From noreply at github.com  Fri Jul  1 14:05:55 2011
From: noreply at github.com (noreply at github.com)
Date: Fri, 1 Jul 2011 11:05:55 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] a5ca17: Add test for
	RPS-BLAST algorithm
Message-ID: <20110701180555.758764249C@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: a5ca17dd6906f2643ca76aedcfb550c40fdbbac5
      https://github.com/bioperl/bioperl-live/commit/a5ca17dd6906f2643ca76aedcfb550c40fdbbac5
  Author: Brian Osborne <briano at bioteam.net>
  Date:   2011-07-01 (Fri, 01 Jul 2011)

  Changed paths:
    M t/SearchIO/blast.t

  Log Message:
  -----------
  Add test for RPS-BLAST algorithm



From noreply at github.com  Sun Jul  3 13:03:48 2011
From: noreply at github.com (noreply at github.com)
Date: Sun, 3 Jul 2011 10:03:48 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 8c5f17: Stockholm.pm did
	not work, fixed now. Add tests. M...
Message-ID: <20110703170348.013224240A@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: 8c5f173e784966dd8352c284e9dd436773dcdd16
      https://github.com/bioperl/bioperl-live/commit/8c5f173e784966dd8352c284e9dd436773dcdd16
  Author: Brian Osborne <briano at bioteam.net>
  Date:   2011-07-03 (Sun, 03 Jul 2011)

  Changed paths:
    M Bio/Index/Stockholm.pm
  M t/LocalDB/Index/Index.t
  M t/data/testaln.stockholm

  Log Message:
  -----------
  Stockholm.pm did not work, fixed now. Add tests. Make ids unique in aligment file.



From noreply at github.com  Tue Jul  5 09:25:48 2011
From: noreply at github.com (noreply at github.com)
Date: Tue, 5 Jul 2011 06:25:48 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 5bbaa1: Minor edits to docs
Message-ID: <20110705132548.B86D1423A1@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: 5bbaa163d6d3a71759e29b828bb9a3147c615c91
      https://github.com/bioperl/bioperl-live/commit/5bbaa163d6d3a71759e29b828bb9a3147c615c91
  Author: Brian Osborne <briano at bioteam.net>
  Date:   2011-07-05 (Tue, 05 Jul 2011)

  Changed paths:
    M Bio/Index/Stockholm.pm

  Log Message:
  -----------
  Minor edits to docs



From redmine at redmine.open-bio.org  Tue Jul  5 16:26:17 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Tue, 5 Jul 2011 20:26:17 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3252] ./Build.PL --network has no
	effect.
References: <redmine.issue-3252.20110618015256@redmine.open-bio.org>
Message-ID: <redmine.journal-14608.20110705202617@redmine.open-bio.org>


Issue #3252 has been updated by Chris Fields.

Assignee set to Bioperl Guts


----------------------------------------
Bug #3252: ./Build.PL --network has no effect.
https://redmine.open-bio.org/issues/3252

Author: Charles Plessy
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: 
Target version: 
URL: 


Because ./Build.PL --network sets $build->notes('network'), but the interactive selection of network tests sets $build->notes('Network Tests'), both methods can not work at the same time.  The attached patch modifies Bio/Root/Build.pm and Bio/Root/Test.pm to set and use $build->notes('network'), so that ./Build.PL --network works again.


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From redmine at redmine.open-bio.org  Tue Jul  5 16:26:19 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Tue, 5 Jul 2011 20:26:19 +0000
Subject: [Bioperl-guts-l] [BioPerl-Run - Bug #3253] Undocumented need for
	Array::Compare.
References: <redmine.issue-3253.20110618020311@redmine.open-bio.org>
Message-ID: <redmine.journal-14609.20110705202619@redmine.open-bio.org>


Issue #3253 has been updated by Chris Fields.

Assignee set to Bioperl Guts


----------------------------------------
Bug #3253: Undocumented need for Array::Compare.
https://redmine.open-bio.org/issues/3253

Author: Charles Plessy
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: 
Target version: 
URL: 


Dear BioPerl developers,

BioPerl-Run needs Array::Compare to run its regression tests (t/lib/Test/Warn.pm), but this is not documented anywhere so it slightly complicates packaging in Linux distributions like Debian (for keeping track of what a package needs).

Have a nice week-end,

-- 
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


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From redmine at redmine.open-bio.org  Tue Jul  5 16:26:20 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Tue, 5 Jul 2011 20:26:20 +0000
Subject: [Bioperl-guts-l] [BioPerl-Run - Bug #3255] /usr/local/bin/perl used
	for scripts/bioperl_application_installer.pl
References: <redmine.issue-3255.20110618040230@redmine.open-bio.org>
Message-ID: <redmine.journal-14611.20110705202620@redmine.open-bio.org>


Issue #3255 has been updated by Chris Fields.

Assignee set to Bioperl Guts


----------------------------------------
Bug #3255: /usr/local/bin/perl used for scripts/bioperl_application_installer.pl
https://redmine.open-bio.org/issues/3255

Author: Charles Plessy
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: 
Target version: 
URL: 


In contrary to the other scripts, scripts/bioperl_application_installer.pl uses /usr/local/bin/perl, which is not available by default on many Linux distributions.  The attached patch changes this path to /usr/bin/perl.


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From redmine at redmine.open-bio.org  Tue Jul  5 16:26:20 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Tue, 5 Jul 2011 20:26:20 +0000
Subject: [Bioperl-guts-l] =?utf-8?q?=5BBioPerl-Run_-_Bug_=233256=5D_Spellc?=
	=?utf-8?q?hecking=E2=80=A6?=
References: <redmine.issue-3256.20110618042027@redmine.open-bio.org>
Message-ID: <redmine.journal-14612.20110705202620@redmine.open-bio.org>


Issue #3256 has been updated by Chris Fields.

Assignee set to Bioperl Guts


----------------------------------------
Bug #3256: Spellchecking?
https://redmine.open-bio.org/issues/3256

Author: Charles Plessy
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: 
Target version: 
URL: 


Please accept this humble spell checking patch from Debian.


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From redmine at redmine.open-bio.org  Tue Jul  5 16:26:21 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Tue, 5 Jul 2011 20:26:21 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3261] incomplete parse of
	entrezgene file
References: <redmine.issue-3261.20110705152403@redmine.open-bio.org>
Message-ID: <redmine.journal-14614.20110705202621@redmine.open-bio.org>


Issue #3261 has been updated by Chris Fields.

Assignee set to Bioperl Guts


----------------------------------------
Bug #3261: incomplete parse of entrezgene file
https://redmine.open-bio.org/issues/3261

Author: Carn? Draug
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: 
Target version: 
URL: 


Hi

Some data on entrezgene file are not parsed completely, and some of the data is inaccessible. I attached a file that causes that problem.

I was looking for the ids "NM_002105" and "NP_002096" which show up several times on the file. However, when I use Data::Dumper to see the contents of the sequence object I couldn't see them.

use Data::Dumper;
use Bio::SeqIO;
my $file = $ARGV[0];
my $seqio_object = Bio::SeqIO->new(-file => $file, -format => 'entrezgene');
my $seq_object = $seqio_object->next_seq;
print Dumper($seq_object);

I can't find 002105 or 002096 anywhere on the output (actually the first can be seen as part of an URL only)

I asked for help on this first on the bioperl mailing list and was told to report it as a bug.


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From redmine at redmine.open-bio.org  Tue Jul  5 16:26:21 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Tue, 5 Jul 2011 20:26:21 +0000
Subject: [Bioperl-guts-l] [BioPerl-Run - Bug #3257] comparison of a string
	with a number
References: <redmine.issue-3257.20110623173145@redmine.open-bio.org>
Message-ID: <redmine.journal-14613.20110705202621@redmine.open-bio.org>


Issue #3257 has been updated by Chris Fields.

Assignee set to Bioperl Guts


----------------------------------------
Bug #3257: comparison of a string with a number
https://redmine.open-bio.org/issues/3257

Author: sixela De bourgogne
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: 
Target version: 
URL: 


In SeqI.pm, the function _delete return a string, which is then compared to a number, leading to the following warning

Argument "AAAAA" isn't numeric in numeric eq (==) at BioPerl-1.6.1/Bio/LiveSeq/SeqI.pm line 558, <GEN0> line 1.
 at BioPerl-1.6.1/Bio/LiveSeq/SeqI.pm line 558




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From redmine at redmine.open-bio.org  Tue Jul  5 16:26:19 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Tue, 5 Jul 2011 20:26:19 +0000
Subject: [Bioperl-guts-l] [BioPerl-Run - Feature #3254] New
	--install_scripts option to request script installation
	non-interactively.
References: <redmine.issue-3254.20110618034750@redmine.open-bio.org>
Message-ID: <redmine.journal-14610.20110705202619@redmine.open-bio.org>


Issue #3254 has been updated by Chris Fields.

Assignee set to Bioperl Guts


----------------------------------------
Feature #3254: New --install_scripts option to request script installation non-interactively.
https://redmine.open-bio.org/issues/3254

Author: Charles Plessy
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: 
Target version: 
URL: 


Hello,

installation of BioPerl-Run scripts is not the default anymore, which slightly complicates packaging in Debian.  The attached patch introduces a new --install_scripts option to request script installation non-interactively.  Would you consider it ?


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From redmine at redmine.open-bio.org  Tue Jul  5 17:01:25 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Tue, 5 Jul 2011 21:01:25 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3262] (New) Test bug
Message-ID: <redmine.issue-3262.20110705210125@redmine.open-bio.org>


Issue #3262 has been reported by Chris Fields.

----------------------------------------
Bug #3262: Test bug
https://redmine.open-bio.org/issues/3262

Author: Chris Fields
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: Core Components
Target version: 
URL: 


GitHub now has a new post-commit hook for Redmine (no plugin required for a generic post-receive URL hook).  This is a test bug to catch these.


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From redmine at redmine.open-bio.org  Tue Jul  5 17:01:25 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Tue, 5 Jul 2011 21:01:25 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3262] (New) Test bug
Message-ID: <redmine.issue-3262.20110705210125@redmine.open-bio.org>


Issue #3262 has been reported by Chris Fields.

----------------------------------------
Bug #3262: Test bug
https://redmine.open-bio.org/issues/3262

Author: Chris Fields
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: Core Components
Target version: 
URL: 


GitHub now has a new post-commit hook for Redmine (no plugin required for a generic post-receive URL hook).  This is a test bug to catch these.


----------------------------------------
You have received this notification because this email was added to the New Issue Alert plugin


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From noreply at github.com  Tue Jul  5 17:03:31 2011
From: noreply at github.com (noreply at github.com)
Date: Tue, 5 Jul 2011 14:03:31 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 470a3c: update Changes,
	refs bug #3262
Message-ID: <20110705210331.C3F5B421BB@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: 470a3c2be217ee5d88c3eb6ccd11677ff099d3c1
      https://github.com/bioperl/bioperl-live/commit/470a3c2be217ee5d88c3eb6ccd11677ff099d3c1
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-05 (Tue, 05 Jul 2011)

  Changed paths:
    M Changes

  Log Message:
  -----------
  update Changes, refs bug #3262



From noreply at github.com  Tue Jul  5 17:13:25 2011
From: noreply at github.com (noreply at github.com)
Date: Tue, 5 Jul 2011 14:13:25 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] a67546: remove $Id$ tag,
	refs #3262
Message-ID: <20110705211325.210AE42457@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: a6754658355e3dc8f9bed9cda60d5e3c0dfd4510
      https://github.com/bioperl/bioperl-live/commit/a6754658355e3dc8f9bed9cda60d5e3c0dfd4510
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-05 (Tue, 05 Jul 2011)

  Changed paths:
    M README

  Log Message:
  -----------
  remove $Id$ tag, refs #3262



From noreply at github.com  Tue Jul  5 17:26:22 2011
From: noreply at github.com (noreply at github.com)
Date: Tue, 5 Jul 2011 14:26:22 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 640ac8: remove superfluous
	line, refs #3262
Message-ID: <20110705212622.438A142341@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: 640ac836fe3f9e7df9039f6467b0c6d8863fd322
      https://github.com/bioperl/bioperl-live/commit/640ac836fe3f9e7df9039f6467b0c6d8863fd322
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-05 (Tue, 05 Jul 2011)

  Changed paths:
    M README

  Log Message:
  -----------
  remove superfluous line, refs #3262



From noreply at github.com  Tue Jul  5 17:34:15 2011
From: noreply at github.com (noreply at github.com)
Date: Tue, 5 Jul 2011 14:34:15 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 771f72: test, refs #3262
Message-ID: <20110705213415.8692D42493@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: 771f7253d84a42891f9c367d1639879ff1a2ff2a
      https://github.com/bioperl/bioperl-live/commit/771f7253d84a42891f9c367d1639879ff1a2ff2a
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-05 (Tue, 05 Jul 2011)

  Changed paths:
    M README

  Log Message:
  -----------
  test, refs #3262



From noreply at github.com  Tue Jul  5 18:13:39 2011
From: noreply at github.com (noreply at github.com)
Date: Tue, 5 Jul 2011 15:13:39 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 35e8b7: test, refs bug #3262
Message-ID: <20110705221339.348F842341@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: 35e8b76113d0a09dbc19ac8ea5cc686243d3b75d
      https://github.com/bioperl/bioperl-live/commit/35e8b76113d0a09dbc19ac8ea5cc686243d3b75d
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-05 (Tue, 05 Jul 2011)

  Changed paths:
    M README

  Log Message:
  -----------
  test, refs bug #3262



From redmine at redmine.open-bio.org  Tue Jul  5 18:27:36 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Tue, 5 Jul 2011 22:27:36 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3261] incomplete parse of
	entrezgene file
References: <redmine.issue-3261.20110705152403@redmine.open-bio.org>
Message-ID: <redmine.journal-14615.20110705222736@redmine.open-bio.org>


Issue #3261 has been updated by Carn? Draug.


Discussing this on the mailing list http://thread.gmane.org/gmane.comp.lang.perl.bio.general/24705 it was shown that the entire data is accessible if the file is parsed using the Bio::ASN1::EntrezGene module directly (just not when using the Bio::SeqIO module).

The following code shows that the entire file is being parsed correctly:

<pre>
use warnings;
use strict;
use Bio::ASN1::EntrezGene;
use Data::Dumper;

my $parser = Bio::ASN1::EntrezGene->new('file' => "entrezgene.asn");
while(my $result = $parser->next_seq){
  print Dumper ($result);
}
</pre>
I looked at the Bio::SeqIO module file, followed it to Bio::SeqIO::entrezgene and it looks like it should be using Bio::ASN1::EntrezGene module to parse the file anyway. Here's initialize method that I found on the code

<pre>
sub _initialize {
    my ( $self, @args ) = @_;
    $self->SUPER::_initialize(@args);
    my %param = @args;
    @param{ map { lc $_ } keys %param } = values %param;    # lowercase keys
    $self->{_debug}          = $param{-debug}          || 'off';
    $self->{_locuslink}      = $param{-locuslink}      || 'no';
    $self->{_service_record} = $param{-service_record} || 'no';
    $self->{_parser} = Bio::ASN1::EntrezGene->new( file => $param{-file} );

    #Instantiate the low level parser here (it is -file in Bioperl
    #-should tell M.)
    #$self->{_parser}->next_seq; #First empty record- bug in Bio::ASN::Parser
}
</pre>
----------------------------------------
Bug #3261: incomplete parse of entrezgene file
https://redmine.open-bio.org/issues/3261

Author: Carn? Draug
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: 
Target version: 
URL: 


Hi

Some data on entrezgene file are not parsed completely, and some of the data is inaccessible. I attached a file that causes that problem.

I was looking for the ids "NM_002105" and "NP_002096" which show up several times on the file. However, when I use Data::Dumper to see the contents of the sequence object I couldn't see them.

use Data::Dumper;
use Bio::SeqIO;
my $file = $ARGV[0];
my $seqio_object = Bio::SeqIO->new(-file => $file, -format => 'entrezgene');
my $seq_object = $seqio_object->next_seq;
print Dumper($seq_object);

I can't find 002105 or 002096 anywhere on the output (actually the first can be seen as part of an URL only)

I asked for help on this first on the bioperl mailing list and was told to report it as a bug.


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From redmine at redmine.open-bio.org  Tue Jul  5 22:20:24 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Wed, 6 Jul 2011 02:20:24 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3252] (Closed) ./Build.PL
	--network has no effect.
References: <redmine.issue-3252.20110618015256@redmine.open-bio.org>
Message-ID: <redmine.journal-14616.20110706022024@redmine.open-bio.org>


Issue #3252 has been updated by Chris Fields.

Status changed from New to Closed
% Done changed from 0 to 100

Applied in changeset commit:6a3c2b8d48fe5166f86c7c5e987b1a4e6bf79117.
----------------------------------------
Bug #3252: ./Build.PL --network has no effect.
https://redmine.open-bio.org/issues/3252

Author: Charles Plessy
Status: Closed
Priority: Normal
Assignee: Bioperl Guts
Category: 
Target version: 
URL: 


Because ./Build.PL --network sets $build->notes('network'), but the interactive selection of network tests sets $build->notes('Network Tests'), both methods can not work at the same time.  The attached patch modifies Bio/Root/Build.pm and Bio/Root/Test.pm to set and use $build->notes('network'), so that ./Build.PL --network works again.


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From noreply at github.com  Tue Jul  5 22:20:25 2011
From: noreply at github.com (noreply at github.com)
Date: Tue, 5 Jul 2011 19:20:25 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 6a3c2b: restore --network
	flag (broke this accidently in l...
Message-ID: <20110706022025.7BAF242355@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: 6a3c2b8d48fe5166f86c7c5e987b1a4e6bf79117
      https://github.com/bioperl/bioperl-live/commit/6a3c2b8d48fe5166f86c7c5e987b1a4e6bf79117
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-05 (Tue, 05 Jul 2011)

  Changed paths:
    M Bio/Root/Build.pm
  M Bio/Root/Test.pm

  Log Message:
  -----------
  restore --network flag (broke this accidently in last release), patch courtesy Charles Plessy, fixes bug #3252



From redmine at redmine.open-bio.org  Tue Jul  5 22:29:21 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Wed, 6 Jul 2011 02:29:21 +0000
Subject: [Bioperl-guts-l] [BioPerl-Run - Bug #3253] Undocumented need for
	Array::Compare.
References: <redmine.issue-3253.20110618020311@redmine.open-bio.org>
Message-ID: <redmine.journal-14617.20110706022921@redmine.open-bio.org>


Issue #3253 has been updated by Chris Fields.


The traditional place to have these is in a @build_requires@ section.  Would that work?
----------------------------------------
Bug #3253: Undocumented need for Array::Compare.
https://redmine.open-bio.org/issues/3253

Author: Charles Plessy
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: 
Target version: 
URL: 


Dear BioPerl developers,

BioPerl-Run needs Array::Compare to run its regression tests (t/lib/Test/Warn.pm), but this is not documented anywhere so it slightly complicates packaging in Linux distributions like Debian (for keeping track of what a package needs).

Have a nice week-end,

-- 
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


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From redmine at redmine.open-bio.org  Tue Jul  5 22:33:35 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Wed, 6 Jul 2011 02:33:35 +0000
Subject: [Bioperl-guts-l] =?utf-8?q?=5BBioPerl-Run_-_Bug_=233256=5D_=28Clo?=
	=?utf-8?b?c2VkKSBTcGVsbGNoZWNraW5n4oCm?=
References: <redmine.issue-3256.20110618042027@redmine.open-bio.org>
Message-ID: <redmine.journal-14618.20110706023335@redmine.open-bio.org>


Issue #3256 has been updated by Chris Fields.

Status changed from New to Closed
% Done changed from 0 to 100

Applied in changeset commit:42649c5308b51c1b87d442ac35e82b8ccfa6545d.
----------------------------------------
Bug #3256: Spellchecking?
https://redmine.open-bio.org/issues/3256

Author: Charles Plessy
Status: Closed
Priority: Normal
Assignee: Bioperl Guts
Category: 
Target version: 
URL: 


Please accept this humble spell checking patch from Debian.


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From redmine at redmine.open-bio.org  Tue Jul  5 22:33:36 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Wed, 6 Jul 2011 02:33:36 +0000
Subject: [Bioperl-guts-l] [BioPerl-Run - Feature #3254] (Closed) New
	--install_scripts option to request script installation
	non-interactively.
References: <redmine.issue-3254.20110618034750@redmine.open-bio.org>
Message-ID: <redmine.journal-14619.20110706023336@redmine.open-bio.org>


Issue #3254 has been updated by Chris Fields.

Status changed from New to Closed
% Done changed from 0 to 100

Applied in changeset commit:20d2c4886f28eeb41465b780b875e6370e3c33ee.
----------------------------------------
Feature #3254: New --install_scripts option to request script installation non-interactively.
https://redmine.open-bio.org/issues/3254

Author: Charles Plessy
Status: Closed
Priority: Normal
Assignee: Bioperl Guts
Category: 
Target version: 
URL: 


Hello,

installation of BioPerl-Run scripts is not the default anymore, which slightly complicates packaging in Debian.  The attached patch introduces a new --install_scripts option to request script installation non-interactively.  Would you consider it ?


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From noreply at github.com  Tue Jul  5 22:33:37 2011
From: noreply at github.com (noreply at github.com)
Date: Tue, 5 Jul 2011 19:33:37 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-run] 20d2c4: add
	--install_scripts option for Build.PL, patch c...
Message-ID: <20110706023337.3E5F842352@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-run

  Commit: 20d2c4886f28eeb41465b780b875e6370e3c33ee
      https://github.com/bioperl/bioperl-run/commit/20d2c4886f28eeb41465b780b875e6370e3c33ee
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-05 (Tue, 05 Jul 2011)

  Changed paths:
    M Build.PL

  Log Message:
  -----------
  add --install_scripts option for Build.PL, patch courtesy Charles Plessy, fixes bug #3254


  Commit: 42649c5308b51c1b87d442ac35e82b8ccfa6545d
      https://github.com/bioperl/bioperl-run/commit/42649c5308b51c1b87d442ac35e82b8ccfa6545d
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-05 (Tue, 05 Jul 2011)

  Changed paths:
    M lib/Bio/Tools/Run/Alignment/Clustalw.pm
  M lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
  M lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
  M lib/Bio/Tools/Run/AssemblerBase.pm
  M lib/Bio/Tools/Run/FootPrinter.pm
  M lib/Bio/Tools/Run/Hmmer.pm
  M lib/Bio/Tools/Run/MCS.pm
  M lib/Bio/Tools/Run/Phylo/Gerp.pm
  M lib/Bio/Tools/Run/Phylo/Gumby.pm
  M lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm
  M lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
  M lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
  M lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm
  M lib/Bio/Tools/Run/Phylo/Phyml.pm
  M lib/Bio/Tools/Run/Phylo/QuickTree.pm
  M lib/Bio/Tools/Run/Phylo/Semphy.pm
  M lib/Bio/Tools/Run/StandAloneBlastPlus.pm
  M lib/Bio/Tools/Run/TigrAssembler.pm
  M t/lib/Test/Builder/Tester.pm

  Log Message:
  -----------
  speelink fixes, patch courtesy Charles Plessy, fixes #3256


Compare: https://github.com/bioperl/bioperl-run/compare/925b83d...42649c5

From noreply at github.com  Tue Jul  5 22:35:43 2011
From: noreply at github.com (noreply at github.com)
Date: Tue, 5 Jul 2011 19:35:43 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-run] e90554: fix path to system
	perl, patch courtesy Charles Pl...
Message-ID: <20110706023543.6D8B1423DD@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-run

  Commit: e90554309810f68142886ef99547cd563043358a
      https://github.com/bioperl/bioperl-run/commit/e90554309810f68142886ef99547cd563043358a
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-05 (Tue, 05 Jul 2011)

  Changed paths:
    M scripts/bioperl_application_installer.PLS

  Log Message:
  -----------
  fix path to system perl, patch courtesy Charles Plessy, fixes bug #3255



From redmine at redmine.open-bio.org  Tue Jul  5 22:35:42 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Wed, 6 Jul 2011 02:35:42 +0000
Subject: [Bioperl-guts-l] [BioPerl-Run - Bug #3255] (Closed)
	/usr/local/bin/perl used for
	scripts/bioperl_application_installer.pl
References: <redmine.issue-3255.20110618040230@redmine.open-bio.org>
Message-ID: <redmine.journal-14620.20110706023542@redmine.open-bio.org>


Issue #3255 has been updated by Chris Fields.

Status changed from New to Closed
% Done changed from 0 to 100

Applied in changeset commit:e90554309810f68142886ef99547cd563043358a.
----------------------------------------
Bug #3255: /usr/local/bin/perl used for scripts/bioperl_application_installer.pl
https://redmine.open-bio.org/issues/3255

Author: Charles Plessy
Status: Closed
Priority: Normal
Assignee: Bioperl Guts
Category: 
Target version: 
URL: 


In contrary to the other scripts, scripts/bioperl_application_installer.pl uses /usr/local/bin/perl, which is not available by default on many Linux distributions.  The attached patch changes this path to /usr/bin/perl.


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From redmine at redmine.open-bio.org  Tue Jul  5 22:37:02 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Wed, 6 Jul 2011 02:37:02 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3257] comparison of a string with
	a number
References: <redmine.issue-3257.20110623173145@redmine.open-bio.org>
Message-ID: <redmine.journal-14621.20110706023702@redmine.open-bio.org>


Issue #3257 has been updated by Chris Fields.

Project changed from BioPerl-Run to BioPerl


----------------------------------------
Bug #3257: comparison of a string with a number
https://redmine.open-bio.org/issues/3257

Author: sixela De bourgogne
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: 
Target version: 
URL: 


In SeqI.pm, the function _delete return a string, which is then compared to a number, leading to the following warning

Argument "AAAAA" isn't numeric in numeric eq (==) at BioPerl-1.6.1/Bio/LiveSeq/SeqI.pm line 558, <GEN0> line 1.
 at BioPerl-1.6.1/Bio/LiveSeq/SeqI.pm line 558




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From noreply at github.com  Tue Jul  5 22:53:46 2011
From: noreply at github.com (noreply at github.com)
Date: Tue, 5 Jul 2011 19:53:46 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-run] b2b2e4: updates for PhyML
	3.0, patch courtesy Jessen Brede...
Message-ID: <20110706025346.5218C42427@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-run

  Commit: b2b2e4c3a9dcb54dbc62445222e500fa78ff9108
      https://github.com/bioperl/bioperl-run/commit/b2b2e4c3a9dcb54dbc62445222e500fa78ff9108
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-05 (Tue, 05 Jul 2011)

  Changed paths:
    M lib/Bio/Tools/Run/Phylo/Phyml.pm

  Log Message:
  -----------
  updates for PhyML 3.0, patch courtesy Jessen Bredeson, refs issue #3226



From noreply at github.com  Tue Jul  5 23:21:57 2011
From: noreply at github.com (noreply at github.com)
Date: Tue, 5 Jul 2011 20:21:57 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-run] c6f898: tested against phyml
	2.4.4 and phyml 3.0 releases, ...
Message-ID: <20110706032157.DD999423C7@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-run

  Commit: c6f898b5031fe178169145a827bbeb0ec1e8a65c
      https://github.com/bioperl/bioperl-run/commit/c6f898b5031fe178169145a827bbeb0ec1e8a65c
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-05 (Tue, 05 Jul 2011)

  Changed paths:
    M lib/Bio/Tools/Run/Phylo/Phyml.pm
  M t/Phyml.t

  Log Message:
  -----------
  tested against phyml 2.4.4 and phyml 3.0 releases, recent releases with dated versions are a bit flaky



From redmine at redmine.open-bio.org  Mon Jul 11 12:34:14 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Mon, 11 Jul 2011 16:34:14 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3262] Test bug
References: <redmine.issue-3262.20110705210125@redmine.open-bio.org>
Message-ID: <redmine.journal-14624.20110711163414@redmine.open-bio.org>


Issue #3262 has been updated by Chris Fields.


At the moment the new hook is essentially useless for our purposes, see "this thread":https://www.chiliproject.org/boards/1/topics/525
----------------------------------------
Bug #3262: Test bug
https://redmine.open-bio.org/issues/3262

Author: Chris Fields
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: Core Components
Target version: 
URL: 


GitHub now has a new post-commit hook for Redmine (no plugin required for a generic post-receive URL hook).  This is a test bug to catch these.


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From noreply at github.com  Mon Jul 11 13:35:25 2011
From: noreply at github.com (noreply at github.com)
Date: Mon, 11 Jul 2011 10:35:25 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 924340: add option to turn
	off summary stats when --create...
Message-ID: <20110711173525.665804229C@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: 92434037e496fa06f34446b5fa9d7e0138096ae6
      https://github.com/bioperl/bioperl-live/commit/92434037e496fa06f34446b5fa9d7e0138096ae6
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-11 (Mon, 11 Jul 2011)

  Changed paths:
    M scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.PLS

  Log Message:
  -----------
  add option to turn off summary stats when --create is specified; fixes bug #3199



From redmine at redmine.open-bio.org  Mon Jul 11 13:35:24 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Mon, 11 Jul 2011 17:35:24 +0000
Subject: [Bioperl-guts-l] [BioPerl - Feature #3199] (Closed)
	bp_seqfeature_load.pl: add --nosummary option
References: <redmine.issue-3199.20110411181759@redmine.open-bio.org>
Message-ID: <redmine.journal-14625.20110711173524@redmine.open-bio.org>


Issue #3199 has been updated by Chris Fields.

Status changed from New to Closed
% Done changed from 0 to 100

Applied in changeset commit:92434037e496fa06f34446b5fa9d7e0138096ae6.
----------------------------------------
Feature #3199: bp_seqfeature_load.pl: add --nosummary option
https://redmine.open-bio.org/issues/3199

Author: Nathan Weeks
Status: Closed
Priority: Normal
Assignee: Bioperl Guts
Category: 
Target version: 
URL: 


Currently, --summary is enabled by default if --create is specified.
This isn't documented, and it's sometimes undesirable if it increases
load time and space for tracks where summary satistics will never be
used.

A couple solutions:
# Do not generate summary statistics by default if "--create" is specified.
   I think this is preferable, as it makes the behavior of bp_seqfeature_load.pl
   more consistent.
# If the first solution isn't satisfactory due to the possibility of a change in
   current behavior impacting existing scripts, a "--nosummary" (-N) option
   could be used to disable the generate summary statistics.

Attached is patch that implements the second solution; here is an example
of where its use is beneficial in terms of disk space and load time for a
track that doesn't need summary statistics:
<pre>
$ bp_seqfeature_load.PLS -c -a DBI::SQLite -d test.sqlite test.gff
loading /mnt/genome_structure/recent_duplication_blocks/output/test.gff...
837 features loaded in  0.96s                                                   
Building object tree... 0.04s
load time:  1.01s
Building summary statistics for coverage graphs...

coverage graph build time: 25.11stotal load time: 26.12s
$ du -h test.sqlite
 51M    test.sqlite
$ rm test.sqlite
remove test.sqlite? y
$ ~/bp_seqfeature_load.PLS -N -c -a DBI::SQLite -d test.sqlite test.gff
loading test.gff...
837 features loaded in  0.96s                                                   
Building object tree... 0.04s
load time:  1.00s
total load time:  1.00s
$ du -h test.sqlite
692K    test.sqlite
</pre>





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From redmine at redmine.open-bio.org  Mon Jul 11 13:37:23 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Mon, 11 Jul 2011 17:37:23 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3204] file/fh checking should be
	in Bio::Root::IO, not in subclasses
References: <redmine.issue-3204.20110413182314@redmine.open-bio.org>
Message-ID: <redmine.journal-14626.20110711173723@redmine.open-bio.org>


Issue #3204 has been updated by Chris Fields.

Target version changed from 1.7 branch to unspecified

We'll probably wait until Bio::Root modules are split out into their own distribution before fixing this (currently underway with Sheena's GSoC 2011 project)
----------------------------------------
Bug #3204: file/fh checking should be in Bio::Root::IO, not in subclasses
https://redmine.open-bio.org/issues/3204

Author: Chris Fields
Status: In Progress
Priority: Low
Assignee: Bioperl Guts
Category: 
Target version: unspecified
URL: 


Any checking of file or filehandle arguments should be handled by the parent Bio::Root::IO class for consistency.  Currently there seems to be inconsistent checking of these in the various subclasses (ex: Bio::SeqIO).  See this thread:

http://lists.open-bio.org/pipermail/bioperl-l/2011-April/034868.html


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From noreply at github.com  Wed Jul 13 03:16:44 2011
From: noreply at github.com (noreply at github.com)
Date: Wed, 13 Jul 2011 00:16:44 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 8dec0e: Fixed issue when
	adding MID to a simulated read th...
Message-ID: <20110713071644.ADAE7424C5@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: 8dec0ef17eae846742a8f5bd8b40341aebff90b8
      https://github.com/bioperl/bioperl-live/commit/8dec0ef17eae846742a8f5bd8b40341aebff90b8
  Author: Florent Angly <florent.angly at gmail.com>
  Date:   2011-07-13 (Wed, 13 Jul 2011)

  Changed paths:
    M Bio/Seq/SimulatedRead.pm
  M t/Seq/SimulatedRead.t

  Log Message:
  -----------
  Fixed issue when adding MID to a simulated read that already has a MID


  Commit: f71e5de6d80e8ad14d2285745bf98300744e4026
      https://github.com/bioperl/bioperl-live/commit/f71e5de6d80e8ad14d2285745bf98300744e4026
  Author: Florent Angly <florent.angly at gmail.com>
  Date:   2011-07-13 (Wed, 13 Jul 2011)

  Changed paths:
    M Bio/Seq/SimulatedRead.pm
  M t/Seq/SimulatedRead.t

  Log Message:
  -----------
  Fixed an edge case when introducing errors in the last bases of a simulated read with MID


Compare: https://github.com/bioperl/bioperl-live/compare/9243403...f71e5de

From redmine at redmine.open-bio.org  Thu Jul 14 19:03:05 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Thu, 14 Jul 2011 23:03:05 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3264] (New) Bio::SearchIO::hmmer2
	fails with Bio::Tools::Run::Hmmer, with diagnosis
Message-ID: <redmine.issue-3264.20110714230305@redmine.open-bio.org>


Issue #3264 has been reported by George Hartzell.

----------------------------------------
Bug #3264: Bio::SearchIO::hmmer2 fails with Bio::Tools::Run::Hmmer, with diagnosis
https://redmine.open-bio.org/issues/3264

Author: George Hartzell
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


I'm working with clones of the git repository from this morning.

I can't get bioperl-run/t/Hmmer.t to pass.

Digging into it I believe that the root of the problem is that Bio::SearchIO:hmmer::new reads a couple of lines off of the filehandle in order to figure out the hmmer version and then assumes that it can use seek to rewind the input stream back to the beginning.

Unfortunately Bio::Tools::Run::Hmmer ends up passing in a filehandle that's reading off of a pipe.

Line 132 of Bio/SearchIO/hmmer.pm should become something like this:

            @seek($fh, 0, 0) or die "Unable to seek to start of input.";@

and then "someone" needs to figure out how to make the format guesser Do The Right Thing when it's input is a pipe.



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From redmine at redmine.open-bio.org  Fri Jul 15 20:50:09 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Sat, 16 Jul 2011 00:50:09 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3265] (New) BioPerl(Bio::SearchIO)
	has different behaviours in parsing blast and blast+ result
Message-ID: <redmine.issue-3265.20110716005009@redmine.open-bio.org>


Issue #3265 has been reported by yi xianfu.

----------------------------------------
Bug #3265: BioPerl(Bio::SearchIO) has different behaviours in parsing blast and blast+ result
https://redmine.open-bio.org/issues/3265

Author: yi xianfu
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: Bio::Search/Bio::SearchIO
Target version: 
URL: http://biostar.stackexchange.com/questions/10295/bioperl-has-different-behaviours-in-parsing-blast-and-blast-result


Hi Developers,

When I was using BioPerl(Bio::SearchIO) to parse the blast results, I found that it can parse the blast(2.2.25) result but not the blast+(2.2.25+) result (all were in the default format).

The result of blast is parsed properly. But the result of parsing blast+ has no output (except the header I printed).

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

Besides, according to BioPerl's wiki(http://www.bioperl.org/wiki/HOWTO%3aSearchIO) (NCBI-BLAST parsing problems), XML format is recommended. But I found that Bioperl has problems in parsing blast or blast+ results in XML format.

The result of parsing blast in XML format outputs the first query only , while I have three queries. The result of parsing blast+ in XML format has the same problem. Besides, it can not get the query id properly: they are all named "Query_1".

BTW: The same bug about XML format has been reported.
Bug #3154: SearchIO:blastxml does not return correct query name for blastp (2.2.24)
https://redmine.open-bio.org/issues/3154
--------------------------------------------------------------------------

All files for test has been attached. BTW, the FASTA file for database building is too big, so I give the website for downloading instead of the real file. "README" is recommended to read.

--------------------------------------------------------------------------
System: Ubuntu 10.10.
Version: Perl-5.10.1; BioPerl-1.6.901(not sure).
BTW: The problem has been asked on BioStar (http://biostar.stackexchange.com/questions/10295/bioperl-has-different-behaviours-in-parsing-blast-and-blast-result).

Thanks,
yixf


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From redmine at redmine.open-bio.org  Fri Jul 15 20:50:10 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Sat, 16 Jul 2011 00:50:10 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3265] (New) BioPerl(Bio::SearchIO)
	has different behaviours in parsing blast and blast+ result
Message-ID: <redmine.issue-3265.20110716005009@redmine.open-bio.org>


Issue #3265 has been reported by yi xianfu.

----------------------------------------
Bug #3265: BioPerl(Bio::SearchIO) has different behaviours in parsing blast and blast+ result
https://redmine.open-bio.org/issues/3265

Author: yi xianfu
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: Bio::Search/Bio::SearchIO
Target version: 
URL: http://biostar.stackexchange.com/questions/10295/bioperl-has-different-behaviours-in-parsing-blast-and-blast-result


Hi Developers,

When I was using BioPerl(Bio::SearchIO) to parse the blast results, I found that it can parse the blast(2.2.25) result but not the blast+(2.2.25+) result (all were in the default format).

The result of blast is parsed properly. But the result of parsing blast+ has no output (except the header I printed).

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

Besides, according to BioPerl's wiki(http://www.bioperl.org/wiki/HOWTO%3aSearchIO) (NCBI-BLAST parsing problems), XML format is recommended. But I found that Bioperl has problems in parsing blast or blast+ results in XML format.

The result of parsing blast in XML format outputs the first query only , while I have three queries. The result of parsing blast+ in XML format has the same problem. Besides, it can not get the query id properly: they are all named "Query_1".

BTW: The same bug about XML format has been reported.
Bug #3154: SearchIO:blastxml does not return correct query name for blastp (2.2.24)
https://redmine.open-bio.org/issues/3154
--------------------------------------------------------------------------

All files for test has been attached. BTW, the FASTA file for database building is too big, so I give the website for downloading instead of the real file. "README" is recommended to read.

--------------------------------------------------------------------------
System: Ubuntu 10.10.
Version: Perl-5.10.1; BioPerl-1.6.901(not sure).
BTW: The problem has been asked on BioStar (http://biostar.stackexchange.com/questions/10295/bioperl-has-different-behaviours-in-parsing-blast-and-blast-result).

Thanks,
yixf


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From redmine at redmine.open-bio.org  Fri Jul 15 21:20:15 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Sat, 16 Jul 2011 01:20:15 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3265] BioPerl(Bio::SearchIO) has
	different behaviours in parsing blast and blast+ result
References: <redmine.issue-3265.20110716005009@redmine.open-bio.org>
Message-ID: <redmine.journal-14629.20110716012015@redmine.open-bio.org>


Issue #3265 has been updated by Jason Stajich.


I'm not aware than anyone has volunteered to test and develop improvements to this module to handle any changes in BLAST+ so I'm not surprised that it isn't working... 


----------------------------------------
Bug #3265: BioPerl(Bio::SearchIO) has different behaviours in parsing blast and blast+ result
https://redmine.open-bio.org/issues/3265

Author: yi xianfu
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: Bio::Search/Bio::SearchIO
Target version: 
URL: http://biostar.stackexchange.com/questions/10295/bioperl-has-different-behaviours-in-parsing-blast-and-blast-result


Hi Developers,

When I was using BioPerl(Bio::SearchIO) to parse the blast results, I found that it can parse the blast(2.2.25) result but not the blast+(2.2.25+) result (all were in the default format).

The result of blast is parsed properly. But the result of parsing blast+ has no output (except the header I printed).

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

Besides, according to BioPerl's wiki(http://www.bioperl.org/wiki/HOWTO%3aSearchIO) (NCBI-BLAST parsing problems), XML format is recommended. But I found that Bioperl has problems in parsing blast or blast+ results in XML format.

The result of parsing blast in XML format outputs the first query only , while I have three queries. The result of parsing blast+ in XML format has the same problem. Besides, it can not get the query id properly: they are all named "Query_1".

BTW: The same bug about XML format has been reported.
Bug #3154: SearchIO:blastxml does not return correct query name for blastp (2.2.24)
https://redmine.open-bio.org/issues/3154
--------------------------------------------------------------------------

All files for test has been attached. BTW, the FASTA file for database building is too big, so I give the website for downloading instead of the real file. "README" is recommended to read.

--------------------------------------------------------------------------
System: Ubuntu 10.10.
Version: Perl-5.10.1; BioPerl-1.6.901(not sure).
BTW: The problem has been asked on BioStar (http://biostar.stackexchange.com/questions/10295/bioperl-has-different-behaviours-in-parsing-blast-and-blast-result).

Thanks,
yixf


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From noreply at github.com  Thu Jul 21 02:06:43 2011
From: noreply at github.com (noreply at github.com)
Date: Wed, 20 Jul 2011 23:06:43 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 1681f9: Fixed a bug in
	Bio::Seq::Meta* modules that preven...
Message-ID: <20110721060643.179A7425F2@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: 1681f9f54f836943fd370737f049afb4ef59f3c0
      https://github.com/bioperl/bioperl-live/commit/1681f9f54f836943fd370737f049afb4ef59f3c0
  Author: Florent Angly <florent.angly at gmail.com>
  Date:   2011-07-20 (Wed, 20 Jul 2011)

  Changed paths:
    M Bio/Seq/Meta.pm
  M Bio/Seq/Meta/Array.pm
  M Bio/Seq/SimulatedRead.pm
  M t/Seq/MetaSeq.t
  M t/Seq/SimulatedRead.t

  Log Message:
  -----------
  Fixed a bug in Bio::Seq::Meta* modules that prevented objects without meta information to be reverse-complemented



From redmine at redmine.open-bio.org  Mon Jul 25 09:37:46 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Mon, 25 Jul 2011 13:37:46 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3269] (New) Incorrect name
	creation in Bio::SimpleAlign:remove_seq
Message-ID: <redmine.issue-3269.20110725133746@redmine.open-bio.org>


Issue #3269 has been reported by James Allen.

----------------------------------------
Bug #3269: Incorrect name creation in Bio::SimpleAlign:remove_seq
https://redmine.open-bio.org/issues/3269

Author: James Allen
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


The @get_nse@ function in the LocatableSeq module was changed to take account of strand information (cf http://lists.open-bio.org/pipermail/bioperl-l/2009-December/031807.html). In SimpleAlign.pm the @add_seq@ function uses @get_nse@ to generate a name for each sequence; but the @remove_seq@ function does not, instead generating a name without reference to the strand. This causes remove_seq to fail if the sequence is on the negative strand, since the names don't match. This is an easy fix, and I've attached a patch in which @remove_seq@ also uses @get_nse@ (diffed against bioperl-live).

Cheers,
James



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From noreply at github.com  Mon Jul 25 14:21:44 2011
From: noreply at github.com (noreply at github.com)
Date: Mon, 25 Jul 2011 11:21:44 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] edc9e5: Merge pull request
	#17 from carandraug/master
Message-ID: <20110725182144.2AE9E42392@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: edc9e522d8a0bba1265b351a892d20de976f7953
      https://github.com/bioperl/bioperl-live/commit/edc9e522d8a0bba1265b351a892d20de976f7953
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-25 (Mon, 25 Jul 2011)

  Changed paths:
    A scripts/Bio-DB-EUtilities/bp_einfo.PLS
  R scripts/Bio-DB-EUtilities/einfo.PLS
  A scripts/Bio-DB-GFF/bp_bulk_load_gff.PLS
  A scripts/Bio-DB-GFF/bp_fast_load_gff.PLS
  A scripts/Bio-DB-GFF/bp_genbank2gff.PLS
  A scripts/Bio-DB-GFF/bp_genbank2gff3.PLS
  A scripts/Bio-DB-GFF/bp_generate_histogram.PLS
  A scripts/Bio-DB-GFF/bp_load_gff.PLS
  A scripts/Bio-DB-GFF/bp_meta_gff.PLS
  A scripts/Bio-DB-GFF/bp_process_gadfly.PLS
  A scripts/Bio-DB-GFF/bp_process_sgd.PLS
  A scripts/Bio-DB-GFF/bp_process_wormbase.PLS
  R scripts/Bio-DB-GFF/bulk_load_gff.PLS
  R scripts/Bio-DB-GFF/fast_load_gff.PLS
  R scripts/Bio-DB-GFF/genbank2gff.PLS
  R scripts/Bio-DB-GFF/genbank2gff3.PLS
  R scripts/Bio-DB-GFF/generate_histogram.PLS
  R scripts/Bio-DB-GFF/load_gff.PLS
  R scripts/Bio-DB-GFF/meta_gff.PLS
  R scripts/Bio-DB-GFF/process_gadfly.PLS
  R scripts/Bio-DB-GFF/process_sgd.PLS
  R scripts/Bio-DB-GFF/process_wormbase.PLS
  M scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.PLS
  M scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.PLS
  M scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.PLS
  A scripts/DB-HIV/bp_hivq.PLS
  R scripts/DB-HIV/hivq.PLS
  R scripts/DB/biofetch_genbank_proxy.PLS
  R scripts/DB/bioflat_index.PLS
  R scripts/DB/biogetseq.PLS
  A scripts/DB/bp_biofetch_genbank_proxy.PLS
  A scripts/DB/bp_bioflat_index.PLS
  A scripts/DB/bp_biogetseq.PLS
  A scripts/DB/bp_flanks.PLS
  R scripts/DB/flanks.PLS
  R scripts/biblio/biblio.PLS
  A scripts/biblio/bp_biblio.PLS
  A scripts/das/bp_das_server.pl
  R scripts/das/das_server.pl
  M scripts/index/bp_fetch.PLS
  M scripts/index/bp_index.PLS
  A scripts/popgen/bp_composite_LD.PLS
  A scripts/popgen/bp_heterogeneity_test.PLS
  R scripts/popgen/composite_LD.PLS
  R scripts/popgen/heterogeneity_test.PLS
  A scripts/searchio/bp_fastam9_to_table.PLS
  A scripts/searchio/bp_filter_search.PLS
  A scripts/searchio/bp_hmmer_to_table.PLS
  A scripts/searchio/bp_parse_hmmsearch.PLS
  A scripts/searchio/bp_search2table.PLS
  R scripts/searchio/fastam9_to_table.PLS
  R scripts/searchio/filter_search.PLS
  R scripts/searchio/hmmer_to_table.PLS
  R scripts/searchio/parse_hmmsearch.PLS
  R scripts/searchio/search2table.PLS
  A scripts/seq/bp_extract_feature_seq.PLS
  A scripts/seq/bp_make_mrna_protein.PLS
  A scripts/seq/bp_seqconvert.PLS
  A scripts/seq/bp_seqretsplit.PLS
  A scripts/seq/bp_split_seq.PLS
  A scripts/seq/bp_translate_seq.PLS
  A scripts/seq/bp_unflatten_seq.PLS
  R scripts/seq/extract_feature_seq.PLS
  R scripts/seq/make_mrna_protein.PLS
  R scripts/seq/seqconvert.PLS
  R scripts/seq/seqretsplit.PLS
  R scripts/seq/split_seq.PLS
  R scripts/seq/translate_seq.PLS
  R scripts/seq/unflatten_seq.PLS
  R scripts/seqstats/aacomp.PLS
  A scripts/seqstats/bp_aacomp.PLS
  A scripts/seqstats/bp_chaos_plot.PLS
  A scripts/seqstats/bp_gccalc.PLS
  A scripts/seqstats/bp_oligo_count.PLS
  R scripts/seqstats/chaos_plot.PLS
  R scripts/seqstats/gccalc.PLS
  R scripts/seqstats/oligo_count.PLS
  A scripts/taxa/bp_classify_hits_kingdom.PLS
  A scripts/taxa/bp_local_taxonomydb_query.PLS
  A scripts/taxa/bp_query_entrez_taxa.PLS
  A scripts/taxa/bp_taxid4species.PLS
  A scripts/taxa/bp_taxonomy2tree.PLS
  R scripts/taxa/classify_hits_kingdom.PLS
  R scripts/taxa/local_taxonomydb_query.PLS
  R scripts/taxa/query_entrez_taxa.PLS
  R scripts/taxa/taxid4species.PLS
  R scripts/taxa/taxonomy2tree.PLS
  R scripts/tree/blast2tree.PLS
  A scripts/tree/bp_blast2tree.PLS
  A scripts/tree/bp_nexus2nh.PLS
  A scripts/tree/bp_tree2pag.PLS
  R scripts/tree/nexus2nh.PLS
  R scripts/tree/tree2pag.PLS
  A scripts/utilities/bp_dbsplit.PLS
  A scripts/utilities/bp_download_query_genbank.PLS
  A scripts/utilities/bp_mask_by_search.PLS
  A scripts/utilities/bp_mutate.PLS
  A scripts/utilities/bp_pairwise_kaks.PLS
  A scripts/utilities/bp_remote_blast.PLS
  A scripts/utilities/bp_revtrans-motif.PLS
  A scripts/utilities/bp_search2BSML.PLS
  A scripts/utilities/bp_search2alnblocks.PLS
  A scripts/utilities/bp_search2gff.PLS
  A scripts/utilities/bp_search2tribe.PLS
  A scripts/utilities/bp_seq_length.PLS
  R scripts/utilities/dbsplit.PLS
  R scripts/utilities/download_query_genbank.PLS
  R scripts/utilities/mask_by_search.PLS
  R scripts/utilities/mutate.PLS
  R scripts/utilities/pairwise_kaks.PLS
  R scripts/utilities/remote_blast.PLS
  R scripts/utilities/revtrans-motif.PLS
  R scripts/utilities/search2BSML.PLS
  R scripts/utilities/search2alnblocks.PLS
  R scripts/utilities/search2gff.PLS
  R scripts/utilities/search2tribe.PLS
  R scripts/utilities/seq_length.PLS

  Log Message:
  -----------
  Merge pull request #17 from carandraug/master

prefix scripts with bp_.  Will possibly run another pull request to change file extension to .pl, depending on feedback.



From noreply at github.com  Mon Jul 25 15:13:13 2011
From: noreply at github.com (noreply at github.com)
Date: Mon, 25 Jul 2011 12:13:13 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 7c156d: scripts: replaced
	-w switch by use warnings
Message-ID: <20110725191315.35FC8424B3@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: 7c156d69589b299f887d88de26ea446120ddd2cd
      https://github.com/bioperl/bioperl-live/commit/7c156d69589b299f887d88de26ea446120ddd2cd
  Author: Carn? Draug <carandraug+dev at gmail.com>
  Date:   2011-07-25 (Mon, 25 Jul 2011)

  Changed paths:
    M scripts/DB/bp_biofetch_genbank_proxy.PLS
  M scripts/DB/bp_biogetseq.PLS
  M scripts/biblio/bp_biblio.PLS
  M scripts/searchio/bp_filter_search.PLS
  M scripts/searchio/bp_hmmer_to_table.PLS
  M scripts/seq/bp_extract_feature_seq.PLS
  M scripts/seq/bp_make_mrna_protein.PLS
  M scripts/seq/bp_seqconvert.PLS
  M scripts/seq/bp_split_seq.PLS
  M scripts/seq/bp_translate_seq.PLS
  M scripts/seq/bp_unflatten_seq.PLS
  M scripts/seqstats/bp_aacomp.PLS
  M scripts/seqstats/bp_chaos_plot.PLS
  M scripts/seqstats/bp_gccalc.PLS
  M scripts/seqstats/bp_oligo_count.PLS
  M scripts/taxa/bp_taxid4species.PLS
  M scripts/tree/bp_nexus2nh.PLS
  M scripts/tree/bp_tree2pag.PLS
  M scripts/utilities/bp_dbsplit.PLS
  M scripts/utilities/bp_mask_by_search.PLS
  M scripts/utilities/bp_nrdb.PLS
  M scripts/utilities/bp_pairwise_kaks.PLS
  M scripts/utilities/bp_search2BSML.PLS
  M scripts/utilities/bp_search2alnblocks.PLS
  M scripts/utilities/bp_search2gff.PLS
  M scripts/utilities/bp_search2tribe.PLS
  M scripts/utilities/bp_seq_length.PLS

  Log Message:
  -----------
  scripts: replaced -w switch by use warnings


  Commit: 9050a06acfe93a976e6471a44c8fd7fd5d030cab
      https://github.com/bioperl/bioperl-live/commit/9050a06acfe93a976e6471a44c8fd7fd5d030cab
  Author: Carn? Draug <carandraug+dev at gmail.com>
  Date:   2011-07-25 (Mon, 25 Jul 2011)

  Changed paths:
    M scripts/Bio-DB-GFF/bp_bulk_load_gff.PLS
  M scripts/Bio-DB-GFF/bp_fast_load_gff.PLS
  M scripts/Bio-DB-GFF/bp_genbank2gff.PLS
  M scripts/Bio-DB-GFF/bp_genbank2gff3.PLS
  M scripts/Bio-DB-GFF/bp_generate_histogram.PLS
  M scripts/Bio-DB-GFF/bp_load_gff.PLS
  M scripts/Bio-DB-GFF/bp_meta_gff.PLS
  M scripts/Bio-DB-GFF/bp_process_gadfly.PLS
  M scripts/Bio-DB-GFF/bp_process_sgd.PLS
  M scripts/Bio-DB-GFF/bp_process_wormbase.PLS
  M scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.PLS
  M scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.PLS
  M scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.PLS
  M scripts/DB-HIV/bp_hivq.PLS
  M scripts/DB/bp_bioflat_index.PLS
  M scripts/DB/bp_flanks.PLS
  M scripts/das/bp_das_server.pl
  M scripts/index/bp_index.PLS
  M scripts/index/bp_seqret.PLS
  M scripts/popgen/bp_composite_LD.PLS
  M scripts/popgen/bp_heterogeneity_test.PLS
  M scripts/searchio/bp_fastam9_to_table.PLS
  M scripts/searchio/bp_parse_hmmsearch.PLS
  M scripts/searchio/bp_search2table.PLS
  M scripts/seq/bp_seqretsplit.PLS
  M scripts/taxa/bp_classify_hits_kingdom.PLS
  M scripts/taxa/bp_local_taxonomydb_query.PLS
  M scripts/taxa/bp_query_entrez_taxa.PLS
  M scripts/taxa/bp_taxonomy2tree.PLS
  M scripts/tree/bp_blast2tree.PLS
  M scripts/utilities/bp_download_query_genbank.PLS
  M scripts/utilities/bp_mrtrans.PLS
  M scripts/utilities/bp_mutate.PLS
  M scripts/utilities/bp_remote_blast.PLS
  M scripts/utilities/bp_sreformat.PLS

  Log Message:
  -----------
  scripts: added 'use warnings' to all scripts without it


  Commit: 1a401d97bf10a343b940b86eaafb41caddc7c978
      https://github.com/bioperl/bioperl-live/commit/1a401d97bf10a343b940b86eaafb41caddc7c978
  Author: Carn? Draug <carandraug+dev at gmail.com>
  Date:   2011-07-25 (Mon, 25 Jul 2011)

  Changed paths:
    M scripts/Bio-DB-GFF/bp_genbank2gff3.PLS

  Log Message:
  -----------
  Don't mess with $^W. Control with warnings pragma instead


  Commit: 39cedcd08241926e1527cd2086e401927a290a1f
      https://github.com/bioperl/bioperl-live/commit/39cedcd08241926e1527cd2086e401927a290a1f
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-25 (Mon, 25 Jul 2011)

  Changed paths:
    M scripts/Bio-DB-GFF/bp_bulk_load_gff.PLS
  M scripts/Bio-DB-GFF/bp_fast_load_gff.PLS
  M scripts/Bio-DB-GFF/bp_genbank2gff.PLS
  M scripts/Bio-DB-GFF/bp_genbank2gff3.PLS
  M scripts/Bio-DB-GFF/bp_generate_histogram.PLS
  M scripts/Bio-DB-GFF/bp_load_gff.PLS
  M scripts/Bio-DB-GFF/bp_meta_gff.PLS
  M scripts/Bio-DB-GFF/bp_process_gadfly.PLS
  M scripts/Bio-DB-GFF/bp_process_sgd.PLS
  M scripts/Bio-DB-GFF/bp_process_wormbase.PLS
  M scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.PLS
  M scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.PLS
  M scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.PLS
  M scripts/DB-HIV/bp_hivq.PLS
  M scripts/DB/bp_biofetch_genbank_proxy.PLS
  M scripts/DB/bp_bioflat_index.PLS
  M scripts/DB/bp_biogetseq.PLS
  M scripts/DB/bp_flanks.PLS
  M scripts/biblio/bp_biblio.PLS
  M scripts/das/bp_das_server.pl
  M scripts/index/bp_index.PLS
  M scripts/index/bp_seqret.PLS
  M scripts/popgen/bp_composite_LD.PLS
  M scripts/popgen/bp_heterogeneity_test.PLS
  M scripts/searchio/bp_fastam9_to_table.PLS
  M scripts/searchio/bp_filter_search.PLS
  M scripts/searchio/bp_hmmer_to_table.PLS
  M scripts/searchio/bp_parse_hmmsearch.PLS
  M scripts/searchio/bp_search2table.PLS
  M scripts/seq/bp_extract_feature_seq.PLS
  M scripts/seq/bp_make_mrna_protein.PLS
  M scripts/seq/bp_seqconvert.PLS
  M scripts/seq/bp_seqretsplit.PLS
  M scripts/seq/bp_split_seq.PLS
  M scripts/seq/bp_translate_seq.PLS
  M scripts/seq/bp_unflatten_seq.PLS
  M scripts/seqstats/bp_aacomp.PLS
  M scripts/seqstats/bp_chaos_plot.PLS
  M scripts/seqstats/bp_gccalc.PLS
  M scripts/seqstats/bp_oligo_count.PLS
  M scripts/taxa/bp_classify_hits_kingdom.PLS
  M scripts/taxa/bp_local_taxonomydb_query.PLS
  M scripts/taxa/bp_query_entrez_taxa.PLS
  M scripts/taxa/bp_taxid4species.PLS
  M scripts/taxa/bp_taxonomy2tree.PLS
  M scripts/tree/bp_blast2tree.PLS
  M scripts/tree/bp_nexus2nh.PLS
  M scripts/tree/bp_tree2pag.PLS
  M scripts/utilities/bp_dbsplit.PLS
  M scripts/utilities/bp_download_query_genbank.PLS
  M scripts/utilities/bp_mask_by_search.PLS
  M scripts/utilities/bp_mrtrans.PLS
  M scripts/utilities/bp_mutate.PLS
  M scripts/utilities/bp_nrdb.PLS
  M scripts/utilities/bp_pairwise_kaks.PLS
  M scripts/utilities/bp_remote_blast.PLS
  M scripts/utilities/bp_search2BSML.PLS
  M scripts/utilities/bp_search2alnblocks.PLS
  M scripts/utilities/bp_search2gff.PLS
  M scripts/utilities/bp_search2tribe.PLS
  M scripts/utilities/bp_seq_length.PLS
  M scripts/utilities/bp_sreformat.PLS

  Log Message:
  -----------
  Merge pull request #18 from carandraug/script/perl-warnings

Script/perl warnings


Compare: https://github.com/bioperl/bioperl-live/compare/edc9e52...39cedcd

From redmine at redmine.open-bio.org  Mon Jul 25 17:51:40 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Mon, 25 Jul 2011 21:51:40 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3270] (New) script:
	bp_extract_feature fails for opening STDOUT
Message-ID: <redmine.issue-3270.20110725215140@redmine.open-bio.org>


Issue #3270 has been reported by Carn? Draug.

----------------------------------------
Bug #3270: script: bp_extract_feature fails for opening STDOUT
https://redmine.open-bio.org/issues/3270

Author: Carn? Draug
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


Hi,

when using the script bp_extract_feature, if no output file is given (so that it uses STDOUT), or the file to save the sequence is not a fasta extension, it will fail. There's two reasons for this:

1) if no extension of no file format, it doesn't know what format to use. returns error:
MSG: Unknown format given or could not determine it []

2) if the format is something else than a simple thing such as fasta, it returns the error (the sequence it tries to write is obtained from spliced_seq):
Can't locate object method "annotation" via package "Bio::PrimarySeq" at /usr/share/perl5/Bio/SeqIO/genbank.pm line 840, <GEN0> line 185.

The following patch fix this:

 my $out;
 if ($output ) {
-    $out = new Bio::SeqIO(-file => ">$output");
+    $out = new Bio::SeqIO(-file => ">$output", -format => 'fasta');
 } else { 
-    $out = new Bio::SeqIO(); # use STDOUT for output
+    $out = new Bio::SeqIO(-format => 'fasta'); # use STDOUT for output
 }

I'll submit a pull request with this fix soon.


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From noreply at github.com  Mon Jul 25 22:18:43 2011
From: noreply at github.com (noreply at github.com)
Date: Mon, 25 Jul 2011 19:18:43 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] c19314: Improvements to POD
Message-ID: <20110726021843.D5C5A4255F@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: c1931481534ce956d0c3fc024612f1bf752ed5d2
      https://github.com/bioperl/bioperl-live/commit/c1931481534ce956d0c3fc024612f1bf752ed5d2
  Author: Carn? Draug <carandraug+dev at gmail.com>
  Date:   2011-07-25 (Mon, 25 Jul 2011)

  Changed paths:
    M scripts/seq/bp_extract_feature_seq.PLS

  Log Message:
  -----------
  Improvements to POD


  Commit: 87ec9d528c6958a55a52f36a1d75399728d8993b
      https://github.com/bioperl/bioperl-live/commit/87ec9d528c6958a55a52f36a1d75399728d8993b
  Author: Carn? Draug <carandraug+dev at gmail.com>
  Date:   2011-07-25 (Mon, 25 Jul 2011)

  Changed paths:
    M scripts/seq/bp_extract_feature_seq.PLS

  Log Message:
  -----------
  Fix bug when using STDOUT or writing to file without extension. Closes bug #3270


  Commit: 93090423e9c2ad7415913608a026a9149289b5c9
      https://github.com/bioperl/bioperl-live/commit/93090423e9c2ad7415913608a026a9149289b5c9
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-25 (Mon, 25 Jul 2011)

  Changed paths:
    M scripts/seq/bp_extract_feature_seq.PLS

  Log Message:
  -----------
  Merge pull request #19 from carandraug/script/extract_feature_seq

Script/extract feature seq, fixes bug#3270


Compare: https://github.com/bioperl/bioperl-live/compare/39cedcd...9309042

From noreply at github.com  Wed Jul 27 16:23:02 2011
From: noreply at github.com (noreply at github.com)
Date: Wed, 27 Jul 2011 13:23:02 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] f4f6cb: fix FASTQ case
	where qual of 0 stops parse (edge c...
Message-ID: <20110727202303.C1A954253A@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: f4f6cbb731e0281b9a20cf6991e4f8e3db869452
      https://github.com/bioperl/bioperl-live/commit/f4f6cbb731e0281b9a20cf6991e4f8e3db869452
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-27 (Wed, 27 Jul 2011)

  Changed paths:
    M Bio/SeqIO/fastq.pm
  M t/SeqIO/fastq.t

  Log Message:
  -----------
  fix FASTQ case where qual of 0 stops parse (edge case)



From noreply at github.com  Wed Jul 27 16:23:43 2011
From: noreply at github.com (noreply at github.com)
Date: Wed, 27 Jul 2011 13:23:43 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 7cd687: test data for last
	FASTQ commit
Message-ID: <20110727202343.03FD1425CB@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: 7cd6878ee81e2cf9b9551ad0e8a01510fea72554
      https://github.com/bioperl/bioperl-live/commit/7cd6878ee81e2cf9b9551ad0e8a01510fea72554
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-27 (Wed, 27 Jul 2011)

  Changed paths:
    A t/data/fastq/zero_qual.fastq

  Log Message:
  -----------
  test data for last FASTQ commit



From noreply at github.com  Wed Jul 27 16:26:24 2011
From: noreply at github.com (noreply at github.com)
Date: Wed, 27 Jul 2011 13:26:24 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 605279: add that last fix
Message-ID: <20110727202624.28929425CB@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: 6052791d5d2b20cf9c5f7f62188b40c3080eff99
      https://github.com/bioperl/bioperl-live/commit/6052791d5d2b20cf9c5f7f62188b40c3080eff99
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-27 (Wed, 27 Jul 2011)

  Changed paths:
    M Changes

  Log Message:
  -----------
  add that last fix



From redmine at redmine.open-bio.org  Fri Jul 29 10:13:56 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Fri, 29 Jul 2011 14:13:56 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3274] (New) genbank2gff3.pl error
	when running on multiple input files
Message-ID: <redmine.issue-3274.20110729141356@redmine.open-bio.org>


Issue #3274 has been reported by Adam Witney.

----------------------------------------
Bug #3274: genbank2gff3.pl error when running on multiple input files
https://redmine.open-bio.org/issues/3274

Author: Adam Witney
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: Bio::DB::GFF
Target version: 
URL: 


When running genbank2gff3 in this way:

genbank2gff3.pl *.gbk

the first file works ok, but subsequent files contain all the previous files' features. This seems to be because two variables are not being reset between files. The attached patch fixes it for me




----------------------------------------
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From redmine at redmine.open-bio.org  Fri Jul 29 10:13:56 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Fri, 29 Jul 2011 14:13:56 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3274] (New) genbank2gff3.pl error
	when running on multiple input files
Message-ID: <redmine.issue-3274.20110729141356@redmine.open-bio.org>


Issue #3274 has been reported by Adam Witney.

----------------------------------------
Bug #3274: genbank2gff3.pl error when running on multiple input files
https://redmine.open-bio.org/issues/3274

Author: Adam Witney
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: Bio::DB::GFF
Target version: 
URL: 


When running genbank2gff3 in this way:

genbank2gff3.pl *.gbk

the first file works ok, but subsequent files contain all the previous files' features. This seems to be because two variables are not being reset between files. The attached patch fixes it for me




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From redmine at redmine.open-bio.org  Fri Jul 29 10:56:21 2011
From: redmine at redmine.open-bio.org (redmine at redmine.open-bio.org)
Date: Fri, 29 Jul 2011 14:56:21 +0000
Subject: [Bioperl-guts-l] [BioPerl - Bug #3274] genbank2gff3.pl error when
	running on multiple input files
References: <redmine.issue-3274.20110729141356@redmine.open-bio.org>
Message-ID: <redmine.journal-14644.20110729145621@redmine.open-bio.org>


Issue #3274 has been updated by Adam Witney.

File genbank2gff3.diff added

looks like a few other variables need to be reset as well. See attached patch
----------------------------------------
Bug #3274: genbank2gff3.pl error when running on multiple input files
https://redmine.open-bio.org/issues/3274

Author: Adam Witney
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: Bio::DB::GFF
Target version: 
URL: 


When running genbank2gff3 in this way:

genbank2gff3.pl *.gbk

the first file works ok, but subsequent files contain all the previous files' features. This seems to be because two variables are not being reset between files. The attached patch fixes it for me




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From noreply at github.com  Sun Jul 31 23:27:03 2011
From: noreply at github.com (noreply at github.com)
Date: Sun, 31 Jul 2011 20:27:03 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 26ecb0: buglet (bad test
	count), reported by George Hartze...
Message-ID: <20110801032703.450C342535@smtp1.rs.github.com>

  Branch: refs/heads/master
  Home:   https://github.com/bioperl/bioperl-live

  Commit: 26ecb042753f5b6c59d6520463d6891ea5c978c7
      https://github.com/bioperl/bioperl-live/commit/26ecb042753f5b6c59d6520463d6891ea5c978c7
  Author: Chris Fields <cjfields at bioperl.org>
  Date:   2011-07-31 (Sun, 31 Jul 2011)

  Changed paths:
    M t/SearchIO/blast.t

  Log Message:
  -----------
  buglet (bad test count), reported by George Hartzell