2: ld returned 1 exit status
>> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
>> lib/Bio/DB/BigFile.o at
>> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
>> ?LDS/Bio-BigFile-1.03.tar.gz
>> ?./Build -- NOT OK
>> ...
>>
>>
>> I tried to 'recompile with -fPIC', but saw further errors about
>> missing symbols that I can't fix.
>>
>> Are there some specific applications of the jkucsc package that I
>> should build and install first?
>>
>>
>> Thanks for any help,
>> Dan.
>>
>>
>> [1] http://genome.ucsc.edu/admin/git.html
>>
>



From lincoln.stein at gmail.com  Thu Oct  7 18:52:09 2010
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Thu, 7 Oct 2010 14:52:09 -0400
Subject: [Bioperl-l] [Gmod-gbrowse] Installing Bio::DB::BigWig ?
In-Reply-To: <AANLkTikPF=qo8dv-PXEaU71tU8UtDYXjJ6cC9DB8ranV@mail.gmail.com>
References: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
	<AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>
	<AANLkTikPF=qo8dv-PXEaU71tU8UtDYXjJ6cC9DB8ranV@mail.gmail.com>
Message-ID: <AANLkTinXx94t-RhyYF8_f4=pdj3YZwF_1Bqfe7oJMAh8@mail.gmail.com>

Sorry, I'll fix the installation documentation to warn people about -fPIC.
This seems to be needed on some platforms and not others.

Lincoln

On Thu, Oct 7, 2010 at 11:01 AM, Dan Bolser <dan.bolser at gmail.com> wrote:

> I finally found the solution to this install problem. The error
> message 'recompile with -fPIC' isn't referring to the Perl code, but
> rather the jkucsc code...
>
> In the directory .../src/kent/src/inc I changed the file common.mk to
> add the -fPIC option to the CFLAGS...
>
> [me at box inc]$ diff common.mk~ common.mk
> 6c6
> < CFLAGS=
> ---
> > CFLAGS=-fPIC
>
>
> I then went back to .../src/kent/src/lib and hit 'make clean && make'.
> Finally, going back to cpan, and re-installing Bio::DB::BigWig,
> everything worked.
>
>
> Sorry for the confusion, but it's been a long time since I needed to
> install anything 'manually' ;-)
>
> Dan.
>
> # fun for everyone!
> irc://irc.perl.org/#gmod
>
> #also good!
> irc://irc.freenode.net/#bioperl
>
>
> On 7 October 2010 15:22, Dan Bolser <dan.bolser at gmail.com> wrote:
> > Trying to run make in .../src/kent/src (also CC'ing BP)
> >
> > Dan.
> >
> > # fun for everyone!
> > irc://irc.perl.org/#gmod
> >
> > #also good!
> > irc://irc.freenode.net/#bioperl
> >
> > On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
> >> Hi,
> >>
> >> I'm having trouble installing Bio::DB::BigWig.
> >>
> >> I grabbed the jkucsc code as described here [1] and built it
> >> successfully after setting 'export MACHTYPE=x86_64'.
> >>
> >> I then set 'export KENT_SRC=.../src/kent/src' and called:
> >> cpan[1]> install Bio::DB::BigWig
> >>
> >> The error comes:
> >> ...
> >> 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: comparison is always false due to
> >> limited range of data type
> >> 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: comparison is always false due to
> >> limited range of data type
> >> 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 -m64 -mtune=generic -o
> >> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> >> .../src/kent/src/lib/x86_64/jkweb.a -lz
> >> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
> >> relocation R_X86_64_32S against `a local symbol' can not be used when
> >> making a shared object; recompile with -fPIC
> >> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
> >> collect2: ld returned 1 exit status
> >> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
> >> lib/Bio/DB/BigFile.o at
> >> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
> >>  LDS/Bio-BigFile-1.03.tar.gz
> >>  ./Build -- NOT OK
> >> ...
> >>
> >>
> >> I tried to 'recompile with -fPIC', but saw further errors about
> >> missing symbols that I can't fix.
> >>
> >> Are there some specific applications of the jkucsc package that I
> >> should build and install first?
> >>
> >>
> >> Thanks for any help,
> >> Dan.
> >>
> >>
> >> [1] http://genome.ucsc.edu/admin/git.html
> >>
> >
>
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



-- 
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  Thu Oct  7 19:58:40 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 7 Oct 2010 20:58:40 +0100
Subject: [Bioperl-l] [Gmod-gbrowse] Installing Bio::DB::BigWig ?
In-Reply-To: <AANLkTinXx94t-RhyYF8_f4=pdj3YZwF_1Bqfe7oJMAh8@mail.gmail.com>
References: <AANLkTiks-QdrhRHva==-DnwFWS9Q-G93XDMbj4m8rEHJ@mail.gmail.com>
	<AANLkTi=ArBFaPTF=aog0TLWn8OL-hpdnSP8=z5_4-CyM@mail.gmail.com>
	<AANLkTikPF=qo8dv-PXEaU71tU8UtDYXjJ6cC9DB8ranV@mail.gmail.com>
	<AANLkTinXx94t-RhyYF8_f4=pdj3YZwF_1Bqfe7oJMAh8@mail.gmail.com>
Message-ID: <AANLkTi=1pnkXFf4XE6K1BgQikf40AnTfbRwzV7CAvnrz@mail.gmail.com>

On 7 October 2010 19:52, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Sorry, I'll fix the installation documentation to warn people about -fPIC.
> This seems to be needed on some platforms and not others.

No problem, thanks for the update. Perhaps it should also be added to
the jkucsc code? any harm in adding -fPIC there anyway?

Here are the details of my box:

ge-002 2.6.18-92.1.22.el5 #1 SMP Tue Dec 16 11:57:43 EST 2008 x86_64
x86_64 x86_64 GNU/Linux

gcc --version
gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)
Copyright (C) 2006 Free Software Foundation, Inc.

perl --version
This is perl, v5.8.8 built for x86_64-linux-thread-multi

jkucsc ... git rev-parse HEAD
cb419933fdc44246e6bac605e65ddc27e7683559


I made some other minor changes to the jkucsc code in an attempt to
get the whole lot to compile:

diff --git a/src/inc/common.mk b/src/inc/common.mk
index 65c9f3c..b7b5389 100644
--- a/src/inc/common.mk
+++ b/src/inc/common.mk
@@ -3,7 +3,7 @@ CC=gcc
 ifeq (${COPT},)
     COPT=-O -g
 endif
-CFLAGS=
+CFLAGS=-fPIC
 HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${M
 HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../i

diff --git a/src/oneShot/smoothWindow/smoothWindow.c b/src/oneShot/smoothWindow/
index b062c91..f0d9c49 100644
--- a/src/oneShot/smoothWindow/smoothWindow.c
+++ b/src/oneShot/smoothWindow/smoothWindow.c
@@ -80,9 +80,9 @@ while (lineFileNext(lf, &line, NULL))
     val = words[1];
     dataValue = strtod(val, &valEnd);
     if ((*val == '\0') || (*valEnd != '\0'))
-       errAbort("Not a valid float at line %d: %s\n", lineCount, words[1]);
+       errAbort("Not a valid float at line %llu: %s\n", lineCount, words[1]);
     if (Offset < 1)
-       errAbort("Illegal offset: %llu at line %d, dataValue: %g", Offset,
+       errAbort("Illegal offset: %llu at line %llu, dataValue: %g", Offset,
            lineCount, dataValue);
     verbose(3, "#\tline: %llu, offset: %llu, data: %g\n",
        lineCount, Offset, dataValue);
diff --git a/src/utils/wigAsciiCrunch/wigAsciiCrunch.c b/src/utils/wigAsciiCrunc
index 04f7692..fc86036 100644
--- a/src/utils/wigAsciiCrunch/wigAsciiCrunch.c
+++ b/src/utils/wigAsciiCrunch/wigAsciiCrunch.c
@@ -103,7 +103,7 @@ while ((wordCount = lineFileChop(lf, words)) != 0)
        if (clFixOverlap)
            {
            minPos = lastOffset;
-           verbose(1, "Removing overlap %d-%d line %d of %s\n",
+           verbose(1, "Removing overlap %ld-%ld line %d of %s\n",
                    lastOffset, offset, lf->lineIx, lf->fileName);
            }
        else


Thanks again,
Dan.

# fun for everyone!
irc://irc.perl.org/#gmod

#also good!
irc://irc.freenode.net/#bioperl


> Lincoln
>
> On Thu, Oct 7, 2010 at 11:01 AM, Dan Bolser <dan.bolser at gmail.com> wrote:
>>
>> I finally found the solution to this install problem. The error
>> message 'recompile with -fPIC' isn't referring to the Perl code, but
>> rather the jkucsc code...
>>
>> In the directory .../src/kent/src/inc I changed the file common.mk to
>> add the -fPIC option to the CFLAGS...
>>
>> [me at box inc]$ diff common.mk~ common.mk
>> 6c6
>> < CFLAGS=
>> ---
>> > CFLAGS=-fPIC
>>
>>
>> I then went back to .../src/kent/src/lib and hit 'make clean && make'.
>> Finally, going back to cpan, and re-installing Bio::DB::BigWig,
>> everything worked.
>>
>>
>> Sorry for the confusion, but it's been a long time since I needed to
>> install anything 'manually' ;-)
>>
>> Dan.
>>
>> # fun for everyone!
>> irc://irc.perl.org/#gmod
>>
>> #also good!
>> irc://irc.freenode.net/#bioperl
>>
>>
>> On 7 October 2010 15:22, Dan Bolser <dan.bolser at gmail.com> wrote:
>> > Trying to run make in .../src/kent/src (also CC'ing BP)
>> >
>> > Dan.
>> >
>> > # fun for everyone!
>> > irc://irc.perl.org/#gmod
>> >
>> > #also good!
>> > irc://irc.freenode.net/#bioperl
>> >
>> > On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
>> >> Hi,
>> >>
>> >> I'm having trouble installing Bio::DB::BigWig.
>> >>
>> >> I grabbed the jkucsc code as described here [1] and built it
>> >> successfully after setting 'export MACHTYPE=x86_64'.
>> >>
>> >> I then set 'export KENT_SRC=.../src/kent/src' and called:
>> >> cpan[1]> install Bio::DB::BigWig
>> >>
>> >> The error comes:
>> >> ...
>> >> 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: comparison is always false due to
>> >> limited range of data type
>> >> 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: comparison is always false due to
>> >> limited range of data type
>> >> 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 -m64 -mtune=generic -o
>> >> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
>> >> .../src/kent/src/lib/x86_64/jkweb.a -lz
>> >> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
>> >> relocation R_X86_64_32S against `a local symbol' can not be used when
>> >> making a shared object; recompile with -fPIC
>> >> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
>> >> collect2: ld returned 1 exit status
>> >> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
>> >> lib/Bio/DB/BigFile.o at
>> >> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
>> >> ?LDS/Bio-BigFile-1.03.tar.gz
>> >> ?./Build -- NOT OK
>> >> ...
>> >>
>> >>
>> >> I tried to 'recompile with -fPIC', but saw further errors about
>> >> missing symbols that I can't fix.
>> >>
>> >> Are there some specific applications of the jkucsc package that I
>> >> should build and install first?
>> >>
>> >>
>> >> Thanks for any help,
>> >> Dan.
>> >>
>> >>
>> >> [1] http://genome.ucsc.edu/admin/git.html
>> >>
>> >
>>
>>
>> ------------------------------------------------------------------------------
>> Beautiful is writing same markup. Internet Explorer 9 supports
>> standards for HTML5, CSS3, SVG 1.1, ?ECMAScript5, and DOM L2 & L3.
>> Spend less time writing and ?rewriting code and more time creating great
>> experiences on the web. Be a part of the beta today.
>> http://p.sf.net/sfu/beautyoftheweb
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> 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 timmcilveen at talktalk.net  Fri Oct  8 09:16:48 2010
From: timmcilveen at talktalk.net (tim)
Date: Fri, 8 Oct 2010 10:16:48 +0100
Subject: [Bioperl-l] Getting BioPerl from Github
Message-ID: <201010081016.48460.timmcilveen@talktalk.net>

Hi,
I'm not an experienced Linux user but have been trying to download Bioperl via 
GitHub as I was getting lots of errors using the package installer. It was 
suggested by a list user that I use GitHub instead.

I installed Git using Yast.

I visited this page:
http://www.bioperl.org/wiki/Using_Git 

and used the installation instructions:
$ git clone git://github.com/bioperl/bioperl-live.git
bash: $ export PERL5LIB="$HOME/src/bioperl-live:$PERL5LIB"

I tested the code:
$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;' 
but the install didn't work.
Here is the ouput from my terminal.
tim at linux-oxgy:~> su
Password: 
linux-oxgy:/home/tim # git clone git://github.com/bioperl/bioperl-live.git
Initialized empty Git repository in /home/tim/bioperl-live/.git/
remote: Counting objects: 88288, done.
remote: Compressing objects: 100% (23829/23829), done.
remote: Total 88288 (delta 66885), reused 85264 (delta 63993)
Receiving objects: 100% (88288/88288), 138.20 MiB | 1.19 MiB/s, done.
Resolving deltas: 100% (66885/66885), done.
linux-oxgy:/home/tim # bash
linux-oxgy:/home/tim # export PERL5LIB="$HOME/src/biooperl-live:$PERL5LIB"
linux-oxgy:/home/tim # perl -MBIO::Perl -le 'print Bio::Perl->VERSION;'
Can't locate BIO/Perl.pm in @INC (@INC contains: /root/src/biooperl-live 
/usr/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi 
/usr/lib/perl5/site_perl/5.12.1 /usr/lib/perl5/vendor_perl/5.12.1/x86_64-
linux-thread-multi /usr/lib/perl5/vendor_perl/5.12.1 
/usr/lib/perl5/5.12.1/x86_64-linux-thread-multi /usr/lib/perl5/5.12.1 .).
BEGIN failed--compilation aborted.
linux-oxgy:/home/tim # 

I assume that something has went wrong at this step:
To use this 'live' version of BioPerl, you need to install it (simply tell 
Perl where to find it). Assuming you checked out the code above into 
$HOME/src; set this in your .bash_profile, .profile, or .cshrc: 

How do I set things up so that the code is in $HOME/src? Where is it likely to 
be if I carried out the installation as root?

Any help would be appreciated.

Thanks,
Tim




From scott at scottcain.net  Fri Oct  8 13:14:24 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 8 Oct 2010 09:14:24 -0400
Subject: [Bioperl-l] Getting BioPerl from Github
In-Reply-To: <201010081016.48460.timmcilveen@talktalk.net>
References: <201010081016.48460.timmcilveen@talktalk.net>
Message-ID: <AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>

Hi Tim,

Could it just be that you misspelled "bioperl-live" (as biooperl-live)
in your export statement?

Scott


On Fri, Oct 8, 2010 at 5:16 AM, tim <timmcilveen at talktalk.net> wrote:
> Hi,
> I'm not an experienced Linux user but have been trying to download Bioperl via
> GitHub as I was getting lots of errors using the package installer. It was
> suggested by a list user that I use GitHub instead.
>
> I installed Git using Yast.
>
> I visited this page:
> http://www.bioperl.org/wiki/Using_Git
>
> and used the installation instructions:
> $ git clone git://github.com/bioperl/bioperl-live.git
> bash: $ export PERL5LIB="$HOME/src/bioperl-live:$PERL5LIB"
>
> I tested the code:
> $ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
> but the install didn't work.
> Here is the ouput from my terminal.
> tim at linux-oxgy:~> su
> Password:
> linux-oxgy:/home/tim # git clone git://github.com/bioperl/bioperl-live.git
> Initialized empty Git repository in /home/tim/bioperl-live/.git/
> remote: Counting objects: 88288, done.
> remote: Compressing objects: 100% (23829/23829), done.
> remote: Total 88288 (delta 66885), reused 85264 (delta 63993)
> Receiving objects: 100% (88288/88288), 138.20 MiB | 1.19 MiB/s, done.
> Resolving deltas: 100% (66885/66885), done.
> linux-oxgy:/home/tim # bash
> linux-oxgy:/home/tim # export PERL5LIB="$HOME/src/biooperl-live:$PERL5LIB"
> linux-oxgy:/home/tim # perl -MBIO::Perl -le 'print Bio::Perl->VERSION;'
> Can't locate BIO/Perl.pm in @INC (@INC contains: /root/src/biooperl-live
> /usr/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi
> /usr/lib/perl5/site_perl/5.12.1 /usr/lib/perl5/vendor_perl/5.12.1/x86_64-
> linux-thread-multi /usr/lib/perl5/vendor_perl/5.12.1
> /usr/lib/perl5/5.12.1/x86_64-linux-thread-multi /usr/lib/perl5/5.12.1 .).
> BEGIN failed--compilation aborted.
> linux-oxgy:/home/tim #
>
> I assume that something has went wrong at this step:
> To use this 'live' version of BioPerl, you need to install it (simply tell
> Perl where to find it). Assuming you checked out the code above into
> $HOME/src; set this in your .bash_profile, .profile, or .cshrc:
>
> How do I set things up so that the code is in $HOME/src? Where is it likely to
> be if I carried out the installation as root?
>
> Any help would be appreciated.
>
> Thanks,
> Tim
>
>
> _______________________________________________
> 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 pjayaraman at mcw.edu  Thu Oct  7 20:46:19 2010
From: pjayaraman at mcw.edu (Jayaraman, Pushkala)
Date: Thu, 7 Oct 2010 15:46:19 -0500
Subject: [Bioperl-l] FW: bp_genbank2gff3- Unflattening error
Message-ID: <1448A38A42714048B9C53E473E13CCF00379E83D@davis.hmgc.mcw.edu>

I apologize, 

I should have sent it to the forum first.. 

 

 

FYI.. 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala 
Sent: Thursday, October 07, 2010 3:07 PM
To: 'cjm at fruitfly.org'
Subject: bp_genbank2gff3- Unflattening error

 

Hi Chris, 

I saw your response in a  post about Unflattener.pm here;

http://generic-model-organism-system-database.450254.n5.nabble.com/genba
nk-to-gff3-conversion-problem-td460065.html

 

hence decided to fwd this to you.. 

I have no clue what is going on.. 

 

NT_010799 Unflattening error:

Details: 

------------- EXCEPTION -------------

MSG: PROBLEM, SEVERITY==1

Container feature does not spatially contain subfeature. Perhaps this is
a dicistronic gene? I am expanding the parent feature

SF [Bio::SeqFeature::Generic=HASH(0x149297a0)]: gene; CCL14

 

SF [Bio::SeqFeature::Generic=HASH(0x1492d860)]: mRNA; CCL14; chemokine
(C-C motif) ligand 14 (CCL14), transcript variant 1

 

STACK Bio::SeqFeature::Tools::Unflattener::problem
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:952

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_group
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:2170

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_groups
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1798

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1503

STACK (eval) /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:915

STACK main::unflatten_seq
/usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:914

STACK toplevel /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:411

 

 

 

 

 

I even get another error under Unflattener.pm in another region.. this
is how it is described:

 

PROBLEM:

NT_024524 Unflattening error:

Details: 

------------- EXCEPTION -------------

MSG: 1 there is a conflict with exons; there was an explicitly stated
exon with location 22748456..22748502, yet I cannot generate this exon
from the supplied mRNA locations

 

1 There are some inferred exons that are not in the explicit exon list;
they are the exons at locations:

10982777..10983033

9516278..9517506

1225346..1225429

33491613..33491816

58797942..58798087

7323184..7323367

21253638..21253755

59172140..59172196

54309290..54310329

8988942..8989171

26569087..26569218

6479986..6480032

32266760..32267377

.....

 

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1631

STACK (eval) /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:915

STACK main::unflatten_seq
/usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:914

STACK toplevel /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:411

-------------------------------------

 

 

I do not know what is going on.. is it something that the data has or
something that I am doing wrong? 

the section of the genbank file that gives out this error is pasted
below.. 

 

 

 

 

Please help,

 

 

 

 

 

gene            complement(9047672..9065992)

                     /gene="CCL14-CCL15"

                     /note="chemokine ligand 14, chemokine ligand 15

                     transcription unit"

                     /db_xref="GeneID:348249"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004166.3"

                     /db_xref="GI:34335177"

                     /db_xref="GeneID:6358"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032964.2"

                     /db_xref="GI:34335178"

                     /db_xref="GeneID:6359"

                     /db_xref="MIM:601393"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032962.2"

                     /db_xref="GI:34335175"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004167.3"

                     /db_xref="GI:34335181"

                     /db_xref="GeneID:6359"

                     /db_xref="HGNC:10613"

                     /db_xref="MIM:601393"

     gene            complement(9047672..9050719)

                     /gene="CCL14"

                     /note="chemokine (C-C motif) ligand 14; synonyms:
CC-1,

                     CC-3, CKb1, MCIF, NCC2, SY14, HCC-1, HCC-3, NCC-2,
SCYL2,

                     SCYA14"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050719))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 3"

                     /transcript_id="NM_032963.2"

                     /db_xref="GI:34335176"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     STS             9047707..9047892

                     /standard_name="STS-H22017"

                     /db_xref="UniSTS:13833"

     STS             9047767..9047885

                     /standard_name="GDB:607751"

                     /db_xref="UniSTS:158278"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_116739.1"

                     /db_xref="GI:14589961"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_004157.1"

                     /db_xref="GI:4759070"

                     /db_xref="CCDS:CCDS32624.1"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 2

                     precursor"

                     /protein_id="NP_116738.1"

                     /db_xref="GI:14589959"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

 

 

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala [mailto:pjayaraman at mcw.edu] 
Sent: Thursday, October 07, 2010 2:56 PM
To: gmod-devel at lists.sourceforge.net
Cc: gmod-gbrowse at lists.sourceforge.net
Subject: [Gmod-gbrowse] FW: bp_genbank2gff3- Unflattening error

 

I am providing the section of the genbank file here as I am not able to
attach the entire genbank file here(duh!):

 

     gene            complement(9047672..9065992)

                     /gene="CCL14-CCL15"

                     /note="chemokine ligand 14, chemokine ligand 15

                     transcription unit"

                     /db_xref="GeneID:348249"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004166.3"

                     /db_xref="GI:34335177"

                     /db_xref="GeneID:6358"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032964.2"

                     /db_xref="GI:34335178"

                     /db_xref="GeneID:6359"

                     /db_xref="MIM:601393"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032962.2"

                     /db_xref="GI:34335175"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004167.3"

                     /db_xref="GI:34335181"

                     /db_xref="GeneID:6359"

                     /db_xref="HGNC:10613"

                     /db_xref="MIM:601393"

     gene            complement(9047672..9050719)

                     /gene="CCL14"

                     /note="chemokine (C-C motif) ligand 14; synonyms:
CC-1,

                     CC-3, CKb1, MCIF, NCC2, SY14, HCC-1, HCC-3, NCC-2,
SCYL2,

                     SCYA14"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050719))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 3"

                     /transcript_id="NM_032963.2"

                     /db_xref="GI:34335176"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     STS             9047707..9047892

                     /standard_name="STS-H22017"

                     /db_xref="UniSTS:13833"

     STS             9047767..9047885

                     /standard_name="GDB:607751"

                     /db_xref="UniSTS:158278"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_116739.1"

                     /db_xref="GI:14589961"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_004157.1"

                     /db_xref="GI:4759070"

                     /db_xref="CCDS:CCDS32624.1"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 2

                     precursor"

                     /protein_id="NP_116738.1"

                     /db_xref="GI:14589959"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

 

 

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala 
Sent: Thursday, October 07, 2010 2:43 PM
To: gmod-gbrowse at lists.sourceforge.net
Subject: bp_genbank2gff3- Unflattening error

 

Hello, 

Running the bp_genbank2gff3.pm gives me:

 

NT_010799 Unflattening error:

Details: 

------------- EXCEPTION -------------

MSG: PROBLEM, SEVERITY==1

Container feature does not spatially contain subfeature. Perhaps this is
a dicistronic gene? I am expanding the parent feature

SF [Bio::SeqFeature::Generic=HASH(0x149297a0)]: gene; CCL14

 

SF [Bio::SeqFeature::Generic=HASH(0x1492d860)]: mRNA; CCL14; chemokine
(C-C motif) ligand 14 (CCL14), transcript variant 1

 

STACK Bio::SeqFeature::Tools::Unflattener::problem
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:952

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_group
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:2170

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_groups
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1798

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1503

STACK (eval) /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:915

STACK main::unflatten_seq
/usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:914

STACK toplevel /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:411

 

 

 

Ive never seen this error before and have no clue how to resolve this as
the input is a .gbk file and the script is a BIOPerl script.  Because we
seem to be losing a  lot of gene information in a particular contig. 

Am I doing anything wrong?

 

Thanks,

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

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From kai.blin at biotech.uni-tuebingen.de  Fri Oct  8 13:35:02 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Fri, 08 Oct 2010 15:35:02 +0200
Subject: [Bioperl-l] Getting BioPerl from Github
In-Reply-To: <AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>
References: <201010081016.48460.timmcilveen@talktalk.net>
	<AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>
Message-ID: <4CAF1E06.2090206@biotech.uni-tuebingen.de>

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

On 2010-10-08 15:14, Scott Cain wrote:

> Could it just be that you misspelled "bioperl-live" (as biooperl-live)
> in your export statement?

Looks mighty suspicious, indeed. Good Catch.

Also, if you install into your home directory, there's no reason at all
to do this as root, and you probably never want to do the git clone as
root. There more stuff you do as root, the more likely you're going to
shoot yourself into the foot. :)

Cheers,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universit?t T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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usoRUwv/eHjEFciz4xp/t+CWkmlQ1YyPNA329FKTBgl1QxTuUxGQnXI+dksMmbra
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From David.Messina at sbc.su.se  Fri Oct  8 14:24:12 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 8 Oct 2010 16:24:12 +0200
Subject: [Bioperl-l] Getting BioPerl from Github
In-Reply-To: <AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>
References: <201010081016.48460.timmcilveen@talktalk.net>
	<AANLkTiktCRbgevK_iJaatVgce3SP-VNXMRO8RxaRS7gp@mail.gmail.com>
Message-ID: <65D590FA-9102-4406-AA86-462CF7EFFD0C@sbc.su.se>


> Could it just be that you misspelled "bioperl-live" (as biooperl-live)
> in your export statement?


I think also the capitalization in the following statement is important. That is, -MBio::Perl not -MBIO::Perl

>> linux-oxgy:/home/tim # perl -MBIO::Perl -le 'print Bio::Perl->VERSION;'



Dave




From David.Messina at sbc.su.se  Fri Oct  8 14:37:27 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 8 Oct 2010 16:37:27 +0200
Subject: [Bioperl-l] Bio::Matrix::MatrixI
In-Reply-To: <35D95AF6C5D146479C328BBBA554FB76028C367E@mailf.lumcnet.prod.intern>
References: <35D95AF6C5D146479C328BBBA554FB76028C367E@mailf.lumcnet.prod.intern>
Message-ID: <9826175D-4FD0-44CD-9E29-348176A2C117@sbc.su.se>

Hi Anna,

You will want to use Bio::Matrix::IO to read in a Phylip matrix.

Something like:

use Bio::Matrix::IO;
my $parser = Bio::Matrix::IO->new(-format   => 'phylip',
                                  -file     => 'phylipdist.out');
my $matrix = $parser->next_matrix;


Dave


On Sep 29, 2010, at 15:28 , <A.Vakhrusheva at lumc.nl> wrote:

> Bio::Matrix::MatrixI
> 
> I have a question concerning this interface.
> 
> I want to calculate p distances matrix, but what format is acceptable
> for input? Phylip doesn't work
> 
> Anna 



From dan.bolser at gmail.com  Fri Oct  8 15:04:44 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Fri, 8 Oct 2010 16:04:44 +0100
Subject: [Bioperl-l] Question about Bio::Coordinate::Pair
In-Reply-To: <AANLkTi=fmjWt95GWw=Fe+-WVkhQYcuHPDCNxE6iLpN0w@mail.gmail.com>
References: <AANLkTi=fmjWt95GWw=Fe+-WVkhQYcuHPDCNxE6iLpN0w@mail.gmail.com>
Message-ID: <AANLkTim3fvNkvaXftcvRb0SnhATOdugtr3Z=2v8HTxrU@mail.gmail.com>

Well... I tried to toggle the strand of the gap sublocation to match
that of the match sublocation, and overall I ended up failing one test
within t/Coordinate/CoordinateMapper.t, test number 55 (line 119)...

This test actually tests for the strandedness of the gap sublocation
that I'm specifically changing because it leads to the 'unexpected'
(or at least, 'inconsistent') behaviour that I'm calling a bug (test
55 is at the end, with enough preceding context to reproduce it):

# propepide
my $match1 = Bio::Location::Simple->new
    (-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
# peptide
my $match2 = Bio::Location::Simple->new
    (-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );

ok my $pair = Bio::Coordinate::Pair->new(-in => $match1,
					 -out => $match2,
					 -negative => 0, # false, default
					);

...

#
# partial match = gap & match
#
$pos2 = Bio::Location::Simple->new
    (-start => 20, -end => 22, -strand=> -1 );

ok $res = $pair->map($pos2);

...

is $res->gap->strand, -1; # TEST 55.  Fails when I 'fix' Bio::Coordinate::Pair



In the absence of any other information, can I take this to mean that
the strand of the gap sublocations are not used for anything
significant?


Cheers,
Dan.



On 5 October 2010 11:36, Dan Bolser <dan.bolser at gmail.com> wrote:
> Hi,
>
> Can someone describe in a bit more detail the purpose of the Gap
> sublocations that are sometimes returned by Bio::Coordinate::Pair [1]?
>
> I found that, according to Bio::Location::Split, if the Match and Gap
> sublocations have a different strand, the strand method (called via
> Bio::Coordinate::Result) returns undef. This is inconsistent with the
> way Bio::Coordinate::Result tends to behave. See the test script and
> results below, also pasted here [2].
>
> The question is, can I just toggle the strand of the Gap sublocation
> to match that of the Match sublocation? Or does the strand of the Gap
> sublocation encode some important but as yet undocumented information?
> If the strand of the Gap and Match sublocations are made to match
> (within Bio::Coordinate::Pair) this will simplify code that uses
> Bio::Coordinate::Pair, making it more consistent, and perhaps help
> with some other bugs [3].
>
>
> Cheers,
> Dan.
>
> [1] http://www.bioperl.org/wiki/Module:Bio::Coordinate::Pair
> [2] http://www.bioperl.org/wiki/Module_Discussion:Bio::Coordinate::Pair
> [3] http://tinyurl.com/36na2cp
>
>
> #!/usr/bin/perl -w
>
> ## Stress test Bio::Coordinate::Pair
>
> use strict;
> use Data::Dumper;
>
> use Bio::Location::Simple;
> use Bio::Coordinate::Pair;
>
> ## A contig
> my $ctg = Bio::Location::Simple->
> ?new( -seq_id => 'ctg',
> ? ? ? -start ?=> ? ?1,
> ? ? ? -end ? ?=> 1001,
> ? ? ? -strand => ? +1,
> ? ? );
>
> ## The contigs position on a chromosome (forward)
> my $ctg_on_chr_f = Bio::Location::Simple->
> ?new( -seq_id => 'ctg on chr r',
> ? ? ? -start ?=> ? ? ? ? ? 5001,
> ? ? ? -end ? ?=> ? ? ? ? ? 6001,
> ? ? ? -strand => ? ? ? ? ? ? +1,
> ? ? );
>
> ## The contigs position on a chromosome (reverse)
> my $ctg_on_chr_r = Bio::Location::Simple->
> ?new( -seq_id => 'ctg on chr r',
> ? ? ? -start ?=> ? ? ? ? ? 5001,
> ? ? ? -end ? ?=> ? ? ? ? ? 6001,
> ? ? ? -strand => ? ? ? ? ? ? -1,
> ? ? );
>
> ## Coordinate mapping (forward)
> my $agp_f = Bio::Coordinate::Pair->
> ?new( -in ?=> $ctg,
> ? ? ? -out => $ctg_on_chr_f
> ? ? );
>
> ## Coordinate mapping (reverse)
> my $agp_r = Bio::Coordinate::Pair->
> ?new( -in ?=> $ctg,
> ? ? ? -out => $ctg_on_chr_r
> ? ? );
>
>
>
> ## A match, in contig coordinates...
> my $match_on_ctg_4 = Bio::Location::Simple->
> ?new( -seq_id => 'hit 4',
> ? ? ? -start ?=> ? ? 925,
> ? ? ? -end ? ?=> ? ?1125,
> ? ? ? -strand => ? ? ?-1,
> ? ? );
>
> ## Map it into chromosome coordinates (forward)
> my $match_on_chr_4_f =
> ?$agp_f->map( $match_on_ctg_4 );
>
> print Dumper $match_on_chr_4_f, "\n";
>
> ## Map it into chromosome coordinates (reverse)
> my $match_on_chr_4_r =
> ?$agp_r->map( $match_on_ctg_4 );
>
> print Dumper $match_on_chr_4_r, "\n";
>
> __END__
>
> $VAR1 = bless( {
> ? ? ? ? ? ? ? ? '_sublocations' => [
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg on chr r',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 5925,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 6001
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? },
> 'Bio::Coordinate::Result::Match' ),
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 1002,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 1125
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result::Gap' )
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?],
> ? ? ? ? ? ? ? ? '_gap' => $VAR1->{'_sublocations'}[1],
> ? ? ? ? ? ? ? ? 'strand' => -1,
> ? ? ? ? ? ? ? ? '_match' => $VAR1->{'_sublocations'}[0],
> ? ? ? ? ? ? ? ? '_splittype' => 'JOIN'
> ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result' );
> $VAR2 = '
> ';
> $VAR1 = bless( {
> ? ? ? ? ? ? ? ? '_sublocations' => [
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => 1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg on chr r',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 5001,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 5077
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? },
> 'Bio::Coordinate::Result::Match' ),
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 1002,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 1125
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result::Gap' )
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?],
> ? ? ? ? ? ? ? ? '_gap' => $VAR1->{'_sublocations'}[1],
> ? ? ? ? ? ? ? ? 'strand' => 1,
> ? ? ? ? ? ? ? ? '_match' => $VAR1->{'_sublocations'}[0],
> ? ? ? ? ? ? ? ? '_splittype' => 'JOIN'
> ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result' );
> $VAR2 = '
> ';
>



From cjfields at illinois.edu  Fri Oct  8 15:16:21 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 8 Oct 2010 10:16:21 -0500
Subject: [Bioperl-l] Bio::Matrix::MatrixI
In-Reply-To: <9826175D-4FD0-44CD-9E29-348176A2C117@sbc.su.se>
References: <35D95AF6C5D146479C328BBBA554FB76028C367E@mailf.lumcnet.prod.intern>
	<9826175D-4FD0-44CD-9E29-348176A2C117@sbc.su.se>
Message-ID: <D4BC1FC6-2A66-4F26-ABF3-EB6D6CD65FE9@illinois.edu>

Correct, MatrixI (and pretty much any other module 'FooI') are interfaces for API consistency.

chris

On Oct 8, 2010, at 9:37 AM, Dave Messina wrote:

> Hi Anna,
> 
> You will want to use Bio::Matrix::IO to read in a Phylip matrix.
> 
> Something like:
> 
> use Bio::Matrix::IO;
> my $parser = Bio::Matrix::IO->new(-format   => 'phylip',
>                                  -file     => 'phylipdist.out');
> my $matrix = $parser->next_matrix;
> 
> 
> Dave
> 
> 
> On Sep 29, 2010, at 15:28 , <A.Vakhrusheva at lumc.nl> wrote:
> 
>> Bio::Matrix::MatrixI
>> 
>> I have a question concerning this interface.
>> 
>> I want to calculate p distances matrix, but what format is acceptable
>> for input? Phylip doesn't work
>> 
>> Anna 
> 
> _______________________________________________
> 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  Fri Oct  8 15:57:38 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Fri, 8 Oct 2010 16:57:38 +0100
Subject: [Bioperl-l] Question about Bio::Coordinate::Pair
In-Reply-To: <AANLkTim3fvNkvaXftcvRb0SnhATOdugtr3Z=2v8HTxrU@mail.gmail.com>
References: <AANLkTi=fmjWt95GWw=Fe+-WVkhQYcuHPDCNxE6iLpN0w@mail.gmail.com>
	<AANLkTim3fvNkvaXftcvRb0SnhATOdugtr3Z=2v8HTxrU@mail.gmail.com>
Message-ID: <AANLkTimFqsJbpZ802GzKPUAnhKHUgyjRvyg3bJNPEQNL@mail.gmail.com>

Actually, I changed the Strand of the gap in a few more places [1],
and now there are a total of 4 failed tests, however, they all appear
to be of the same form as the one reported below:


not ok 84
#   Failed test at t/Coordinate/CoordinateMapper.t line 229.
#          got: '1'
#     expected: '-1'

not ok 93
#   Failed test at t/Coordinate/CoordinateMapper.t line 246.
#          got: '1'
#     expected: '-1'

not ok 99
#   Failed test at t/Coordinate/CoordinateMapper.t line 262.
#          got: '1'
#     expected: '-1'

not ok 102
#   Failed test at t/Coordinate/CoordinateMapper.t line 265.
#          got: '1'
#     expected: '-1'


So now you know.


Dan.

[1] http://github.com/dbolser/bioperl-live/tree/dbolser_bio_coordinate_pair_tests

On 8 October 2010 16:04, Dan Bolser <dan.bolser at gmail.com> wrote:
> Well... I tried to toggle the strand of the gap sublocation to match
> that of the match sublocation, and overall I ended up failing one test
> within t/Coordinate/CoordinateMapper.t, test number 55 (line 119)...
>
> This test actually tests for the strandedness of the gap sublocation
> that I'm specifically changing because it leads to the 'unexpected'
> (or at least, 'inconsistent') behaviour that I'm calling a bug (test
> 55 is at the end, with enough preceding context to reproduce it):
>
> # propepide
> my $match1 = Bio::Location::Simple->new
> ? ?(-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
> # peptide
> my $match2 = Bio::Location::Simple->new
> ? ?(-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );
>
> ok my $pair = Bio::Coordinate::Pair->new(-in => $match1,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -out => $match2,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -negative => 0, # false, default
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?);
>
> ...
>
> #
> # partial match = gap & match
> #
> $pos2 = Bio::Location::Simple->new
> ? ?(-start => 20, -end => 22, -strand=> -1 );
>
> ok $res = $pair->map($pos2);
>
> ...
>
> is $res->gap->strand, -1; # TEST 55. ?Fails when I 'fix' Bio::Coordinate::Pair
>
>
>
> In the absence of any other information, can I take this to mean that
> the strand of the gap sublocations are not used for anything
> significant?
>
>
> Cheers,
> Dan.
>
>
>
> On 5 October 2010 11:36, Dan Bolser <dan.bolser at gmail.com> wrote:
>> Hi,
>>
>> Can someone describe in a bit more detail the purpose of the Gap
>> sublocations that are sometimes returned by Bio::Coordinate::Pair [1]?
>>
>> I found that, according to Bio::Location::Split, if the Match and Gap
>> sublocations have a different strand, the strand method (called via
>> Bio::Coordinate::Result) returns undef. This is inconsistent with the
>> way Bio::Coordinate::Result tends to behave. See the test script and
>> results below, also pasted here [2].
>>
>> The question is, can I just toggle the strand of the Gap sublocation
>> to match that of the Match sublocation? Or does the strand of the Gap
>> sublocation encode some important but as yet undocumented information?
>> If the strand of the Gap and Match sublocations are made to match
>> (within Bio::Coordinate::Pair) this will simplify code that uses
>> Bio::Coordinate::Pair, making it more consistent, and perhaps help
>> with some other bugs [3].
>>
>>
>> Cheers,
>> Dan.
>>
>> [1] http://www.bioperl.org/wiki/Module:Bio::Coordinate::Pair
>> [2] http://www.bioperl.org/wiki/Module_Discussion:Bio::Coordinate::Pair
>> [3] http://tinyurl.com/36na2cp
>>
>>
>> #!/usr/bin/perl -w
>>
>> ## Stress test Bio::Coordinate::Pair
>>
>> use strict;
>> use Data::Dumper;
>>
>> use Bio::Location::Simple;
>> use Bio::Coordinate::Pair;
>>
>> ## A contig
>> my $ctg = Bio::Location::Simple->
>> ?new( -seq_id => 'ctg',
>> ? ? ? -start ?=> ? ?1,
>> ? ? ? -end ? ?=> 1001,
>> ? ? ? -strand => ? +1,
>> ? ? );
>>
>> ## The contigs position on a chromosome (forward)
>> my $ctg_on_chr_f = Bio::Location::Simple->
>> ?new( -seq_id => 'ctg on chr r',
>> ? ? ? -start ?=> ? ? ? ? ? 5001,
>> ? ? ? -end ? ?=> ? ? ? ? ? 6001,
>> ? ? ? -strand => ? ? ? ? ? ? +1,
>> ? ? );
>>
>> ## The contigs position on a chromosome (reverse)
>> my $ctg_on_chr_r = Bio::Location::Simple->
>> ?new( -seq_id => 'ctg on chr r',
>> ? ? ? -start ?=> ? ? ? ? ? 5001,
>> ? ? ? -end ? ?=> ? ? ? ? ? 6001,
>> ? ? ? -strand => ? ? ? ? ? ? -1,
>> ? ? );
>>
>> ## Coordinate mapping (forward)
>> my $agp_f = Bio::Coordinate::Pair->
>> ?new( -in ?=> $ctg,
>> ? ? ? -out => $ctg_on_chr_f
>> ? ? );
>>
>> ## Coordinate mapping (reverse)
>> my $agp_r = Bio::Coordinate::Pair->
>> ?new( -in ?=> $ctg,
>> ? ? ? -out => $ctg_on_chr_r
>> ? ? );
>>
>>
>>
>> ## A match, in contig coordinates...
>> my $match_on_ctg_4 = Bio::Location::Simple->
>> ?new( -seq_id => 'hit 4',
>> ? ? ? -start ?=> ? ? 925,
>> ? ? ? -end ? ?=> ? ?1125,
>> ? ? ? -strand => ? ? ?-1,
>> ? ? );
>>
>> ## Map it into chromosome coordinates (forward)
>> my $match_on_chr_4_f =
>> ?$agp_f->map( $match_on_ctg_4 );
>>
>> print Dumper $match_on_chr_4_f, "\n";
>>
>> ## Map it into chromosome coordinates (reverse)
>> my $match_on_chr_4_r =
>> ?$agp_r->map( $match_on_ctg_4 );
>>
>> print Dumper $match_on_chr_4_r, "\n";
>>
>> __END__
>>
>> $VAR1 = bless( {
>> ? ? ? ? ? ? ? ? '_sublocations' => [
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg on chr r',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 5925,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 6001
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? },
>> 'Bio::Coordinate::Result::Match' ),
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 1002,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 1125
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result::Gap' )
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?],
>> ? ? ? ? ? ? ? ? '_gap' => $VAR1->{'_sublocations'}[1],
>> ? ? ? ? ? ? ? ? 'strand' => -1,
>> ? ? ? ? ? ? ? ? '_match' => $VAR1->{'_sublocations'}[0],
>> ? ? ? ? ? ? ? ? '_splittype' => 'JOIN'
>> ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result' );
>> $VAR2 = '
>> ';
>> $VAR1 = bless( {
>> ? ? ? ? ? ? ? ? '_sublocations' => [
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => 1,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg on chr r',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 5001,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 5077
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? },
>> 'Bio::Coordinate::Result::Match' ),
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bless( {
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_strand' => -1,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_seqid' => 'ctg',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_location_type' => 'EXACT',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_start' => 1002,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '_end' => 1125
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result::Gap' )
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?],
>> ? ? ? ? ? ? ? ? '_gap' => $VAR1->{'_sublocations'}[1],
>> ? ? ? ? ? ? ? ? 'strand' => 1,
>> ? ? ? ? ? ? ? ? '_match' => $VAR1->{'_sublocations'}[0],
>> ? ? ? ? ? ? ? ? '_splittype' => 'JOIN'
>> ? ? ? ? ? ? ? }, 'Bio::Coordinate::Result' );
>> $VAR2 = '
>> ';
>>
>



From mauricio at open-bio.org  Fri Oct  8 16:47:56 2010
From: mauricio at open-bio.org (Mauricio Herrera Cuadra)
Date: Fri, 08 Oct 2010 11:47:56 -0500
Subject: [Bioperl-l] Pdoc documentation & test coverage updated
Message-ID: <4CAF4B3C.1060001@open-bio.org>

The cron scripts that generate the live code Pdoc documentation and the 
test coverage reports are now updated to pull from the GitHub 
repository. Please let me know if you notice anything wonky.

Mauricio.


From cjfields at illinois.edu  Fri Oct  8 20:13:08 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 8 Oct 2010 15:13:08 -0500
Subject: [Bioperl-l] Pdoc documentation & test coverage updated
In-Reply-To: <4CAF4B3C.1060001@open-bio.org>
References: <4CAF4B3C.1060001@open-bio.org>
Message-ID: <DA23CAB1-6A1C-4EC5-9EEF-06ED68C35AE9@illinois.edu>

Thanks Mauricio!  That completely feel off my radar.

chris

On Oct 8, 2010, at 11:47 AM, Mauricio Herrera Cuadra wrote:

> The cron scripts that generate the live code Pdoc documentation and the test coverage reports are now updated to pull from the GitHub repository. Please let me know if you notice anything wonky.
> 
> Mauricio.
> _______________________________________________
> 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  Fri Oct  8 21:08:40 2010
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 08 Oct 2010 14:08:40 -0700
Subject: [Bioperl-l] Pdoc documentation & test coverage updated
In-Reply-To: <DA23CAB1-6A1C-4EC5-9EEF-06ED68C35AE9@illinois.edu>
References: <4CAF4B3C.1060001@open-bio.org>
	<DA23CAB1-6A1C-4EC5-9EEF-06ED68C35AE9@illinois.edu>
Message-ID: <4CAF8858.5090302@bioperl.org>

nice -- thanks for doing that Mauricio.


Chris Fields wrote, On 10/8/10 1:13 PM:
> Thanks Mauricio!  That completely feel off my radar.
>
> chris
>
> On Oct 8, 2010, at 11:47 AM, Mauricio Herrera Cuadra wrote:
>
>> The cron scripts that generate the live code Pdoc documentation and the test coverage reports are now updated to pull from the GitHub repository. Please let me know if you notice anything wonky.
>>
>> Mauricio.
>> _______________________________________________
>> 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

-- 
Jason Stajich
jason at bioperl.org



From avilella at gmail.com  Tue Oct 12 12:34:14 2010
From: avilella at gmail.com (Albert Vilella)
Date: Tue, 12 Oct 2010 13:34:14 +0100
Subject: [Bioperl-l] possible bug in Bio::SeqIO::fastq
Message-ID: <AANLkTi=XNY9skUoTpJYJ=cp8wcpRPiskjFeuc3RquDUk@mail.gmail.com>

Hi,

I found what seems to me could be a bug in the fastq module, which is
that if the
last line of the raw_quality section is a single "0" character, a
"if($line)" isn't
returning it properly, because it should be "if(defined $line)" instead.

Find here a test case and the line in question:

----
use strict;
use Bio::SeqIO;

my $consio = Bio::SeqIO->new
  (-format => 'fastq',
   -fh => \*DATA);

my $onelineconsout = Bio::SeqIO->new
  (-format => 'fastq',
   -fh => \*STDOUT);

while (my $seq = $consio->next_seq) {
  next if ($seq->seq =~ /^n+$/);
  $seq->seq(uc($seq->seq));
  $onelineconsout->write_seq($seq);
}
$consio->close;
$onelineconsout->close;

__DATA__
@SRR031652.634472
agtgcgctgatctgtggcccgtattgcctcaacgcaagctcaatagcttgagtatattaa
a
+
01111111111111100111111--,,011111101111111110111111111111110
0
----

--- /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm
2010-10-12 13:26:06.491743000 +0100
+++ /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm~
2010-10-12 13:07:27.462833000 +0100
@@ -80,7 +80,7 @@
                 last FASTQ
             }
             chomp $line;
-            if (!defined($line)) {
+            if (!$line) {
                 delete $self->{lastline};
                 last FASTQ;
             }


From shalabh.sharma7 at gmail.com  Tue Oct 12 14:20:58 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 12 Oct 2010 10:20:58 -0400
Subject: [Bioperl-l] fastq Problem
Message-ID: <AANLkTikTASuFtDhvwZDpvn4N4k-nMR2S1y9noQ2OcY12@mail.gmail.com>

Hi,
    I have data from illumina, i can read the data by using Bio::SeqIO but
when i am writing it back its writing in fasta format.

Is there anyway i can write it back in fastq format?

Thanks
Shalabh


From avilella at gmail.com  Tue Oct 12 14:54:46 2010
From: avilella at gmail.com (Albert Vilella)
Date: Tue, 12 Oct 2010 15:54:46 +0100
Subject: [Bioperl-l] possible bug in Bio::SeqIO::fastq
In-Reply-To: <76631143-1043-4A02-BF4C-AC7F9D8A3274@illinois.edu>
References: <AANLkTi=XNY9skUoTpJYJ=cp8wcpRPiskjFeuc3RquDUk@mail.gmail.com>
	<76631143-1043-4A02-BF4C-AC7F9D8A3274@illinois.edu>
Message-ID: <AANLkTi=m3-rR4yGLRPLTVW0azSdS3AUwQQ1u1gtvzWoP@mail.gmail.com>

aah! thanks!

On Tue, Oct 12, 2010 at 3:50 PM, Chris Fields <cjfields at illinois.edu> wrote:
> Albert,
>
> Have you tried bioperl-live? ?This is already fixed there.
>
> chris
>
> On Oct 12, 2010, at 7:34 AM, Albert Vilella wrote:
>
>> Hi,
>>
>> I found what seems to me could be a bug in the fastq module, which is
>> that if the
>> last line of the raw_quality section is a single "0" character, a
>> "if($line)" isn't
>> returning it properly, because it should be "if(defined $line)" instead.
>>
>> Find here a test case and the line in question:
>>
>> ----
>> use strict;
>> use Bio::SeqIO;
>>
>> my $consio = Bio::SeqIO->new
>> ?(-format => 'fastq',
>> ? -fh => \*DATA);
>>
>> my $onelineconsout = Bio::SeqIO->new
>> ?(-format => 'fastq',
>> ? -fh => \*STDOUT);
>>
>> while (my $seq = $consio->next_seq) {
>> ?next if ($seq->seq =~ /^n+$/);
>> ?$seq->seq(uc($seq->seq));
>> ?$onelineconsout->write_seq($seq);
>> }
>> $consio->close;
>> $onelineconsout->close;
>>
>> __DATA__
>> @SRR031652.634472
>> agtgcgctgatctgtggcccgtattgcctcaacgcaagctcaatagcttgagtatattaa
>> a
>> +
>> 01111111111111100111111--,,011111101111111110111111111111110
>> 0
>> ----
>>
>> --- /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm
>> 2010-10-12 13:26:06.491743000 +0100
>> +++ /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm~
>> 2010-10-12 13:07:27.462833000 +0100
>> @@ -80,7 +80,7 @@
>> ? ? ? ? ? ? ? ? last FASTQ
>> ? ? ? ? ? ? }
>> ? ? ? ? ? ? chomp $line;
>> - ? ? ? ? ? ?if (!defined($line)) {
>> + ? ? ? ? ? ?if (!$line) {
>> ? ? ? ? ? ? ? ? delete $self->{lastline};
>> ? ? ? ? ? ? ? ? last FASTQ;
>> ? ? ? ? ? ? }
>> _______________________________________________
>> 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 Oct 12 14:50:30 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 12 Oct 2010 09:50:30 -0500
Subject: [Bioperl-l] possible bug in Bio::SeqIO::fastq
In-Reply-To: <AANLkTi=XNY9skUoTpJYJ=cp8wcpRPiskjFeuc3RquDUk@mail.gmail.com>
References: <AANLkTi=XNY9skUoTpJYJ=cp8wcpRPiskjFeuc3RquDUk@mail.gmail.com>
Message-ID: <76631143-1043-4A02-BF4C-AC7F9D8A3274@illinois.edu>

Albert, 

Have you tried bioperl-live?  This is already fixed there.

chris

On Oct 12, 2010, at 7:34 AM, Albert Vilella wrote:

> Hi,
> 
> I found what seems to me could be a bug in the fastq module, which is
> that if the
> last line of the raw_quality section is a single "0" character, a
> "if($line)" isn't
> returning it properly, because it should be "if(defined $line)" instead.
> 
> Find here a test case and the line in question:
> 
> ----
> use strict;
> use Bio::SeqIO;
> 
> my $consio = Bio::SeqIO->new
>  (-format => 'fastq',
>   -fh => \*DATA);
> 
> my $onelineconsout = Bio::SeqIO->new
>  (-format => 'fastq',
>   -fh => \*STDOUT);
> 
> while (my $seq = $consio->next_seq) {
>  next if ($seq->seq =~ /^n+$/);
>  $seq->seq(uc($seq->seq));
>  $onelineconsout->write_seq($seq);
> }
> $consio->close;
> $onelineconsout->close;
> 
> __DATA__
> @SRR031652.634472
> agtgcgctgatctgtggcccgtattgcctcaacgcaagctcaatagcttgagtatattaa
> a
> +
> 01111111111111100111111--,,011111101111111110111111111111110
> 0
> ----
> 
> --- /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm
> 2010-10-12 13:26:06.491743000 +0100
> +++ /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm~
> 2010-10-12 13:07:27.462833000 +0100
> @@ -80,7 +80,7 @@
>                 last FASTQ
>             }
>             chomp $line;
> -            if (!defined($line)) {
> +            if (!$line) {
>                 delete $self->{lastline};
>                 last FASTQ;
>             }
> _______________________________________________
> 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 Oct 12 14:51:41 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 12 Oct 2010 09:51:41 -0500
Subject: [Bioperl-l] fastq Problem
In-Reply-To: <AANLkTikTASuFtDhvwZDpvn4N4k-nMR2S1y9noQ2OcY12@mail.gmail.com>
References: <AANLkTikTASuFtDhvwZDpvn4N4k-nMR2S1y9noQ2OcY12@mail.gmail.com>
Message-ID: <03B2F4BE-4E32-4A28-BB9E-B2B59EAEFE00@illinois.edu>

Yes, but you need to use the latest CPAN release or bioperl-live; anything older than v. 1.6.1 will not convert Illumina reads correctly.

chris

On Oct 12, 2010, at 9:20 AM, shalabh sharma wrote:

> Hi,
>    I have data from illumina, i can read the data by using Bio::SeqIO but
> when i am writing it back its writing in fasta format.
> 
> Is there anyway i can write it back in fastq format?
> 
> Thanks
> Shalabh
> _______________________________________________
> 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  Tue Oct 12 15:09:50 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 12 Oct 2010 11:09:50 -0400
Subject: [Bioperl-l] fastq Problem
In-Reply-To: <03B2F4BE-4E32-4A28-BB9E-B2B59EAEFE00@illinois.edu>
References: <AANLkTikTASuFtDhvwZDpvn4N4k-nMR2S1y9noQ2OcY12@mail.gmail.com>
	<03B2F4BE-4E32-4A28-BB9E-B2B59EAEFE00@illinois.edu>
Message-ID: <AANLkTim3Hx3SLrEoQa8D9Ha_x-ECTOjCCQY4CjHBJOaV@mail.gmail.com>

Thanks Chris,
I realized that after writing that mail. Its working now.

Thanks
Shalabh


On Tue, Oct 12, 2010 at 10:51 AM, Chris Fields <cjfields at illinois.edu>wrote:

> Yes, but you need to use the latest CPAN release or bioperl-live; anything
> older than v. 1.6.1 will not convert Illumina reads correctly.
>
> chris
>
> On Oct 12, 2010, at 9:20 AM, shalabh sharma wrote:
>
> > Hi,
> >    I have data from illumina, i can read the data by using Bio::SeqIO but
> > when i am writing it back its writing in fasta format.
> >
> > Is there anyway i can write it back in fastq format?
> >
> > Thanks
> > Shalabh
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From maj at fortinbras.us  Thu Oct 14 03:52:05 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Wed, 13 Oct 2010 23:52:05 -0400
Subject: [Bioperl-l] Next-gen flu informatics
Message-ID: <81299466177D467091763FEA84CA00FD@NewLife>

Hi All, 

Sorry about the job spam, but you are the best talent pool I know. SRA
(the company now interfering with my BioPerl work) is looking for
next-gen experienced bioinformaticists for a new contract with
CDC. Please have a look at http://www.sra.com/careers/search.php,
requisition numbers 31385, 31402 and 31467.

Thanks!
MAJ



From dichmann at berkeley.edu  Fri Oct 15 01:16:29 2010
From: dichmann at berkeley.edu (Darwin Sorento Dichmann)
Date: Thu, 14 Oct 2010 18:16:29 -0700
Subject: [Bioperl-l] Extracting sequences from MySQL DB with Bio::DB::GFF
Message-ID: <36D60149-EEC5-4A45-85B9-E7FD4F3C005C@berkeley.edu>

Greetings, 

I am trying to extract sequences from a MySQL DB with Bio::DB::GFF. The database is the same as I use for my gbrowse2 and it works fine for that. Also, I can extract all sorts of features but not sequence. 

When I run this script I thought I'd get a sequence output but apparently I get the memory address instead. 

I have very little experience with perl or other programming, but I try to follow the directions in the manual. I suspect that I overlook something very basic and any help would be greatly appreciated. 

Thanks,
Darwin 



The script:
------------
#! usr/bin/perl -w
# module to test if Bio::DB::GFF can be used to extract sequences from frog2 database.

use strict;
use Bio::Seq;
use Bio::SeqIO;
use Bio::DB::GFF;

# Open database
my $db = Bio::DB::GFF->
new( 	-adaptor => 'DBI::mysql',
     	-dsn     => 'frog2',
		-user => 'darwin',
		-password => '****',
		);

# fetch scaffold_1 (1-100000)
my $segment = $db->segment('scaffold_1', 1 => 100000) or die;

# get its DNA
 my $dna = $segment->seq or die;
print $segment, "\n";
print $dna,"\n";

# get an iterator on all curated features of type 'exon' or 'intron'
# this prints all exons and intron with transcript name on screen
	my $iterator = $segment->get_seq_stream(-type     => ['mRNA']);
	while (my $s = $iterator->next_seq) {
    print $s,"\n";
}

exit;
---------------

The output:
Macintosh:perlscripts darwin$ perl frog2_parser.pl 
scaffold_1:1,100000
Bio::PrimarySeq=HASH(0x100bb4d68)
mRNA:pick(xt42f011730m)
mRNA:pick(xt42f014902m)
mRNA:pick(xt42f016160m)
mRNA:pick(xt42f017353m)
mRNA:pick(xt42f029332m)
---------------


From scott at scottcain.net  Fri Oct 15 02:01:24 2010
From: scott at scottcain.net (Scott Cain)
Date: Thu, 14 Oct 2010 22:01:24 -0400
Subject: [Bioperl-l] Extracting sequences from MySQL DB with Bio::DB::GFF
In-Reply-To: <36D60149-EEC5-4A45-85B9-E7FD4F3C005C@berkeley.edu>
References: <36D60149-EEC5-4A45-85B9-E7FD4F3C005C@berkeley.edu>
Message-ID: <AANLkTi=i1xAoyeQJGAnT9X5wEmdchJk1v4YWMSqk7fH1@mail.gmail.com>

Hi Darwin,

The "seq" method returns a Bio::PrimarySeq object (I forget why this
is--I think it's to fulfill the contract with the Bio::SeqFeatureI
interface).  To get the sequence, you can do a few things: 1) call the
seq method on the Bio::PrimarySeq object, like this:

  my $dna = $segment->seq->seq;

or 2) use the dna method:

  my $dna = $segment->dna;

The perldoc section from Bio::DB::GFF::Segment is below.

Scott

       seq

        Title   : seq
        Usage   : $s->seq
        Function: get the sequence string for this segment
        Returns : a Bio::PrimarySeq
        Args    : none
        Status  : Public

       Returns the sequence for this segment as a Bio::PrimarySeq.  (-) strand
       segments are automatically reverse complemented

       The method is called dna() return the data as a simple sequence string.

       dna

        Title   : dna
        Usage   : $s->dna
        Function: get the DNA string for this segment
        Returns : a string
        Args    : none
        Status  : Public

       Returns the sequence for this segment as a simple string. (-) strand
       segments are automatically reverse complemented

       The method is also called protein().


On Thu, Oct 14, 2010 at 9:16 PM, Darwin Sorento Dichmann
<dichmann at berkeley.edu> wrote:
> Greetings,
>
> I am trying to extract sequences from a MySQL DB with Bio::DB::GFF. The database is the same as I use for my gbrowse2 and it works fine for that. Also, I can extract all sorts of features but not sequence.
>
> When I run this script I thought I'd get a sequence output but apparently I get the memory address instead.
>
> I have very little experience with perl or other programming, but I try to follow the directions in the manual. I suspect that I overlook something very basic and any help would be greatly appreciated.
>
> Thanks,
> Darwin
>
>
>
> The script:
> ------------
> #! usr/bin/perl -w
> # module to test if Bio::DB::GFF can be used to extract sequences from frog2 database.
>
> use strict;
> use Bio::Seq;
> use Bio::SeqIO;
> use Bio::DB::GFF;
>
> # Open database
> my $db = Bio::DB::GFF->
> new(    -adaptor => 'DBI::mysql',
>        -dsn     => 'frog2',
>                -user => 'darwin',
>                -password => '****',
>                );
>
> # fetch scaffold_1 (1-100000)
> my $segment = $db->segment('scaffold_1', 1 => 100000) or die;
>
> # get its DNA
>  my $dna = $segment->seq or die;
> print $segment, "\n";
> print $dna,"\n";
>
> # get an iterator on all curated features of type 'exon' or 'intron'
> # this prints all exons and intron with transcript name on screen
>        my $iterator = $segment->get_seq_stream(-type     => ['mRNA']);
>        while (my $s = $iterator->next_seq) {
>    print $s,"\n";
> }
>
> exit;
> ---------------
>
> The output:
> Macintosh:perlscripts darwin$ perl frog2_parser.pl
> scaffold_1:1,100000
> Bio::PrimarySeq=HASH(0x100bb4d68)
> mRNA:pick(xt42f011730m)
> mRNA:pick(xt42f014902m)
> mRNA:pick(xt42f016160m)
> mRNA:pick(xt42f017353m)
> mRNA:pick(xt42f029332m)
> ---------------
> _______________________________________________
> 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 dichmann at berkeley.edu  Fri Oct 15 17:34:02 2010
From: dichmann at berkeley.edu (Darwin Sorento Dichmann)
Date: Fri, 15 Oct 2010 10:34:02 -0700
Subject: [Bioperl-l] Extracting sequences from MySQL DB with Bio::DB::GFF
In-Reply-To: <AANLkTi=i1xAoyeQJGAnT9X5wEmdchJk1v4YWMSqk7fH1@mail.gmail.com>
References: <36D60149-EEC5-4A45-85B9-E7FD4F3C005C@berkeley.edu>
	<AANLkTi=i1xAoyeQJGAnT9X5wEmdchJk1v4YWMSqk7fH1@mail.gmail.com>
Message-ID: <9E7B9E6F-9440-4BAC-AD8D-2A739A863C1B@berkeley.edu>

It's a beauty to behold!
Thanks Scott!

Best,
Darwin

On Oct 14, 2010, at 7:01 PM, Scott Cain wrote:

> Hi Darwin,
> 
> The "seq" method returns a Bio::PrimarySeq object (I forget why this
> is--I think it's to fulfill the contract with the Bio::SeqFeatureI
> interface).  To get the sequence, you can do a few things: 1) call the
> seq method on the Bio::PrimarySeq object, like this:
> 
>  my $dna = $segment->seq->seq;
> 
> or 2) use the dna method:
> 
>  my $dna = $segment->dna;
> 
> The perldoc section from Bio::DB::GFF::Segment is below.
> 
> Scott
> 
>       seq
> 
>        Title   : seq
>        Usage   : $s->seq
>        Function: get the sequence string for this segment
>        Returns : a Bio::PrimarySeq
>        Args    : none
>        Status  : Public
> 
>       Returns the sequence for this segment as a Bio::PrimarySeq.  (-) strand
>       segments are automatically reverse complemented
> 
>       The method is called dna() return the data as a simple sequence string.
> 
>       dna
> 
>        Title   : dna
>        Usage   : $s->dna
>        Function: get the DNA string for this segment
>        Returns : a string
>        Args    : none
>        Status  : Public
> 
>       Returns the sequence for this segment as a simple string. (-) strand
>       segments are automatically reverse complemented
> 
>       The method is also called protein().
> 
> 
> On Thu, Oct 14, 2010 at 9:16 PM, Darwin Sorento Dichmann
> <dichmann at berkeley.edu> wrote:
>> Greetings,
>> 
>> I am trying to extract sequences from a MySQL DB with Bio::DB::GFF. The database is the same as I use for my gbrowse2 and it works fine for that. Also, I can extract all sorts of features but not sequence.
>> 
>> When I run this script I thought I'd get a sequence output but apparently I get the memory address instead.
>> 
>> I have very little experience with perl or other programming, but I try to follow the directions in the manual. I suspect that I overlook something very basic and any help would be greatly appreciated.
>> 
>> Thanks,
>> Darwin
>> 
>> 
>> 
>> The script:
>> ------------
>> #! usr/bin/perl -w
>> # module to test if Bio::DB::GFF can be used to extract sequences from frog2 database.
>> 
>> use strict;
>> use Bio::Seq;
>> use Bio::SeqIO;
>> use Bio::DB::GFF;
>> 
>> # Open database
>> my $db = Bio::DB::GFF->
>> new(    -adaptor => 'DBI::mysql',
>>       -dsn     => 'frog2',
>>               -user => 'darwin',
>>               -password => '****',
>>               );
>> 
>> # fetch scaffold_1 (1-100000)
>> my $segment = $db->segment('scaffold_1', 1 => 100000) or die;
>> 
>> # get its DNA
>> my $dna = $segment->seq or die;
>> print $segment, "\n";
>> print $dna,"\n";
>> 
>> # get an iterator on all curated features of type 'exon' or 'intron'
>> # this prints all exons and intron with transcript name on screen
>>       my $iterator = $segment->get_seq_stream(-type     => ['mRNA']);
>>       while (my $s = $iterator->next_seq) {
>>   print $s,"\n";
>> }
>> 
>> exit;
>> ---------------
>> 
>> The output:
>> Macintosh:perlscripts darwin$ perl frog2_parser.pl
>> scaffold_1:1,100000
>> Bio::PrimarySeq=HASH(0x100bb4d68)
>> mRNA:pick(xt42f011730m)
>> mRNA:pick(xt42f014902m)
>> mRNA:pick(xt42f016160m)
>> mRNA:pick(xt42f017353m)
>> mRNA:pick(xt42f029332m)
>> ---------------
>> _______________________________________________
>> 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 mcestep at gmail.com  Fri Oct 15 20:59:57 2010
From: mcestep at gmail.com (Matt Estep)
Date: Fri, 15 Oct 2010 15:59:57 -0500
Subject: [Bioperl-l] Installing BioPerl on New mac 10.6.4
Message-ID: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>

Hi

When running the ./build install script I get an error because it can
not make a directory in /usr/local/share/man/man3  I looked around a
bit and I have a file titled /usr/share/man/man3. I am guessing the
script does not know how to skip the local bit of the first line.

Can you tell me how to run the script so that it will make the file in
the right place. I am guessing the file struture of the new mac is a
little different.

Thanks in advance for any help.

Matt


From scott at scottcain.net  Sat Oct 16 03:41:40 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 15 Oct 2010 23:41:40 -0400
Subject: [Bioperl-l] Installing BioPerl on New mac 10.6.4
In-Reply-To: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>
References: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>
Message-ID: <AANLkTimUSO7ohhN6L80tjYhsrHk+2oQx6JWcRE11g4ob@mail.gmail.com>

Hi Matt,

Usually, when ./Build install fails to create a directory or file it
is because the user that executed the script didn't have permission to
perform that action.  Did you use "sudo" when you executed the install
command?

Scott


On Fri, Oct 15, 2010 at 4:59 PM, Matt Estep <mcestep at gmail.com> wrote:
> Hi
>
> When running the ./build install script I get an error because it can
> not make a directory in /usr/local/share/man/man3 ?I looked around a
> bit and I have a file titled /usr/share/man/man3. I am guessing the
> script does not know how to skip the local bit of the first line.
>
> Can you tell me how to run the script so that it will make the file in
> the right place. I am guessing the file struture of the new mac is a
> little different.
>
> Thanks in advance for any help.
>
> Matt
> _______________________________________________
> 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 fij at elte.hu  Sat Oct 16 11:34:06 2010
From: fij at elte.hu (Farkas, Illes)
Date: Sat, 16 Oct 2010 13:34:06 +0200
Subject: [Bioperl-l] cis-regulatory elements
Message-ID: <AANLkTinCN+qFBZeGtKiYLMWg+yzitkEP497pHMgG-ULn@mail.gmail.com>

Dear All,

Which (BioPerl or other) module/algorithm would you recommend for predicting
cis-regulatory elements (mainly TFBSs) in a variety of organisms? We (= 1
colleague and I) have looked at
http://www.nature.com/nbt/journal/v23/n1/full/nbt1053.html so far.

Thanks,
Illes
--
http://hal.elte.hu/fij


From grapeguy at gmail.com  Sat Oct 16 19:46:32 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Sat, 16 Oct 2010 15:46:32 -0400
Subject: [Bioperl-l] Installing BioPerl on New mac 10.6.4
In-Reply-To: <AANLkTimUSO7ohhN6L80tjYhsrHk+2oQx6JWcRE11g4ob@mail.gmail.com>
References: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>
	<AANLkTimUSO7ohhN6L80tjYhsrHk+2oQx6JWcRE11g4ob@mail.gmail.com>
Message-ID: <AANLkTikbZnnno5oNDi1Q0HYe9QEFhp9xuF3wH5C8NhXG@mail.gmail.com>

Matt,

I just installed on OSX 10.6.3.  Definitely use sudo to perform the install.

I actually used the PPM install.  I used this command to start PPM: sudo
perl -MCPAN -e shell

http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_CPAN

Thanks,
Bill S.
Dept. of Biomedical Informatics
Ohio State University

On Fri, Oct 15, 2010 at 11:41 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Matt,
>
> Usually, when ./Build install fails to create a directory or file it
> is because the user that executed the script didn't have permission to
> perform that action.  Did you use "sudo" when you executed the install
> command?
>
> Scott
>
>
> On Fri, Oct 15, 2010 at 4:59 PM, Matt Estep <mcestep at gmail.com> wrote:
> > Hi
> >
> > When running the ./build install script I get an error because it can
> > not make a directory in /usr/local/share/man/man3  I looked around a
> > bit and I have a file titled /usr/share/man/man3. I am guessing the
> > script does not know how to skip the local bit of the first line.
> >
> > Can you tell me how to run the script so that it will make the file in
> > the right place. I am guessing the file struture of the new mac is a
> > little different.
> >
> > Thanks in advance for any help.
> >
> > Matt
> > _______________________________________________
> > 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
>


From jun.yin at ucd.ie  Sat Oct 16 20:41:37 2010
From: jun.yin at ucd.ie (Jun Yin)
Date: Sat, 16 Oct 2010 21:41:37 +0100
Subject: [Bioperl-l] cis-regulatory elements
In-Reply-To: <AANLkTinCN+qFBZeGtKiYLMWg+yzitkEP497pHMgG-ULn@mail.gmail.com>
References: <AANLkTinCN+qFBZeGtKiYLMWg+yzitkEP497pHMgG-ULn@mail.gmail.com>
Message-ID: <001501cb6d72$8771c2b0$96554810$%yin@ucd.ie>

Hi, Illes,

Sorry I don't know any package in BioPerl predicting TFBS binding motifs. As
far as I know, neither Bio::Align nor Bio::Assembly has such functions,
though Bio::SimpleAlign can be used to manipulate your promoter alignment.
For TFBS prediction, I personally use PScan and TFFind at the moment.

I am also interested in this question. I will wait for the answer in the
mail list with you :)

Cheers,
Jun Yin
Ph.D.?student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Farkas, Illes
Sent: Saturday, October 16, 2010 12:34 PM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] cis-regulatory elements

Dear All,

Which (BioPerl or other) module/algorithm would you recommend for predicting
cis-regulatory elements (mainly TFBSs) in a variety of organisms? We (= 1
colleague and I) have looked at
http://www.nature.com/nbt/journal/v23/n1/full/nbt1053.html so far.

Thanks,
Illes
--
http://hal.elte.hu/fij
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com


 

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com
 
 

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com
 




From cjfields at illinois.edu  Sun Oct 17 03:24:32 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Sat, 16 Oct 2010 22:24:32 -0500
Subject: [Bioperl-l] cis-regulatory elements
In-Reply-To: <001501cb6d72$8771c2b0$96554810$%yin@ucd.ie>
References: <AANLkTinCN+qFBZeGtKiYLMWg+yzitkEP497pHMgG-ULn@mail.gmail.com>
	<001501cb6d72$8771c2b0$96554810$%yin@ucd.ie>
Message-ID: <ECB68538-3F18-4AEB-A097-773A913935B5@illinois.edu>

Sendu Bala delved into this a bit; you can look at a few of his modules in BioPerl, specifically Bio::DB::TFBS (which is only configured for transfac_pro at the moment).

chris

On Oct 16, 2010, at 3:41 PM, Jun Yin wrote:

> Hi, Illes,
> 
> Sorry I don't know any package in BioPerl predicting TFBS binding motifs. As
> far as I know, neither Bio::Align nor Bio::Assembly has such functions,
> though Bio::SimpleAlign can be used to manipulate your promoter alignment.
> For TFBS prediction, I personally use PScan and TFFind at the moment.
> 
> I am also interested in this question. I will wait for the answer in the
> mail list with you :)
> 
> Cheers,
> Jun Yin
> Ph.D. student in U.C.D.
> 
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Farkas, Illes
> Sent: Saturday, October 16, 2010 12:34 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] cis-regulatory elements
> 
> Dear All,
> 
> Which (BioPerl or other) module/algorithm would you recommend for predicting
> cis-regulatory elements (mainly TFBSs) in a variety of organisms? We (= 1
> colleague and I) have looked at
> http://www.nature.com/nbt/journal/v23/n1/full/nbt1053.html so far.
> 
> Thanks,
> Illes
> --
> http://hal.elte.hu/fij
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
> 
> The message was checked by ESET Smart Security.
> 
> http://www.eset.com
> 
> 
> 
> 
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
> 
> The message was checked by ESET Smart Security.
> 
> http://www.eset.com
> 
> 
> 
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
> 
> The message was checked by ESET Smart Security.
> 
> http://www.eset.com
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From grapeguy at gmail.com  Mon Oct 18 13:58:24 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Mon, 18 Oct 2010 09:58:24 -0400
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal alignment
Message-ID: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>

All,

I'm in my first week with bioperl for a class project (although I've used
Perl for years). I've successfully run a clustal alignment of several DNA
sequences to produce the aln and dnd files. Now I would like to generate a
consensus sequence from the alignment.  I see that Pise Cons does this
satisfactorily on my example data (
http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1 distribution
that I installed.

Is this another module that I need to install separately?

"cpan[2]> m /Pise/
Module    Bio::Tools::Run::AnalysisFactory::Pise
(BIRNEY/bioperl-run-1.4.tar.gz)
Module    Bio::Tools::Run::PiseApplication (BIRNEY/bioperl-run-1.4.tar.gz)"

Bill S.


From cjfields at illinois.edu  Mon Oct 18 14:54:32 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 18 Oct 2010 09:54:32 -0500
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
Message-ID: <DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>

Bill,

Actually, the page you reached at Pasteur is not Pise, but Mobyle (their replacement for the older Pise tools).  The Pise modules were in BioPerl-Run, but they were deprecated a few years ago and removed from the latest BioPerl-Run releases b/c the remote service is no longer active; there is no Perl-based replacement for Mobyle interaction.  

Have you thought about just using the functionality within the Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there are methods in place to do that.

chris

On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:

> All,
> 
> I'm in my first week with bioperl for a class project (although I've used
> Perl for years). I've successfully run a clustal alignment of several DNA
> sequences to produce the aln and dnd files. Now I would like to generate a
> consensus sequence from the alignment.  I see that Pise Cons does this
> satisfactorily on my example data (
> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1 distribution
> that I installed.
> 
> Is this another module that I need to install separately?
> 
> "cpan[2]> m /Pise/
> Module    Bio::Tools::Run::AnalysisFactory::Pise
> (BIRNEY/bioperl-run-1.4.tar.gz)
> Module    Bio::Tools::Run::PiseApplication (BIRNEY/bioperl-run-1.4.tar.gz)"
> 
> Bill S.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From grapeguy at gmail.com  Mon Oct 18 15:52:03 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Mon, 18 Oct 2010 11:52:03 -0400
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
Message-ID: <AANLkTimF5N_AnTV380fT5hPAEjjSgSP37+KVaoHNwbXN@mail.gmail.com>

Chris,

Well, That explains it.

I'll take a 2 pronged approach:
1. Try SimpleAlign
2. Driving the Mobyle UI using LWP::UserAgent, HTML::Form and
HTML::TableExtract (I do this for Tm calculations);

Thanks,
Bill S.



On Mon, Oct 18, 2010 at 10:54 AM, Chris Fields <cjfields at illinois.edu>wrote:

> Bill,
>
> Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
> replacement for the older Pise tools).  The Pise modules were in
> BioPerl-Run, but they were deprecated a few years ago and removed from the
> latest BioPerl-Run releases b/c the remote service is no longer active;
> there is no Perl-based replacement for Mobyle interaction.
>
> Have you thought about just using the functionality within the
> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there are
> methods in place to do that.
>
> chris
>
> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
>
> > All,
> >
> > I'm in my first week with bioperl for a class project (although I've used
> > Perl for years). I've successfully run a clustal alignment of several DNA
> > sequences to produce the aln and dnd files. Now I would like to generate
> a
> > consensus sequence from the alignment.  I see that Pise Cons does this
> > satisfactorily on my example data (
> > http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However,
> I'm
> > not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
> distribution
> > that I installed.
> >
> > Is this another module that I need to install separately?
> >
> > "cpan[2]> m /Pise/
> > Module    Bio::Tools::Run::AnalysisFactory::Pise
> > (BIRNEY/bioperl-run-1.4.tar.gz)
> > Module    Bio::Tools::Run::PiseApplication
> (BIRNEY/bioperl-run-1.4.tar.gz)"
> >
> > Bill S.
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From jun.yin at ucd.ie  Mon Oct 18 16:09:32 2010
From: jun.yin at ucd.ie (Jun Yin)
Date: Mon, 18 Oct 2010 17:09:32 +0100
Subject: [Bioperl-l] Generating a consensus sequence from a
	Clustal	alignment
In-Reply-To: <DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
Message-ID: <001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>

Hi, Bill,

You may consider to use consensus_iupac or consensus_string methods in
Bio::SimpleAlign to generate consensus sequence.

Cheers,
Jun Yin
Ph.D.?student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Monday, October 18, 2010 3:55 PM
To: Bill Stephens
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
alignment

Bill,

Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
replacement for the older Pise tools).  The Pise modules were in
BioPerl-Run, but they were deprecated a few years ago and removed from the
latest BioPerl-Run releases b/c the remote service is no longer active;
there is no Perl-based replacement for Mobyle interaction.  

Have you thought about just using the functionality within the
Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there are
methods in place to do that.

chris

On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:

> All,
> 
> I'm in my first week with bioperl for a class project (although I've used
> Perl for years). I've successfully run a clustal alignment of several DNA
> sequences to produce the aln and dnd files. Now I would like to generate a
> consensus sequence from the alignment.  I see that Pise Cons does this
> satisfactorily on my example data (
> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
distribution
> that I installed.
> 
> Is this another module that I need to install separately?
> 
> "cpan[2]> m /Pise/
> Module    Bio::Tools::Run::AnalysisFactory::Pise
> (BIRNEY/bioperl-run-1.4.tar.gz)
> Module    Bio::Tools::Run::PiseApplication
(BIRNEY/bioperl-run-1.4.tar.gz)"
> 
> Bill S.
> _______________________________________________
> 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

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com


 

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com
 




From mcestep at gmail.com  Sun Oct 17 02:59:24 2010
From: mcestep at gmail.com (Matt Estep)
Date: Sat, 16 Oct 2010 21:59:24 -0500
Subject: [Bioperl-l] Installing BioPerl on New mac 10.6.4
In-Reply-To: <AANLkTikbZnnno5oNDi1Q0HYe9QEFhp9xuF3wH5C8NhXG@mail.gmail.com>
References: <AANLkTinC8edEuzwsSvphAzw+BnYmjWCDjRdBxao4vHGQ@mail.gmail.com>
	<AANLkTimUSO7ohhN6L80tjYhsrHk+2oQx6JWcRE11g4ob@mail.gmail.com>
	<AANLkTikbZnnno5oNDi1Q0HYe9QEFhp9xuF3wH5C8NhXG@mail.gmail.com>
Message-ID: <AANLkTimiPDKCFKZwDT1UM-OG=jKqxVMe2fD5hdY_jPW-@mail.gmail.com>

Thank you both. I think this has solved my troubles.

Matt

On Sat, Oct 16, 2010 at 2:46 PM, Bill Stephens <grapeguy at gmail.com> wrote:
> Matt,
>
> I just installed on OSX 10.6.3.? Definitely use sudo to perform the install.
>
> I actually used the PPM install.? I used this command to start PPM: sudo
> perl -MCPAN -e shell
>
> http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_CPAN
>
> Thanks,
> Bill S.
> Dept. of Biomedical Informatics
> Ohio State University
>
> On Fri, Oct 15, 2010 at 11:41 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Matt,
>>
>> Usually, when ./Build install fails to create a directory or file it
>> is because the user that executed the script didn't have permission to
>> perform that action. ?Did you use "sudo" when you executed the install
>> command?
>>
>> Scott
>>
>>
>> On Fri, Oct 15, 2010 at 4:59 PM, Matt Estep <mcestep at gmail.com> wrote:
>> > Hi
>> >
>> > When running the ./build install script I get an error because it can
>> > not make a directory in /usr/local/share/man/man3 ?I looked around a
>> > bit and I have a file titled /usr/share/man/man3. I am guessing the
>> > script does not know how to skip the local bit of the first line.
>> >
>> > Can you tell me how to run the script so that it will make the file in
>> > the right place. I am guessing the file struture of the new mac is a
>> > little different.
>> >
>> > Thanks in advance for any help.
>> >
>> > Matt
>> > _______________________________________________
>> > 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
>
>



From e.cristiano at Dkfz-Heidelberg.de  Mon Oct 18 14:33:05 2010
From: e.cristiano at Dkfz-Heidelberg.de (Cristiano Elena)
Date: Mon, 18 Oct 2010 16:33:05 +0200
Subject: [Bioperl-l] bioperl easy way installation using cpan
Message-ID: <FC756E55-13EF-449F-B324-3BB76032A22B@Dkfz-Heidelberg.de>

Hi,
I am a beginner and i am trying to install bioperl via CPAN following the instructions on wiki.
i have a leopard mac 10.6 and perl version 5.10 i have X11 and i also installed fink (but the installation of bioperl wasn't successful trough fink either).

the error that i got at the end of the installation via CPAN is the following:

 SHAWNPW/PostScript-0.06.tar.gz
  /usr/bin/make install  -- OK
Warning (usually harmless): 'YAML' not installed, will not store persistent state
Running Build for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
  Has already been unwrapped into directory /Users/ecristiano/.cpan/build/BioPerl-1.6.1-66fecx
Could not make: cannot resolve circular dependency
Warning (usually harmless): 'YAML' not installed, will not store persistent state
Running Build test
  Can't test without successful make
Running Build install
  Make had returned bad status, install seems impossible
Could not read '/Users/ecristiano/.cpan/build/GraphViz-2.04-f7G5nl/META.yml'. Falling back to other methods to determine prerequisites
Failed during this command:
 MINGYILIU/Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz: make NO cannot resolve circular dependency
 CJFIELDS/BioPerl-1.6.1.tar.gz                : make NO cannot resolve circular dependency
 LBROCARD/GraphViz-2.04.tar.gz                : writemakefile NO '/usr/bin/perl Makefile.PL' returned status 512


thanks in advance



Elena




From sarahdoom at gmail.com  Mon Oct 18 15:20:25 2010
From: sarahdoom at gmail.com (Sarah Kingan)
Date: Mon, 18 Oct 2010 08:20:25 -0700 (PDT)
Subject: [Bioperl-l] DNAStatistics
Message-ID: <780929ef-4b06-43ae-9d9c-78a62e84a4d7@g18g2000yqk.googlegroups.com>

Hello,
I am trying to calculate Ka/Ks statistics using the
Align:DNAStatistics module. When I use the function, calc_KaKs_pair, I
get a long list of errors. The calculation is performed but I don't
understand the source of the errors. They include:

Use of uninitialized value in addition (+) at /usr/lib/perl5/site_perl/
5.8.8/Bio/Align/DNAStatistics.pm line 1673, <GEN0> line 25.

Use of uninitialized value in addition (+) at /usr/lib/perl5/site_perl/
5.8.8/Bio/Align/DNAStatistics.pm line 1505, <GEN0> line 25.

Use of uninitialized value in subtraction (-) at /usr/lib/perl5/
site_perl/5.8.8/Bio/Align/DNAStatistics.pm line 1506, <GEN0> line 25.

My alignment object has gaps, but I believe this module handles gaps.
The data I am analyzing comes from recently diverged species, so I
wonder if the errors could originate from a lack of substitutions.

Any help would be much appreciated.

Thanks!
Sarah.Kingan at rochester.edu


From scott at scottcain.net  Mon Oct 18 17:26:53 2010
From: scott at scottcain.net (Scott Cain)
Date: Mon, 18 Oct 2010 13:26:53 -0400
Subject: [Bioperl-l] bioperl easy way installation using cpan
In-Reply-To: <FC756E55-13EF-449F-B324-3BB76032A22B@Dkfz-Heidelberg.de>
References: <FC756E55-13EF-449F-B324-3BB76032A22B@Dkfz-Heidelberg.de>
Message-ID: <AANLkTim6NxZx2-MCNJQ190-za6TkCYF_m9WZvPfO+LhC@mail.gmail.com>

Hi Elena,

I would suggest that you answer the question about installing optional
prerequisites with a "no"; I think that will eliminate the circular
dependency problem.  Of course the only problem is if you need
Bio-ASN1-EntrezGene, but even if you do, you can probably install it
after the BioPerl install completes.

Scott


On Mon, Oct 18, 2010 at 10:33 AM, Cristiano Elena
<e.cristiano at dkfz-heidelberg.de> wrote:
> Hi,
> I am a beginner and i am trying to install bioperl via CPAN following the instructions on wiki.
> i have a leopard mac 10.6 and perl version 5.10 i have X11 and i also installed fink (but the installation of bioperl wasn't successful trough fink either).
>
> the error that i got at the end of the installation via CPAN is the following:
>
> ?SHAWNPW/PostScript-0.06.tar.gz
> ?/usr/bin/make install ?-- OK
> Warning (usually harmless): 'YAML' not installed, will not store persistent state
> Running Build for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
> ?Has already been unwrapped into directory /Users/ecristiano/.cpan/build/BioPerl-1.6.1-66fecx
> Could not make: cannot resolve circular dependency
> Warning (usually harmless): 'YAML' not installed, will not store persistent state
> Running Build test
> ?Can't test without successful make
> Running Build install
> ?Make had returned bad status, install seems impossible
> Could not read '/Users/ecristiano/.cpan/build/GraphViz-2.04-f7G5nl/META.yml'. Falling back to other methods to determine prerequisites
> Failed during this command:
> ?MINGYILIU/Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz: make NO cannot resolve circular dependency
> ?CJFIELDS/BioPerl-1.6.1.tar.gz ? ? ? ? ? ? ? ?: make NO cannot resolve circular dependency
> ?LBROCARD/GraphViz-2.04.tar.gz ? ? ? ? ? ? ? ?: writemakefile NO '/usr/bin/perl Makefile.PL' returned status 512
>
>
> thanks in advance
>
>
>
> Elena
>
>
> _______________________________________________
> 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 Oct 18 17:37:02 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 18 Oct 2010 12:37:02 -0500
Subject: [Bioperl-l] bioperl easy way installation using cpan
In-Reply-To: <AANLkTim6NxZx2-MCNJQ190-za6TkCYF_m9WZvPfO+LhC@mail.gmail.com>
References: <FC756E55-13EF-449F-B324-3BB76032A22B@Dkfz-Heidelberg.de>
	<AANLkTim6NxZx2-MCNJQ190-za6TkCYF_m9WZvPfO+LhC@mail.gmail.com>
Message-ID: <6081844C-D4CB-4926-968D-9CACAE017E57@illinois.edu>

Agreed.  Unfortunately, this is an issue that has repeatedly popped up.  The best way I can think of to solve it is to remove Bio::ASN1::EntrezGene 'recommends' from Build.PL file, manually check for it's presence, and indicate the procedure for installing (basically post-bioperl install).

chris

On Oct 18, 2010, at 12:26 PM, Scott Cain wrote:

> Hi Elena,
> 
> I would suggest that you answer the question about installing optional
> prerequisites with a "no"; I think that will eliminate the circular
> dependency problem.  Of course the only problem is if you need
> Bio-ASN1-EntrezGene, but even if you do, you can probably install it
> after the BioPerl install completes.
> 
> Scott
> 
> 
> On Mon, Oct 18, 2010 at 10:33 AM, Cristiano Elena
> <e.cristiano at dkfz-heidelberg.de> wrote:
>> Hi,
>> I am a beginner and i am trying to install bioperl via CPAN following the instructions on wiki.
>> i have a leopard mac 10.6 and perl version 5.10 i have X11 and i also installed fink (but the installation of bioperl wasn't successful trough fink either).
>> 
>> the error that i got at the end of the installation via CPAN is the following:
>> 
>>  SHAWNPW/PostScript-0.06.tar.gz
>>  /usr/bin/make install  -- OK
>> Warning (usually harmless): 'YAML' not installed, will not store persistent state
>> Running Build for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
>>  Has already been unwrapped into directory /Users/ecristiano/.cpan/build/BioPerl-1.6.1-66fecx
>> Could not make: cannot resolve circular dependency
>> Warning (usually harmless): 'YAML' not installed, will not store persistent state
>> Running Build test
>>  Can't test without successful make
>> Running Build install
>>  Make had returned bad status, install seems impossible
>> Could not read '/Users/ecristiano/.cpan/build/GraphViz-2.04-f7G5nl/META.yml'. Falling back to other methods to determine prerequisites
>> Failed during this command:
>>  MINGYILIU/Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz: make NO cannot resolve circular dependency
>>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make NO cannot resolve circular dependency
>>  LBROCARD/GraphViz-2.04.tar.gz                : writemakefile NO '/usr/bin/perl Makefile.PL' returned status 512
>> 
>> 
>> thanks in advance
>> 
>> 
>> 
>> Elena
>> 
>> 
>> _______________________________________________
>> 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




From David.Messina at sbc.su.se  Mon Oct 18 18:23:18 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 18 Oct 2010 14:23:18 -0400
Subject: [Bioperl-l] DNAStatistics
In-Reply-To: <780929ef-4b06-43ae-9d9c-78a62e84a4d7@g18g2000yqk.googlegroups.com>
References: <780929ef-4b06-43ae-9d9c-78a62e84a4d7@g18g2000yqk.googlegroups.com>
Message-ID: <B1ABB50A-0B78-44D9-85C3-4A316B52278F@sbc.su.se>

Hi Sarah,

Usually "unintialized value" errors mean you're not trying to read from an empty variable.

I would check that all of the data you're passing to calc_KaKs_pair does contain a value.


> My alignment object has gaps, but I believe this module handles gaps.

I'm not sure about that; I'd have to check. Did you try handing it some ungapped data to see if the errors go away?



Dave




From grapeguy at gmail.com  Tue Oct 19 00:02:47 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Mon, 18 Oct 2010 20:02:47 -0400
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
Message-ID: <AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>

So, I've got the SimpleAlign running. It looks like it's running the
alignment based upon the input sequence location only (first residue from
each sequence).  This is not what I need.

I'm back to to clustal, tcoffee or dalign.

Bill

On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:

> Hi, Bill,
>
> You may consider to use consensus_iupac or consensus_string methods in
> Bio::SimpleAlign to generate consensus sequence.
>
> Cheers,
> Jun Yin
> Ph.D. student in U.C.D.
>
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Monday, October 18, 2010 3:55 PM
> To: Bill Stephens
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
> alignment
>
> Bill,
>
> Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
> replacement for the older Pise tools).  The Pise modules were in
> BioPerl-Run, but they were deprecated a few years ago and removed from the
> latest BioPerl-Run releases b/c the remote service is no longer active;
> there is no Perl-based replacement for Mobyle interaction.
>
> Have you thought about just using the functionality within the
> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there
> are
> methods in place to do that.
>
> chris
>
> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
>
> > All,
> >
> > I'm in my first week with bioperl for a class project (although I've used
> > Perl for years). I've successfully run a clustal alignment of several DNA
> > sequences to produce the aln and dnd files. Now I would like to generate
> a
> > consensus sequence from the alignment.  I see that Pise Cons does this
> > satisfactorily on my example data (
> > http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However,
> I'm
> > not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
> distribution
> > that I installed.
> >
> > Is this another module that I need to install separately?
> >
> > "cpan[2]> m /Pise/
> > Module    Bio::Tools::Run::AnalysisFactory::Pise
> > (BIRNEY/bioperl-run-1.4.tar.gz)
> > Module    Bio::Tools::Run::PiseApplication
> (BIRNEY/bioperl-run-1.4.tar.gz)"
> >
> > Bill S.
> > _______________________________________________
> > 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
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>


From thomas.sharpton at gmail.com  Tue Oct 19 02:30:40 2010
From: thomas.sharpton at gmail.com (Thomas Sharpton)
Date: Mon, 18 Oct 2010 19:30:40 -0700
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
	<AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
Message-ID: <16917B57-A1EE-495C-A541-D5C666701C31@gmail.com>

While the tools you mention are sufficient, you might be interested to  
know that HMMER can also generate consensus sequences. Briefly, you  
would use the alignment you generated with clustal (or any other  
multiple sequence alignment tool) to build an HMM via the hmmbuild  
function. You can then emit a consensus sequence from the HMM file  
using the hmmemit function:

hmmemit -c HMM_file.hmm

Just FYI.

T

On Oct 18, 2010, at 5:02 PM, Bill Stephens wrote:

> So, I've got the SimpleAlign running. It looks like it's running the
> alignment based upon the input sequence location only (first residue  
> from
> each sequence).  This is not what I need.
>
> I'm back to to clustal, tcoffee or dalign.
>
> Bill
>
> On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:
>
>> Hi, Bill,
>>
>> You may consider to use consensus_iupac or consensus_string methods  
>> in
>> Bio::SimpleAlign to generate consensus sequence.
>>
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>>
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris  
>> Fields
>> Sent: Monday, October 18, 2010 3:55 PM
>> To: Bill Stephens
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] Generating a consensus sequence from a  
>> Clustal
>> alignment
>>
>> Bill,
>>
>> Actually, the page you reached at Pasteur is not Pise, but Mobyle  
>> (their
>> replacement for the older Pise tools).  The Pise modules were in
>> BioPerl-Run, but they were deprecated a few years ago and removed  
>> from the
>> latest BioPerl-Run releases b/c the remote service is no longer  
>> active;
>> there is no Perl-based replacement for Mobyle interaction.
>>
>> Have you thought about just using the functionality within the
>> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure  
>> there
>> are
>> methods in place to do that.
>>
>> chris
>>
>> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
>>
>>> All,
>>>
>>> I'm in my first week with bioperl for a class project (although  
>>> I've used
>>> Perl for years). I've successfully run a clustal alignment of  
>>> several DNA
>>> sequences to produce the aln and dnd files. Now I would like to  
>>> generate
>> a
>>> consensus sequence from the alignment.  I see that Pise Cons does  
>>> this
>>> satisfactorily on my example data (
>>> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) .  
>>> However,
>> I'm
>>> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
>> distribution
>>> that I installed.
>>>
>>> Is this another module that I need to install separately?
>>>
>>> "cpan[2]> m /Pise/
>>> Module    Bio::Tools::Run::AnalysisFactory::Pise
>>> (BIRNEY/bioperl-run-1.4.tar.gz)
>>> Module    Bio::Tools::Run::PiseApplication
>> (BIRNEY/bioperl-run-1.4.tar.gz)"
>>>
>>> Bill S.
>>> _______________________________________________
>>> 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
>>
>> __________ Information from ESET Smart Security, version of virus  
>> signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus  
>> signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jun.yin at ucd.ie  Tue Oct 19 08:17:58 2010
From: jun.yin at ucd.ie (Jun Yin)
Date: Tue, 19 Oct 2010 09:17:58 +0100
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
 alignment
In-Reply-To: <AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
	<AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
Message-ID: <003501cb6f66$23c37330$6b4a5990$%yin@ucd.ie>

Hi, Bill,

 

There are several methods you can choose from Bio::SimpleAlign to build
subalignment. For example, you can use $aln->slice  to get part of your
alignment, and then you can calculate concensus sequence from subalignment.
Another method $aln->remove_gaps, which can remove gap containing columns.

 

Cheers,

Jun Yin

Ph.D. student in U.C.D.

 

Bioinformatics Laboratory

Conway Institute

University College Dublin

 

From: Bill Stephens [mailto:grapeguy at gmail.com] 
Sent: Tuesday, October 19, 2010 1:03 AM
To: Jun Yin
Cc: Chris Fields; bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
alignment

 

So, I've got the SimpleAlign running. It looks like it's running the
alignment based upon the input sequence location only (first residue from
each sequence).  This is not what I need. 

I'm back to to clustal, tcoffee or dalign.

Bill

On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:

Hi, Bill,

You may consider to use consensus_iupac or consensus_string methods in
Bio::SimpleAlign to generate consensus sequence.

Cheers,
Jun Yin
Ph.D. student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Monday, October 18, 2010 3:55 PM
To: Bill Stephens
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
alignment

Bill,

Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
replacement for the older Pise tools).  The Pise modules were in
BioPerl-Run, but they were deprecated a few years ago and removed from the
latest BioPerl-Run releases b/c the remote service is no longer active;
there is no Perl-based replacement for Mobyle interaction.

Have you thought about just using the functionality within the
Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there are
methods in place to do that.

chris

On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:

> All,
>
> I'm in my first week with bioperl for a class project (although I've used
> Perl for years). I've successfully run a clustal alignment of several DNA
> sequences to produce the aln and dnd files. Now I would like to generate a
> consensus sequence from the alignment.  I see that Pise Cons does this
> satisfactorily on my example data (
> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
distribution
> that I installed.
>
> Is this another module that I need to install separately?
>
> "cpan[2]> m /Pise/
> Module    Bio::Tools::Run::AnalysisFactory::Pise
> (BIRNEY/bioperl-run-1.4.tar.gz)
> Module    Bio::Tools::Run::PiseApplication
(BIRNEY/bioperl-run-1.4.tar.gz)"
>
> Bill S.
> _______________________________________________
> 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

__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com




__________ Information from ESET Smart Security, version of virus signature
database 5377 (20100818) __________

The message was checked by ESET Smart Security.

http://www.eset.com



 



From joseramonblas at gmail.com  Tue Oct 19 09:34:12 2010
From: joseramonblas at gmail.com (=?ISO-8859-1?Q?Jos=E9_Ram=F3n_Blas_Pastor?=)
Date: Tue, 19 Oct 2010 11:34:12 +0200
Subject: [Bioperl-l] correlated mutations analysis
Message-ID: <AANLkTimtudsQqppZtVz2+cCxKZ7gxEKXuHYPg85TC87M@mail.gmail.com>

Hi,

I have 2 protein sequences (or more). I want...
-to perform an analysis of correlated mutations in these proteins
(considering variations across 10 or 20 sps)
-obtain an statistical parameter on the significance of these mutations to
predict/hint interacting residues

Can you help me in this issue?. (Bioperl or not bioperl-based solutions are
welcome)

Thank you very much.

JR

-- 
Jos? Ram?n Blas - PhD
Dept. Biochemistry - Medicine School
University of Castilla-La Mancha

C Almansa, 14
02006 Albacete (Spain)



From cjfields at illinois.edu  Tue Oct 19 15:47:16 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 19 Oct 2010 10:47:16 -0500
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
	<AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
Message-ID: <16EDEBED-BAD4-4D57-B51B-C3234D1E8C39@illinois.edu>

Bio::SimpleAlign is the class that contains the alignment data; it does not generate the alignment for you.  You can use modules from BioPerl-Run that run ClustalW, MUSCLE, T-Coffee, etc to get a Bio::SimpleAlign instance, or parse the already-generated alignment output via Bio::AlignIO.

>From the Bio::Tools::Run::Alignment::ClustalW docs:

=================================================================

  #  Build a clustalw alignment factory
  @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
  $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);

  #  Pass the factory a list of sequences to be aligned.	
  $inputfilename = 't/data/cysprot.fa';
  $aln = $factory->align($inputfilename); # $aln is a SimpleAlign object.

  # ...or
  $seq_array_ref = \@seq_array;

  # where @seq_array is an array of Bio::Seq objects
  $aln = $factory->align($seq_array_ref);

=================================================================

$aln is a Bio::SimpleAlign derived from ClustalW output.  

>From Bio::SimpleAlign (note the use of Bio::AlignIO):

=================================================================

  # Use Bio::AlignIO to read in the alignment
  $str = Bio::AlignIO->new(-file => 't/data/testaln.pfam');
  $aln = $str->next_aln();

  # Describe
  print $aln->length;
  print $aln->num_residues;
  print $aln->is_flush;
  print $aln->num_sequences;
  print $aln->score;
  print $aln->percentage_identity;
  print $aln->consensus_string(50);

=================================================================

Note the consensus_string() method:

 Title     : consensus_string
 Usage     : $str = $ali->consensus_string($threshold_percent)
 Function  : Makes a strict consensus
 Returns   : Consensus string
 Argument  : Optional treshold ranging from 0 to 100.
             The consensus residue has to appear at least threshold %
             of the sequences at a given location, otherwise a '?'
             character will be placed at that location.
             (Default value = 0%)

chris

On Oct 18, 2010, at 7:02 PM, Bill Stephens wrote:

> So, I've got the SimpleAlign running. It looks like it's running the
> alignment based upon the input sequence location only (first residue from
> each sequence).  This is not what I need.
> 
> I'm back to to clustal, tcoffee or dalign.
> 
> Bill
> 
> On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:
> 
>> Hi, Bill,
>> 
>> You may consider to use consensus_iupac or consensus_string methods in
>> Bio::SimpleAlign to generate consensus sequence.
>> 
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>> 
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>> 
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
>> Sent: Monday, October 18, 2010 3:55 PM
>> To: Bill Stephens
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
>> alignment
>> 
>> Bill,
>> 
>> Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
>> replacement for the older Pise tools).  The Pise modules were in
>> BioPerl-Run, but they were deprecated a few years ago and removed from the
>> latest BioPerl-Run releases b/c the remote service is no longer active;
>> there is no Perl-based replacement for Mobyle interaction.
>> 
>> Have you thought about just using the functionality within the
>> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there
>> are
>> methods in place to do that.
>> 
>> chris
>> 
>> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
>> 
>>> All,
>>> 
>>> I'm in my first week with bioperl for a class project (although I've used
>>> Perl for years). I've successfully run a clustal alignment of several DNA
>>> sequences to produce the aln and dnd files. Now I would like to generate
>> a
>>> consensus sequence from the alignment.  I see that Pise Cons does this
>>> satisfactorily on my example data (
>>> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However,
>> I'm
>>> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
>> distribution
>>> that I installed.
>>> 
>>> Is this another module that I need to install separately?
>>> 
>>> "cpan[2]> m /Pise/
>>> Module    Bio::Tools::Run::AnalysisFactory::Pise
>>> (BIRNEY/bioperl-run-1.4.tar.gz)
>>> Module    Bio::Tools::Run::PiseApplication
>> (BIRNEY/bioperl-run-1.4.tar.gz)"
>>> 
>>> Bill S.
>>> _______________________________________________
>>> 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
>> 
>> __________ Information from ESET Smart Security, version of virus signature
>> database 5377 (20100818) __________
>> 
>> The message was checked by ESET Smart Security.
>> 
>> http://www.eset.com
>> 
>> 
>> 
>> 
>> __________ Information from ESET Smart Security, version of virus signature
>> database 5377 (20100818) __________
>> 
>> The message was checked by ESET Smart Security.
>> 
>> http://www.eset.com
>> 
>> 
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From td8pub at gmail.com  Tue Oct 19 17:28:07 2010
From: td8pub at gmail.com (T D)
Date: Tue, 19 Oct 2010 13:28:07 -0400
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
Message-ID: <AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>

Hi,

I'm new to BioPerl and Perl in general, and I'm trying to get
StandAloneBlastPlus to run. I got the latest versions using git and
downloaded bioperl-live  and bioperl-run.  I am having issues with Perl not
finding modules. Here is my error:

Can't locate IPC/Run.pm in @INC

Where is this module located? I am running Windows 7. I did a search for the
Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
Run.pm the older version? I have Perl v5.12.1 installed.

Thanks in advance!
Tracey


From cjfields at illinois.edu  Tue Oct 19 17:33:19 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 19 Oct 2010 12:33:19 -0500
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
	<AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>
Message-ID: <9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>

No, IPC::Run is different than IPC::Run3:

http://search.cpan.org/dist/IPC-Run/
http://search.cpan.org/dist/IPC-Run3/

Both should work under Windows, not sure about Windows7 but I can't see why they wouldn't work.

chris

On Oct 19, 2010, at 12:28 PM, T D wrote:

> Hi,
> 
> I'm new to BioPerl and Perl in general, and I'm trying to get
> StandAloneBlastPlus to run. I got the latest versions using git and
> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl not
> finding modules. Here is my error:
> 
> Can't locate IPC/Run.pm in @INC
> 
> Where is this module located? I am running Windows 7. I did a search for the
> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
> Run.pm the older version? I have Perl v5.12.1 installed.
> 
> Thanks in advance!
> Tracey
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From td8pub at gmail.com  Tue Oct 19 13:27:20 2010
From: td8pub at gmail.com (T D)
Date: Tue, 19 Oct 2010 09:27:20 -0400
Subject: [Bioperl-l] IPC/Run.pm?
Message-ID: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>

Hi,

I'm new to BioPerl and I'm trying to get StandAloneBlastPlus to run. I got
the latest versions using git and downloaded bioperl-live and and
bioperl-run.  I am having issues with Perl not finding modules. Here is my
error:

Can't locate IPC/Run.pm in @INC

Where is this module located? I am running Windows 7. I did a search for the
Run.pm and could only find IPC/*Run3.pm* under my Perl installation.

Thanks in advance!
Tracey


From anjan.purkayastha at gmail.com  Tue Oct 19 17:49:11 2010
From: anjan.purkayastha at gmail.com (ANJAN PURKAYASTHA)
Date: Tue, 19 Oct 2010 13:49:11 -0400
Subject: [Bioperl-l] Help in retrieving the DEFINITION line
Message-ID: <AANLkTimC=1mD3YBys8mOe9AUVZgo3QeNiWSydRRrfrNu@mail.gmail.com>

Hi,
I need to retrieve the DEFINITION line of a GenBank file, given the GenBank
accession ID.
The following code does not seem to do it:

use strict;
use warnings;
use Bio::Perl;
use Bio::DB::GenBank;
my $gb= new Bio::DB::GenBank;

open(F, "test_id");

while(<F>){
chomp;
my $id= $_;
my $seq= $gb->get_Seq_by_acc("$id");
my $anno_collection = $seq->annotation;
my @annotations = $anno_collection->get_Annotations('definition');
print ("@annotations\n");
}

Any thoughts on how to get this done will be deeply appreciated.
Thanks,
Anjan

-- 
===================================
anjan purkayastha, phd.
research associate
fas center for systems biology,
harvard university
52 oxford street
cambridge ma 02138
phone-703.740.6939
===================================


From David.Messina at sbc.su.se  Tue Oct 19 20:03:08 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 19 Oct 2010 16:03:08 -0400
Subject: [Bioperl-l] Help in retrieving the DEFINITION line
In-Reply-To: <AANLkTimC=1mD3YBys8mOe9AUVZgo3QeNiWSydRRrfrNu@mail.gmail.com>
References: <AANLkTimC=1mD3YBys8mOe9AUVZgo3QeNiWSydRRrfrNu@mail.gmail.com>
Message-ID: <0E6779A3-BD3E-469F-8C23-8BFA92135915@sbc.su.se>

Hi Anjan,

You can get to the definition directly, via the desc() method.

So, this works:

use strict;
use warnings;
use Bio::Perl;
use Bio::DB::GenBank;
my $gb= new Bio::DB::GenBank;

open(F, "test_id");

while(<F>){
	chomp;
	my $id= $_;
	my $seq= $gb->get_Seq_by_acc("$id");

	# I added these lines:
	my $definition      = $seq->desc;
        print $definition, "\n";}
}



Dave



From td8pub at gmail.com  Tue Oct 19 20:38:32 2010
From: td8pub at gmail.com (T D)
Date: Tue, 19 Oct 2010 16:38:32 -0400
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
	<AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>
	<9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>
Message-ID: <AANLkTi=LKy-UMPkQkDXN=83sjRFdJMgOn7Du9vVdh6x7@mail.gmail.com>

Thank you. I downloaded IPC::Run and the code seems to be working now. Is
Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?


On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:

> No, IPC::Run is different than IPC::Run3:
>
> http://search.cpan.org/dist/IPC-Run/
> http://search.cpan.org/dist/IPC-Run3/
>
> Both should work under Windows, not sure about Windows7 but I can't see why
> they wouldn't work.
>
> chris
>
> On Oct 19, 2010, at 12:28 PM, T D wrote:
>
> > Hi,
> >
> > I'm new to BioPerl and Perl in general, and I'm trying to get
> > StandAloneBlastPlus to run. I got the latest versions using git and
> > downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
> not
> > finding modules. Here is my error:
> >
> > Can't locate IPC/Run.pm in @INC
> >
> > Where is this module located? I am running Windows 7. I did a search for
> the
> > Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
> > Run.pm the older version? I have Perl v5.12.1 installed.
> >
> > Thanks in advance!
> > Tracey
> > _______________________________________________
> > 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 Oct 19 20:45:55 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 19 Oct 2010 15:45:55 -0500
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <AANLkTi=LKy-UMPkQkDXN=83sjRFdJMgOn7Du9vVdh6x7@mail.gmail.com>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>
	<AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>
	<9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>
	<AANLkTi=LKy-UMPkQkDXN=83sjRFdJMgOn7Du9vVdh6x7@mail.gmail.com>
Message-ID: <840CF652-BAE0-4DD6-A375-30A817F20351@illinois.edu>

If you mean IPC::Run, I'm not sure.  I don't think BioPerl-Run was ever a part of Strawberry Perl Pro.

I do know there are some warnings that will pop up with BioPerl when using perl 5.12; these have been fixed in the github repo but haven't made their way into a release yet.

chris

On Oct 19, 2010, at 3:38 PM, T D wrote:

> Thank you. I downloaded IPC::Run and the code seems to be working now. Is
> Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?
> 
> 
> On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> No, IPC::Run is different than IPC::Run3:
>> 
>> http://search.cpan.org/dist/IPC-Run/
>> http://search.cpan.org/dist/IPC-Run3/
>> 
>> Both should work under Windows, not sure about Windows7 but I can't see why
>> they wouldn't work.
>> 
>> chris
>> 
>> On Oct 19, 2010, at 12:28 PM, T D wrote:
>> 
>>> Hi,
>>> 
>>> I'm new to BioPerl and Perl in general, and I'm trying to get
>>> StandAloneBlastPlus to run. I got the latest versions using git and
>>> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
>> not
>>> finding modules. Here is my error:
>>> 
>>> Can't locate IPC/Run.pm in @INC
>>> 
>>> Where is this module located? I am running Windows 7. I did a search for
>> the
>>> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
>>> Run.pm the older version? I have Perl v5.12.1 installed.
>>> 
>>> Thanks in advance!
>>> Tracey
>>> _______________________________________________
>>> 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 shalabh.sharma7 at gmail.com  Wed Oct 20 15:00:26 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 20 Oct 2010 11:00:26 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
Message-ID: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>

Hi All,
        Is there any module for mummer in Bioperl?

Also i need some suggestions and ideas (i think this is the best place to
ask).
I am working with huge data (around 200 million illumina reads), earlier i
was using blastx and other similar approaches to annotate but now i think
thats not possible, i would be very grateful if anyone can give me some idea
regarding this.

Thanks
Shalabh


From David.Messina at sbc.su.se  Wed Oct 20 15:25:02 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Wed, 20 Oct 2010 11:25:02 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
Message-ID: <C3E45590-33DD-4A27-87FF-533D8E8C9C09@sbc.su.se>


> Is there any module for mummer in Bioperl?

Did you try searching for mummer on the bioperl website?




From shalabh.sharma7 at gmail.com  Wed Oct 20 15:31:09 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 20 Oct 2010 11:31:09 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <C3E45590-33DD-4A27-87FF-533D8E8C9C09@sbc.su.se>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
	<C3E45590-33DD-4A27-87FF-533D8E8C9C09@sbc.su.se>
Message-ID: <AANLkTim3ig2Aa+=TUqb0Cr5HsH0f-eHoi+aZCX-pctEp@mail.gmail.com>

Yes , i did but its saying there aren't any modules available so i jsu
wanted to make sure.

-Shalabh


On Wed, Oct 20, 2010 at 11:25 AM, Dave Messina <David.Messina at sbc.su.se>wrote:

>
> > Is there any module for mummer in Bioperl?
>
> Did you try searching for mummer on the bioperl website?
>
>
>


From jimhu at tamu.edu  Wed Oct 20 15:27:08 2010
From: jimhu at tamu.edu (Jim Hu)
Date: Wed, 20 Oct 2010 10:27:08 -0500
Subject: [Bioperl-l] treeio->write_tree problem
Message-ID: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>

Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.

Jim

use Data::Dumper;
use Bio::TreeIO;
my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
                            -format => "newick");
while( my $tree = $treeio->next_tree ) {
	$treeio->write_tree($tree);
	print Dumper($tree);

}

=====================================
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 Oct 20 15:45:45 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 10:45:45 -0500
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
Message-ID: <572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>

On Oct 20, 2010, at 10:00 AM, shalabh sharma wrote:

> Hi All,
>        Is there any module for mummer in Bioperl?
> 
> Also i need some suggestions and ideas (i think this is the best place to
> ask).
> I am working with huge data (around 200 million illumina reads), earlier i
> was using blastx and other similar approaches to annotate but now i think
> thats not possible, i would be very grateful if anyone can give me some idea
> regarding this.
> 
> Thanks
> Shalabh

Hard to say unless we know a little more about what you are attempting to do.  Not sure why you are using mummer here, but...

This is something fairly well-covered in the literature for most use cases, and on places like seqanswers.  If you are doing something like aligning reads to reference genome(s) or set of gene models, you should be using something like bowtie/tophat, bwa, etc., with the output in SAM (BioPerl has perl wrappers for most of these modules).  

You can also do the same for metagenome analyses, but you may need to run BLAST and convert to SAM (maybe that's what you are doing?).  The samtools package comes with perl scripts to do that and can be further used to sort the matches, convert/index a BAM file for fast accession, etc.  From there you can then use tools like Bio::DB::SAM, R/BioConductor/RSamtools, or similar to access the sequences, find coverage statistics, run SNP calls, etc.

And, for the record, we do have an experimental mummer parser, but I believe it lies in a branch at the moment (don't think it has been merged yet):

http://github.com/bioperl/bioperl-live/tree/topic/bug-2701

chris


From cjfields at illinois.edu  Wed Oct 20 15:46:42 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 10:46:42 -0500
Subject: [Bioperl-l] treeio->write_tree problem
In-Reply-To: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
References: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
Message-ID: <112B35F0-77B6-4B46-9E3A-AAB840E7D349@illinois.edu>

Try '-format => "nhx"'.

chris

On Oct 20, 2010, at 10:27 AM, Jim Hu wrote:

> Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.
> 
> Jim
> 
> use Data::Dumper;
> use Bio::TreeIO;
> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>                            -format => "newick");
> while( my $tree = $treeio->next_tree ) {
> 	$treeio->write_tree($tree);
> 	print Dumper($tree);
> 
> }
> 
> =====================================
> Jim Hu
> Associate Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jimhu at tamu.edu  Wed Oct 20 16:16:52 2010
From: jimhu at tamu.edu (Jim Hu)
Date: Wed, 20 Oct 2010 11:16:52 -0500
Subject: [Bioperl-l] treeio->write_tree problem
In-Reply-To: <534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>
References: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
	<534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>
Message-ID: <BADE3FC8-A40F-4832-8C63-B20CB7C40631@tamu.edu>

Doh!  I suspected it was something brain-dead that I was doing.

Thanks very much.  That worked.

Jim

On Oct 20, 2010, at 11:01 AM, Adam Witney wrote:

> 
> you are writing to your input stream. I think you need to create a separate output stream. Maybe something like this (untested):
> 
> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>                           -format => "newick");
> 
> my $treeio_out = new Bio::TreeIO(-fh   => \*STDOUT,
>                           -format => "newick");
> 
> while( my $tree = $treeio->next_tree ) {
> 	$treeio_out->write_tree($tree);
> 	print Dumper($tree);
> }
> 
> 
> 
> On 20 Oct 2010, at 16:27, Jim Hu wrote:
> 
>> Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.
>> 
>> Jim
>> 
>> use Data::Dumper;
>> use Bio::TreeIO;
>> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>>                           -format => "newick");
>> while( my $tree = $treeio->next_tree ) {
>> 	$treeio->write_tree($tree);
>> 	print Dumper($tree);
>> 
>> }
>> 
>> =====================================
>> Jim Hu
>> Associate Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>> 
>> 
>> 
>> _______________________________________________
>> 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 awitney at sgul.ac.uk  Wed Oct 20 16:01:45 2010
From: awitney at sgul.ac.uk (Adam Witney)
Date: Wed, 20 Oct 2010 17:01:45 +0100
Subject: [Bioperl-l] treeio->write_tree problem
In-Reply-To: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
References: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
Message-ID: <534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>


you are writing to your input stream. I think you need to create a separate output stream. Maybe something like this (untested):

my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
                           -format => "newick");

my $treeio_out = new Bio::TreeIO(-fh   => \*STDOUT,
                           -format => "newick");

while( my $tree = $treeio->next_tree ) {
	$treeio_out->write_tree($tree);
	print Dumper($tree);
}



On 20 Oct 2010, at 16:27, Jim Hu wrote:

> Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.
> 
> Jim
> 
> use Data::Dumper;
> use Bio::TreeIO;
> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>                            -format => "newick");
> while( my $tree = $treeio->next_tree ) {
> 	$treeio->write_tree($tree);
> 	print Dumper($tree);
> 
> }
> 
> =====================================
> Jim Hu
> Associate Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
> 
> 
> 
> _______________________________________________
> 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 Oct 20 16:35:40 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 20 Oct 2010 12:35:40 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
	<572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>
Message-ID: <AANLkTimfSXRn1u-wvqSGM+B=j0Ohhnu5SGDcO413pSBm@mail.gmail.com>

Hey Chris,
             Thanks for the reply , it was really useful.
Actually you are right, it is metagenomics sample. The thing is i've never
worked with that huge amount of data, so i am trying to test some alignment
programs (i am just trying to see if i can avoid blastx) so i am trying all
the available programs.

Blasting 200 million reads doesn't seems a right option (may be i will go
with assembly then blasting it).

Thanks
Shalabh


On Wed, Oct 20, 2010 at 11:45 AM, Chris Fields <cjfields at illinois.edu>wrote:

> On Oct 20, 2010, at 10:00 AM, shalabh sharma wrote:
>
> > Hi All,
> >        Is there any module for mummer in Bioperl?
> >
> > Also i need some suggestions and ideas (i think this is the best place to
> > ask).
> > I am working with huge data (around 200 million illumina reads), earlier
> i
> > was using blastx and other similar approaches to annotate but now i think
> > thats not possible, i would be very grateful if anyone can give me some
> idea
> > regarding this.
> >
> > Thanks
> > Shalabh
>
> Hard to say unless we know a little more about what you are attempting to
> do.  Not sure why you are using mummer here, but...
>
> This is something fairly well-covered in the literature for most use cases,
> and on places like seqanswers.  If you are doing something like aligning
> reads to reference genome(s) or set of gene models, you should be using
> something like bowtie/tophat, bwa, etc., with the output in SAM (BioPerl has
> perl wrappers for most of these modules).
>
> You can also do the same for metagenome analyses, but you may need to run
> BLAST and convert to SAM (maybe that's what you are doing?).  The samtools
> package comes with perl scripts to do that and can be further used to sort
> the matches, convert/index a BAM file for fast accession, etc.  From there
> you can then use tools like Bio::DB::SAM, R/BioConductor/RSamtools, or
> similar to access the sequences, find coverage statistics, run SNP calls,
> etc.
>
> And, for the record, we do have an experimental mummer parser, but I
> believe it lies in a branch at the moment (don't think it has been merged
> yet):
>
> http://github.com/bioperl/bioperl-live/tree/topic/bug-2701
>
> chris


From cjfields at illinois.edu  Wed Oct 20 18:15:09 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 13:15:09 -0500
Subject: [Bioperl-l] treeio->write_tree problem
In-Reply-To: <534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>
References: <84ED8CA0-7561-41D5-B870-0CA89F548555@tamu.edu>
	<534641DC-2888-4D8E-892A-80444F4AFDD4@sgul.ac.uk>
Message-ID: <8A7F4396-D88F-438E-B045-F2CD58293DD1@illinois.edu>

Nice catch!  Completely missed that.

chris

On Oct 20, 2010, at 11:01 AM, Adam Witney wrote:

> 
> you are writing to your input stream. I think you need to create a separate output stream. Maybe something like this (untested):
> 
> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>                           -format => "newick");
> 
> my $treeio_out = new Bio::TreeIO(-fh   => \*STDOUT,
>                           -format => "newick");
> 
> while( my $tree = $treeio->next_tree ) {
> 	$treeio_out->write_tree($tree);
> 	print Dumper($tree);
> }
> 
> 
> 
> On 20 Oct 2010, at 16:27, Jim Hu wrote:
> 
>> Help! In the script below, I'm not getting any output from treeio->write_tree.  Dumper shows that the tree is populated.
>> 
>> Jim
>> 
>> use Data::Dumper;
>> use Bio::TreeIO;
>> my $treeio = new Bio::TreeIO(-file   => "PF03466_seed.nhx.txt",
>>                           -format => "newick");
>> while( my $tree = $treeio->next_tree ) {
>> 	$treeio->write_tree($tree);
>> 	print Dumper($tree);
>> 
>> }
>> 
>> =====================================
>> Jim Hu
>> Associate Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>> 
>> 
>> 
>> _______________________________________________
>> 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  Wed Oct 20 18:25:09 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 13:25:09 -0500
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <AANLkTimfSXRn1u-wvqSGM+B=j0Ohhnu5SGDcO413pSBm@mail.gmail.com>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
	<572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>
	<AANLkTimfSXRn1u-wvqSGM+B=j0Ohhnu5SGDcO413pSBm@mail.gmail.com>
Message-ID: <8B2DB10D-0E81-4426-8678-893669DFD0F9@illinois.edu>

I recall there being a lot of tools available for these.  In particular, one of my colleagues has used MEGAN with some success:

http://www-ab.informatik.uni-tuebingen.de/software/megan

If the sample is from a specific host (i.e. gut microbiome, etc), you can set up initial short read runs that act to filter out sequences you might not be interested in (namely those that belong to the host), then run alignments against more focused databases (rRNA, for instance, if one is doing meta-transcriptomic analyses).  Beyond that, I agree that assembly should be included early in the analysis, if it isn't already the initial step.

chris

On Oct 20, 2010, at 11:35 AM, shalabh sharma wrote:

> Hey Chris,
>              Thanks for the reply , it was really useful.
> Actually you are right, it is metagenomics sample. The thing is i've never worked with that huge amount of data, so i am trying to test some alignment programs (i am just trying to see if i can avoid blastx) so i am trying all the available programs.
> 
> Blasting 200 million reads doesn't seems a right option (may be i will go with assembly then blasting it).
> 
> Thanks
> Shalabh
> 
> 
> On Wed, Oct 20, 2010 at 11:45 AM, Chris Fields <cjfields at illinois.edu> wrote:
> On Oct 20, 2010, at 10:00 AM, shalabh sharma wrote:
> 
> > Hi All,
> >        Is there any module for mummer in Bioperl?
> >
> > Also i need some suggestions and ideas (i think this is the best place to
> > ask).
> > I am working with huge data (around 200 million illumina reads), earlier i
> > was using blastx and other similar approaches to annotate but now i think
> > thats not possible, i would be very grateful if anyone can give me some idea
> > regarding this.
> >
> > Thanks
> > Shalabh
> 
> Hard to say unless we know a little more about what you are attempting to do.  Not sure why you are using mummer here, but...
> 
> This is something fairly well-covered in the literature for most use cases, and on places like seqanswers.  If you are doing something like aligning reads to reference genome(s) or set of gene models, you should be using something like bowtie/tophat, bwa, etc., with the output in SAM (BioPerl has perl wrappers for most of these modules).
> 
> You can also do the same for metagenome analyses, but you may need to run BLAST and convert to SAM (maybe that's what you are doing?).  The samtools package comes with perl scripts to do that and can be further used to sort the matches, convert/index a BAM file for fast accession, etc.  From there you can then use tools like Bio::DB::SAM, R/BioConductor/RSamtools, or similar to access the sequences, find coverage statistics, run SNP calls, etc.
> 
> And, for the record, we do have an experimental mummer parser, but I believe it lies in a branch at the moment (don't think it has been merged yet):
> 
> http://github.com/bioperl/bioperl-live/tree/topic/bug-2701
> 
> chris
> 




From shalabh.sharma7 at gmail.com  Wed Oct 20 18:35:54 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 20 Oct 2010 14:35:54 -0400
Subject: [Bioperl-l] Mummer parser and data anlysis
In-Reply-To: <8B2DB10D-0E81-4426-8678-893669DFD0F9@illinois.edu>
References: <AANLkTintTTxPf9zEHApZBLDoqtA5aOxdp4s1YtrxRK60@mail.gmail.com>
	<572A4CDD-E370-4743-867B-02E7B2521092@illinois.edu>
	<AANLkTimfSXRn1u-wvqSGM+B=j0Ohhnu5SGDcO413pSBm@mail.gmail.com>
	<8B2DB10D-0E81-4426-8678-893669DFD0F9@illinois.edu>
Message-ID: <AANLkTinxFKdMkOaejxpFDN-qf0pF=Lg7brHHvqYuXk4s@mail.gmail.com>

I have used MEGAN a lot in past, but again it takes blast files as input and
here i just want to avoid blast.
The problem is its environmental sample so i cant throw any of the data.

I know its not a bioperl question but i was just wondering is there any
program that can align my reads against a huge database at amino acid level
(like with refseq or subset of refseq).
or even alignment is a good option?

I really appreciate your input.

Thanks
Shalabh


On Wed, Oct 20, 2010 at 2:25 PM, Chris Fields <cjfields at illinois.edu> wrote:

> I recall there being a lot of tools available for these.  In particular,
> one of my colleagues has used MEGAN with some success:
>
> http://www-ab.informatik.uni-tuebingen.de/software/megan
>
> If the sample is from a specific host (i.e. gut microbiome, etc), you can
> set up initial short read runs that act to filter out sequences you might
> not be interested in (namely those that belong to the host), then run
> alignments against more focused databases (rRNA, for instance, if one is
> doing meta-transcriptomic analyses).  Beyond that, I agree that assembly
> should be included early in the analysis, if it isn't already the initial
> step.
>
> chris
>
> On Oct 20, 2010, at 11:35 AM, shalabh sharma wrote:
>
> > Hey Chris,
> >              Thanks for the reply , it was really useful.
> > Actually you are right, it is metagenomics sample. The thing is i've
> never worked with that huge amount of data, so i am trying to test some
> alignment programs (i am just trying to see if i can avoid blastx) so i am
> trying all the available programs.
> >
> > Blasting 200 million reads doesn't seems a right option (may be i will go
> with assembly then blasting it).
> >
> > Thanks
> > Shalabh
> >
> >
> > On Wed, Oct 20, 2010 at 11:45 AM, Chris Fields <cjfields at illinois.edu>
> wrote:
> > On Oct 20, 2010, at 10:00 AM, shalabh sharma wrote:
> >
> > > Hi All,
> > >        Is there any module for mummer in Bioperl?
> > >
> > > Also i need some suggestions and ideas (i think this is the best place
> to
> > > ask).
> > > I am working with huge data (around 200 million illumina reads),
> earlier i
> > > was using blastx and other similar approaches to annotate but now i
> think
> > > thats not possible, i would be very grateful if anyone can give me some
> idea
> > > regarding this.
> > >
> > > Thanks
> > > Shalabh
> >
> > Hard to say unless we know a little more about what you are attempting to
> do.  Not sure why you are using mummer here, but...
> >
> > This is something fairly well-covered in the literature for most use
> cases, and on places like seqanswers.  If you are doing something like
> aligning reads to reference genome(s) or set of gene models, you should be
> using something like bowtie/tophat, bwa, etc., with the output in SAM
> (BioPerl has perl wrappers for most of these modules).
> >
> > You can also do the same for metagenome analyses, but you may need to run
> BLAST and convert to SAM (maybe that's what you are doing?).  The samtools
> package comes with perl scripts to do that and can be further used to sort
> the matches, convert/index a BAM file for fast accession, etc.  From there
> you can then use tools like Bio::DB::SAM, R/BioConductor/RSamtools, or
> similar to access the sequences, find coverage statistics, run SNP calls,
> etc.
> >
> > And, for the record, we do have an experimental mummer parser, but I
> believe it lies in a branch at the moment (don't think it has been merged
> yet):
> >
> > http://github.com/bioperl/bioperl-live/tree/topic/bug-2701
> >
> > chris
> >
>
>


From rmb32 at cornell.edu  Thu Oct 21 00:27:36 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Wed, 20 Oct 2010 17:27:36 -0700
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <840CF652-BAE0-4DD6-A375-30A817F20351@illinois.edu>
References: <AANLkTikBHHL30X8AqEiSgiHOeOG=MPNGFksUdA2PQRYD@mail.gmail.com>	<AANLkTi=G_0pf5x-7sDmhuyK3xsh1oYmK8i63oBDtxs6O@mail.gmail.com>	<9FF796A1-BFC1-41AA-A14F-C362252818EC@illinois.edu>	<AANLkTi=LKy-UMPkQkDXN=83sjRFdJMgOn7Du9vVdh6x7@mail.gmail.com>
	<840CF652-BAE0-4DD6-A375-30A817F20351@illinois.edu>
Message-ID: <4CBF88F8.2030601@cornell.edu>

Ah, the joys of optional deps.

You know, bioperl-run does not have that many deps right now.  Why don't 
we just make those optional ones required?

R


Chris Fields wrote:
> If you mean IPC::Run, I'm not sure.  I don't think BioPerl-Run was ever a part of Strawberry Perl Pro.
> 
> I do know there are some warnings that will pop up with BioPerl when using perl 5.12; these have been fixed in the github repo but haven't made their way into a release yet.
> 
> chris
> 
> On Oct 19, 2010, at 3:38 PM, T D wrote:
> 
>> Thank you. I downloaded IPC::Run and the code seems to be working now. Is
>> Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?
>>
>>
>> On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>
>>> No, IPC::Run is different than IPC::Run3:
>>>
>>> http://search.cpan.org/dist/IPC-Run/
>>> http://search.cpan.org/dist/IPC-Run3/
>>>
>>> Both should work under Windows, not sure about Windows7 but I can't see why
>>> they wouldn't work.
>>>
>>> chris
>>>
>>> On Oct 19, 2010, at 12:28 PM, T D wrote:
>>>
>>>> Hi,
>>>>
>>>> I'm new to BioPerl and Perl in general, and I'm trying to get
>>>> StandAloneBlastPlus to run. I got the latest versions using git and
>>>> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
>>> not
>>>> finding modules. Here is my error:
>>>>
>>>> Can't locate IPC/Run.pm in @INC
>>>>
>>>> Where is this module located? I am running Windows 7. I did a search for
>>> the
>>>> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
>>>> Run.pm the older version? I have Perl v5.12.1 installed.
>>>>
>>>> Thanks in advance!
>>>> Tracey
>>>> _______________________________________________
>>>> 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 maj at fortinbras.us  Thu Oct 21 01:21:56 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Thu, 21 Oct 2010 01:21:56 +0000
Subject: [Bioperl-l] IPC/Run.pm?
Message-ID: <W2403825015265021287624116@webmail11>

I would +1 making IPC::Run required. It's got some nice features and it much safer than system(). Might even want to make it a dev recommendation for all system calls. MAJ

>-----Original Message-----
>From: Robert Buels [mailto:rmb32 at cornell.edu]
>Sent: Wednesday, October 20, 2010 08:27 PM
>To: 'Chris Fields'
>Cc: bioperl-l at lists.open-bio.org
>Subject: Re: [Bioperl-l] IPC/Run.pm?
>
>Ah, the joys of optional deps.
>
>You know, bioperl-run does not have that many deps right now.  Why don't 
>we just make those optional ones required?
>
>R
>
>
>Chris Fields wrote:
>> If you mean IPC::Run, I'm not sure.  I don't think BioPerl-Run was ever a part of Strawberry Perl Pro.
>> 
>> I do know there are some warnings that will pop up with BioPerl when using perl 5.12; these have been fixed in the github repo but haven't made their way into a release yet.
>> 
>> chris
>> 
>> On Oct 19, 2010, at 3:38 PM, T D wrote:
>> 
>>> Thank you. I downloaded IPC::Run and the code seems to be working now. Is
>>> Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?
>>>
>>>
>>> On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>
>>>> No, IPC::Run is different than IPC::Run3:
>>>>
>>>> http://search.cpan.org/dist/IPC-Run/
>>>> http://search.cpan.org/dist/IPC-Run3/
>>>>
>>>> Both should work under Windows, not sure about Windows7 but I can't see why
>>>> they wouldn't work.
>>>>
>>>> chris
>>>>
>>>> On Oct 19, 2010, at 12:28 PM, T D wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I'm new to BioPerl and Perl in general, and I'm trying to get
>>>>> StandAloneBlastPlus to run. I got the latest versions using git and
>>>>> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
>>>> not
>>>>> finding modules. Here is my error:
>>>>>
>>>>> Can't locate IPC/Run.pm in @INC
>>>>>
>>>>> Where is this module located? I am running Windows 7. I did a search for
>>>> the
>>>>> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
>>>>> Run.pm the older version? I have Perl v5.12.1 installed.
>>>>>
>>>>> Thanks in advance!
>>>>> Tracey
>>>>> _______________________________________________
>>>>> 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 cjfields at illinois.edu  Thu Oct 21 01:54:48 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 20 Oct 2010 20:54:48 -0500
Subject: [Bioperl-l] IPC/Run.pm?
In-Reply-To: <W2403825015265021287624116@webmail11>
References: <W2403825015265021287624116@webmail11>
Message-ID: <697C7C00-5ED9-4A69-9F55-6C8C6F349DF4@illinois.edu>

+1.  Quite a few modules there use it.

chris

On Oct 20, 2010, at 8:21 PM, Mark A. Jensen wrote:

> I would +1 making IPC::Run required. It's got some nice features and it much safer than system(). Might even want to make it a dev recommendation for all system calls. MAJ
> 
>> -----Original Message-----
>> From: Robert Buels [mailto:rmb32 at cornell.edu]
>> Sent: Wednesday, October 20, 2010 08:27 PM
>> To: 'Chris Fields'
>> Cc: bioperl-l at lists.open-bio.org
>> Subject: Re: [Bioperl-l] IPC/Run.pm?
>> 
>> Ah, the joys of optional deps.
>> 
>> You know, bioperl-run does not have that many deps right now.  Why don't 
>> we just make those optional ones required?
>> 
>> R
>> 
>> 
>> Chris Fields wrote:
>>> If you mean IPC::Run, I'm not sure.  I don't think BioPerl-Run was ever a part of Strawberry Perl Pro.
>>> 
>>> I do know there are some warnings that will pop up with BioPerl when using perl 5.12; these have been fixed in the github repo but haven't made their way into a release yet.
>>> 
>>> chris
>>> 
>>> On Oct 19, 2010, at 3:38 PM, T D wrote:
>>> 
>>>> Thank you. I downloaded IPC::Run and the code seems to be working now. Is
>>>> Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?
>>>> 
>>>> 
>>>> On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>> 
>>>>> No, IPC::Run is different than IPC::Run3:
>>>>> 
>>>>> http://search.cpan.org/dist/IPC-Run/
>>>>> http://search.cpan.org/dist/IPC-Run3/
>>>>> 
>>>>> Both should work under Windows, not sure about Windows7 but I can't see why
>>>>> they wouldn't work.
>>>>> 
>>>>> chris
>>>>> 
>>>>> On Oct 19, 2010, at 12:28 PM, T D wrote:
>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I'm new to BioPerl and Perl in general, and I'm trying to get
>>>>>> StandAloneBlastPlus to run. I got the latest versions using git and
>>>>>> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
>>>>> not
>>>>>> finding modules. Here is my error:
>>>>>> 
>>>>>> Can't locate IPC/Run.pm in @INC
>>>>>> 
>>>>>> Where is this module located? I am running Windows 7. I did a search for
>>>>> the
>>>>>> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
>>>>>> Run.pm the older version? I have Perl v5.12.1 installed.
>>>>>> 
>>>>>> Thanks in advance!
>>>>>> Tracey
>>>>>> _______________________________________________
>>>>>> 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 ashwani.iiit at gmail.com  Thu Oct 21 08:39:22 2010
From: ashwani.iiit at gmail.com (ashwani sharma)
Date: Thu, 21 Oct 2010 14:09:22 +0530
Subject: [Bioperl-l] how to download PDB files using Bioperl script
Message-ID: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>

Hi All,


I have around 150 pdb file names and I need to download them from Protein
Data Bank. I wonder if someone could tell me how to do it by using Bioperl.

Thanks in advance.

Regards,
Ashwani


From hanbobio at 126.com  Tue Oct 19 11:50:07 2010
From: hanbobio at 126.com (yusheng liao)
Date: Tue, 19 Oct 2010 11:50:07 +0000 (UTC)
Subject: [Bioperl-l] Can't locate Bio/seqIO.pm in @INC
Message-ID: <loom.20101019T134347-528@post.gmane.org>

Can't locate Bio/seqIO.pm in @INC 
I try to run a .pl file to get multi sequences for t
he GenBank using the
Bioperl. The following were the error message:
linux:/home/liaoy # perl hsv-1.pl
Can't locate Bio/seqIO.pm in @INC (@INC contains:
/usr/lib/perl5/5.8.7/i586-linux-thread-multi /usr/lib/perl5/5.8.7
/usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.7 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .)
 at hsv-1.pl line 4.
BEGIN failed--compilation aborted at hsv-1.pl line 4.

what is the problem? And how to corret it? 



From cgzheng86 at gmail.com  Thu Oct 21 08:45:40 2010
From: cgzheng86 at gmail.com (Chaogu Zheng)
Date: Thu, 21 Oct 2010 01:45:40 -0700 (PDT)
Subject: [Bioperl-l] Failed to load module Bio::SeqIO::swiss
Message-ID: <63e01ab5-99f2-46a0-8901-3bdb24562c5f@g13g2000yqj.googlegroups.com>

I am extremely new to Bioperl and got a problem immediately after I
installed it.

I installed Bioperl-pm5100 and Bioperl-run-pm5100 using fink.
Everything seems to be fine. However, when I tried to retrieve some
sequences from swissprot, I found the following errors.

It seems the module Bio::SeqIO::swiss can not be loaded, though I
indeed found it under the correct directory. By the way, if I change
'swiss' to 'genbank' I can successfully run the program.

I don't know how to fix it. Anyone can help me?


Ryan

>>>>>>>>>>>>>>
Bio::SeqIO: swiss cannot be found
Exception
------------- EXCEPTION -------------
MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/
Stag.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-
multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-
multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/
5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/
Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/
5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/
5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /
Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/
Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/
5.10.0 .) at /sw/lib/perl5/5.10.0/Bio/Annotation/TagTree.pm line 123.
BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/
Annotation/TagTree.pm line 123.
Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/SeqIO/
swiss.pm line 208.
BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/SeqIO/
swiss.pm line 208.
Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/Root/Root.pm
line 439.

STACK Bio::Root::Root::_load_module /sw/lib/perl5/5.10.0/Bio/Root/
Root.pm:441
STACK (eval) /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:570
STACK Bio::SeqIO::_load_format_module /sw/lib/perl5/5.10.0/Bio/
SeqIO.pm:569
STACK Bio::SeqIO::new /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:389
STACK Bio::DB::WebDBSeqI::get_seq_stream /sw/lib/perl5/5.10.0/Bio/DB/
WebDBSeqI.pm:472
STACK Bio::DB::WebDBSeqI::get_Stream_by_acc /sw/lib/perl5/5.10.0/Bio/
DB/WebDBSeqI.pm:314
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
WebDBSeqI.pm:186
STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
STACK toplevel ./Documents/perl-programs/perl_test:8
-------------------------------------


For more information about the SeqIO system please see the SeqIO docs.
This includes ways of checking for formats at compile time, not run
time

------------- EXCEPTION -------------
MSG: acc P11217 does not exist
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
WebDBSeqI.pm:187
STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
STACK toplevel ./Documents/perl-programs/perl_test:8
-------------------------------------


From cjfields at illinois.edu  Thu Oct 21 15:02:35 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 21 Oct 2010 10:02:35 -0500
Subject: [Bioperl-l] Can't locate Bio/seqIO.pm in @INC
In-Reply-To: <loom.20101019T134347-528@post.gmane.org>
References: <loom.20101019T134347-528@post.gmane.org>
Message-ID: <9E5A48C0-4509-429B-8F16-9A1D1A440CC8@illinois.edu>

Check your spelling (note the caps below):

use Bio::SeqIO;

chris

On Oct 19, 2010, at 6:50 AM, yusheng liao wrote:

> Can't locate Bio/seqIO.pm in @INC 
> I try to run a .pl file to get multi sequences for t
> he GenBank using the
> Bioperl. The following were the error message:
> linux:/home/liaoy # perl hsv-1.pl
> Can't locate Bio/seqIO.pm in @INC (@INC contains:
> /usr/lib/perl5/5.8.7/i586-linux-thread-multi /usr/lib/perl5/5.8.7
> /usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.7 /usr/lib/perl5/site_perl
> /usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .)
> at hsv-1.pl line 4.
> BEGIN failed--compilation aborted at hsv-1.pl line 4.
> 
> what is the problem? And how to corret it? 
> 
> _______________________________________________
> 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 Oct 21 15:05:17 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 21 Oct 2010 10:05:17 -0500
Subject: [Bioperl-l] Failed to load module Bio::SeqIO::swiss
In-Reply-To: <63e01ab5-99f2-46a0-8901-3bdb24562c5f@g13g2000yqj.googlegroups.com>
References: <63e01ab5-99f2-46a0-8901-3bdb24562c5f@g13g2000yqj.googlegroups.com>
Message-ID: <23FDD4AF-3E56-4E05-AFD7-21A54DECD1C6@illinois.edu>

Like the error message says, you need to install Data::Stag (so, for some reason, this way left off).  However, I'm not sure why you are using fink as the version in stable is still 1.5.1; bioperl 1.6.1 is in fink-unstable.

chris

On Oct 21, 2010, at 3:45 AM, Chaogu Zheng wrote:

> I am extremely new to Bioperl and got a problem immediately after I
> installed it.
> 
> I installed Bioperl-pm5100 and Bioperl-run-pm5100 using fink.
> Everything seems to be fine. However, when I tried to retrieve some
> sequences from swissprot, I found the following errors.
> 
> It seems the module Bio::SeqIO::swiss can not be loaded, though I
> indeed found it under the correct directory. By the way, if I change
> 'swiss' to 'genbank' I can successfully run the program.
> 
> I don't know how to fix it. Anyone can help me?
> 
> 
> Ryan
> 
>>>>>>>>>>>>>>> 
> Bio::SeqIO: swiss cannot be found
> Exception
> ------------- EXCEPTION -------------
> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/
> Stag.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-
> multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-
> multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/
> 5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/
> Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/
> 5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/
> 5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /
> Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/
> Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/
> 5.10.0 .) at /sw/lib/perl5/5.10.0/Bio/Annotation/TagTree.pm line 123.
> BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/
> Annotation/TagTree.pm line 123.
> Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> swiss.pm line 208.
> BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> swiss.pm line 208.
> Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/Root/Root.pm
> line 439.
> 
> STACK Bio::Root::Root::_load_module /sw/lib/perl5/5.10.0/Bio/Root/
> Root.pm:441
> STACK (eval) /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:570
> STACK Bio::SeqIO::_load_format_module /sw/lib/perl5/5.10.0/Bio/
> SeqIO.pm:569
> STACK Bio::SeqIO::new /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:389
> STACK Bio::DB::WebDBSeqI::get_seq_stream /sw/lib/perl5/5.10.0/Bio/DB/
> WebDBSeqI.pm:472
> STACK Bio::DB::WebDBSeqI::get_Stream_by_acc /sw/lib/perl5/5.10.0/Bio/
> DB/WebDBSeqI.pm:314
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> WebDBSeqI.pm:186
> STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> STACK toplevel ./Documents/perl-programs/perl_test:8
> -------------------------------------
> 
> 
> For more information about the SeqIO system please see the SeqIO docs.
> This includes ways of checking for formats at compile time, not run
> time
> 
> ------------- EXCEPTION -------------
> MSG: acc P11217 does not exist
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> WebDBSeqI.pm:187
> STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> STACK toplevel ./Documents/perl-programs/perl_test:8
> -------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jimhu at tamu.edu  Thu Oct 21 17:52:32 2010
From: jimhu at tamu.edu (Jim Hu)
Date: Thu, 21 Oct 2010 12:52:32 -0500
Subject: [Bioperl-l] Does $tree->remove_Node prune or splice?
Message-ID: <927BEE54-ABC2-428A-AF42-DDEBDEABB878@tamu.edu>

I'm trying to take an unreadable tree from PFAM and prune it down to just show the paralogs from E. coli.

When you run remove_Node on an internal node, is it supposed to reconnect the ancestors to the descendants?  This seems to be way to aggressive in what it's removing.

while( my $tree = $treeio->next_tree ) {
	for my $node ( $tree->get_nodes ) {
		if ($node->id =~ m/_ECOLI/){
			#	leave this node alone
			#	print $node->id."\n";
		}else{
			if ($node->is_Leaf){
				$tree->remove_Node($node);
			}else{
				my $num_children = scalar($node->each_Descendent);
				if ($num_children == 1){ 
					print "removing ".$node->id."\n";
					$tree->remove_Node($node);
				}	
			}	
		}
	}
	$treeio_out->write_tree($tree);
}

The idea is that when I've pruned the non-ECOLI leaves, some internal nodes will not be branches anymore.  But at the end, all the ECOLI nodes are gone, presumably because an ancestor got removed and the whole branch was lost.  Is there a way to remove just a node and graft the tree back together?  My plan, once I get that working is to repeat the traversal until the output stops changing.

Jim


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





From cgzheng86 at gmail.com  Thu Oct 21 17:57:06 2010
From: cgzheng86 at gmail.com (Chaogu Zheng)
Date: Thu, 21 Oct 2010 10:57:06 -0700 (PDT)
Subject: [Bioperl-l] Failed to load module Bio::SeqIO::swiss
In-Reply-To: <23FDD4AF-3E56-4E05-AFD7-21A54DECD1C6@illinois.edu>
References: <63e01ab5-99f2-46a0-8901-3bdb24562c5f@g13g2000yqj.googlegroups.com>
	<23FDD4AF-3E56-4E05-AFD7-21A54DECD1C6@illinois.edu>
Message-ID: <974a993b-fbdf-4ca6-a59b-a7f247669eff@j18g2000yqd.googlegroups.com>

Maybe my reason for this is silly. I am using the Mac OS X 10.6, which
has the pre-installed perl 5.10.0. Fink only has the unstable bioperl
1.6.1 for Mac OS X 10.6. If I want to install bioperl-pm588 that is
the fink-stable 1.5.1 version, I guess I have to install an earlier
version of perl 5.8.8. I did not bother to do that.

So, do you think I really need to uninstall bioperl-pm5100 and get
perl 5.8.8 to try the fink-stable one?

Ryan

On Oct 21, 11:05?am, Chris Fields <cjfie... at illinois.edu> wrote:
> Like the error message says, you need to install Data::Stag (so, for some reason, this way left off). ?However, I'm not sure why you are using fink as the version in stable is still 1.5.1; bioperl 1.6.1 is in fink-unstable.
>
> chris
>
> On Oct 21, 2010, at 3:45 AM, Chaogu Zheng wrote:
>
>
>
>
>
> > I am extremely new to Bioperl and got a problem immediately after I
> > installed it.
>
> > I installed Bioperl-pm5100 and Bioperl-run-pm5100 using fink.
> > Everything seems to be fine. However, when I tried to retrieve some
> > sequences from swissprot, I found the following errors.
>
> > It seems the module Bio::SeqIO::swiss can not be loaded, though I
> > indeed found it under the correct directory. By the way, if I change
> > 'swiss' to 'genbank' I can successfully run the program.
>
> > I don't know how to fix it. Anyone can help me?
>
> > Ryan
>
> > Bio::SeqIO: swiss cannot be found
> > Exception
> > ------------- EXCEPTION -------------
> > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/
> > Stag.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-
> > multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-
> > multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/
> > 5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/
> > Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/
> > 5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/
> > 5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /
> > Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/
> > Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/
> > 5.10.0 .) at /sw/lib/perl5/5.10.0/Bio/Annotation/TagTree.pm line 123.
> > BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/
> > Annotation/TagTree.pm line 123.
> > Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> > swiss.pm line 208.
> > BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> > swiss.pm line 208.
> > Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/Root/Root.pm
> > line 439.
>
> > STACK Bio::Root::Root::_load_module /sw/lib/perl5/5.10.0/Bio/Root/
> > Root.pm:441
> > STACK (eval) /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:570
> > STACK Bio::SeqIO::_load_format_module /sw/lib/perl5/5.10.0/Bio/
> > SeqIO.pm:569
> > STACK Bio::SeqIO::new /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:389
> > STACK Bio::DB::WebDBSeqI::get_seq_stream /sw/lib/perl5/5.10.0/Bio/DB/
> > WebDBSeqI.pm:472
> > STACK Bio::DB::WebDBSeqI::get_Stream_by_acc /sw/lib/perl5/5.10.0/Bio/
> > DB/WebDBSeqI.pm:314
> > STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> > WebDBSeqI.pm:186
> > STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> > STACK toplevel ./Documents/perl-programs/perl_test:8
> > -------------------------------------
>
> > For more information about the SeqIO system please see the SeqIO docs.
> > This includes ways of checking for formats at compile time, not run
> > time
>
> > ------------- EXCEPTION -------------
> > MSG: acc P11217 does not exist
> > STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> > WebDBSeqI.pm:187
> > STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> > STACK toplevel ./Documents/perl-programs/perl_test:8
> > -------------------------------------
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioper... at lists.open-bio.org
> >http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l



From izlowe at ucdavis.edu  Fri Oct 22 02:00:24 2010
From: izlowe at ucdavis.edu (Iago Lowe)
Date: Thu, 21 Oct 2010 22:00:24 -0400
Subject: [Bioperl-l] Specifying the search set in NCBI BLAST
Message-ID: <AANLkTi=s_RstcyKyoGws0ykcK8VAb7DVcLtMrRyt2O4X@mail.gmail.com>

In the "Choose Search Set" tab on the NCBI BLAST webpage, there are some
convenient ways to restrict the size of the database for queries.  In there
a way to apply these restrictions in a remote search via Bioperl?

For example, in our research, we want to search only the "Non-human,
non-mouse ESTs" for the organism "Triticum" rather than the entire NCBI
database.

Thanks very much for any guidance.
Iago Lowe


From David.Messina at sbc.su.se  Fri Oct 22 15:29:36 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 22 Oct 2010 11:29:36 -0400
Subject: [Bioperl-l] Specifying the search set in NCBI BLAST
In-Reply-To: <AANLkTi=s_RstcyKyoGws0ykcK8VAb7DVcLtMrRyt2O4X@mail.gmail.com>
References: <AANLkTi=s_RstcyKyoGws0ykcK8VAb7DVcLtMrRyt2O4X@mail.gmail.com>
Message-ID: <C7922411-92DE-46D0-B4AA-E32A606C7415@sbc.su.se>

Hi Iago,

It is possible to do this with BioPerl, but I would recommend simply downloading Blast+ (note the +) and using the -entrez_query and -remote options.

Dave




From MEC at stowers.org  Fri Oct 22 15:40:24 2010
From: MEC at stowers.org (Cook, Malcolm)
Date: Fri, 22 Oct 2010 10:40:24 -0500
Subject: [Bioperl-l] Specifying the search set in NCBI BLAST
In-Reply-To: <C7922411-92DE-46D0-B4AA-E32A606C7415@sbc.su.se>
References: <AANLkTi=s_RstcyKyoGws0ykcK8VAb7DVcLtMrRyt2O4X@mail.gmail.com>
	<C7922411-92DE-46D0-B4AA-E32A606C7415@sbc.su.se>
Message-ID: <BD62CBAC4395B94096109020651BE2EC138AFB720D@EXCHMB-02.stowers-institute.org>

I agree with Dave.

But, if you must use BioPerl, see http://doc.bioperl.org/releases/bioperl-1.4/Bio/Tools/Run/RemoteBlast.html where it shows this code:

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

You'll probably want to set your database to  est_others (c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html#2 )

--Malcolm
 

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dave Messina
Sent: Friday, October 22, 2010 10:30 AM
To: Iago Lowe
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Specifying the search set in NCBI BLAST

Hi Iago,

It is possible to do this with BioPerl, but I would recommend simply downloading Blast+ (note the +) and using the -entrez_query and -remote options.

Dave


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



From jun.yin at ucd.ie  Fri Oct 22 16:12:45 2010
From: jun.yin at ucd.ie (Jun Yin)
Date: Fri, 22 Oct 2010 17:12:45 +0100
Subject: [Bioperl-l] how to download PDB files using Bioperl script
In-Reply-To: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
Message-ID: <01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>

Hi, Ashwani,

I havenot found any module in BioPerl for downloading PDB files, though
Bio::Structure::IO::pdb can parse PDB files.

However, PDB provides RESTful service
(http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
batch downloading the proteins.

Cheers,
Jun Yin
Ph.D.?student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
Sent: Thursday, October 21, 2010 9:39 AM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] how to download PDB files using Bioperl script

Hi All,


I have around 150 pdb file names and I need to download them from Protein
Data Bank. I wonder if someone could tell me how to do it by using Bioperl.

Thanks in advance.

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

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From jason at bioperl.org  Sat Oct 23 15:33:49 2010
From: jason at bioperl.org (Jason Stajich)
Date: Sat, 23 Oct 2010 08:33:49 -0700
Subject: [Bioperl-l] Question on BioPerl modules
In-Reply-To: <1287838391.5784.19.camel@ubuntu>
References: <1287838391.5784.19.camel@ubuntu>
Message-ID: <4CC3005D.1070708@bioperl.org>

Lincoln overloaded the "" method for the objects that are returned from 
Bio::DB::Fasta so that attempts to print them directly will instead 
print out the display_id field.

If you want to know what kind of object you getting back you use 'ref', 
as in:
print ref($seq),"\n";

Tao Zhu wrote, On 10/23/10 5:53 AM:
> Dear Professor Stajich,
>
> Recently I was puzzled when using two BioPerl modules, Bio::Index::Fasta
> and Bio::DB::Fasta;
>
> For example, I have a fasta file: sequence.fa, on my computer. That is:
>
>> ORFN:87
> ATGGAAGCCCCTTCAGAAATTACCGATTCCAA
>
> I hope to make a local index, then I use Bio::Index::Fasta and write:
>
> use Bio::Index::Fasta;
> $file_name = "sequence.fa";
> $id = "ORFN:87";
> $inx = Bio::Index::Fasta->new (-filename =>  $file_name . ".idx", -write_flag =>  1);
> $inx->make_index($file_name);
> $seq_obj = $inx->fetch($id);
> print "$seq_obj\n";
>
> Running the perl script, it prints "Bio::Seq=HASH(0x66590a0)" on screen.
> That means the scalar "$seq_obj" is a Bio::Seq object.
>
> However, I try another method, using Bio::DB::Fasta,
>
> use Bio::DB::Fasta;
> ($file,$id) = ("sequence.fa","ORFN:87");
> $db = Bio::DB::Fasta->new($file);
> $seq_obj = $db->get_Seq_by_id($id);
> print "$seq_obj\n";
>
> I expect it should also print "Bio::Seq=HASH(sth)",because I also get a
> Bio::Seq object. Surprisingly it prints "ORFN:87"
>
> How it comes to be?
>

-- 
Jason Stajich
jason at bioperl.org



From yifangt at hotmail.com  Sat Oct 23 06:21:40 2010
From: yifangt at hotmail.com (yifangt)
Date: Fri, 22 Oct 2010 23:21:40 -0700 (PDT)
Subject: [Bioperl-l] Can't locate Bio/seqIO.pm in @INC
In-Reply-To: <loom.20101019T134347-528@post.gmane.org>
References: <loom.20101019T134347-528@post.gmane.org>
Message-ID: <30034148.post@talk.nabble.com>


Probably your Bioperl installation is not correct. Re-install your bioperl
and try again!

Good luck!




yusheng liao wrote:
> 
> Can't locate Bio/seqIO.pm in @INC 
> I try to run a .pl file to get multi sequences for t
> he GenBank using the
> Bioperl. The following were the error message:
> linux:/home/liaoy # perl hsv-1.pl
> Can't locate Bio/seqIO.pm in @INC (@INC contains:
> /usr/lib/perl5/5.8.7/i586-linux-thread-multi /usr/lib/perl5/5.8.7
> /usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.7 /usr/lib/perl5/site_perl
> /usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .)
>  at hsv-1.pl line 4.
> BEGIN failed--compilation aborted at hsv-1.pl line 4.
> 
> what is the problem? And how to corret it? 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/Can%27t-locate-Bio-seqIO.pm-in-%40INC-tp30019789p30034148.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From timmcilveen at talktalk.net  Mon Oct 25 00:45:15 2010
From: timmcilveen at talktalk.net (Tim)
Date: Mon, 25 Oct 2010 01:45:15 +0100
Subject: [Bioperl-l] Installing Bioperl  from Git Hub
Message-ID: <4CC4D31B.1080905@talktalk.net>

Hi everyone,
A couple of weeks ago, I posted a query about installing Bioperl from 
GitHub. I was getting installation errors and someone on the list had 
picked up on  a typo I had made while trying to install it.
Bioperl is now installed and working properly. I forgot to acknowledge 
your help. Thanks for your advice.

Tim



From edwardsa at cs.man.ac.uk  Mon Oct 25 16:33:21 2010
From: edwardsa at cs.man.ac.uk (Andrea Edwards)
Date: Mon, 25 Oct 2010 17:33:21 +0100
Subject: [Bioperl-l] can't install bioperl 1.6.1
Message-ID: <4CC5B151.8030606@cs.man.ac.uk>

  Hi

I can't install Bioperl 1.6.1 on windows using Active Perl 5.8.8.822

I have added the repositories as mentioned in the user guide but get 
this error message

?ERROR: File conflict for 'C:/Perl/html/bin/bp_aacomp.html'.The package 
BioPerl has already installed a file that package bioperl wants to install.?

I have seen a forum thread which says the problem is due to the 
trouchelle repository.

http://www.perlmonks.org/?node_id=817531

I did remove the trouchelle repository as suggested and bioperl 1.6.1 
does seem to have installed but I don't know enough about Perl to know 
if it will have installed correctly by removing this repository.

I installed BioPerl 1.6 successfully on a different PC running 
ActivePerl 5.8.9.827 without needing to remove the trouchelle so I 'm 
not sure what to think.

Many thanks




From sahasangi at gmail.com  Tue Oct 26 11:41:01 2010
From: sahasangi at gmail.com (sangita saha)
Date: Tue, 26 Oct 2010 17:11:01 +0530
Subject: [Bioperl-l] Fwd: Need Help regarding reciprocal BLAST using BioPerl
In-Reply-To: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>
References: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>
Message-ID: <AANLkTimidEhyj=nJ4U9vwp1He45fgUg-d1LOs+dEYoq=@mail.gmail.com>

---------- Forwarded message ----------
From: sangita saha <sahasangi at gmail.com>
Date: Tue, Oct 26, 2010 at 4:32 PM
Subject: Need Help regarding reciprocal BLAST using BioPerl
To: bioperl-l at lists.open-bio.org


Hello Sir,
I have installed BioPerl and standalone BLAST in my PC.I faced problem in
doing the Reciprocal BLAST.Will anyone kindly tell me how to link between
BioPerl and Standalone BLAST ?How to use Bioperl itself to identify the
ortholog?What is the command to be used for reciprocal Blast?Since I am the
new user of it and need help to your concerned.If anybody have any
experience regarding reciprocal blast please give me a suggestion.

I will be happy to hear you from.

Thank you

With Regards,
Sangita Saha


From shalabh.sharma7 at gmail.com  Tue Oct 26 14:04:31 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 26 Oct 2010 10:04:31 -0400
Subject: [Bioperl-l] Fwd: Need Help regarding reciprocal BLAST using
	BioPerl
In-Reply-To: <AANLkTimidEhyj=nJ4U9vwp1He45fgUg-d1LOs+dEYoq=@mail.gmail.com>
References: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>
	<AANLkTimidEhyj=nJ4U9vwp1He45fgUg-d1LOs+dEYoq=@mail.gmail.com>
Message-ID: <AANLkTinhKE_KTzr3_Xftu96dyhyC4fc0QYm_2FhQ6HPU@mail.gmail.com>

Hey Sangita,
               I am not sure if bioperl has any direct command for
reciprocal blast.
But it is fairly simple, you can use all vs all blast then post process your
results in finding orthologs according to your cutoff parameters.

Other way is to use OrthoMCL :
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403725/?tool=pubmed

Also read this:
http://bioperl.org/wiki/HOWTO:PhylogeneticAnalysisPipeline
 Since you are a beginner it will help you a lot.

Hope this helps.

Shalabh
-----------------------------------
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636
On Tue, Oct 26, 2010 at 7:41 AM, sangita saha <sahasangi at gmail.com> wrote:

> ---------- Forwarded message ----------
> From: sangita saha <sahasangi at gmail.com>
> Date: Tue, Oct 26, 2010 at 4:32 PM
> Subject: Need Help regarding reciprocal BLAST using BioPerl
> To: bioperl-l at lists.open-bio.org
>
>
> Hello Sir,
> I have installed BioPerl and standalone BLAST in my PC.I faced problem in
> doing the Reciprocal BLAST.Will anyone kindly tell me how to link between
> BioPerl and Standalone BLAST ?How to use Bioperl itself to identify the
> ortholog?What is the command to be used for reciprocal Blast?Since I am the
> new user of it and need help to your concerned.If anybody have any
> experience regarding reciprocal blast please give me a suggestion.
>
> I will be happy to hear you from.
>
> Thank you
>
> With Regards,
> Sangita Saha
> _______________________________________________
> 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  Tue Oct 26 14:09:48 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 26 Oct 2010 10:09:48 -0400
Subject: [Bioperl-l] Genome Information
Message-ID: <AANLkTikLfZa-FSFXiriqPGHf63kcTgkY0+rT2Mq=7hCu@mail.gmail.com>

Hi All,
       I have thousands of taxaIds and i need to find out the following
information regarding genomes:
1) Taxonomy information
2) GC%
3) total coding genes %

I can easily find the taxonomy info by using Bio::DB::Taxonomy but for the
other two i am stuck.
Is there any way i can find this info?
I would really appreciate your help.

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


From cjfields at illinois.edu  Tue Oct 26 15:40:02 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 26 Oct 2010 10:40:02 -0500
Subject: [Bioperl-l] Fwd: Need Help regarding reciprocal BLAST using
	BioPerl
In-Reply-To: <AANLkTinhKE_KTzr3_Xftu96dyhyC4fc0QYm_2FhQ6HPU@mail.gmail.com>
References: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>
	<AANLkTimidEhyj=nJ4U9vwp1He45fgUg-d1LOs+dEYoq=@mail.gmail.com>
	<AANLkTinhKE_KTzr3_Xftu96dyhyC4fc0QYm_2FhQ6HPU@mail.gmail.com>
Message-ID: <02B10B6A-5E4A-4889-AACA-A47D8FA39E88@illinois.edu>

BioPerl does have Bio::Tools::Run::TribeMCL in BioPerl-Run, but I don't suggest using that.  mcl has a few tools in-place already within the distribition, but I personally have been using the latest version of OrthoMCL (v2), and have also started setting up a pipeline using InParanoid.

chris

On Oct 26, 2010, at 9:04 AM, shalabh sharma wrote:

> Hey Sangita,
>               I am not sure if bioperl has any direct command for
> reciprocal blast.
> But it is fairly simple, you can use all vs all blast then post process your
> results in finding orthologs according to your cutoff parameters.
> 
> Other way is to use OrthoMCL :
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403725/?tool=pubmed
> 
> Also read this:
> http://bioperl.org/wiki/HOWTO:PhylogeneticAnalysisPipeline
> Since you are a beginner it will help you a lot.
> 
> Hope this helps.
> 
> Shalabh
> -----------------------------------
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
> On Tue, Oct 26, 2010 at 7:41 AM, sangita saha <sahasangi at gmail.com> wrote:
> 
>> ---------- Forwarded message ----------
>> From: sangita saha <sahasangi at gmail.com>
>> Date: Tue, Oct 26, 2010 at 4:32 PM
>> Subject: Need Help regarding reciprocal BLAST using BioPerl
>> To: bioperl-l at lists.open-bio.org
>> 
>> 
>> Hello Sir,
>> I have installed BioPerl and standalone BLAST in my PC.I faced problem in
>> doing the Reciprocal BLAST.Will anyone kindly tell me how to link between
>> BioPerl and Standalone BLAST ?How to use Bioperl itself to identify the
>> ortholog?What is the command to be used for reciprocal Blast?Since I am the
>> new user of it and need help to your concerned.If anybody have any
>> experience regarding reciprocal blast please give me a suggestion.
>> 
>> I will be happy to hear you from.
>> 
>> Thank you
>> 
>> With Regards,
>> Sangita Saha
>> _______________________________________________
>> 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 Oct 26 16:11:05 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 26 Oct 2010 11:11:05 -0500
Subject: [Bioperl-l] Genome Information
In-Reply-To: <AANLkTikLfZa-FSFXiriqPGHf63kcTgkY0+rT2Mq=7hCu@mail.gmail.com>
References: <AANLkTikLfZa-FSFXiriqPGHf63kcTgkY0+rT2Mq=7hCu@mail.gmail.com>
Message-ID: <7A662ADB-506C-439E-9C0C-44F8DE540428@illinois.edu>

Shalabh,

I don't know if there is a quick one-step way of getting this information via NCBI w/o wrangling with query term limit magic, and even then you will be bound to whatever version of the genome is present within the database of interest.  

For instance, via eutils you can get summary information for various taxa, genomes, and genome projects using the following example code (prints the first 10 archaeal genome project summaries; set the '-db' parameter to one of 'genomeprj', 'taxonomy', 'genome'):

=================================

use Bio::DB::EUtilities;

my $term = "Archaea[ORGN]";

my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                     -db    => 'genome',
                                     -email => 'cjfields at bioperl.org',
                                     -usehistory => 'y',
                                     -term  => $term);

my $hist = $eutil->next_History || die "No history returned";

$eutil->set_parameters(-eutil   => 'esummary',
                       -history => $hist,
                       -retmax  => 10);

$eutil->print_all; # print summary info to STDOUT

=================================

GC and coding % don't appear to be stored in any of the above databases, but they are displayed via the genome overview.  You could probably use something like WWW::Mechanize to grab the summary table information displayed using the Genome UID:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=ShowDetailView&TermToSearch=25024

Just don't spam the server with a billion requests (use a timeout!) or you'll find yourself blocked.  I may pop an email to NCBI to see if this information is programmatically accessible.

chris

On Oct 26, 2010, at 9:09 AM, shalabh sharma wrote:

> Hi All,
>       I have thousands of taxaIds and i need to find out the following
> information regarding genomes:
> 1) Taxonomy information
> 2) GC%
> 3) total coding genes %
> 
> I can easily find the taxonomy info by using Bio::DB::Taxonomy but for the
> other two i am stuck.
> Is there any way i can find this info?
> I would really appreciate your help.
> 
> Thanks
> Shalabh
> -------------------------------
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
> _______________________________________________
> 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  Tue Oct 26 16:23:02 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 26 Oct 2010 12:23:02 -0400
Subject: [Bioperl-l] Genome Information
In-Reply-To: <7A662ADB-506C-439E-9C0C-44F8DE540428@illinois.edu>
References: <AANLkTikLfZa-FSFXiriqPGHf63kcTgkY0+rT2Mq=7hCu@mail.gmail.com>
	<7A662ADB-506C-439E-9C0C-44F8DE540428@illinois.edu>
Message-ID: <AANLkTin_JuaAi9Op_T9N9YVzjpOtN1hnXV=X02kPutBA@mail.gmail.com>

Hey Chris,
            This information is really useful.
Actually i was using Bio::DB::Taxonomy for taxonomy information
and Bio::DB::EUtilities to get the genome size (i didn't know that i can
just use Bio::DB::EUtilities for all the information).
I was very confused about getting GC% and coding% info but i
think WWW::Mechanize might help me out.
I really appreciate your help.

-Shalabh


On Tue, Oct 26, 2010 at 12:11 PM, Chris Fields <cjfields at illinois.edu>wrote:

> Shalabh,
>
> I don't know if there is a quick one-step way of getting this information
> via NCBI w/o wrangling with query term limit magic, and even then you will
> be bound to whatever version of the genome is present within the database of
> interest.
>
> For instance, via eutils you can get summary information for various taxa,
> genomes, and genome projects using the following example code (prints the
> first 10 archaeal genome project summaries; set the '-db' parameter to one
> of 'genomeprj', 'taxonomy', 'genome'):
>
> =================================
>
> use Bio::DB::EUtilities;
>
> my $term = "Archaea[ORGN]";
>
> my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
>                                     -db    => 'genome',
>                                     -email => 'cjfields at bioperl.org',
>                                     -usehistory => 'y',
>                                     -term  => $term);
>
> my $hist = $eutil->next_History || die "No history returned";
>
> $eutil->set_parameters(-eutil   => 'esummary',
>                       -history => $hist,
>                       -retmax  => 10);
>
> $eutil->print_all; # print summary info to STDOUT
>
> =================================
>
> GC and coding % don't appear to be stored in any of the above databases,
> but they are displayed via the genome overview.  You could probably use
> something like WWW::Mechanize to grab the summary table information
> displayed using the Genome UID:
>
>
> http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=ShowDetailView&TermToSearch=25024
>
> Just don't spam the server with a billion requests (use a timeout!) or
> you'll find yourself blocked.  I may pop an email to NCBI to see if this
> information is programmatically accessible.
>
> chris
>
> On Oct 26, 2010, at 9:09 AM, shalabh sharma wrote:
>
> > Hi All,
> >       I have thousands of taxaIds and i need to find out the following
> > information regarding genomes:
> > 1) Taxonomy information
> > 2) GC%
> > 3) total coding genes %
> >
> > I can easily find the taxonomy info by using Bio::DB::Taxonomy but for
> the
> > other two i am stuck.
> > Is there any way i can find this info?
> > I would really appreciate your help.
> >
> > Thanks
> > Shalabh
> > -------------------------------
> > Shalabh Sharma
> > Scientific Computing Professional Associate (Bioinformatics Specialist)
> > Department of Marine Sciences
> > University of Georgia
> > Athens, GA 30602-3636
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From mconte at umd.edu  Tue Oct 26 18:25:28 2010
From: mconte at umd.edu (Matthew Conte)
Date: Tue, 26 Oct 2010 14:25:28 -0400
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
Message-ID: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>

Hello,

I have a custom script for parsing out UniProt accessions from a GFF3 file
and fetching the description of the UniProt entry using Bio::DB::SwissProt
and *get_Seq_by_acc*.  This script has been working for months without any
problems until now.  The script and the format of the input files has not
changed at all.

I now get an error like this:

*------------- EXCEPTION: Bio::Root::Exception -------------*
*MSG: acc O95342 does not exist*
*STACK: Error::throw*
*STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
*STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
/Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
*STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
*-----------------------------------------------------------*

The relevant portion of my original code looks something like this:

*#!/usr/bin/perl*
*use strict;*
*use Bio::DB::SwissProt;*
*#parse out accession number*
*..*
*my $acc_num = "**O95342";*
*my $db_obj = Bio::DB::SwissProt->new;*
*my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
*
*
Looking at the documentation for Bio::DB::SwissProt, I noticed you can
specify -servertype and -hostlocation.  So I changed my code to look
something like this:

*
#!/usr/bin/perl
use strict;
use Bio::DB::SwissProt;
#parse out accession number
..
my $acc_num = "O95342";
my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
                                                           '-hostlocation'
=> 'us');
my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
*

This fixes my problem and my script works again.

The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
  Both of these urls work in a browser, though the default throws the error
in my script. Interestingly, the 'us' url has a notice that says
"*Notice:* This
page will be replaced with www.uniprot.org. Please send us your
feedback<http://www.uniprot.org/contact>
!", so hopefully it doesn't break soon as well.  Perhaps the default ebi url
was recently changed in some way?  Anyway, I figured I'd post here in case
anyone else ran into this problem.

cheers,
Matt


From grapeguy at gmail.com  Tue Oct 26 19:15:09 2010
From: grapeguy at gmail.com (Bill Stephens)
Date: Tue, 26 Oct 2010 15:15:09 -0400
Subject: [Bioperl-l] Generating a consensus sequence from a Clustal
	alignment
In-Reply-To: <16EDEBED-BAD4-4D57-B51B-C3234D1E8C39@illinois.edu>
References: <AANLkTik18CbsBZO4pPF3Y=Zn2phKavz6YhA-A0qWCHRB@mail.gmail.com>
	<DB24DCA6-E2FD-47DC-A4F9-551EBB39DFA5@illinois.edu>
	<001101cb6ede$d9e80e10$8db82a30$%yin@ucd.ie>
	<AANLkTi=4Qv_0miTTCP4yHxk-jqCp8u6EZAL5OEet=u0F@mail.gmail.com>
	<16EDEBED-BAD4-4D57-B51B-C3234D1E8C39@illinois.edu>
Message-ID: <AANLkTim5_UF-AQd8HRD9v4_5SF8T5z+awWN8KAORoUGs@mail.gmail.com>

I've got my script running.

In order to support the identification of degenerate primers I had to create
a new method that would alter the IUPAC consensus. We're interested in
15-30bp sections of the consensus with high, but not 100%, conservation. We
would like to have a couple of "slices" with 2-3 mismatches to allow for the
ordering of a variety of primers.

To be completed:

   - I would *love* to hide the Clustal output that is being printed to the
   screen
   - Primer candidate identification (min_primerlength to max_primerlength)
   based on our scoring matrix
   - Primer melting temperature calculation
   - 3' Clamping identification
   - Self complementary primers

This has been a nice change from Java.

Bill


*Code*

assume: I have already read fasta input, performed Clustal align and
obtained the IUPAC consensus

sub getDegenerateConsensusIupac {
    my ($aln, $maxGapPercent, $iupacConsensus, $numSequences) = @_;

  # convert consensus into array
  my @cons = split(//, $iupacConsensus);

  # loop over the alignment "columns"
  foreach my $position ( 1 .. $aln->length() ) {
      my $consCode = $cons[$position-1];
      my %slice = getSliceHash($aln, $position);

      my $out = _applyGapPercentToConsensus ($maxGapPercent, $consCode,
$numSequences, %slice);

      # Convert consensus value new value
      if ($out ne $consCode) {
          $cons[$position-1] = $out;
      }
  }

  #rebuild consensus
  my $degenerateConsensus = join '', @cons;

  return $degenerateConsensus;
}

sub _applyGapPercentToConsensus {
    my ($maxGapPercent, $consCode, $numSequences, %slice) = @_;

        my $gapCount = $slice{'.'};

        # no gaps!
        if ($gapCount !~ /\d/) {
            return $consCode;
        }

        my $pctGap = ($gapCount / $numSequences) * 100;

        if ($pctGap > $maxGapPercent) {
            if ($consCode =~ /[A-Z]/) {
                return lc $consCode;
            }
            if ($consCode =~ /[a-z]/) {
                return '.';
            }
        }

    return $consCode;
}

sub getSliceHash{
    my ($aln, $position) = @_;

    my %sliceHash;
    foreach my $seq ($aln->each_seq) {
        my $res = $seq->subseq($position, $position);
        $sliceHash{$res}++;
    }

    return %sliceHash;
}


On Tue, Oct 19, 2010 at 11:47 AM, Chris Fields <cjfields at illinois.edu>wrote:

> Bio::SimpleAlign is the class that contains the alignment data; it does not
> generate the alignment for you.  You can use modules from BioPerl-Run that
> run ClustalW, MUSCLE, T-Coffee, etc to get a Bio::SimpleAlign instance, or
> parse the already-generated alignment output via Bio::AlignIO.
>
> From the Bio::Tools::Run::Alignment::ClustalW docs:
>
> =================================================================
>
>  #  Build a clustalw alignment factory
>  @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
>  $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
>
>  #  Pass the factory a list of sequences to be aligned.
>  $inputfilename = 't/data/cysprot.fa';
>  $aln = $factory->align($inputfilename); # $aln is a SimpleAlign object.
>
>  # ...or
>  $seq_array_ref = \@seq_array;
>
>  # where @seq_array is an array of Bio::Seq objects
>  $aln = $factory->align($seq_array_ref);
>
> =================================================================
>
> $aln is a Bio::SimpleAlign derived from ClustalW output.
>
> From Bio::SimpleAlign (note the use of Bio::AlignIO):
>
> =================================================================
>
>  # Use Bio::AlignIO to read in the alignment
>  $str = Bio::AlignIO->new(-file => 't/data/testaln.pfam');
>  $aln = $str->next_aln();
>
>  # Describe
>  print $aln->length;
>  print $aln->num_residues;
>  print $aln->is_flush;
>  print $aln->num_sequences;
>  print $aln->score;
>  print $aln->percentage_identity;
>  print $aln->consensus_string(50);
>
> =================================================================
>
> Note the consensus_string() method:
>
>  Title     : consensus_string
>  Usage     : $str = $ali->consensus_string($threshold_percent)
>  Function  : Makes a strict consensus
>  Returns   : Consensus string
>  Argument  : Optional treshold ranging from 0 to 100.
>             The consensus residue has to appear at least threshold %
>             of the sequences at a given location, otherwise a '?'
>             character will be placed at that location.
>             (Default value = 0%)
>
> chris
>
> On Oct 18, 2010, at 7:02 PM, Bill Stephens wrote:
>
> > So, I've got the SimpleAlign running. It looks like it's running the
> > alignment based upon the input sequence location only (first residue from
> > each sequence).  This is not what I need.
> >
> > I'm back to to clustal, tcoffee or dalign.
> >
> > Bill
> >
> > On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:
> >
> >> Hi, Bill,
> >>
> >> You may consider to use consensus_iupac or consensus_string methods in
> >> Bio::SimpleAlign to generate consensus sequence.
> >>
> >> Cheers,
> >> Jun Yin
> >> Ph.D. student in U.C.D.
> >>
> >> Bioinformatics Laboratory
> >> Conway Institute
> >> University College Dublin
> >>
> >> -----Original Message-----
> >> From: bioperl-l-bounces at lists.open-bio.org
> >> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
> >> Sent: Monday, October 18, 2010 3:55 PM
> >> To: Bill Stephens
> >> Cc: bioperl-l at bioperl.org
> >> Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
> >> alignment
> >>
> >> Bill,
> >>
> >> Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
> >> replacement for the older Pise tools).  The Pise modules were in
> >> BioPerl-Run, but they were deprecated a few years ago and removed from
> the
> >> latest BioPerl-Run releases b/c the remote service is no longer active;
> >> there is no Perl-based replacement for Mobyle interaction.
> >>
> >> Have you thought about just using the functionality within the
> >> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there
> >> are
> >> methods in place to do that.
> >>
> >> chris
> >>
> >> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
> >>
> >>> All,
> >>>
> >>> I'm in my first week with bioperl for a class project (although I've
> used
> >>> Perl for years). I've successfully run a clustal alignment of several
> DNA
> >>> sequences to produce the aln and dnd files. Now I would like to
> generate
> >> a
> >>> consensus sequence from the alignment.  I see that Pise Cons does this
> >>> satisfactorily on my example data (
> >>> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However,
> >> I'm
> >>> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
> >> distribution
> >>> that I installed.
> >>>
> >>> Is this another module that I need to install separately?
> >>>
> >>> "cpan[2]> m /Pise/
> >>> Module    Bio::Tools::Run::AnalysisFactory::Pise
> >>> (BIRNEY/bioperl-run-1.4.tar.gz)
> >>> Module    Bio::Tools::Run::PiseApplication
> >> (BIRNEY/bioperl-run-1.4.tar.gz)"
> >>>
> >>> Bill S.
> >>> _______________________________________________
> >>> 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
> >>
> >> __________ Information from ESET Smart Security, version of virus
> signature
> >> database 5377 (20100818) __________
> >>
> >> The message was checked by ESET Smart Security.
> >>
> >> http://www.eset.com
> >>
> >>
> >>
> >>
> >> __________ Information from ESET Smart Security, version of virus
> signature
> >> database 5377 (20100818) __________
> >>
> >> The message was checked by ESET Smart Security.
> >>
> >> http://www.eset.com
> >>
> >>
> >>
> > _______________________________________________
> > 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 Oct 26 22:02:03 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 26 Oct 2010 17:02:03 -0500
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
Message-ID: <FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>

The default was changed recently in github to 'expasy'.  My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.

chris

On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:

> Hello,
> 
> I have a custom script for parsing out UniProt accessions from a GFF3 file
> and fetching the description of the UniProt entry using Bio::DB::SwissProt
> and *get_Seq_by_acc*.  This script has been working for months without any
> problems until now.  The script and the format of the input files has not
> changed at all.
> 
> I now get an error like this:
> 
> *------------- EXCEPTION: Bio::Root::Exception -------------*
> *MSG: acc O95342 does not exist*
> *STACK: Error::throw*
> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
> *-----------------------------------------------------------*
> 
> The relevant portion of my original code looks something like this:
> 
> *#!/usr/bin/perl*
> *use strict;*
> *use Bio::DB::SwissProt;*
> *#parse out accession number*
> *..*
> *my $acc_num = "**O95342";*
> *my $db_obj = Bio::DB::SwissProt->new;*
> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
> *
> *
> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
> specify -servertype and -hostlocation.  So I changed my code to look
> something like this:
> 
> *
> #!/usr/bin/perl
> use strict;
> use Bio::DB::SwissProt;
> #parse out accession number
> ..
> my $acc_num = "O95342";
> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>                                                           '-hostlocation'
> => 'us');
> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
> *
> 
> This fixes my problem and my script works again.
> 
> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>  Both of these urls work in a browser, though the default throws the error
> in my script. Interestingly, the 'us' url has a notice that says
> "*Notice:* This
> page will be replaced with www.uniprot.org. Please send us your
> feedback<http://www.uniprot.org/contact>
> !", so hopefully it doesn't break soon as well.  Perhaps the default ebi url
> was recently changed in some way?  Anyway, I figured I'd post here in case
> anyone else ran into this problem.
> 
> cheers,
> Matt
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From sahasangi at gmail.com  Tue Oct 26 11:02:04 2010
From: sahasangi at gmail.com (sangita saha)
Date: Tue, 26 Oct 2010 16:32:04 +0530
Subject: [Bioperl-l] Need Help regarding reciprocal BLAST using BioPerl
Message-ID: <AANLkTi=JeRr0P4v4U0g_fMkPz6gVCHPjXW6hW=cp9bp0@mail.gmail.com>

Hello Sir,
I have installed BioPerl and standalone BLAST in my PC.I faced problem in
doing the Reciprocal BLAST.Will anyone kindly tell me how to link between
BioPerl and Standalone BLAST ?How to use Bioperl itself to identify the
ortholog?What is the command to be used for reciprocal Blast?Since I am the
new user of it and need help to your concerned.If anybody have any
experience regarding reciprocal blast please give me a suggestion.

I will be happy to hear you from.

Thank you

With Regards,
Sangita Saha


From ameet at eecs.berkeley.edu  Tue Oct 26 23:51:17 2010
From: ameet at eecs.berkeley.edu (Ameet Talwalkar)
Date: Tue, 26 Oct 2010 16:51:17 -0700
Subject: [Bioperl-l] TreeIO for NHX format
Message-ID: <AANLkTim2hsO=rRCfa5H4Uu7waF7iVbJo9NDfTq2q8yrN@mail.gmail.com>

Hi,

I would like to use BIOPerl to convert a tree in PhyloXML format to NHX
format, and I have tried the following code:

*use Bio::TreeIO;

my $input = new Bio::TreeIO(-file   => "reconciled_test.xml",
                            -format => "phyloxml");
my $treeout = new Bio::TreeIO(-fh => \*STDOUT,
                              -format => 'nhx');

while (my $tree = $input->next_tree) {
  $treeout->write_tree($tree);
}
*

The output is indeed in NHX format, but the tags (in particular I have a
duplication / speciation tag) does not appear in the output.  Am I doing
something wrong?

Thanks.

-Ameet


From bill_zt at sina.com  Wed Oct 27 01:08:11 2010
From: bill_zt at sina.com (Tao Zhu)
Date: Wed, 27 Oct 2010 09:08:11 +0800
Subject: [Bioperl-l] A problem on BioPerl module Bio::DB::Fasta
Message-ID: <1288141691.2377.1.camel@ubuntu>

Hello, everyone!

I hope it isn't true, but I really find a problem on BioPerl module
Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
Osborne wrote that we could catch sub-sequences like this,


use Bio::DB::Fasta;
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
$db = Bio::DB::Fasta->new($file);
$seqobj = $db->get_Seq_by_id($id,$start,$end);
print $seqobj->seq,"\n";


In fact it didn't work. I only got the whole sequence after running the
script. Therefore I referred to the Pdoc documentation and realized it
should be written as follows,


use Bio::DB::Fasta;
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
$db = Bio::DB::Fasta->new($file);
$seq = $db->seq($id,$start,$end);
print $seq,"\n";


Then it would return the sub-sequence from 6 to 10.

Probably Dr Osborne had made a mistake when writing the use-guide
HOWTO:Beginners.


-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
email: tzhu at mail.bnu.edu.cn



From cjfields at illinois.edu  Wed Oct 27 03:41:40 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 26 Oct 2010 22:41:40 -0500
Subject: [Bioperl-l] TreeIO for NHX format
In-Reply-To: <AANLkTim2hsO=rRCfa5H4Uu7waF7iVbJo9NDfTq2q8yrN@mail.gmail.com>
References: <AANLkTim2hsO=rRCfa5H4Uu7waF7iVbJo9NDfTq2q8yrN@mail.gmail.com>
Message-ID: <55546218-9878-421F-B4A7-FADA7760C374@illinois.edu>

Ameet,

You should file this as a bug, along with example code and data (http://bugzilla.open-bio.org/).  It's possible the tags are parsed but the NHX writer is not finding the data somehow.

chris

On Oct 26, 2010, at 6:51 PM, Ameet Talwalkar wrote:

> Hi,
> 
> I would like to use BIOPerl to convert a tree in PhyloXML format to NHX
> format, and I have tried the following code:
> 
> *use Bio::TreeIO;
> 
> my $input = new Bio::TreeIO(-file   => "reconciled_test.xml",
>                            -format => "phyloxml");
> my $treeout = new Bio::TreeIO(-fh => \*STDOUT,
>                              -format => 'nhx');
> 
> while (my $tree = $input->next_tree) {
>  $treeout->write_tree($tree);
> }
> *
> 
> The output is indeed in NHX format, but the tags (in particular I have a
> duplication / speciation tag) does not appear in the output.  Am I doing
> something wrong?
> 
> Thanks.
> 
> -Ameet
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hamish.mcwilliam at bioinfo-user.org.uk  Wed Oct 27 10:32:22 2010
From: hamish.mcwilliam at bioinfo-user.org.uk (Hamish McWilliam)
Date: Wed, 27 Oct 2010 11:32:22 +0100
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
	<FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
Message-ID: <AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>

Hi Chris,

The dbfetch service at EBI has changed, see
http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010. On
of the effects of this is the main endpoint used for dbfetch has
changed from http://www.ebi.ac.uk/cgi-bin/dbfetch to
http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. With the old endpoints
being supported via a HTTP redirect. It looks like the
Bio::DB::SwissProt module does not support redirects and is thus
getting an empty document back from the service. Looks like the URL
used in the code needs to be updated.

All the best,

Hamish

On 26 October 2010 23:02, Chris Fields <cjfields at illinois.edu> wrote:
> The default was changed recently in github to 'expasy'. ?My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.
>
> chris
>
> On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:
>
>> Hello,
>>
>> I have a custom script for parsing out UniProt accessions from a GFF3 file
>> and fetching the description of the UniProt entry using Bio::DB::SwissProt
>> and *get_Seq_by_acc*. ?This script has been working for months without any
>> problems until now. ?The script and the format of the input files has not
>> changed at all.
>>
>> I now get an error like this:
>>
>> *------------- EXCEPTION: Bio::Root::Exception -------------*
>> *MSG: acc O95342 does not exist*
>> *STACK: Error::throw*
>> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
>> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
>> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
>> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
>> *-----------------------------------------------------------*
>>
>> The relevant portion of my original code looks something like this:
>>
>> *#!/usr/bin/perl*
>> *use strict;*
>> *use Bio::DB::SwissProt;*
>> *#parse out accession number*
>> *..*
>> *my $acc_num = "**O95342";*
>> *my $db_obj = Bio::DB::SwissProt->new;*
>> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
>> *
>> *
>> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
>> specify -servertype and -hostlocation. ?So I changed my code to look
>> something like this:
>>
>> *
>> #!/usr/bin/perl
>> use strict;
>> use Bio::DB::SwissProt;
>> #parse out accession number
>> ..
>> my $acc_num = "O95342";
>> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '-hostlocation'
>> => 'us');
>> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
>> *
>>
>> This fixes my problem and my script works again.
>>
>> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
>> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>> ?Both of these urls work in a browser, though the default throws the error
>> in my script. Interestingly, the 'us' url has a notice that says
>> "*Notice:* This
>> page will be replaced with www.uniprot.org. Please send us your
>> feedback<http://www.uniprot.org/contact>
>> !", so hopefully it doesn't break soon as well. ?Perhaps the default ebi url
>> was recently changed in some way? ?Anyway, I figured I'd post here in case
>> anyone else ran into this problem.
>>
>> cheers,
>> Matt
>> _______________________________________________
>> 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
>



-- 
----
"Saying the internet has changed dramatically over the last five years
is clich? ? the internet is always changing dramatically" - Craig
Labovitz, Arbor Networks.



From cjfields at illinois.edu  Wed Oct 27 14:51:22 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 27 Oct 2010 09:51:22 -0500
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
	<FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
	<AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>
Message-ID: <FAB70AF7-B56C-4DEA-BF4D-AA9F001D6E9F@illinois.edu>

Hamish,

Thanks, but I already caught that and fixed it in main trunk where appropriate yesterday (specifically, both Bio::DB::SwissProt and Bio::DB::BioFetch).  

chris

On Oct 27, 2010, at 5:32 AM, Hamish McWilliam wrote:

> Hi Chris,
> 
> The dbfetch service at EBI has changed, see
> http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010. On
> of the effects of this is the main endpoint used for dbfetch has
> changed from http://www.ebi.ac.uk/cgi-bin/dbfetch to
> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. With the old endpoints
> being supported via a HTTP redirect. It looks like the
> Bio::DB::SwissProt module does not support redirects and is thus
> getting an empty document back from the service. Looks like the URL
> used in the code needs to be updated.
> 
> All the best,
> 
> Hamish
> 
> On 26 October 2010 23:02, Chris Fields <cjfields at illinois.edu> wrote:
>> The default was changed recently in github to 'expasy'.  My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.
>> 
>> chris
>> 
>> On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:
>> 
>>> Hello,
>>> 
>>> I have a custom script for parsing out UniProt accessions from a GFF3 file
>>> and fetching the description of the UniProt entry using Bio::DB::SwissProt
>>> and *get_Seq_by_acc*.  This script has been working for months without any
>>> problems until now.  The script and the format of the input files has not
>>> changed at all.
>>> 
>>> I now get an error like this:
>>> 
>>> *------------- EXCEPTION: Bio::Root::Exception -------------*
>>> *MSG: acc O95342 does not exist*
>>> *STACK: Error::throw*
>>> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
>>> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
>>> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
>>> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
>>> *-----------------------------------------------------------*
>>> 
>>> The relevant portion of my original code looks something like this:
>>> 
>>> *#!/usr/bin/perl*
>>> *use strict;*
>>> *use Bio::DB::SwissProt;*
>>> *#parse out accession number*
>>> *..*
>>> *my $acc_num = "**O95342";*
>>> *my $db_obj = Bio::DB::SwissProt->new;*
>>> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
>>> *
>>> *
>>> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
>>> specify -servertype and -hostlocation.  So I changed my code to look
>>> something like this:
>>> 
>>> *
>>> #!/usr/bin/perl
>>> use strict;
>>> use Bio::DB::SwissProt;
>>> #parse out accession number
>>> ..
>>> my $acc_num = "O95342";
>>> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>>>                                                           '-hostlocation'
>>> => 'us');
>>> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
>>> *
>>> 
>>> This fixes my problem and my script works again.
>>> 
>>> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
>>> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>>>  Both of these urls work in a browser, though the default throws the error
>>> in my script. Interestingly, the 'us' url has a notice that says
>>> "*Notice:* This
>>> page will be replaced with www.uniprot.org. Please send us your
>>> feedback<http://www.uniprot.org/contact>
>>> !", so hopefully it doesn't break soon as well.  Perhaps the default ebi url
>>> was recently changed in some way?  Anyway, I figured I'd post here in case
>>> anyone else ran into this problem.
>>> 
>>> cheers,
>>> Matt
>>> _______________________________________________
>>> 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
>> 
> 
> 
> 
> -- 
> ----
> "Saying the internet has changed dramatically over the last five years
> is clich? ? the internet is always changing dramatically" - Craig
> Labovitz, Arbor Networks.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hamish.mcwilliam at bioinfo-user.org.uk  Wed Oct 27 15:34:09 2010
From: hamish.mcwilliam at bioinfo-user.org.uk (Hamish McWilliam)
Date: Wed, 27 Oct 2010 16:34:09 +0100
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <FAB70AF7-B56C-4DEA-BF4D-AA9F001D6E9F@illinois.edu>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
	<FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
	<AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>
	<FAB70AF7-B56C-4DEA-BF4D-AA9F001D6E9F@illinois.edu>
Message-ID: <AANLkTik0tKy2B1W8Avd7ap=Fg4prR3p0w9OXpka5PXHP@mail.gmail.com>

Hi Chris,

Although they handle the redirect, the other modules which use dbfetch
should probably have the URLs updated too:

Bio::DB::Biblio::biofetch
Bio::DB::EMBL
Bio::DB::RefSeq

Hamish

On 27 October 2010 15:51, Chris Fields <cjfields at illinois.edu> wrote:
> Hamish,
>
> Thanks, but I already caught that and fixed it in main trunk where appropriate yesterday (specifically, both Bio::DB::SwissProt and Bio::DB::BioFetch).
>
> chris
>
> On Oct 27, 2010, at 5:32 AM, Hamish McWilliam wrote:
>
>> Hi Chris,
>>
>> The dbfetch service at EBI has changed, see
>> http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010. On
>> of the effects of this is the main endpoint used for dbfetch has
>> changed from http://www.ebi.ac.uk/cgi-bin/dbfetch to
>> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. With the old endpoints
>> being supported via a HTTP redirect. It looks like the
>> Bio::DB::SwissProt module does not support redirects and is thus
>> getting an empty document back from the service. Looks like the URL
>> used in the code needs to be updated.
>>
>> All the best,
>>
>> Hamish
>>
>> On 26 October 2010 23:02, Chris Fields <cjfields at illinois.edu> wrote:
>>> The default was changed recently in github to 'expasy'. ?My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.
>>>
>>> chris
>>>
>>> On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:
>>>
>>>> Hello,
>>>>
>>>> I have a custom script for parsing out UniProt accessions from a GFF3 file
>>>> and fetching the description of the UniProt entry using Bio::DB::SwissProt
>>>> and *get_Seq_by_acc*. ?This script has been working for months without any
>>>> problems until now. ?The script and the format of the input files has not
>>>> changed at all.
>>>>
>>>> I now get an error like this:
>>>>
>>>> *------------- EXCEPTION: Bio::Root::Exception -------------*
>>>> *MSG: acc O95342 does not exist*
>>>> *STACK: Error::throw*
>>>> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
>>>> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
>>>> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
>>>> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
>>>> *-----------------------------------------------------------*
>>>>
>>>> The relevant portion of my original code looks something like this:
>>>>
>>>> *#!/usr/bin/perl*
>>>> *use strict;*
>>>> *use Bio::DB::SwissProt;*
>>>> *#parse out accession number*
>>>> *..*
>>>> *my $acc_num = "**O95342";*
>>>> *my $db_obj = Bio::DB::SwissProt->new;*
>>>> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
>>>> *
>>>> *
>>>> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
>>>> specify -servertype and -hostlocation. ?So I changed my code to look
>>>> something like this:
>>>>
>>>> *
>>>> #!/usr/bin/perl
>>>> use strict;
>>>> use Bio::DB::SwissProt;
>>>> #parse out accession number
>>>> ..
>>>> my $acc_num = "O95342";
>>>> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? '-hostlocation'
>>>> => 'us');
>>>> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
>>>> *
>>>>
>>>> This fixes my problem and my script works again.
>>>>
>>>> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
>>>> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>>>> ?Both of these urls work in a browser, though the default throws the error
>>>> in my script. Interestingly, the 'us' url has a notice that says
>>>> "*Notice:* This
>>>> page will be replaced with www.uniprot.org. Please send us your
>>>> feedback<http://www.uniprot.org/contact>
>>>> !", so hopefully it doesn't break soon as well. ?Perhaps the default ebi url
>>>> was recently changed in some way? ?Anyway, I figured I'd post here in case
>>>> anyone else ran into this problem.
>>>>
>>>> cheers,
>>>> Matt
>>>> _______________________________________________
>>>> 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
>>>
>>
>>
>>
>> --
>> ----
>> "Saying the internet has changed dramatically over the last five years
>> is clich? ? the internet is always changing dramatically" - Craig
>> Labovitz, Arbor Networks.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
----
"Saying the internet has changed dramatically over the last five years
is clich? ? the internet is always changing dramatically" - Craig
Labovitz, Arbor Networks.



From cjfields at illinois.edu  Wed Oct 27 16:20:48 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 27 Oct 2010 11:20:48 -0500
Subject: [Bioperl-l] default Bio::DB::SwissProt server broken?
In-Reply-To: <AANLkTik0tKy2B1W8Avd7ap=Fg4prR3p0w9OXpka5PXHP@mail.gmail.com>
References: <AANLkTimqqxHvHFXM6NUJO+RHDMmTUnqJXLH3wcjcxTt6@mail.gmail.com>
	<FC12313C-C872-4B1B-91D1-C9DAA3355ECD@illinois.edu>
	<AANLkTi=5cJvNWc4WyLOqm7fD5bYLYxhOQoEiRKjdi4Au@mail.gmail.com>
	<FAB70AF7-B56C-4DEA-BF4D-AA9F001D6E9F@illinois.edu>
	<AANLkTik0tKy2B1W8Avd7ap=Fg4prR3p0w9OXpka5PXHP@mail.gmail.com>
Message-ID: <BC746329-82A8-4215-BE8D-4CCDE6911FDB@illinois.edu>

Hamish,

Ah, missed those!  That's what I get for relying on tests alone.  Thanks for pointing them out; I'll double-check the various distributions for more, just in case.

chris

On Oct 27, 2010, at 10:34 AM, Hamish McWilliam wrote:

> Hi Chris,
> 
> Although they handle the redirect, the other modules which use dbfetch
> should probably have the URLs updated too:
> 
> Bio::DB::Biblio::biofetch
> Bio::DB::EMBL
> Bio::DB::RefSeq
> 
> Hamish
> 
> On 27 October 2010 15:51, Chris Fields <cjfields at illinois.edu> wrote:
>> Hamish,
>> 
>> Thanks, but I already caught that and fixed it in main trunk where appropriate yesterday (specifically, both Bio::DB::SwissProt and Bio::DB::BioFetch).
>> 
>> chris
>> 
>> On Oct 27, 2010, at 5:32 AM, Hamish McWilliam wrote:
>> 
>>> Hi Chris,
>>> 
>>> The dbfetch service at EBI has changed, see
>>> http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010. On
>>> of the effects of this is the main endpoint used for dbfetch has
>>> changed from http://www.ebi.ac.uk/cgi-bin/dbfetch to
>>> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. With the old endpoints
>>> being supported via a HTTP redirect. It looks like the
>>> Bio::DB::SwissProt module does not support redirects and is thus
>>> getting an empty document back from the service. Looks like the URL
>>> used in the code needs to be updated.
>>> 
>>> All the best,
>>> 
>>> Hamish
>>> 
>>> On 26 October 2010 23:02, Chris Fields <cjfields at illinois.edu> wrote:
>>>> The default was changed recently in github to 'expasy'.  My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.
>>>> 
>>>> chris
>>>> 
>>>> On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:
>>>> 
>>>>> Hello,
>>>>> 
>>>>> I have a custom script for parsing out UniProt accessions from a GFF3 file
>>>>> and fetching the description of the UniProt entry using Bio::DB::SwissProt
>>>>> and *get_Seq_by_acc*.  This script has been working for months without any
>>>>> problems until now.  The script and the format of the input files has not
>>>>> changed at all.
>>>>> 
>>>>> I now get an error like this:
>>>>> 
>>>>> *------------- EXCEPTION: Bio::Root::Exception -------------*
>>>>> *MSG: acc O95342 does not exist*
>>>>> *STACK: Error::throw*
>>>>> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
>>>>> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
>>>>> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
>>>>> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
>>>>> *-----------------------------------------------------------*
>>>>> 
>>>>> The relevant portion of my original code looks something like this:
>>>>> 
>>>>> *#!/usr/bin/perl*
>>>>> *use strict;*
>>>>> *use Bio::DB::SwissProt;*
>>>>> *#parse out accession number*
>>>>> *..*
>>>>> *my $acc_num = "**O95342";*
>>>>> *my $db_obj = Bio::DB::SwissProt->new;*
>>>>> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
>>>>> *
>>>>> *
>>>>> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
>>>>> specify -servertype and -hostlocation.  So I changed my code to look
>>>>> something like this:
>>>>> 
>>>>> *
>>>>> #!/usr/bin/perl
>>>>> use strict;
>>>>> use Bio::DB::SwissProt;
>>>>> #parse out accession number
>>>>> ..
>>>>> my $acc_num = "O95342";
>>>>> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>>>>>                                                           '-hostlocation'
>>>>> => 'us');
>>>>> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
>>>>> *
>>>>> 
>>>>> This fixes my problem and my script works again.
>>>>> 
>>>>> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
>>>>> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>>>>>  Both of these urls work in a browser, though the default throws the error
>>>>> in my script. Interestingly, the 'us' url has a notice that says
>>>>> "*Notice:* This
>>>>> page will be replaced with www.uniprot.org. Please send us your
>>>>> feedback<http://www.uniprot.org/contact>
>>>>> !", so hopefully it doesn't break soon as well.  Perhaps the default ebi url
>>>>> was recently changed in some way?  Anyway, I figured I'd post here in case
>>>>> anyone else ran into this problem.
>>>>> 
>>>>> cheers,
>>>>> Matt
>>>>> _______________________________________________
>>>>> 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
>>>> 
>>> 
>>> 
>>> 
>>> --
>>> ----
>>> "Saying the internet has changed dramatically over the last five years
>>> is clich? ? the internet is always changing dramatically" - Craig
>>> Labovitz, Arbor Networks.
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> ----
> "Saying the internet has changed dramatically over the last five years
> is clich? ? the internet is always changing dramatically" - Craig
> Labovitz, Arbor Networks.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From maizemu at gmail.com  Wed Oct 27 16:53:26 2010
From: maizemu at gmail.com (Christopher Bottoms)
Date: Wed, 27 Oct 2010 11:53:26 -0500
Subject: [Bioperl-l] how to download PDB files using Bioperl script
In-Reply-To: <01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
Message-ID: <AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>

Ashwani,

Do you need to download the files once or does this need to be automated?

If you just need to do it once, check out
http://www.rcsb.org/pdb/download/download.do for downloading multiple
files.

If you need to automate the process, let me know and I'll help you
figure it out. The easiest way I can think of, which I used to do, is
downloading them from the ftp site.

Sincerely,

Christopher Bottoms

On Fri, Oct 22, 2010 at 11:12 AM, Jun Yin <jun.yin at ucd.ie> wrote:
> Hi, Ashwani,
>
> I havenot found any module in BioPerl for downloading PDB files, though
> Bio::Structure::IO::pdb can parse PDB files.
>
> However, PDB provides RESTful service
> (http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
> batch downloading the proteins.
>
> Cheers,
> Jun Yin
> Ph.D.?student in U.C.D.
>
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
> Sent: Thursday, October 21, 2010 9:39 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] how to download PDB files using Bioperl script
>
> Hi All,
>
>
> I have around 150 pdb file names and I need to download them from Protein
> Data Bank. I wonder if someone could tell me how to do it by using Bioperl.
>
> Thanks in advance.
>
> Regards,
> Ashwani
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>
> __________ Information from ESET Smart Security, version of virus signature
> database 5377 (20100818) __________
>
> The message was checked by ESET Smart Security.
>
> http://www.eset.com
>
>
>
> _______________________________________________
> 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 Oct 27 18:40:02 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 27 Oct 2010 13:40:02 -0500
Subject: [Bioperl-l] A problem on BioPerl module Bio::DB::Fasta
In-Reply-To: <1288141691.2377.1.camel@ubuntu>
References: <1288141691.2377.1.camel@ubuntu>
Message-ID: <25CA46EE-B73B-4C27-9CA6-28BED05C7AEB@illinois.edu>

Tao,

I've made that correction to the HOWTO.  In the future, if you see an error on the wiki you are free to make changes to correct them.  

Thanks!

chris

On Oct 26, 2010, at 8:08 PM, Tao Zhu wrote:

> Hello, everyone!
> 
> I hope it isn't true, but I really find a problem on BioPerl module
> Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
> Osborne wrote that we could catch sub-sequences like this,
> 
> 
> use Bio::DB::Fasta;
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> $db = Bio::DB::Fasta->new($file);
> $seqobj = $db->get_Seq_by_id($id,$start,$end);
> print $seqobj->seq,"\n";
> 
> 
> In fact it didn't work. I only got the whole sequence after running the
> script. Therefore I referred to the Pdoc documentation and realized it
> should be written as follows,
> 
> 
> use Bio::DB::Fasta;
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> $db = Bio::DB::Fasta->new($file);
> $seq = $db->seq($id,$start,$end);
> print $seq,"\n";
> 
> 
> Then it would return the sub-sequence from 6 to 10.
> 
> Probably Dr Osborne had made a mistake when writing the use-guide
> HOWTO:Beginners.
> 
> 
> -- 
> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> 100875, China
> email: tzhu at mail.bnu.edu.cn
> 
> _______________________________________________
> 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 Oct 28 15:10:25 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 28 Oct 2010 10:10:25 -0500
Subject: [Bioperl-l] A problem on BioPerl module Bio::DB::Fasta
In-Reply-To: <1288251535.4408.18.camel@ubuntu>
References: <1288141691.2377.1.camel@ubuntu>
	<25CA46EE-B73B-4C27-9CA6-28BED05C7AEB@illinois.edu>
	<1288251535.4408.18.camel@ubuntu>
Message-ID: <C3335F92-724B-48C7-A05F-17AF27B244D9@illinois.edu>

Very true, didn't catch that; I was just making the correction you mentioned.  That's what happens when I don't have enough coffee!

chris

On Oct 28, 2010, at 2:38 AM, Tao Zhu wrote:

> Dear Chris,
> 
> Thank you for correcting the HOWTO, but in fact it hasn't been
> completely correct yet. I've made some changes to the passage again like
> this,
> 
> ************************
> use Bio::DB::Fasta; 
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
> $db = Bio::DB::Fasta->new($file);
> $seq = $db->seq($id,$start,$end);
> print $seq,"\n";
> ************************
> 
> The original passage is like this,
> ************************
> use Bio::DB::Fasta;
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
> $db = Bio::DB::Fasta->new($file);
> $seqobj = $db->seq($id,$start,$end); 
> print $seqobj->seq;
> ************************
> 
> We should notice that if method '$db->seq()' is called, then it would
> return a simple string, not a Bio::Seq object.
> 
> 
> 
> ? 2010-10-27?? 13:40 -0500?Chris Fields???
>> Tao,
>> 
>> I've made that correction to the HOWTO.  In the future, if you see an error on the wiki you are free to make changes to correct them.  
>> 
>> Thanks!
>> 
>> chris
>> 
>> On Oct 26, 2010, at 8:08 PM, Tao Zhu wrote:
>> 
>>> Hello, everyone!
>>> 
>>> I hope it isn't true, but I really find a problem on BioPerl module
>>> Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
>>> Osborne wrote that we could catch sub-sequences like this,
>>> 
>>> 
>>> use Bio::DB::Fasta;
>>> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
>>> $db = Bio::DB::Fasta->new($file);
>>> $seqobj = $db->get_Seq_by_id($id,$start,$end);
>>> print $seqobj->seq,"\n";
>>> 
>>> 
>>> In fact it didn't work. I only got the whole sequence after running the
>>> script. Therefore I referred to the Pdoc documentation and realized it
>>> should be written as follows,
>>> 
>>> 
>>> use Bio::DB::Fasta;
>>> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
>>> $db = Bio::DB::Fasta->new($file);
>>> $seq = $db->seq($id,$start,$end);
>>> print $seq,"\n";
>>> 
>>> 
>>> Then it would return the sub-sequence from 6 to 10.
>>> 
>>> Probably Dr Osborne had made a mistake when writing the use-guide
>>> HOWTO:Beginners.
>>> 
>>> 
>>> -- 
>>> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
>>> 100875, China
>>> email: tzhu at mail.bnu.edu.cn
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 
> 
> 




From Seidl-Michael at t-online.de  Wed Oct 27 08:58:03 2010
From: Seidl-Michael at t-online.de (seidl-michael)
Date: Wed, 27 Oct 2010 10:58:03 +0200
Subject: [Bioperl-l] Tiling of hsps using Bioperl
Message-ID: <041D7AC1-99F2-4760-B709-29FE138E05FA@web.de>

Hi everyone,

I have a question about the Bio::Search::Tiling::MapTiling  package. I  
want to get the range of my tilled hsps using the "range" function.  
The reported range is, unfortunately, not what I would expect while  
looking at my data:

 >A
          Length = 1967

Score = 70.1 bits (170), Expect = 1e-11,   Method: Compositional  
matrix adjust.
Identities = 47/110 (42%), Positives = 66/110 (60%), Gaps = 29/110 (26%)

Query: 358   
EAARQEEVARELEVKSSMATKIQSHWRGMAARSEVSTLRAEAAAAEAAASEAARQEEVAR 417
            E ARQEE+AR+ E +S+MATKIQSHWRG  ARSEV+++R+ AA A+        Q +++R
Sbjct: 1344 ELARQEELARQAEAESAMATKIQSHWRGSVARSEVASMRS-AAIADV------- 
QTQLSR 1395

Query: 418  QEEDARRKEAARQEEVARELEVKSSMATKIQSHWRGTAARSEVSTLRAEA 467
                                 +++  A +IQS WRG  AR +V++LRAEA
Sbjct: 1396 ---------------------IENLTAVRIQSRWRGVLARVKVASLRAEA 1424



Score = 57.8 bits (138), Expect = 7e-08,   Method: Compositional  
matrix adjust.
Identities = 28/39 (71%), Positives = 33/39 (84%)

Query: 358  EAARQEEVARELEVKSSMATKIQSHWRGMAARSEVSTLR 396
            E ARQEE+AR+ E +S+MATKIQSHWRG  ARSEV+ LR
Sbjct: 1222 ELARQEELARQAEAESAMATKIQSHWRGSVARSEVAVLR 1260



Score = 47.4 bits (111), Expect = 1e-04,   Method: Compositional  
matrix adjust.
Identities = 43/115 (37%), Positives = 58/115 (50%), Gaps = 29/115 (25%)

Query: 299  
RELEVKSSMATKIQSHWRGMAARSEVSTLRAEAAAAEAAASEAARQEEVARQEEDARRKE 358
           +E + K+ MAT+IQS  RG+ AR        EA + + AASE        R + + RR++
Sbjct: 433 KETQRKNDMATQIQSGVRGVIAR--------EAYSEKLAASERI---- 
AIRIQTEFRRRQ 480

Query: 359 AARQEEVARE-----------------LEVKSSMATKIQSHWRGMAARSEVSTLR 396
           A +Q E  R+                  +   S ATKIQSHWRG  ARSEV+ LR
Sbjct: 481 AQKQLEALRQQLQREQTCAVVIQKILSSDSNESAATKIQSHWRGSVARSEVAVLR 535

I would expect to get [433,1424] when using:

my $tiling = Bio::Search::Tiling::MapTiling->new($hit);
my @range = $tiling->range('subject');

Instead my array includes [1344,535]. Do I have a conceptional problem  
with the function of "range" or is there something wired happening?

Thanks a lot for any help and suggestions,

Michael


From tzhu at mail.bnu.edu.cn  Thu Oct 28 07:38:55 2010
From: tzhu at mail.bnu.edu.cn (Tao Zhu)
Date: Thu, 28 Oct 2010 15:38:55 +0800
Subject: [Bioperl-l] A problem on BioPerl module Bio::DB::Fasta
In-Reply-To: <25CA46EE-B73B-4C27-9CA6-28BED05C7AEB@illinois.edu>
References: <1288141691.2377.1.camel@ubuntu>
	<25CA46EE-B73B-4C27-9CA6-28BED05C7AEB@illinois.edu>
Message-ID: <1288251535.4408.18.camel@ubuntu>

Dear Chris,

Thank you for correcting the HOWTO, but in fact it hasn't been
completely correct yet. I've made some changes to the passage again like
this,

************************
use Bio::DB::Fasta; 
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
$db = Bio::DB::Fasta->new($file);
$seq = $db->seq($id,$start,$end);
print $seq,"\n";
************************

The original passage is like this,
************************
use Bio::DB::Fasta;
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
$db = Bio::DB::Fasta->new($file);
$seqobj = $db->seq($id,$start,$end); 
print $seqobj->seq;
************************

We should notice that if method '$db->seq()' is called, then it would
return a simple string, not a Bio::Seq object.



? 2010-10-27?? 13:40 -0500?Chris Fields???
> Tao,
> 
> I've made that correction to the HOWTO.  In the future, if you see an error on the wiki you are free to make changes to correct them.  
> 
> Thanks!
> 
> chris
> 
> On Oct 26, 2010, at 8:08 PM, Tao Zhu wrote:
> 
> > Hello, everyone!
> > 
> > I hope it isn't true, but I really find a problem on BioPerl module
> > Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
> > Osborne wrote that we could catch sub-sequences like this,
> > 
> > 
> > use Bio::DB::Fasta;
> > ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> > $db = Bio::DB::Fasta->new($file);
> > $seqobj = $db->get_Seq_by_id($id,$start,$end);
> > print $seqobj->seq,"\n";
> > 
> > 
> > In fact it didn't work. I only got the whole sequence after running the
> > script. Therefore I referred to the Pdoc documentation and realized it
> > should be written as follows,
> > 
> > 
> > use Bio::DB::Fasta;
> > ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> > $db = Bio::DB::Fasta->new($file);
> > $seq = $db->seq($id,$start,$end);
> > print $seq,"\n";
> > 
> > 
> > Then it would return the sub-sequence from 6 to 10.
> > 
> > Probably Dr Osborne had made a mistake when writing the use-guide
> > HOWTO:Beginners.
> > 
> > 
> > -- 
> > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> > 100875, China
> > email: tzhu at mail.bnu.edu.cn
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 





From edwardsa at cs.man.ac.uk  Thu Oct 28 20:52:58 2010
From: edwardsa at cs.man.ac.uk (Andrea Edwards)
Date: Thu, 28 Oct 2010 21:52:58 +0100
Subject: [Bioperl-l] Installation of bioperl on Ubuntu
Message-ID: <4CC9E2AA.6020302@cs.man.ac.uk>

Hi

I'm new to Perl and linux and I think I may have messed up my 
installation of Bioperl.

I followed the instructions on this page verbatim
http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server

However the

./Build test


command failed and I noticed a lot of modules were missing from the 
output of the test. I then used CPAN to install these modules. One of 
them was Bio::FeatureIO. When I installed this it seemed to be 
installing lots of BioPerl 1.6.1 files. However when i downloaded the 
bioperl as instructed here

wget -N http://bioperl.org/DIST/current_core_unstable.tar.bz2

the version that I got was 1.5.2_102

I am confused by the presence of 2 different version numbers and don't 
know how to proceed. It looks as if I have installed a lot of BioPerl 
1.6.1 and if i carry on with the make test/install instructions from the 
website I will then install version 1.5.

When i looked at the files installed in the Bio folder in my perl 
libraries there were 88 files and the only files missing compared to my 
other BioPerl installations were:
ANSI directory
BioEntry.pm
ConfigData.pm

I looked at some of the modules to try and see which version they were 
but they all had different version numbers. I think I have inadvertently 
used CPAN to install 1.6.1. What do you think?

many thanks


From buiduyminh at gmail.com  Thu Oct 28 21:07:06 2010
From: buiduyminh at gmail.com (Minh Bui)
Date: Thu, 28 Oct 2010 17:07:06 -0400
Subject: [Bioperl-l] Installation of bioperl on Ubuntu
In-Reply-To: <4CC9E2AA.6020302@cs.man.ac.uk>
References: <4CC9E2AA.6020302@cs.man.ac.uk>
Message-ID: <AANLkTi=Vr3zYRdtUaDptrxexkDmo_wj-2f5BiLvAAzfr@mail.gmail.com>

Hi Andrea,

You don't have to install Bioperl manually on Ubuntu.

You can go to *System* > *Administration* > "*Synaptic Package Manager*" ,
search for "Bioperl" and install it. I believe it has the latest version.

Minh.


On Thu, Oct 28, 2010 at 4:52 PM, Andrea Edwards <edwardsa at cs.man.ac.uk>wrote:

> Hi
>
> I'm new to Perl and linux and I think I may have messed up my installation
> of Bioperl.
>
> I followed the instructions on this page verbatim
> http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server
>
> However the
>
> ./Build test
>
>
> command failed and I noticed a lot of modules were missing from the output
> of the test. I then used CPAN to install these modules. One of them was
> Bio::FeatureIO. When I installed this it seemed to be installing lots of
> BioPerl 1.6.1 files. However when i downloaded the bioperl as instructed
> here
>
> wget -N http://bioperl.org/DIST/current_core_unstable.tar.bz2
>
> the version that I got was 1.5.2_102
>
> I am confused by the presence of 2 different version numbers and don't know
> how to proceed. It looks as if I have installed a lot of BioPerl 1.6.1 and
> if i carry on with the make test/install instructions from the website I
> will then install version 1.5.
>
> When i looked at the files installed in the Bio folder in my perl libraries
> there were 88 files and the only files missing compared to my other BioPerl
> installations were:
> ANSI directory
> BioEntry.pm
> ConfigData.pm
>
> I looked at some of the modules to try and see which version they were but
> they all had different version numbers. I think I have inadvertently used
> CPAN to install 1.6.1. What do you think?
>
> many thanks
> _______________________________________________
> 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 Oct 28 21:28:17 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 28 Oct 2010 16:28:17 -0500
Subject: [Bioperl-l] Installation of bioperl on Ubuntu
In-Reply-To: <4CC9E2AA.6020302@cs.man.ac.uk>
References: <4CC9E2AA.6020302@cs.man.ac.uk>
Message-ID: <22C0CD13-6081-4FC4-97B7-939696D85A74@illinois.edu>

On Oct 28, 2010, at 3:52 PM, Andrea Edwards wrote:

> Hi
> 
> I'm new to Perl and linux and I think I may have messed up my installation of Bioperl.
> 
> I followed the instructions on this page verbatim
> http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server
> 
> However the
> 
> ./Build test
> 
> 
> command failed and I noticed a lot of modules were missing from the output of the test. I then used CPAN to install these modules. One of them was Bio::FeatureIO. When I installed this it seemed to be installing lots of BioPerl 1.6.1 files. However when i downloaded the bioperl as instructed here
> 
> wget -N http://bioperl.org/DIST/current_core_unstable.tar.bz2
> 
> the version that I got was 1.5.2_102

Ugh, that's not good; that should be removed (we're now at v 1.6.1 stable, but about 10 months past that release now and sorely due for another).  For the latest 'unstable' code, you can go to github:

http://github.com/bioperl/bioperl-live

Click on the 'Downloads' button.

Just a warning, but FeatureIO will likely disappear from the github bioperl-live repo master branch.  We're breaking out chunks of code that can be released independently, FeatureIO being one.

> I am confused by the presence of 2 different version numbers and don't know how to proceed. It looks as if I have installed a lot of BioPerl 1.6.1 and if i carry on with the make test/install instructions from the website I will then install version 1.5.
> 
> When i looked at the files installed in the Bio folder in my perl libraries there were 88 files and the only files missing compared to my other BioPerl installations were:
> ANSI directory
> BioEntry.pm
> ConfigData.pm

ConfigData is only for the installation.  Not sure about the others.

> I looked at some of the modules to try and see which version they were but they all had different version numbers. I think I have inadvertently used CPAN to install 1.6.1. What do you think?
> 
> many thanks

Since we moved to github this past May we no longer have different revision numbers per module (git doesn't support them, but so far we haven't seen many actually missing them).  

chris


From daniel.standage at gmail.com  Fri Oct 29 02:45:24 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Thu, 28 Oct 2010 19:45:24 -0700 (PDT)
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
Message-ID: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>

I am using the Bio::Tools::GFF parser to process and store GFF3 data
in an application. Calls to next_feature() return
Bio::SeqFeature::Generic objects. I have written a class that extends
the Bio::SeqFeature::Generic class, but I still want to use the
Bio::Tools::GFF class to do the initial parsing of the data.

Is there a way for me to tell the Bio::Tools::GFF parser that I want
it to give me objects from my custom class? Or should I just re-bless
the objects it gives me? Will I run into garbage collection problems
if I re-bless the Bio::SeqFeature::Generic objects to my custom class
(that extends the Bio::SeqFeature::Generic class)?

Thanks!

Daniel


From scott at scottcain.net  Fri Oct 29 03:41:09 2010
From: scott at scottcain.net (Scott Cain)
Date: Thu, 28 Oct 2010 23:41:09 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
In-Reply-To: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
References: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
Message-ID: <AANLkTika2Nkx5T-Gf_y74NhEij9udqF6V3DFibzMf90G@mail.gmail.com>

Hi Daniel,

It seems like the easiest thing to do would be to subclass
Bio::Tools::GFF.  BSFGeneric is only mentioned explicitly a few times
(maybe only once), so subclassing and having it use your class instead
would probably be the easiest thing to do.

Also, about having it produce GFF3: make sure you're actually getting
valid GFF3.  Bio::Tools::GFF is fairly old, and I am sure you could
give it valid SeqFeature objects and get invalid GFF3 out in some
circumstances.

Scott


On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> I am using the Bio::Tools::GFF parser to process and store GFF3 data
> in an application. Calls to next_feature() return
> Bio::SeqFeature::Generic objects. I have written a class that extends
> the Bio::SeqFeature::Generic class, but I still want to use the
> Bio::Tools::GFF class to do the initial parsing of the data.
>
> Is there a way for me to tell the Bio::Tools::GFF parser that I want
> it to give me objects from my custom class? Or should I just re-bless
> the objects it gives me? Will I run into garbage collection problems
> if I re-bless the Bio::SeqFeature::Generic objects to my custom class
> (that extends the Bio::SeqFeature::Generic class)?
>
> Thanks!
>
> Daniel
> _______________________________________________
> 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 dimitark at bii.a-star.edu.sg  Fri Oct 29 08:29:53 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Fri, 29 Oct 2010 16:29:53 +0800
Subject: [Bioperl-l] about git and perl5lib
Message-ID: <4CCA8601.6020607@bii.a-star.edu.sg>

Hi guys,
i am sorry if this sounds stupid but i have problem with the PERL5LIB 
and the GIT version of BioPerl(BP). I downloaded the BP-live and BP-run 
from git. I use Slackware so I added the following line in bashrc:

  export 
PERL5LIB=$HOME/Bioperl_git/bioperl-live:$HOME/Bioperl_git/bioperl-run:$PERL5LIB

But when i start a script using StandAloneBlastPlus i see perl cant find it:

Can't locate Bio/Tools/Run/StandAloneBlastPlus.pm in @INC (@INC 
contains: /home/domine/Bioperl_git/bioperl-live 
/home/domine/Bioperl_git/bioperl-run 
/usr/lib64/perl5/5.10.1/x86_64-linux-thread-multi 
/usr/lib64/perl5/5.10.1 
/usr/lib64/perl5/site_perl/5.10.1/x86_64-linux-thread-multi 
/usr/lib64/perl5/site_perl/5.10.1 /usr/lib64/perl5/site_perl 
/usr/lib64/perl5/vendor_perl/5.10.1/x86_64-linux-thread-multi 
/usr/lib64/perl5/vendor_perl/5.10.1 /usr/lib64/perl5/vendor_perl

It seems Perl should find the module but it doesnt. Any idea where i 
could have made a mistake?

Btw with:  perl -MBio::Perl -le 'print Bio::Perl->VERSION;' i get 1.0069

Thank you
Dimitar





From David.Messina at sbc.su.se  Fri Oct 29 12:18:40 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 29 Oct 2010 08:18:40 -0400
Subject: [Bioperl-l] about git and perl5lib
In-Reply-To: <4CCA8601.6020607@bii.a-star.edu.sg>
References: <4CCA8601.6020607@bii.a-star.edu.sg>
Message-ID: <DACCDE9C-B82D-4D71-84BC-4119B6E242FD@sbc.su.se>

There's a minor inconsistency on our part: the path to the bioperl-run modules is actually bioperl-run/lib


Note that bioperl-live will I believe also be switching to this at some point; having the modules in a lib subdir is standard Perl practice.


Dave






On Oct 29, 2010, at 4:29, Dimitar Kenanov <dimitark at bii.a-star.edu.sg> wrote:

> Hi guys,
> i am sorry if this sounds stupid but i have problem with the PERL5LIB and the GIT version of BioPerl(BP). I downloaded the BP-live and BP-run from git. I use Slackware so I added the following line in bashrc:
> 
> export PERL5LIB=$HOME/Bioperl_git/bioperl-live:$HOME/Bioperl_git/bioperl-run:$PERL5LIB
> 
> But when i start a script using StandAloneBlastPlus i see perl cant find it:
> 
> Can't locate Bio/Tools/Run/StandAloneBlastPlus.pm in @INC (@INC contains: /home/domine/Bioperl_git/bioperl-live /home/domine/Bioperl_git/bioperl-run /usr/lib64/perl5/5.10.1/x86_64-linux-thread-multi /usr/lib64/perl5/5.10.1 /usr/lib64/perl5/site_perl/5.10.1/x86_64-linux-thread-multi /usr/lib64/perl5/site_perl/5.10.1 /usr/lib64/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.10.1/x86_64-linux-thread-multi /usr/lib64/perl5/vendor_perl/5.10.1 /usr/lib64/perl5/vendor_perl
> 
> It seems Perl should find the module but it doesnt. Any idea where i could have made a mistake?
> 
> Btw with:  perl -MBio::Perl -le 'print Bio::Perl->VERSION;' i get 1.0069
> 
> Thank you
> Dimitar
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From scott at scottcain.net  Fri Oct 29 14:03:54 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 29 Oct 2010 10:03:54 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
In-Reply-To: <AANLkTimVseFgymk+MaumosOkh=jP3bR9LwGVLxmB26Xf@mail.gmail.com>
References: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
	<AANLkTika2Nkx5T-Gf_y74NhEij9udqF6V3DFibzMf90G@mail.gmail.com>
	<AANLkTimVseFgymk+MaumosOkh=jP3bR9LwGVLxmB26Xf@mail.gmail.com>
Message-ID: <AANLkTinKbEtuWetY7avw6uH8w_GcXvrTxD1t7R8t9jc3@mail.gmail.com>

Hi Daniel,

I cc'ed the bioperl mailing list back in and attached your tarball.  I
don't really know what it is you want to do, and you already know that
your code compiles and runs, so I'm not sure what advice you're
looking for.

Scott

On Fri, Oct 29, 2010 at 9:28 AM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> I don't see how to attach files to the mailing list, so I'm just going to
> reply to you. Sorry if that is against the protocol.
>
> I have attached a working implementation of what I think you were
> suggesting. I have a parser class that subclasses Bio::Tools::GFF, and it
> has a method that will return objects of my class that subclasses
> Bio::SeqFeature::Generic. This is a rough test and I still need to clean
> things up and add the rest of the functionality that I originally needed, I
> just wanted to make sure that there aren't going to be any problems with the
> approach I'm taking.
>
> If you unpack and run './temptest' it should print out 7 valid features and
> 1 invalid feature.
>
> Thanks for your suggestions!
>
> Daniel
>
> On Thu, Oct 28, 2010 at 10:41 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Daniel,
>>
>> It seems like the easiest thing to do would be to subclass
>> Bio::Tools::GFF. ?BSFGeneric is only mentioned explicitly a few times
>> (maybe only once), so subclassing and having it use your class instead
>> would probably be the easiest thing to do.
>>
>> Also, about having it produce GFF3: make sure you're actually getting
>> valid GFF3. ?Bio::Tools::GFF is fairly old, and I am sure you could
>> give it valid SeqFeature objects and get invalid GFF3 out in some
>> circumstances.
>>
>> Scott
>>
>>
>> On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
>> <daniel.standage at gmail.com> wrote:
>> > I am using the Bio::Tools::GFF parser to process and store GFF3 data
>> > in an application. Calls to next_feature() return
>> > Bio::SeqFeature::Generic objects. I have written a class that extends
>> > the Bio::SeqFeature::Generic class, but I still want to use the
>> > Bio::Tools::GFF class to do the initial parsing of the data.
>> >
>> > Is there a way for me to tell the Bio::Tools::GFF parser that I want
>> > it to give me objects from my custom class? Or should I just re-bless
>> > the objects it gives me? Will I run into garbage collection problems
>> > if I re-bless the Bio::SeqFeature::Generic objects to my custom class
>> > (that extends the Bio::SeqFeature::Generic class)?
>> >
>> > Thanks!
>> >
>> > Daniel
>> > _______________________________________________
>> > 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
>
>
>
> --
> Daniel S. Standage
> Graduate Research Assistant
> Bioinformatics and Computational Biology Program
> Iowa State University
>
>



-- 
------------------------------------------------------------------------
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 scott at scottcain.net  Fri Oct 29 14:21:51 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 29 Oct 2010 10:21:51 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
In-Reply-To: <AANLkTinKbEtuWetY7avw6uH8w_GcXvrTxD1t7R8t9jc3@mail.gmail.com>
References: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
	<AANLkTika2Nkx5T-Gf_y74NhEij9udqF6V3DFibzMf90G@mail.gmail.com>
	<AANLkTimVseFgymk+MaumosOkh=jP3bR9LwGVLxmB26Xf@mail.gmail.com>
	<AANLkTinKbEtuWetY7avw6uH8w_GcXvrTxD1t7R8t9jc3@mail.gmail.com>
Message-ID: <AANLkTikoPX7ep5QfOd-EDxoGqYU43kJZtwv5MaBHawXC@mail.gmail.com>

Hi all,

I'm resending this because it seems that some mail clients don't like
having executable files hidden inside of a tarball, so I removed the
executable bit.

Scott


On Fri, Oct 29, 2010 at 10:03 AM, Scott Cain <scott at scottcain.net> wrote:
> Hi Daniel,
>
> I cc'ed the bioperl mailing list back in and attached your tarball. ?I
> don't really know what it is you want to do, and you already know that
> your code compiles and runs, so I'm not sure what advice you're
> looking for.
>
> Scott
>
> On Fri, Oct 29, 2010 at 9:28 AM, Daniel Standage
> <daniel.standage at gmail.com> wrote:
>> I don't see how to attach files to the mailing list, so I'm just going to
>> reply to you. Sorry if that is against the protocol.
>>
>> I have attached a working implementation of what I think you were
>> suggesting. I have a parser class that subclasses Bio::Tools::GFF, and it
>> has a method that will return objects of my class that subclasses
>> Bio::SeqFeature::Generic. This is a rough test and I still need to clean
>> things up and add the rest of the functionality that I originally needed, I
>> just wanted to make sure that there aren't going to be any problems with the
>> approach I'm taking.
>>
>> If you unpack and run './temptest' it should print out 7 valid features and
>> 1 invalid feature.
>>
>> Thanks for your suggestions!
>>
>> Daniel
>>
>> On Thu, Oct 28, 2010 at 10:41 PM, Scott Cain <scott at scottcain.net> wrote:
>>>
>>> Hi Daniel,
>>>
>>> It seems like the easiest thing to do would be to subclass
>>> Bio::Tools::GFF. ?BSFGeneric is only mentioned explicitly a few times
>>> (maybe only once), so subclassing and having it use your class instead
>>> would probably be the easiest thing to do.
>>>
>>> Also, about having it produce GFF3: make sure you're actually getting
>>> valid GFF3. ?Bio::Tools::GFF is fairly old, and I am sure you could
>>> give it valid SeqFeature objects and get invalid GFF3 out in some
>>> circumstances.
>>>
>>> Scott
>>>
>>>
>>> On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
>>> <daniel.standage at gmail.com> wrote:
>>> > I am using the Bio::Tools::GFF parser to process and store GFF3 data
>>> > in an application. Calls to next_feature() return
>>> > Bio::SeqFeature::Generic objects. I have written a class that extends
>>> > the Bio::SeqFeature::Generic class, but I still want to use the
>>> > Bio::Tools::GFF class to do the initial parsing of the data.
>>> >
>>> > Is there a way for me to tell the Bio::Tools::GFF parser that I want
>>> > it to give me objects from my custom class? Or should I just re-bless
>>> > the objects it gives me? Will I run into garbage collection problems
>>> > if I re-bless the Bio::SeqFeature::Generic objects to my custom class
>>> > (that extends the Bio::SeqFeature::Generic class)?
>>> >
>>> > Thanks!
>>> >
>>> > Daniel
>>> > _______________________________________________
>>> > 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
>>
>>
>>
>> --
>> Daniel S. Standage
>> Graduate Research Assistant
>> Bioinformatics and Computational Biology Program
>> Iowa State University
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> 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
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From daniel.standage at gmail.com  Fri Oct 29 14:34:41 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Fri, 29 Oct 2010 09:34:41 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Generic and Inheritance Question
In-Reply-To: <AANLkTikoPX7ep5QfOd-EDxoGqYU43kJZtwv5MaBHawXC@mail.gmail.com>
References: <dec53f06-e667-4304-a895-841589181fed@f33g2000yqh.googlegroups.com>
	<AANLkTika2Nkx5T-Gf_y74NhEij9udqF6V3DFibzMf90G@mail.gmail.com>
	<AANLkTimVseFgymk+MaumosOkh=jP3bR9LwGVLxmB26Xf@mail.gmail.com>
	<AANLkTinKbEtuWetY7avw6uH8w_GcXvrTxD1t7R8t9jc3@mail.gmail.com>
	<AANLkTikoPX7ep5QfOd-EDxoGqYU43kJZtwv5MaBHawXC@mail.gmail.com>
Message-ID: <AANLkTikwhSvoEHJECSGV9GzKdXk7Yu7O6nwkk=-Mccba@mail.gmail.com>

I guess my concern is that I haven't used inheritance much in Perl and I'm
unclear about the possible consequences of the approach I've taken. I've
seen people warning against re-blessing objects, and I just wanted to make
sure that the approach that I seem to have working now isn't going to cause
any problems down the line.

Sorry I wasn't clear. Thanks for your help.

Daniel

On Fri, Oct 29, 2010 at 9:21 AM, Scott Cain <scott at scottcain.net> wrote:

> Hi all,
>
> I'm resending this because it seems that some mail clients don't like
> having executable files hidden inside of a tarball, so I removed the
> executable bit.
>
> Scott
>
>
> On Fri, Oct 29, 2010 at 10:03 AM, Scott Cain <scott at scottcain.net> wrote:
> > Hi Daniel,
> >
> > I cc'ed the bioperl mailing list back in and attached your tarball.  I
> > don't really know what it is you want to do, and you already know that
> > your code compiles and runs, so I'm not sure what advice you're
> > looking for.
> >
> > Scott
> >
> > On Fri, Oct 29, 2010 at 9:28 AM, Daniel Standage
> > <daniel.standage at gmail.com> wrote:
> >> I don't see how to attach files to the mailing list, so I'm just going
> to
> >> reply to you. Sorry if that is against the protocol.
> >>
> >> I have attached a working implementation of what I think you were
> >> suggesting. I have a parser class that subclasses Bio::Tools::GFF, and
> it
> >> has a method that will return objects of my class that subclasses
> >> Bio::SeqFeature::Generic. This is a rough test and I still need to clean
> >> things up and add the rest of the functionality that I originally
> needed, I
> >> just wanted to make sure that there aren't going to be any problems with
> the
> >> approach I'm taking.
> >>
> >> If you unpack and run './temptest' it should print out 7 valid features
> and
> >> 1 invalid feature.
> >>
> >> Thanks for your suggestions!
> >>
> >> Daniel
> >>
> >> On Thu, Oct 28, 2010 at 10:41 PM, Scott Cain <scott at scottcain.net>
> wrote:
> >>>
> >>> Hi Daniel,
> >>>
> >>> It seems like the easiest thing to do would be to subclass
> >>> Bio::Tools::GFF.  BSFGeneric is only mentioned explicitly a few times
> >>> (maybe only once), so subclassing and having it use your class instead
> >>> would probably be the easiest thing to do.
> >>>
> >>> Also, about having it produce GFF3: make sure you're actually getting
> >>> valid GFF3.  Bio::Tools::GFF is fairly old, and I am sure you could
> >>> give it valid SeqFeature objects and get invalid GFF3 out in some
> >>> circumstances.
> >>>
> >>> Scott
> >>>
> >>>
> >>> On Thu, Oct 28, 2010 at 10:45 PM, Daniel Standage
> >>> <daniel.standage at gmail.com> wrote:
> >>> > I am using the Bio::Tools::GFF parser to process and store GFF3 data
> >>> > in an application. Calls to next_feature() return
> >>> > Bio::SeqFeature::Generic objects. I have written a class that extends
> >>> > the Bio::SeqFeature::Generic class, but I still want to use the
> >>> > Bio::Tools::GFF class to do the initial parsing of the data.
> >>> >
> >>> > Is there a way for me to tell the Bio::Tools::GFF parser that I want
> >>> > it to give me objects from my custom class? Or should I just re-bless
> >>> > the objects it gives me? Will I run into garbage collection problems
> >>> > if I re-bless the Bio::SeqFeature::Generic objects to my custom class
> >>> > (that extends the Bio::SeqFeature::Generic class)?
> >>> >
> >>> > Thanks!
> >>> >
> >>> > Daniel
> >>> > _______________________________________________
> >>> > 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
> >>
> >>
> >>
> >> --
> >> Daniel S. Standage
> >> Graduate Research Assistant
> >> Bioinformatics and Computational Biology Program
> >> Iowa State University
> >>
> >>
> >
> >
> >
> > --
> > ------------------------------------------------------------------------
> > 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
>



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