From noreply at github.com  Thu Jul  1 11:56:54 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 1 Jul 2010 08:56:54 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-run] 749ab0: contigs off with
	Ubuntu packaged MAQ
Message-ID: <20100701155654.8E816422FF@smtp1.rs.github.com>

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

Commit: 749ab047e091dfeb79d4f92db7aac9e09ddad39c
    http://github.com/bioperl/bioperl-run/commit/749ab047e091dfeb79d4f92db7aac9e09ddad39c
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-01 (Thu, 01 Jul 2010)

Changed paths:
  M t/Maq.t

Log Message:
-----------
contigs off with Ubuntu packaged MAQ



From noreply at github.com  Thu Jul  1 12:34:57 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 1 Jul 2010 09:34:57 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] b984f4: fix edge case when
	adding gaps
Message-ID: <20100701163457.34FEA42306@smtp1.rs.github.com>

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

Commit: b984f4a36bcbb59a8482aee5a35245326933b526
    http://github.com/bioperl/bioperl-live/commit/b984f4a36bcbb59a8482aee5a35245326933b526
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-01 (Thu, 01 Jul 2010)

Changed paths:
  M Bio/Assembly/Contig.pm

Log Message:
-----------
fix edge case when adding gaps



From noreply at github.com  Thu Jul  1 12:43:21 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 1 Jul 2010 09:43:21 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-run] 718cad: algorithm can be
	SSEARCH as well; use test_output_...
Message-ID: <20100701164321.376D74230A@smtp1.rs.github.com>

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

Commit: 718cada19b420ad6b6a0ff761654c81534bfab4f
    http://github.com/bioperl/bioperl-run/commit/718cada19b420ad6b6a0ff761654c81534bfab4f
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-01 (Thu, 01 Jul 2010)

Changed paths:
  M t/StandAloneFasta.t

Log Message:
-----------
algorithm can be SSEARCH as well; use test_output_file() for tempfile cleanup



From noreply at github.com  Thu Jul  1 13:16:39 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 1 Jul 2010 10:16:39 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-run] 97f73d: move to tempfiles
	for cleanup
Message-ID: <20100701171639.B111D422B3@smtp1.rs.github.com>

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

Commit: 97f73d63834d93ba364f102de8c7518706f6be2d
    http://github.com/bioperl/bioperl-run/commit/97f73d63834d93ba364f102de8c7518706f6be2d
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-01 (Thu, 01 Jul 2010)

Changed paths:
  M t/BWA.t

Log Message:
-----------
move to tempfiles for cleanup



From noreply at github.com  Thu Jul  1 13:45:12 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 1 Jul 2010 10:45:12 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-run] fe1195: move tests over to
	tempfile use (tmpdir not being ...
Message-ID: <20100701174512.05BF742301@smtp1.rs.github.com>

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

Commit: fe11959026c567fe6616afa1b3c7c64376086700
    http://github.com/bioperl/bioperl-run/commit/fe11959026c567fe6616afa1b3c7c64376086700
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-01 (Thu, 01 Jul 2010)

Changed paths:
  M t/Bowtie.t
  M t/Samtools.t

Log Message:
-----------
move tests over to tempfile use (tmpdir not being cleaned up)



From noreply at github.com  Fri Jul  2 11:14:50 2010
From: noreply at github.com (noreply at github.com)
Date: Fri, 2 Jul 2010 08:14:50 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 8fefbb: test commit for org
	setup
Message-ID: <20100702151450.02CDB422CE@smtp1.rs.github.com>

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

Commit: 8fefbb81f34f772bfb0187f5519a453cc2b27f6e
    http://github.com/bioperl/bioperl-live/commit/8fefbb81f34f772bfb0187f5519a453cc2b27f6e
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-02 (Fri, 02 Jul 2010)

Changed paths:
  M Changes

Log Message:
-----------
test commit for org setup



From noreply at github.com  Fri Jul  2 12:36:42 2010
From: noreply at github.com (noreply at github.com)
Date: Fri, 2 Jul 2010 09:36:42 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 2c4036: updated for SeqXML
	v0.2
Message-ID: <20100702163642.9AFD64202F@smtp1.rs.github.com>

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

Commit: 2c40363b5c47a75c7a3a1344d19a3fe0b38600b3
    http://github.com/bioperl/bioperl-live/commit/2c40363b5c47a75c7a3a1344d19a3fe0b38600b3
Author: DaveMessina <dave_messina at bioperl.org>
Date:   2010-07-02 (Fri, 02 Jul 2010)

Changed paths:
  M Bio/SeqIO/seqxml.pm
  M t/SeqIO/seqxml.t
  M t/data/seqxml.xml

Log Message:
-----------
updated for SeqXML v0.2



From noreply at github.com  Sat Jul  3 14:42:06 2010
From: noreply at github.com (noreply at github.com)
Date: Sat, 3 Jul 2010 11:42:06 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] c41d7f: Merge branch
	'topic/species_proxy'
Message-ID: <20100703184206.C420F422E2@smtp1.rs.github.com>

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

Commit: c41d7fac68e0cf67075e7b643c8bd847f75de0a6
    http://github.com/bioperl/bioperl-live/commit/c41d7fac68e0cf67075e7b643c8bd847f75de0a6
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-03 (Sat, 03 Jul 2010)

Changed paths:
  M Bio/Species.pm
  M Bio/Taxon.pm
  M Bio/Tree/Node.pm
  M Bio/Tree/Tree.pm
  M t/SeqIO/Handler.t
  M t/SeqIO/swiss.t
  M t/Species.t

Log Message:
-----------
Merge branch 'topic/species_proxy'



From noreply at github.com  Mon Jul  5 11:13:07 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 5 Jul 2010 08:13:07 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] e785d8: add some
	significant milestones
Message-ID: <20100705151307.0D45D42170@smtp1.rs.github.com>

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

Commit: e785d82f55dce183f45ed374eeb2d93053b2734f
    http://github.com/bioperl/bioperl-live/commit/e785d82f55dce183f45ed374eeb2d93053b2734f
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-05 (Mon, 05 Jul 2010)

Changed paths:
  M Bio/DB/EUtilities.pm
  M Bio/Tools/EUtilities/EUtilParameters.pm

Log Message:
-----------
add some significant milestones



From noreply at github.com  Mon Jul  5 12:13:25 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 5 Jul 2010 09:13:25 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-run] 03e09b: small fixes,
	but the previous code does work when ...
Message-ID: <20100705161325.02BE342173@smtp1.rs.github.com>

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

Commit: 03e09b98ce29421536c7dd48460a40e903aed497
    http://github.com/bioperl/bioperl-run/commit/03e09b98ce29421536c7dd48460a40e903aed497
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-05 (Mon, 05 Jul 2010)

Changed paths:
  M lib/Bio/Tools/Run/Infernal.pm

Log Message:
-----------
small fixes, but the previous code does work when setting INFERNALDIR



From noreply at github.com  Mon Jul  5 15:25:28 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 5 Jul 2010 12:25:28 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-run] 4908bb: remove samtool cruft
	from MANIFEST
Message-ID: <20100705192528.070F642036@smtp1.rs.github.com>

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

Commit: 4908bb2d7c1b50a98edbb9b1598fa39dbe5b40e9
    http://github.com/bioperl/bioperl-run/commit/4908bb2d7c1b50a98edbb9b1598fa39dbe5b40e9
Author: maj <maj at fortinbras.us>
Date:   2010-07-05 (Mon, 05 Jul 2010)

Changed paths:
  M MANIFEST

Log Message:
-----------
remove samtool cruft from MANIFEST



From noreply at github.com  Tue Jul  6 11:13:05 2010
From: noreply at github.com (noreply at github.com)
Date: Tue, 6 Jul 2010 08:13:05 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 51c937: added summary mode
	to bio::db::gff mysql adaptor
Message-ID: <20100706151305.3A1604208F@smtp1.rs.github.com>

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

Commit: 51c93744fff1e665ab96d04a387bf1c1490ec251
    http://github.com/bioperl/bioperl-live/commit/51c93744fff1e665ab96d04a387bf1c1490ec251
Author: Lincoln Stein <lstein at tunno.(none)>
Date:   2010-07-06 (Tue, 06 Jul 2010)

Changed paths:
  M Bio/DB/GFF.pm
  M Bio/DB/GFF/Adaptor/dbi/mysql.pm
  M Bio/DB/SeqFeature/Store/DBI/mysql.pm
  M scripts/Bio-DB-GFF/bulk_load_gff.PLS
  M scripts/Bio-DB-GFF/fast_load_gff.PLS
  M scripts/Bio-DB-GFF/load_gff.PLS

Log Message:
-----------
added summary mode to bio::db::gff mysql adaptor



From noreply at github.com  Tue Jul  6 16:06:23 2010
From: noreply at github.com (noreply at github.com)
Date: Tue, 6 Jul 2010 13:06:23 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 58bde5: added interval
	statistics gathering to Pg adaptor
Message-ID: <20100706200623.6CCF24204A@smtp1.rs.github.com>

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

Commit: 58bde583fca9c92dc6ba521cd813ad56a4b4116f
    http://github.com/bioperl/bioperl-live/commit/58bde583fca9c92dc6ba521cd813ad56a4b4116f
Author: Lincoln Stein <lstein at tunno.(none)>
Date:   2010-07-06 (Tue, 06 Jul 2010)

Changed paths:
  M Bio/DB/GFF.pm
  M Bio/DB/GFF/Adaptor/dbi.pm
  M Bio/DB/GFF/Adaptor/dbi/mysql.pm
  M Bio/DB/GFF/Adaptor/dbi/pg.pm
  M Bio/DB/SeqFeature/Store.pm

Log Message:
-----------
added interval statistics gathering to Pg adaptor


Commit: 5d9a696ba55ecf5e755b3c3c91a55cb21369ea45
    http://github.com/bioperl/bioperl-live/commit/5d9a696ba55ecf5e755b3c3c91a55cb21369ea45
Author: Lincoln Stein <lstein at tunno.(none)>
Date:   2010-07-06 (Tue, 06 Jul 2010)

Changed paths:
  M Bio/DB/GFF/Adaptor/dbi/oracle.pm

Log Message:
-----------
ported interval statistics to oracle adaptor, but not testedperl -cw Bio/DB/GFF/Adaptor/dbi/oracle.pmperl -cw Bio/DB/GFF/Adaptor/dbi/oracle.pm



From bugzilla-daemon at portal.open-bio.org  Wed Jul  7 04:08:28 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 7 Jul 2010 04:08:28 -0400
Subject: [Bioperl-guts-l] [Bug 3107] New: column_from_residue_number()
	provides weird position translation on BLAST minus strand
Message-ID: <bug-3107-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3107

           Summary: column_from_residue_number() provides weird position
                    translation on BLAST minus strand
           Product: BioPerl
           Version: 1.6 branch
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Bio::Search/Bio::SearchIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: jiandingzhe at msn.com


It used the reverse strand's LocatableSeq object with strand property
undefined. This undefined strand property is treated as positive strand by
default.

After manually set:

$reverse_seq_obj->strand(-1);

it will provide correct result.


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From bugzilla-daemon at portal.open-bio.org  Wed Jul  7 04:11:38 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 7 Jul 2010 04:11:38 -0400
Subject: [Bioperl-guts-l] [Bug 3107] column_from_residue_number() provides
	weird position translation on BLAST minus strand
In-Reply-To: <bug-3107-25@http.bugzilla.open-bio.org/>
Message-ID: <201007070811.o678Bc5K008700@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3107





------- Comment #1 from jiandingzhe at msn.com  2010-07-07 04:11 EST -------
Created an attachment (id=1520)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1520&action=view)
test script

run with the test blast result as its argument


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From bugzilla-daemon at portal.open-bio.org  Wed Jul  7 04:19:09 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 7 Jul 2010 04:19:09 -0400
Subject: [Bioperl-guts-l] [Bug 3107] column_from_residue_number() provides
	weird position translation on BLAST minus strand
In-Reply-To: <bug-3107-25@http.bugzilla.open-bio.org/>
Message-ID: <201007070819.o678J9Ts009351@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3107





------- Comment #2 from jiandingzhe at msn.com  2010-07-07 04:19 EST -------
Created an attachment (id=1521)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1521&action=view)
blast result for testing


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From noreply at github.com  Wed Jul  7 14:29:27 2010
From: noreply at github.com (noreply at github.com)
Date: Wed, 7 Jul 2010 11:29:27 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 0fe064: Clarify warnings
	when defaulting the value of end(...
Message-ID: <20100707182927.87E7B422D7@smtp1.rs.github.com>

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

Commit: 0fe0648f24bf537685f5d99aec4ab068070b08e3
    http://github.com/bioperl/bioperl-live/commit/0fe0648f24bf537685f5d99aec4ab068070b08e3
Author: Heikki Lehvaslaiho <Heikki.Lehvaslaiho at kaust.edu.sa>
Date:   2010-07-07 (Wed, 07 Jul 2010)

Changed paths:
  M Bio/Location/Simple.pm

Log Message:
-----------
Clarify warnings when defaulting the value of end()



From bugzilla-daemon at portal.open-bio.org  Wed Jul  7 16:02:30 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 7 Jul 2010 16:02:30 -0400
Subject: [Bioperl-guts-l] [Bug 3108] New: Bio::SearchIO
Message-ID: <bug-3108-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3108

           Summary: Bio::SearchIO
           Product: BioPerl
           Version: 1.6 branch
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Bio::Search/Bio::SearchIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: griffith.dan at gmail.com


While parsing blast results from blastall (BLASTN 2.2.13 [Nov-27-2005]) with
Bio::SearchIO I get an error when using a larger version of a test subset that
I was using.  The error appears similar to older problems with the next_result
midline data.  The error looks like:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: no data for midline 
Identi.............................................done
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:368
STACK: Bio::SearchIO::blast::next_result
/usr/lib/perl5/site_perl/5.8.8/Bio/SearchIO/blast.pm:1805
STACK: AiptasiaAnalysisALL.pl:46
-----------------------------------------------------------

I will gladly supply more details, but thought since you have fixed something
like this before, that you might know what was wrong.


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From bugzilla-daemon at portal.open-bio.org  Thu Jul  8 00:34:18 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 8 Jul 2010 00:34:18 -0400
Subject: [Bioperl-guts-l] [Bug 3108] Bio::SearchIO
In-Reply-To: <bug-3108-25@http.bugzilla.open-bio.org/>
Message-ID: <201007080434.o684YIes014446@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3108





------- Comment #1 from jason at bioperl.org  2010-07-08 00:34 EST -------
you should attach an example report to this bug report - but the error
basically means it is out of register when parsing query/homology/subject
alignment data from the BLAST report because there is probably something
unparseable in a previous line and the parser is out of phase.


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From bugzilla-daemon at portal.open-bio.org  Thu Jul  8 10:31:26 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 8 Jul 2010 10:31:26 -0400
Subject: [Bioperl-guts-l] [Bug 3111] New: Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
Message-ID: <bug-3111-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3111

           Summary: Found a few bugs in bp_seqfeature_load.PLS when using -
                    namespace
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: dan.bolser at gmail.com


The code had inconsistent use of the '_qualify' function, and one instance of a
hard-coded table name. These issues were not apparent until "-namespace
anything" was used.

First I got the fatal error:
%0


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From bugzilla-daemon at portal.open-bio.org  Thu Jul  8 10:31:57 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 8 Jul 2010 10:31:57 -0400
Subject: [Bioperl-guts-l] [Bug 3112] New: Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
Message-ID: <bug-3112-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3112

           Summary: Found a few bugs in bp_seqfeature_load.PLS when using -
                    namespace
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: dan.bolser at gmail.com


The code had inconsistent use of the '_qualify' function, and one instance of a
hard-coded table name. These issues were not apparent until "-namespace
anything" was used.

First I got the fatal error:
%0


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From bugzilla-daemon at portal.open-bio.org  Thu Jul  8 10:33:08 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 8 Jul 2010 10:33:08 -0400
Subject: [Bioperl-guts-l] [Bug 3113] New: Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
Message-ID: <bug-3113-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3113

           Summary: Found a few bugs in bp_seqfeature_load.PLS when using -
                    namespace
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: dan.bolser at gmail.com


The code had inconsistent use of the '_qualify' function, and one instance of a
hard-coded table name. These issues were not apparent until "-namespace
anything" was used.

First I got the fatal error:
%0


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From bugzilla-daemon at portal.open-bio.org  Thu Jul  8 10:25:19 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 8 Jul 2010 10:25:19 -0400
Subject: [Bioperl-guts-l] [Bug 3110] New: Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
Message-ID: <bug-3110-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3110

           Summary: Found a few bugs in bp_seqfeature_load.PLS when using -
                    namespace
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: dan.bolser at gmail.com


The code had inconsistent use of the '_qualify' function, and one instance of a
hard-coded table name. These issues were not apparent until "-namespace
anything" was used.

First I got the fatal error:
%0


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From bugzilla-daemon at portal.open-bio.org  Thu Jul  8 12:06:41 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 8 Jul 2010 12:06:41 -0400
Subject: [Bioperl-guts-l] [Bug 3114] New: Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
Message-ID: <bug-3114-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3114

           Summary: Found a few bugs in bp_seqfeature_load.PLS when using -
                    namespace
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: dan.bolser at gmail.com


The code had inconsistent use of the '_qualify' function, and one instance of a
hard-coded table name. These issues were not apparent until "-namespace
anything" was used.

First I got the fatal error:
%0


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From noreply at github.com  Thu Jul  8 12:33:56 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 8 Jul 2010 09:33:56 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 3f8e73: added Dan Bolser's
	patches to fix inconsistent nam...
Message-ID: <20100708163356.9A383422C2@smtp1.rs.github.com>

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

Commit: 3f8e73612ae46de22da11fa843eaccd4ed6c48a2
    http://github.com/bioperl/bioperl-live/commit/3f8e73612ae46de22da11fa843eaccd4ed6c48a2
Author: Lincoln Stein <lstein at itsybitsy.(none)>
Date:   2010-07-08 (Thu, 08 Jul 2010)

Changed paths:
  M Bio/DB/SeqFeature/Store/DBI/mysql.pm

Log Message:
-----------
added Dan Bolser's patches to fix inconsistent namespacing issues in the mysql adaptor


Commit: 111994e4aeca87ae9804ba6d8b9261107e52f5bb
    http://github.com/bioperl/bioperl-live/commit/111994e4aeca87ae9804ba6d8b9261107e52f5bb
Author: Lincoln Stein <lincoln.stein at gmail.com>
Date:   2010-07-08 (Thu, 08 Jul 2010)

Changed paths:
  M Bio/Location/Simple.pm

Log Message:
-----------
Merge branch 'master' of github.com:bioperl/bioperl-live



From noreply at github.com  Thu Jul  8 14:29:49 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 8 Jul 2010 11:29:49 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] fb81d7: adding optional
	-type parameter (and support for i...
Message-ID: <20100708182949.A116642177@smtp1.rs.github.com>

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

Commit: fb81d7b9f6af33f80886292cff12a129b042587e
    http://github.com/bioperl/bioperl-live/commit/fb81d7b9f6af33f80886292cff12a129b042587e
Author: DaveMessina <dave_messina at bioperl.org>
Date:   2010-07-08 (Thu, 08 Jul 2010)

Changed paths:
  M Bio/Annotation/DBLink.pm
  M Bio/SeqIO/seqxml.pm

Log Message:
-----------
adding optional -type parameter (and support for it in SeqIO::seqxml



From bugzilla-daemon at portal.open-bio.org  Thu Jul  8 14:32:41 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 8 Jul 2010 14:32:41 -0400
Subject: [Bioperl-guts-l] [Bug 3115] New: Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
Message-ID: <bug-3115-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3115

           Summary: Found a few bugs in bp_seqfeature_load.PLS when using -
                    namespace
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: dan.bolser at gmail.com


The code had inconsistent use of the '_qualify' function, and one instance of a
hard-coded table name. These issues were not apparent until "-namespace
anything" was used.

First I got the fatal error:
%0


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From bugzilla-daemon at portal.open-bio.org  Thu Jul  8 15:54:17 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 8 Jul 2010 15:54:17 -0400
Subject: [Bioperl-guts-l] [Bug 3111] Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
In-Reply-To: <bug-3111-25@http.bugzilla.open-bio.org/>
Message-ID: <201007081954.o68JsHbd023319@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3111


online at davemessina.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |DUPLICATE




------- Comment #1 from online at davemessina.com  2010-07-08 15:54 EST -------


*** This bug has been marked as a duplicate of bug 3110 ***


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From bugzilla-daemon at portal.open-bio.org  Thu Jul  8 15:54:19 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 8 Jul 2010 15:54:19 -0400
Subject: [Bioperl-guts-l] [Bug 3110] New: Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
Message-ID: <bug-3110-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3110

           Summary: Found a few bugs in bp_seqfeature_load.PLS when using -
                    namespace
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: dan.bolser at gmail.com


The code had inconsistent use of the '_qualify' function, and one instance of a
hard-coded table name. These issues were not apparent until "-namespace
anything" was used.

First I got the fatal error:
%0


------- Comment #1 from online at davemessina.com  2010-07-08 15:54 EST -------
*** Bug 3111 has been marked as a duplicate of this bug. ***


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From bugzilla-daemon at portal.open-bio.org  Thu Jul  8 15:55:28 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 8 Jul 2010 15:55:28 -0400
Subject: [Bioperl-guts-l] [Bug 3112] New: Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
Message-ID: <bug-3112-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3112

           Summary: Found a few bugs in bp_seqfeature_load.PLS when using -
                    namespace
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: RESOLVED
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: dan.bolser at gmail.com


The code had inconsistent use of the '_qualify' function, and one instance of a
hard-coded table name. These issues were not apparent until "-namespace
anything" was used.

First I got the fatal error:
%0


------- Comment #1 from online at davemessina.com  2010-07-08 15:55 EST -------


*** This bug has been marked as a duplicate of bug 3110 ***


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From bugzilla-daemon at portal.open-bio.org  Thu Jul  8 15:55:33 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 8 Jul 2010 15:55:33 -0400
Subject: [Bioperl-guts-l] [Bug 3110] Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
In-Reply-To: <bug-3110-25@http.bugzilla.open-bio.org/>
Message-ID: <201007081955.o68JtXJ9023448@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3110





------- Comment #2 from online at davemessina.com  2010-07-08 15:55 EST -------
*** Bug 3112 has been marked as a duplicate of this bug. ***


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From bugzilla-daemon at portal.open-bio.org  Thu Jul  8 15:56:23 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 8 Jul 2010 15:56:23 -0400
Subject: [Bioperl-guts-l] [Bug 3114] Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
In-Reply-To: <bug-3114-25@http.bugzilla.open-bio.org/>
Message-ID: <201007081956.o68JuLdd023502@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3114


online at davemessina.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |DUPLICATE




------- Comment #1 from online at davemessina.com  2010-07-08 15:56 EST -------


*** This bug has been marked as a duplicate of bug 3110 ***


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From bugzilla-daemon at portal.open-bio.org  Thu Jul  8 15:56:33 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 8 Jul 2010 15:56:33 -0400
Subject: [Bioperl-guts-l] [Bug 3110] Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
In-Reply-To: <bug-3110-25@http.bugzilla.open-bio.org/>
Message-ID: <201007081956.o68JuXWE023525@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3110





------- Comment #3 from online at davemessina.com  2010-07-08 15:56 EST -------
*** Bug 3114 has been marked as a duplicate of this bug. ***


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From bugzilla-daemon at portal.open-bio.org  Thu Jul  8 15:56:50 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 8 Jul 2010 15:56:50 -0400
Subject: [Bioperl-guts-l] [Bug 3113] Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
In-Reply-To: <bug-3113-25@http.bugzilla.open-bio.org/>
Message-ID: <201007081956.o68JuosL023563@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3113


online at davemessina.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |DUPLICATE




------- Comment #1 from online at davemessina.com  2010-07-08 15:56 EST -------


*** This bug has been marked as a duplicate of bug 3110 ***


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From bugzilla-daemon at portal.open-bio.org  Thu Jul  8 15:56:54 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 8 Jul 2010 15:56:54 -0400
Subject: [Bioperl-guts-l] [Bug 3110] Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
In-Reply-To: <bug-3110-25@http.bugzilla.open-bio.org/>
Message-ID: <201007081956.o68JusVS023576@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3110





------- Comment #4 from online at davemessina.com  2010-07-08 15:56 EST -------
*** Bug 3113 has been marked as a duplicate of this bug. ***


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From bugzilla-daemon at portal.open-bio.org  Thu Jul  8 15:59:38 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 8 Jul 2010 15:59:38 -0400
Subject: [Bioperl-guts-l] [Bug 3115] Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
In-Reply-To: <bug-3115-25@http.bugzilla.open-bio.org/>
Message-ID: <201007081959.o68Jxc4G023745@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3115


online at davemessina.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |DUPLICATE




------- Comment #1 from online at davemessina.com  2010-07-08 15:59 EST -------


*** This bug has been marked as a duplicate of bug 3110 ***


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From bugzilla-daemon at portal.open-bio.org  Thu Jul  8 15:59:39 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 8 Jul 2010 15:59:39 -0400
Subject: [Bioperl-guts-l] [Bug 3110] Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
In-Reply-To: <bug-3110-25@http.bugzilla.open-bio.org/>
Message-ID: <201007081959.o68JxdMW023758@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3110





------- Comment #5 from online at davemessina.com  2010-07-08 15:59 EST -------
*** Bug 3115 has been marked as a duplicate of this bug. ***


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From noreply at github.com  Thu Jul  8 16:17:29 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 8 Jul 2010 13:17:29 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] cb475a: adding a bioperl
	commandline netinstaller based on...
Message-ID: <20100708201729.6B7FF422F6@smtp1.rs.github.com>

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

Commit: cb475a30112c8d2ccbfde94d1e36ed81ed082975
    http://github.com/bioperl/bioperl-live/commit/cb475a30112c8d2ccbfde94d1e36ed81ed082975
Author: Scott Cain <scott at scottcain.net>
Date:   2010-07-08 (Thu, 08 Jul 2010)

Changed paths:
  A scripts/bioperl_netinstall.pl

Log Message:
-----------
adding a bioperl commandline netinstaller based on the gbrowse
netinstaller.  Tested on Mac OS X 10.5, a recent Debian and
WinXP.


Commit: cc09af26a1999071170c4da6ee6a91ae64cd9314
    http://github.com/bioperl/bioperl-live/commit/cc09af26a1999071170c4da6ee6a91ae64cd9314
Author: Scott Cain <cain at scott-cains-macbook-pro.local>
Date:   2010-07-08 (Thu, 08 Jul 2010)

Changed paths:
  M .gitignore
  M Bio/Align/ProteinStatistics.pm
  M Bio/Annotation/DBLink.pm
  M Bio/Assembly/Contig.pm
  M Bio/Assembly/IO/ace.pm
  M Bio/Assembly/Tools/ContigSpectrum.pm
  M Bio/DB/EUtilities.pm
  M Bio/DB/Fasta.pm
  M Bio/DB/GFF.pm
  M Bio/DB/GFF/Adaptor/dbi.pm
  M Bio/DB/GFF/Adaptor/dbi/mysql.pm
  M Bio/DB/GFF/Adaptor/dbi/oracle.pm
  M Bio/DB/GFF/Adaptor/dbi/pg.pm
  M Bio/DB/SeqFeature/Store.pm
  M Bio/DB/SeqFeature/Store/DBI/SQLite.pm
  M Bio/DB/SeqFeature/Store/DBI/mysql.pm
  M Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
  M Bio/DB/SeqFeature/Store/GFF3Loader.pm
  M Bio/DB/SeqFeature/Store/Loader.pm
  M Bio/DB/SeqFeature/Store/berkeleydb.pm
  M Bio/DB/SeqFeature/Store/berkeleydb3.pm
  M Bio/DB/SeqFeature/Store/memory.pm
  R Bio/Expression/Contact.pm
  R Bio/Expression/DataSet.pm
  R Bio/Expression/FeatureGroup.pm
  R Bio/Expression/FeatureGroup/FeatureGroupMas50.pm
  R Bio/Expression/FeatureI.pm
  R Bio/Expression/FeatureSet/FeatureSetMas50.pm
  R Bio/Expression/Platform.pm
  R Bio/Expression/ProbeI.pm
  R Bio/Expression/Sample.pm
  M Bio/Location/Atomic.pm
  M Bio/Location/Simple.pm
  M Bio/LocationI.pm
  R Bio/Microarray/Tools/MitoChipV2Parser.pm
  R Bio/Microarray/Tools/ReseqChip.pm
  M Bio/OntologyIO/obo.pm
  M Bio/PrimarySeqI.pm
  M Bio/Root/Root.pm
  M Bio/Root/Test.pm
  M Bio/Search/HSP/GenericHSP.pm
  A Bio/Search/HSP/hmmer3HSP.pm
  M Bio/Search/Hit/GenericHit.pm
  A Bio/Search/Hit/hmmer3Hit.pm
  A Bio/Search/Result/hmmer3Result.pm
  M Bio/SearchIO/blast.pm
  M Bio/SearchIO/fasta.pm
  A Bio/SearchIO/hmmer3.pm
  M Bio/Seq.pm
  M Bio/SeqIO/genbank.pm
  A Bio/SeqIO/msout.pm
  M Bio/SeqIO/phd.pm
  M Bio/SeqIO/seqxml.pm
  M Bio/Species.pm
  M Bio/Taxon.pm
  M Bio/Tools/CodonTable.pm
  M Bio/Tools/EUtilities.pm
  M Bio/Tools/EUtilities/EUtilParameters.pm
  M Bio/Tools/EUtilities/Info/FieldInfo.pm
  M Bio/Tools/EUtilities/Info/LinkInfo.pm
  M Bio/Tools/EUtilities/Query.pm
  M Bio/Tools/Run/WrapperBase/CommandExts.pm
  A Bio/Tools/Run/hmmer3.pm
  M Bio/Tree/Node.pm
  M Bio/Tree/Tree.pm
  M Bio/Tree/TreeFunctionsI.pm
  M Bio/TreeIO/nexus.pm
  M Build.PL
  M Changes
  M DEPRECATED
  M MANIFEST
  R examples/root/lib/Bio/PrimarySeq.pm
  R examples/root/lib/Bio/PrimarySeqI.pm
  R examples/root/lib/Bio/Seq.pm
  R examples/root/lib/Bio/SeqI.pm
  M scripts/Bio-DB-GFF/bulk_load_gff.PLS
  M scripts/Bio-DB-GFF/fast_load_gff.PLS
  M scripts/Bio-DB-GFF/load_gff.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
  M scripts/utilities/download_query_genbank.PLS
  M t/Align/Graphics.t
  M t/Assembly/Assembly.t
  M t/Assembly/ContigSpectrum.t
  R t/Microarray/Tools/ReseqChip.t
  M t/RemoteDB/SwissProt.t
  M t/Root/RootI.t
  M t/SearchIO/blast.t
  M t/SearchIO/fasta.t
  A t/SearchIO/hmmer3.t
  M t/Seq/PrimarySeq.t
  A t/SeqFeature/Clone.t
  M t/SeqIO/Handler.t
  M t/SeqIO/genbank.t
  A t/SeqIO/msout.t
  M t/SeqIO/phd.t
  M t/SeqIO/seqxml.t
  M t/SeqIO/swiss.t
  M t/Species.t
  R t/data/ReseqChip_ExampleData.fasta
  R t/data/ReseqChip_ParamsNcall.csv
  R t/data/ReseqChip_RefSeq.fasta
  R t/data/ReseqChip_mtDNA_design_annotation_file_FINAL.xls
  A t/data/ZABJ4EA7014.CH878695.1.blast.txt
  A t/data/hmmscan.out
  A t/data/hmmscan_multi_domain.out
  A t/data/hmmsearch3.out
  A t/data/msout_infile1
  A t/data/msout_infile1.gz
  A t/data/msout_infile2
  A t/data/msout_infile2.gz
  A t/data/multiseq_tags.phd
  M t/data/seqxml.xml

Log Message:
-----------
Merge branch 'master' of github.com:bioperl/bioperl-live



From noreply at github.com  Tue Jul 13 18:40:34 2010
From: noreply at github.com (noreply at github.com)
Date: Tue, 13 Jul 2010 15:40:34 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 39652b: fix POD
Message-ID: <20100713224034.65AFA4236A@smtp1.rs.github.com>

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

Commit: 39652b01e3f489f039513a8a278865147dc12002
    http://github.com/bioperl/bioperl-live/commit/39652b01e3f489f039513a8a278865147dc12002
Author: Jason Stajich <jason at bioperl.org>
Date:   2010-07-13 (Tue, 13 Jul 2010)

Changed paths:
  M scripts/bioperl_netinstall.pl

Log Message:
-----------
fix POD


Commit: ec09eb36f93eed8542351208e9be37793c891f9e
    http://github.com/bioperl/bioperl-live/commit/ec09eb36f93eed8542351208e9be37793c891f9e
Author: Jason Stajich <jason at bioperl.org>
Date:   2010-07-13 (Tue, 13 Jul 2010)

Changed paths:
  M scripts/bioperl_netinstall.pl

Log Message:
-----------
removed the leading typo



From bugzilla-daemon at portal.open-bio.org  Wed Jul 14 07:07:54 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 14 Jul 2010 07:07:54 -0400
Subject: [Bioperl-guts-l] [Bug 2899] problem with t/LocalDB/SeqFeature.t
	when host ne localhost
In-Reply-To: <bug-2899-25@http.bugzilla.open-bio.org/>
Message-ID: <201007141107.o6EB7sY1003695@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2899





------- Comment #4 from dan.bolser at gmail.com  2010-07-14 07:07 EST -------
The test still fails for this reason. My diff should point to a simple
solution, but I don't know where this string is created.

Note that this is a separate issue from the SQL definitions problem fixed by
Daniel Lang.

Additionally, it would be nice to test with / without the namespace option and
with / without the fast (mysql_local_infile=1) option (see
bp_seqfeature_load.pl).


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From bugzilla-daemon at portal.open-bio.org  Wed Jul 14 14:40:49 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 14 Jul 2010 14:40:49 -0400
Subject: [Bioperl-guts-l] [Bug 3117] New: Bio::Tree::TreeFunctionsI use()ing
	UNIVERSAL
Message-ID: <bug-3117-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3117

           Summary: Bio::Tree::TreeFunctionsI use()ing UNIVERSAL
           Product: BioPerl
           Version: main-trunk
          Platform: HP
               URL: http://code.open-
                    bio.org/svnweb/index.cgi/bioperl/view/bioperl-
                    live/trunk/Bio/Tree/TreeFunctionsI.pm
        OS/Version: Linux
            Status: NEW
          Severity: minor
          Priority: P2
         Component: Unclassified
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: charles.tilford at bms.com


Using Perl 5.12 with -w will result in the following warning for
Bio::Tree::TreeFunctionsI:

UNIVERSAL->import is deprecated and will be removed in a future perl

... via line 94 (16123 2009-09-17 12:57:27Z cjfields):

use UNIVERSAL qw(isa);

I've never seen UNIVERSAL explicitly invoked like that, so I'm not sure what
it's trying to do here. My understanding was that blessed objects get UNIVERSAL
"for free" and never need to isa it. Perldoc says you shouldn't:

http://perldoc.perl.org/UNIVERSAL.html
"You do not need to use UNIVERSAL to make these methods available to your
program (and you should not do so)."

I presume the line could be safely deleted, but am not sure if it's serving a
required function (eg in very old versions of Perl?).


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From bugzilla-daemon at portal.open-bio.org  Wed Jul 14 10:56:27 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 14 Jul 2010 10:56:27 -0400
Subject: [Bioperl-guts-l] [Bug 3116] New: tr/// warning with Bio::Range in
	Perl 5.12
Message-ID: <bug-3116-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3116

           Summary: tr/// warning with Bio::Range in Perl 5.12
           Product: BioPerl
           Version: main-trunk
          Platform: HP
               URL: http://code.open-
                    bio.org/svnweb/index.cgi/bioperl/view/bioperl-
                    live/trunk/Bio/Range.pm
        OS/Version: Linux
            Status: NEW
          Severity: minor
          Priority: P2
         Component: Unclassified
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: charles.tilford at bms.com


We had to upgrade from Perl 5.10 to 5.12 to address a memory leak when using
weaken(). BioPerl appears to be running fine, but is throwing warnings on two
modules. One is Bio::Range, where this line in strand():

$val =~ tr/-/-1/;

(16123 2009-09-17 12:57:27Z cjfields, line 251) warns (when using Perl's -w
flag):
Replacement list is longer than search list

I generally don't use tr/// much, but I presume it's irritated that 1 character
("-") is being replaced with two ("-1"). The full code block is:

    my $val = shift;
    $val =~ tr/+/1/;
    $val =~ tr/-/-1/;
    $val =~ tr/./0/;
    if($val == -1 || $val == 0 || $val == 1 ) {
      $self->{'strand'} = $val;
    }

... which is designed to map alternative strand inputs of  { '+' => 1, '-' =>
-1, '.' => 0 }. It seems like a somewhat baroque way to do so; I don't know if
the tr construct can be fixed (or if it does not need fixing and the warning
just needs suppression), but it might just be easier / more robust to use a
lookup hash like the one above, or even elsif structures ala

if ($val eq '+') {
   $self->{'strand'} = 1;
} elsif ($val eq '.') {
   $self->{'strand'} = 0;
} elsif ($val eq '-') {
   $self->{'strand'} = -1;
} elsif ($val eq '1' || $val eq '-1' || $val eq '0') {
   $self->{'strand'} = $val;  # or $val + 0 if you want to force as int
} else {
   # optional complain
}


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From bugzilla-daemon at portal.open-bio.org  Thu Jul 15 14:28:22 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 15 Jul 2010 14:28:22 -0400
Subject: [Bioperl-guts-l] [Bug 3117] Bio::Tree::TreeFunctionsI use()ing
	UNIVERSAL
In-Reply-To: <bug-3117-25@http.bugzilla.open-bio.org/>
Message-ID: <201007151828.o6FISMVw031579@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3117





------- Comment #1 from cjfields at bioperl.org  2010-07-15 14:28 EST -------
All perl 5.12-related warnings (including these) have been fixed on the github
master brancg.  We have talked at BOSC about pushing out a new release, so I am
planning on that (would be the 1.6.2 release, prefixed by a few of alphas
starting possibly next week).  


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From bugzilla-daemon at portal.open-bio.org  Thu Jul 15 14:58:22 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 15 Jul 2010 14:58:22 -0400
Subject: [Bioperl-guts-l] [Bug 3116] tr/// warning with Bio::Range in Perl
	5.12
In-Reply-To: <bug-3116-25@http.bugzilla.open-bio.org/>
Message-ID: <201007151858.o6FIwM4o010611@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3116





------- Comment #1 from cjfields at bioperl.org  2010-07-15 14:58 EST -------
All perl 5.12 warnings were fixed in github master branch.  I'll close this out
when the next bioperl release (1.6.2) is pushed to CPAN.


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From bugzilla-daemon at portal.open-bio.org  Thu Jul 15 23:33:49 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 15 Jul 2010 23:33:49 -0400
Subject: [Bioperl-guts-l] [Bug 3108] Bio::SearchIO
In-Reply-To: <bug-3108-25@http.bugzilla.open-bio.org/>
Message-ID: <201007160333.o6G3Xnoe030264@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3108





------- Comment #2 from cjfields at bioperl.org  2010-07-15 23:33 EST -------
Daniel, just a reminder that we need an example report attached for this bug. 
Might be worth checking the latest code to see if that fixes the problem.


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From noreply at github.com  Fri Jul 16 00:12:33 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 15 Jul 2010 21:12:33 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 2a240f: [bug 3107] pass
	strand info to alns
Message-ID: <20100716041233.A67264239B@smtp1.rs.github.com>

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

Commit: 2a240f64bb1a45e95f4b8116002463f27ef5f064
    http://github.com/bioperl/bioperl-live/commit/2a240f64bb1a45e95f4b8116002463f27ef5f064
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-15 (Thu, 15 Jul 2010)

Changed paths:
  M Bio/Search/HSP/GenericHSP.pm

Log Message:
-----------
[bug 3107] pass strand info to alns


Commit: 9ec50475b92b0d2dfc640e6b4fae1eca62771f46
    http://github.com/bioperl/bioperl-live/commit/9ec50475b92b0d2dfc640e6b4fae1eca62771f46
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-15 (Thu, 15 Jul 2010)

Changed paths:
  M t/RemoteDB/Taxonomy.t

Log Message:
-----------
remote data change; make test more flexible


Commit: d741467ffaff2c41c132e410058e57bc21aa8c52
    http://github.com/bioperl/bioperl-live/commit/d741467ffaff2c41c132e410058e57bc21aa8c52
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-15 (Thu, 15 Jul 2010)

Changed paths:
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
tests skipped off by 3, fixed



From bugzilla-daemon at portal.open-bio.org  Fri Jul 16 00:27:46 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 16 Jul 2010 00:27:46 -0400
Subject: [Bioperl-guts-l] [Bug 3107] column_from_residue_number() provides
	weird position translation on BLAST minus strand
In-Reply-To: <bug-3107-25@http.bugzilla.open-bio.org/>
Message-ID: <201007160427.o6G4RkKL011202@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3107


cjfields at bioperl.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #3 from cjfields at bioperl.org  2010-07-16 00:27 EST -------
In github master I have added the strand information for the LocatableSeqs so
that it is derived from the HSP data in GenericHSP.  You should now be getting
the correct coordinates.  Feel free to reopen if this is not the case.


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From bugzilla-daemon at portal.open-bio.org  Fri Jul 16 00:29:45 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 16 Jul 2010 00:29:45 -0400
Subject: [Bioperl-guts-l] [Bug 3104] Bio::Species::classification() unhappy
	with single node "hierarchies"
In-Reply-To: <bug-3104-25@http.bugzilla.open-bio.org/>
Message-ID: <201007160429.o6G4TjSF012736@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3104


cjfields at bioperl.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #2 from cjfields at bioperl.org  2010-07-16 00:29 EST -------
Merged into master branch, all tests pass.  Closing...


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From bugzilla-daemon at portal.open-bio.org  Fri Jul 16 16:22:39 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 16 Jul 2010 16:22:39 -0400
Subject: [Bioperl-guts-l] [Bug 2594] Bio::Species memory leak
In-Reply-To: <bug-2594-25@http.bugzilla.open-bio.org/>
Message-ID: <201007162022.o6GKMd7u013668@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2594


cjfields at bioperl.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #8 from cjfields at bioperl.org  2010-07-16 16:22 EST -------
This appears to be fixed and has been merged to trunk.  I'll be pushing 1.6.2
for testing in the meantime.  Sendu, if you see problems with this please feel
free to reopen.


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From bugzilla-daemon at portal.open-bio.org  Fri Jul 16 16:27:58 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 16 Jul 2010 16:27:58 -0400
Subject: [Bioperl-guts-l] [Bug 3110] Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
In-Reply-To: <bug-3110-25@http.bugzilla.open-bio.org/>
Message-ID: <201007162027.o6GKRwcj013869@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3110





------- Comment #6 from cjfields at bioperl.org  2010-07-16 16:27 EST -------
Dan, any way you can add a bit more information to this?  Not sure exactly what
the bug is.


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From bugzilla-daemon at portal.open-bio.org  Fri Jul 16 17:29:08 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 16 Jul 2010 17:29:08 -0400
Subject: [Bioperl-guts-l] [Bug 3095] seq_version() in Bio::PrimarySeq not
	found
In-Reply-To: <bug-3095-25@http.bugzilla.open-bio.org/>
Message-ID: <201007162129.o6GLT8EV015734@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3095





------- Comment #3 from cjfields at bioperl.org  2010-07-16 17:29 EST -------
The consensus on this is that version() and seq_version() can be two different
things; version() corresponds to any sequence version (local, remote,
whatever), whereas seq_version() corresponds to the sequence database version
(e.g. what one gets from a seq record).  

Saying that, I've noticed several inconsistencies with how the two are used. 
For instance, SeqIO::genbank and SeqIO::embl use seq_version (which seems
correct), whereas SeqIO::swiss uses vanilla PrimarySeq::version().  In cases
such as this, I suggest we always set seq_version() for sequence record
versions via SeqIO, then have seq_version() fall back to returning version()
unless explicitly set.  This should catch issues with legacy cases like
SeqIO::swiss being the odd one out.

If I don't see much objection, I'll implement the latter behavior on a branch.  


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From noreply at github.com  Fri Jul 16 17:38:12 2010
From: noreply at github.com (noreply at github.com)
Date: Fri, 16 Jul 2010 14:38:12 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 566e13: [bug 3095] doc
	changes to indicate difference betw...
Message-ID: <20100716213812.6E954422E4@smtp1.rs.github.com>

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

Commit: 566e1341f1cb24b2097cb88f037b0049af2fc1ae
    http://github.com/bioperl/bioperl-live/commit/566e1341f1cb24b2097cb88f037b0049af2fc1ae
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-16 (Fri, 16 Jul 2010)

Changed paths:
  M Bio/Seq.pm
  M Bio/Seq/RichSeq.pm
  M Bio/Seq/RichSeqI.pm

Log Message:
-----------
[bug 3095] doc changes to indicate difference between version and seq_version; remove mention of seq_version from Bio::Seq (method is in RichSeq)



From bugzilla-daemon at portal.open-bio.org  Fri Jul 16 18:58:09 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 16 Jul 2010 18:58:09 -0400
Subject: [Bioperl-guts-l] [Bug 3110] Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
In-Reply-To: <bug-3110-25@http.bugzilla.open-bio.org/>
Message-ID: <201007162258.o6GMw9WH029073@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3110





------- Comment #7 from dan.bolser at gmail.com  2010-07-16 18:58 EST -------
(In reply to comment #6)
> Dan, any way you can add a bit more information to this?  Not sure exactly what
> the bug is.
> 

Sorry, I think it's patched now. Some queries were using hard coded table
names, yet the adaptor allows a parameter called '--namespace x', which
qualifies all table names like 'x_features', 'x_meta', etc.

i.e. it was broken when --namespace was used because of these hard coded table
names.

The name of the table should (apparently) be obtained via a function called
'_qualify', and they now all are.


However, I found the module is still buggy... it doesn't crash, but it fails to
load data into all tables when both --namespace and -f are used together...


Looking closely at the resulting tables I see that the following tables are
empty

volvox_attribute
volvox_parent2child
volvox_feature
volvox_interval_stats
volvox_name
volvox_parent2child

they are not empty when created without the "--namespace x" prefix,
which is why DBI::mysql 'normally' works.


All the other tables:

volvox_attributelist
volvox_locationlist
volvox_meta
volvox_sequence
volvox_typelist

appear to be created correctly, with or without the "--namespace x" prefix.


Note, this is not a problem if you don't use -f!


Hope this is a bit clearer now.


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From bugzilla-daemon at portal.open-bio.org  Fri Jul 16 19:09:23 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 16 Jul 2010 19:09:23 -0400
Subject: [Bioperl-guts-l] [Bug 3110] Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
In-Reply-To: <bug-3110-25@http.bugzilla.open-bio.org/>
Message-ID: <201007162309.o6GN9N1v000521@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3110





------- Comment #8 from dan.bolser at gmail.com  2010-07-16 19:09 EST -------
Oh, I just remembered, why the original but report looks weird (and why I ended
up submitting it 6 times). Something in the bug report was causing a
mod_security rule to fire (I guess) and was giving me a time out when I hit
submit... Lets see if I can submit it again...

The code had inconsistent use of the '_qualif


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From bugzilla-daemon at portal.open-bio.org  Fri Jul 16 19:12:24 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 16 Jul 2010 19:12:24 -0400
Subject: [Bioperl-guts-l] [Bug 3110] Found a few bugs in
	bp_seqfeature_load.PLS when using -namespace
In-Reply-To: <bug-3110-25@http.bugzilla.open-bio.org/>
Message-ID: <201007162312.o6GNCOMN000577@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3110





------- Comment #9 from dan.bolser at gmail.com  2010-07-16 19:12 EST -------

Oh, I just remembered, why the original but report looks weird (and why I ended
up submitting it 6 times). Something in the bug report was causing a
mod_security rule to fire (I guess) and was giving me a time out when I hit
submit... Lets see if I can submit it again... nope... 

The code had inconsistent use of the '_qualify' function, and one instance of a
hard-coded table name. These issues were not apparent until "-namespace
anything" was used. 

First I got the fatal error:
ERROR REMOVED BECAUSE I CANT SUBMIT THE BUG OTHERWISE!

which was due to a hard-coded table name. Then, after fixing, I got the error: 
ERROR REMOVED BECAUSE I CANT SUBMIT THE BUG OTHERWISE! 

i.e. the prefix was being added to the table name twice. 

I went through the code and tried to make all references to table names
consistent to ensure that bugs like this won't creep in again... however, the
code for this module isn't very consistent.


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From bugzilla-daemon at portal.open-bio.org  Sun Jul 18 00:14:56 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 18 Jul 2010 00:14:56 -0400
Subject: [Bioperl-guts-l] [Bug 3017] use threads to get genbank file error
In-Reply-To: <bug-3017-25@http.bugzilla.open-bio.org/>
Message-ID: <201007180414.o6I4EuCv022285@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3017


cjfields at bioperl.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #5 from cjfields at bioperl.org  2010-07-18 00:14 EST -------
Code has been merged to the master branch on github and will appear in the next
BioPerl CPAN release.


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From noreply at github.com  Mon Jul 19 04:47:38 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 19 Jul 2010 01:47:38 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] bcd98d: Merge branch
	'master' of github.com:bioperl/bioper...
Message-ID: <20100719084738.889FC422EA@smtp1.rs.github.com>

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

Commit: bcd98d4be7106b3df5dff7c925c0ae1d8d7d387a
    http://github.com/bioperl/bioperl-live/commit/bcd98d4be7106b3df5dff7c925c0ae1d8d7d387a
Author: Florent Angly <florent.angly at gmail.com>
Date:   2010-07-18 (Sun, 18 Jul 2010)

Changed paths:
  M Bio/Search/HSP/GenericHSP.pm
  M Bio/Seq.pm
  M Bio/Seq/RichSeq.pm
  M Bio/Seq/RichSeqI.pm
  M scripts/bioperl_netinstall.pl
  M t/LocalDB/SeqFeature.t
  M t/RemoteDB/Taxonomy.t

Log Message:
-----------
Merge branch 'master' of github.com:bioperl/bioperl-live


Commit: 893390fbe809ee983c6e8a29b7b6439d652ed008
    http://github.com/bioperl/bioperl-live/commit/893390fbe809ee983c6e8a29b7b6439d652ed008
Author: Florent Angly <florent.angly at gmail.com>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M Bio/Root/IO.pm
  M t/Root/RootIO.t

Log Message:
-----------
New Bio::Root::IO method to insert text at an arbitrary line in a file



From bugzilla-daemon at portal.open-bio.org  Mon Jul 19 18:01:13 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 19 Jul 2010 18:01:13 -0400
Subject: [Bioperl-guts-l] [Bug 3120] New:
	Bio::DB::SeqFeature::Store::DBI::SQLite +
	bp_seqfeature_gff3.PLS = unhappy?
Message-ID: <bug-3120-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3120

           Summary: Bio::DB::SeqFeature::Store::DBI::SQLite +
                    bp_seqfeature_gff3.PLS = unhappy?
           Product: BioPerl
           Version: main-trunk
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: jay at jays.net


Howdy. I hit some oddities yesterday, so abandoned my attempts to use these
modules. I hope you find this bug report useful. I'll attach all the details
shortly.


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From bugzilla-daemon at portal.open-bio.org  Mon Jul 19 18:10:33 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 19 Jul 2010 18:10:33 -0400
Subject: [Bioperl-guts-l] [Bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite
	+ bp_seqfeature_gff3.PLS = unhappy?
In-Reply-To: <bug-3120-25@http.bugzilla.open-bio.org/>
Message-ID: <201007192210.o6JMAXCV010176@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3120





------- Comment #1 from jay at jays.net  2010-07-19 18:10 EST -------
Created an attachment (id=1526)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1526&action=view)
Description of the problem, reproduction steps (bioperl-live)


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From bugzilla-daemon at portal.open-bio.org  Mon Jul 19 18:43:11 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 19 Jul 2010 18:43:11 -0400
Subject: [Bioperl-guts-l] [Bug 3121] New: Bio::OntologyIO cannot parse the
	full InterPro XML file
Message-ID: <bug-3121-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3121

           Summary: Bio::OntologyIO cannot parse the full InterPro XML file
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: jonathan at leto.net


Currently the code does not check if subject_term or object_term are undef
before
calling methods on them, so parsing the interpo.xml from
ftp://ftp.ebi.ac.uk/pub/databases/interpro/
fails with calling a method on an undefined value.

I ran xmllint on the interpro.xml and it does indeed seem to be valid according
to the DTD.


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From bugzilla-daemon at portal.open-bio.org  Mon Jul 19 18:45:25 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 19 Jul 2010 18:45:25 -0400
Subject: [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full
	InterPro XML file
In-Reply-To: <bug-3121-25@http.bugzilla.open-bio.org/>
Message-ID: <201007192245.o6JMjPbu022923@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3121





------- Comment #1 from jonathan at leto.net  2010-07-19 18:45 EST -------
Created an attachment (id=1527)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1527&action=view)
Fixes described but with InterPro parsing


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From bugzilla-daemon at portal.open-bio.org  Mon Jul 19 18:46:04 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 19 Jul 2010 18:46:04 -0400
Subject: [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full
	InterPro XML file
In-Reply-To: <bug-3121-25@http.bugzilla.open-bio.org/>
Message-ID: <201007192246.o6JMk4VZ022964@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3121


jonathan at leto.net changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |jonathan at leto.net




------- Comment #2 from jonathan at leto.net  2010-07-19 18:46 EST -------
I have a github branch that fixes this bug, with a test case:

http://github.com/leto/bioperl-live/tree/fix_ontology_engine


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From bugzilla-daemon at portal.open-bio.org  Mon Jul 19 18:46:41 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 19 Jul 2010 18:46:41 -0400
Subject: [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full
	InterPro XML file
In-Reply-To: <bug-3121-25@http.bugzilla.open-bio.org/>
Message-ID: <201007192246.o6JMkfxK022994@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3121





------- Comment #3 from jonathan at leto.net  2010-07-19 18:46 EST -------
Created an attachment (id=1528)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1528&action=view)
Test case for InterPro parsing bug


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From bugzilla-daemon at portal.open-bio.org  Mon Jul 19 18:47:21 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 19 Jul 2010 18:47:21 -0400
Subject: [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full
	InterPro XML file
In-Reply-To: <bug-3121-25@http.bugzilla.open-bio.org/>
Message-ID: <201007192247.o6JMlL1X023026@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3121





------- Comment #4 from jonathan at leto.net  2010-07-19 18:47 EST -------
Created an attachment (id=1529)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1529&action=view)
Small InterPro XML file which exhibits the bug


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From bugzilla-daemon at portal.open-bio.org  Mon Jul 19 18:53:27 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 19 Jul 2010 18:53:27 -0400
Subject: [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full
	InterPro XML file
In-Reply-To: <bug-3121-25@http.bugzilla.open-bio.org/>
Message-ID: <201007192253.o6JMrRQj023177@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3121


rmb32 at cornell.edu changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED




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From bugzilla-daemon at portal.open-bio.org  Mon Jul 19 18:55:16 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 19 Jul 2010 18:55:16 -0400
Subject: [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full
	InterPro XML file
In-Reply-To: <bug-3121-25@http.bugzilla.open-bio.org/>
Message-ID: <201007192255.o6JMtGlB023234@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3121





------- Comment #5 from rmb32 at cornell.edu  2010-07-19 18:55 EST -------
I don't think this is a good fix, it's basically band-aiding over the fact that
Bio/OntologyIO/Handlers/InterProHandler.pm is sometimes making relationships
with a null object_term.

Need to figure out why it's doing that in the first place.


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From noreply at github.com  Mon Jul 19 19:06:34 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 19 Jul 2010 16:06:34 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 3819ef: interpro parser now
	throws an error when it cannot...
Message-ID: <20100719230634.A72564219D@smtp1.rs.github.com>

Branch: refs/heads/topic/leto_interpro_parse
Home:   http://github.com/bioperl/bioperl-live

Commit: 3819ef764f543db7cbe3c773d34324942e831c3f
    http://github.com/bioperl/bioperl-live/commit/3819ef764f543db7cbe3c773d34324942e831c3f
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M Bio/OntologyIO/Handlers/InterProHandler.pm

Log Message:
-----------
interpro parser now throws an error when it cannot find the term for an interpro type



From bugzilla-daemon at portal.open-bio.org  Mon Jul 19 19:21:22 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 19 Jul 2010 19:21:22 -0400
Subject: [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full
	InterPro XML file
In-Reply-To: <bug-3121-25@http.bugzilla.open-bio.org/>
Message-ID: <201007192321.o6JNLMp4029827@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3121





------- Comment #6 from cjfields at bioperl.org  2010-07-19 19:21 EST -------
Sounds like a case for some tests!

(In reply to comment #5)
> I don't think this is a good fix, it's basically band-aiding over the fact that
> Bio/OntologyIO/Handlers/InterProHandler.pm is sometimes making relationships
> with a null object_term.
> 
> Need to figure out why it's doing that in the first place.


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From noreply at github.com  Mon Jul 19 19:21:45 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 19 Jul 2010 16:21:45 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] d1d9d1: added a little
	defensive error checking when addin...
Message-ID: <20100719232145.125DC4229C@smtp1.rs.github.com>

Branch: refs/heads/topic/leto_interpro_parse
Home:   http://github.com/bioperl/bioperl-live

Commit: d1d9d1ab26ddcb8f92e3663035623e96e193c5f4
    http://github.com/bioperl/bioperl-live/commit/d1d9d1ab26ddcb8f92e3663035623e96e193c5f4
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M Bio/Ontology/SimpleOntologyEngine.pm

Log Message:
-----------
added a little defensive error checking when adding ontology relationships.

throws an error when either subject or object are not defined.  also
reverts 25403c7fbcdf9364fcc03b5d3a637553011c965a, which allowed this
method to succeed in this case.



From bugzilla-daemon at portal.open-bio.org  Mon Jul 19 19:23:43 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 19 Jul 2010 19:23:43 -0400
Subject: [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full
	InterPro XML file
In-Reply-To: <bug-3121-25@http.bugzilla.open-bio.org/>
Message-ID: <201007192323.o6JNNh3o032091@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3121





------- Comment #7 from rmb32 at cornell.edu  2010-07-19 19:23 EST -------
work on this is now going on in topic/leto_interpro_parse


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From noreply at github.com  Mon Jul 19 19:36:38 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 19 Jul 2010 16:36:38 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 3cde0b:
	Bio::Root::IO->_insert() special case when inserti...
Message-ID: <20100719233638.9C1BA422BB@smtp1.rs.github.com>

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

Commit: 3cde0befb0ad314aee0cbfd5620a0fdba1cdc279
    http://github.com/bioperl/bioperl-live/commit/3cde0befb0ad314aee0cbfd5620a0fdba1cdc279
Author: Florent Angly <florent.angly at gmail.com>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M Bio/Root/IO.pm
  M t/Root/RootIO.t

Log Message:
-----------
Bio::Root::IO->_insert() special case when inserting at first line of
an empty file


Commit: 8ecdf9043b15e07313de93dbb17f6b4b2ef50c93
    http://github.com/bioperl/bioperl-live/commit/8ecdf9043b15e07313de93dbb17f6b4b2ef50c93
Author: Florent Angly <florent.angly at gmail.com>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M Bio/Assembly/IO/ace.pm

Log Message:
-----------
Improved Bio::Assembly::IO::ace->write_header



From noreply at github.com  Mon Jul 19 19:45:37 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 19 Jul 2010 16:45:37 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] f1f67a: more perltidy
Message-ID: <20100719234537.273F1422C7@smtp1.rs.github.com>

Branch: refs/heads/topic/leto_interpro_parse
Home:   http://github.com/bioperl/bioperl-live

Commit: f1f67ab09bcdaea923549f3a7aca9871749e619a
    http://github.com/bioperl/bioperl-live/commit/f1f67ab09bcdaea923549f3a7aca9871749e619a
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M t/Ontology/Ontology.t

Log Message:
-----------
more perltidy


Commit: 99d580471349240826f35035dd44513ae15592f2
    http://github.com/bioperl/bioperl-live/commit/99d580471349240826f35035dd44513ae15592f2
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M Bio/OntologyIO/Handlers/InterProHandler.pm

Log Message:
-----------
more perltidy


Commit: cd2c47735db536a601b984f72a15a3a60bed605d
    http://github.com/bioperl/bioperl-live/commit/cd2c47735db536a601b984f72a15a3a60bed605d
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M Bio/OntologyIO/Handlers/InterProHandler.pm

Log Message:
-----------
added 'Region' interpro type.  recently-added test from leto now passes.

this type was added in InterPro release 19.0, according to http://www.ebi.ac.uk/interpro/tutorial.html



From noreply at github.com  Mon Jul 19 19:55:38 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 19 Jul 2010 16:55:38 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] c08e27: more perltidy
Message-ID: <20100719235538.D5328422C9@smtp1.rs.github.com>

Branch: refs/heads/topic/leto_interpro_parse
Home:   http://github.com/bioperl/bioperl-live

Commit: c08e274bcc67349248e8c9bff16765a997273e2e
    http://github.com/bioperl/bioperl-live/commit/c08e274bcc67349248e8c9bff16765a997273e2e
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M t/Ontology/OntologyEngine.t

Log Message:
-----------
more perltidy



From noreply at github.com  Mon Jul 19 21:08:40 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 19 Jul 2010 18:08:40 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 12aa17: Add tests for the
	exceptions thrown by invalid Bio...
Message-ID: <20100720010840.E8A26422C7@smtp1.rs.github.com>

Branch: refs/heads/topic/leto_interpro_parse
Home:   http://github.com/bioperl/bioperl-live

Commit: 12aa1779798057d36090f3d31fd15a7f80e554ac
    http://github.com/bioperl/bioperl-live/commit/12aa1779798057d36090f3d31fd15a7f80e554ac
Author: Duke Leto <jonathan at leto.net>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M t/Ontology/OntologyEngine.t

Log Message:
-----------
Add tests for the exceptions thrown by invalid Bio::Ontology::Relationship's

This adds tests for the functionality added in d1d9d1ab26ddcb8f92e3663035623e96e193c5f4



From noreply at github.com  Mon Jul 19 21:27:31 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 19 Jul 2010 18:27:31 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] cfafb2: Fix some failing
	InterPro tests, since the number ...
Message-ID: <20100720012731.D0D2A422D7@smtp1.rs.github.com>

Branch: refs/heads/topic/leto_interpro_parse
Home:   http://github.com/bioperl/bioperl-live

Commit: cfafb29e4d285eb86b9a3c36dca234f109578c5e
    http://github.com/bioperl/bioperl-live/commit/cfafb29e4d285eb86b9a3c36dca234f109578c5e
Author: Duke Leto <jonathan at leto.net>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M t/Ontology/IO/interpro.t

Log Message:
-----------
Fix some failing InterPro tests, since the number of root terms changed



From noreply at github.com  Mon Jul 19 22:13:48 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 19 Jul 2010 19:13:48 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 244ba4: Fix bug which
	prevents the parsing of the InterPro...
Message-ID: <20100720021348.C6C54422DD@smtp1.rs.github.com>

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

Commit: 244ba412853bef84a1ab899d755f5a2b764edbca
    http://github.com/bioperl/bioperl-live/commit/244ba412853bef84a1ab899d755f5a2b764edbca
Author: Duke Leto <jonathan at leto.net>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M Bio/Ontology/SimpleOntologyEngine.pm

Log Message:
-----------
Fix bug which prevents the parsing of the InterPro XML file

Currently the code does not check if subject_term or object_term are undef before
calling methods on them, so parsing the interpo.xml from ftp://ftp.ebi.ac.uk/pub/databases/interpro/
fails with calling a method on an undefined value.

I ran xmllint on the interpro.xml and it does indeed seem to be valid according to the DTD.


Commit: f06774116fc91f8c9efad932d27260425f897a8b
    http://github.com/bioperl/bioperl-live/commit/f06774116fc91f8c9efad932d27260425f897a8b
Author: Duke Leto <jonathan at leto.net>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M t/Ontology/Ontology.t

Log Message:
-----------
Add test case for parsing interpro XML


Commit: 0b72fdba60c88a1bd0b37a4b954193e2c195812d
    http://github.com/bioperl/bioperl-live/commit/0b72fdba60c88a1bd0b37a4b954193e2c195812d
Author: Duke Leto <jonathan at leto.net>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  A t/data/interpro.xml

Log Message:
-----------
Add a small InterPro XML file that shows the parsing bug


Commit: 40385cef701b9bb5084329ff4fe6844c85e6bb4d
    http://github.com/bioperl/bioperl-live/commit/40385cef701b9bb5084329ff4fe6844c85e6bb4d
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M Bio/Index/Fasta.pm

Log Message:
-----------
moved platform detection out of inner loop of Bio::Index::Fasta indexing


Commit: f24b71369f1c575ef5339a0732166dc591ce549c
    http://github.com/bioperl/bioperl-live/commit/f24b71369f1c575ef5339a0732166dc591ce549c
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M Bio/Ontology/SimpleOntologyEngine.pm

Log Message:
-----------
perltidy on SimpleOntologyEngine.pm using bioperl perltidy conf.  a definite improvement.


Commit: 3c0aa931da0acd75d05393e68ea0846233d29ec7
    http://github.com/bioperl/bioperl-live/commit/3c0aa931da0acd75d05393e68ea0846233d29ec7
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M Bio/OntologyIO/Handlers/InterProHandler.pm

Log Message:
-----------
interpro parser now throws an error when it cannot find the term for an interpro type


Commit: c75d63dee635c41d2382be3f3a6a2b610b535b13
    http://github.com/bioperl/bioperl-live/commit/c75d63dee635c41d2382be3f3a6a2b610b535b13
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M Bio/Ontology/SimpleOntologyEngine.pm

Log Message:
-----------
added a little defensive error checking when adding ontology relationships.

throws an error when either subject or object are not defined.  also
reverts 25403c7fbcdf9364fcc03b5d3a637553011c965a, which allowed this
method to succeed in this case.


Commit: ddfaee203f7174c7c49b29dbbd97e76eb233a2fd
    http://github.com/bioperl/bioperl-live/commit/ddfaee203f7174c7c49b29dbbd97e76eb233a2fd
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M t/Ontology/Ontology.t

Log Message:
-----------
more perltidy


Commit: d8a5d4d93390dfea49452fb23534b415f0519672
    http://github.com/bioperl/bioperl-live/commit/d8a5d4d93390dfea49452fb23534b415f0519672
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M Bio/OntologyIO/Handlers/InterProHandler.pm

Log Message:
-----------
more perltidy


Commit: 417ac454c7749c2e62f93e9059f13d59f559a23b
    http://github.com/bioperl/bioperl-live/commit/417ac454c7749c2e62f93e9059f13d59f559a23b
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M Bio/OntologyIO/Handlers/InterProHandler.pm

Log Message:
-----------
added 'Region' interpro type.  recently-added test from leto now passes.

this type was added in InterPro release 19.0, according to http://www.ebi.ac.uk/interpro/tutorial.html


Commit: b0a88e1a9cecf5e571595e35c4550695654083c4
    http://github.com/bioperl/bioperl-live/commit/b0a88e1a9cecf5e571595e35c4550695654083c4
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M t/Ontology/OntologyEngine.t

Log Message:
-----------
more perltidy


Commit: 4a6f440db7a09e8619490c1692cd3fdf02442825
    http://github.com/bioperl/bioperl-live/commit/4a6f440db7a09e8619490c1692cd3fdf02442825
Author: Duke Leto <jonathan at leto.net>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M t/Ontology/OntologyEngine.t

Log Message:
-----------
Add tests for the exceptions thrown by invalid Bio::Ontology::Relationship's

This adds tests for the functionality added in d1d9d1ab26ddcb8f92e3663035623e96e193c5f4


Commit: ada02634281ae4cd9628521cd9737ac6bfe45afd
    http://github.com/bioperl/bioperl-live/commit/ada02634281ae4cd9628521cd9737ac6bfe45afd
Author: Duke Leto <jonathan at leto.net>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M t/Ontology/IO/interpro.t

Log Message:
-----------
Fix some failing InterPro tests, since the number of root terms changed


Commit: b500f65988b7492fe4bc0023f09ff197883f90b5
    http://github.com/bioperl/bioperl-live/commit/b500f65988b7492fe4bc0023f09ff197883f90b5
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  A t/Assembly/10_core.t
  A t/Assembly/20_bowtie.t
  A t/Assembly/30_sam.t
  R t/Assembly/Assembly.t

Log Message:
-----------
broke t/Assembly/Assembly.t into 3 sane test files



From bugzilla-daemon at portal.open-bio.org  Mon Jul 19 23:00:08 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 19 Jul 2010 23:00:08 -0400
Subject: [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full
	InterPro XML file
In-Reply-To: <bug-3121-25@http.bugzilla.open-bio.org/>
Message-ID: <201007200300.o6K308XY001467@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3121


rmb32 at cornell.edu changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|ASSIGNED                    |RESOLVED
         Resolution|                            |FIXED




------- Comment #8 from rmb32 at cornell.edu  2010-07-19 23:00 EST -------
topic/leto_interpro_parse is merged in now, with some additional tests for the
tweaks to Bio::Ontology::* things that were modified.  closing.


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From noreply at github.com  Tue Jul 20 02:09:34 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 19 Jul 2010 23:09:34 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] be8dd8: Removed warning
	when Bio::Assembly::IO::ace parsin...
Message-ID: <20100720060934.A3FBA422BB@smtp1.rs.github.com>

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

Commit: be8dd8df914e7ec0c349b576b323ee5545bc841a
    http://github.com/bioperl/bioperl-live/commit/be8dd8df914e7ec0c349b576b323ee5545bc841a
Author: Florent Angly <florent.angly at gmail.com>
Date:   2010-07-19 (Mon, 19 Jul 2010)

Changed paths:
  M Bio/Assembly/IO/ace.pm

Log Message:
-----------
Removed warning when Bio::Assembly::IO::ace parsing quality strings
starting with a whitespace



From noreply at github.com  Tue Jul 20 03:21:16 2010
From: noreply at github.com (noreply at github.com)
Date: Tue, 20 Jul 2010 00:21:16 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 783e04: Bio::Root::IO
	insert() with no backup file
Message-ID: <20100720072116.78426422B0@smtp1.rs.github.com>

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

Commit: 783e04c0689d0e4a55b75332bd90123e051896d2
    http://github.com/bioperl/bioperl-live/commit/783e04c0689d0e4a55b75332bd90123e051896d2
Author: Florent Angly <florent.angly at gmail.com>
Date:   2010-07-20 (Tue, 20 Jul 2010)

Changed paths:
  M Bio/Root/IO.pm
  M t/Root/RootIO.t

Log Message:
-----------
Bio::Root::IO insert() with no backup file



From noreply at github.com  Tue Jul 20 17:57:53 2010
From: noreply at github.com (noreply at github.com)
Date: Tue, 20 Jul 2010 14:57:53 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] bcde3b: Update MANIFEST and
	MANIFEST.SKIP
Message-ID: <20100720215753.891FF422CC@smtp1.rs.github.com>

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

Commit: bcde3be3cb425e56219f20fe3069b90166da6778
    http://github.com/bioperl/bioperl-live/commit/bcde3be3cb425e56219f20fe3069b90166da6778
Author: Duke Leto <jonathan at leto.net>
Date:   2010-07-20 (Tue, 20 Jul 2010)

Changed paths:
  M MANIFEST
  M MANIFEST.SKIP

Log Message:
-----------
Update MANIFEST and MANIFEST.SKIP



From noreply at github.com  Tue Jul 20 17:58:41 2010
From: noreply at github.com (noreply at github.com)
Date: Tue, 20 Jul 2010 14:58:41 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 29cf23: allow POST for ID
	lists longer than 200 or terms l...
Message-ID: <20100720215841.E46EB422C5@smtp1.rs.github.com>

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

Commit: 29cf230da064b20743d7417e63a3b39d0d825b79
    http://github.com/bioperl/bioperl-live/commit/29cf230da064b20743d7417e63a3b39d0d825b79
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-20 (Tue, 20 Jul 2010)

Changed paths:
  M Bio/Tools/EUtilities/EUtilParameters.pm

Log Message:
-----------
allow POST for ID lists longer than 200 or terms longer than 300 (with optional setting); beginnings of carryover, but NYI



From noreply at github.com  Tue Jul 20 18:00:32 2010
From: noreply at github.com (noreply at github.com)
Date: Tue, 20 Jul 2010 15:00:32 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 29cf23: allow POST for ID
	lists longer than 200 or terms l...
Message-ID: <20100720220032.7170B422C5@smtp1.rs.github.com>

Branch: refs/heads/topic/eutils_carryover
Home:   http://github.com/bioperl/bioperl-live

Commit: 29cf230da064b20743d7417e63a3b39d0d825b79
    http://github.com/bioperl/bioperl-live/commit/29cf230da064b20743d7417e63a3b39d0d825b79
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-20 (Tue, 20 Jul 2010)

Changed paths:
  M Bio/Tools/EUtilities/EUtilParameters.pm

Log Message:
-----------
allow POST for ID lists longer than 200 or terms longer than 300 (with optional setting); beginnings of carryover, but NYI



From noreply at github.com  Tue Jul 20 20:41:35 2010
From: noreply at github.com (noreply at github.com)
Date: Tue, 20 Jul 2010 17:41:35 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 19d5b7: Refactor some tests
	in t/Ontology/IO/interpro.t
Message-ID: <20100721004135.EF00042281@smtp1.rs.github.com>

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

Commit: 19d5b75172cf69b7b406826d0edac30edbc79967
    http://github.com/bioperl/bioperl-live/commit/19d5b75172cf69b7b406826d0edac30edbc79967
Author: Duke Leto <jonathan at leto.net>
Date:   2010-07-20 (Tue, 20 Jul 2010)

Changed paths:
  M t/Ontology/IO/interpro.t

Log Message:
-----------
Refactor some tests in t/Ontology/IO/interpro.t



From noreply at github.com  Tue Jul 20 21:39:50 2010
From: noreply at github.com (noreply at github.com)
Date: Tue, 20 Jul 2010 18:39:50 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 7314af: Add Conserved_site
	as an InterPro root term and up...
Message-ID: <20100721013950.5F986422A5@smtp1.rs.github.com>

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

Commit: 7314afb87a294043cd2c8d7b9861b96186019cb8
    http://github.com/bioperl/bioperl-live/commit/7314afb87a294043cd2c8d7b9861b96186019cb8
Author: Duke Leto <jonathan at leto.net>
Date:   2010-07-20 (Tue, 20 Jul 2010)

Changed paths:
  M Bio/OntologyIO/Handlers/InterProHandler.pm
  M t/Ontology/IO/interpro.t
  M t/data/interpro.xml

Log Message:
-----------
Add Conserved_site as an InterPro root term and update relevant tests



From bugzilla-daemon at portal.open-bio.org  Tue Jul 20 23:22:58 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 20 Jul 2010 23:22:58 -0400
Subject: [Bioperl-guts-l] [Bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite
	+ bp_seqfeature_gff3.PLS = unhappy?
In-Reply-To: <bug-3120-25@http.bugzilla.open-bio.org/>
Message-ID: <201007210322.o6L3MwNv005043@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3120


genehack at genehack.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED




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From bugzilla-daemon at portal.open-bio.org  Tue Jul 20 23:26:29 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 20 Jul 2010 23:26:29 -0400
Subject: [Bioperl-guts-l] [Bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite
	+ bp_seqfeature_gff3.PLS = unhappy?
In-Reply-To: <bug-3120-25@http.bugzilla.open-bio.org/>
Message-ID: <201007210326.o6L3QTGv006559@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3120


genehack at genehack.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |genehack at genehack.org




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From noreply at github.com  Wed Jul 21 13:53:24 2010
From: noreply at github.com (noreply at github.com)
Date: Wed, 21 Jul 2010 10:53:24 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 7c6739: Add a test to show
	that there is a bug with get_db...
Message-ID: <20100721175324.200BD421A2@smtp1.rs.github.com>

Branch: refs/heads/topic/leto_interpro_get_dbxref
Home:   http://github.com/bioperl/bioperl-live

Commit: 7c6739b8526e0cf5f24c4a66c28c591876a81a1a
    http://github.com/bioperl/bioperl-live/commit/7c6739b8526e0cf5f24c4a66c28c591876a81a1a
Author: Duke Leto <jonathan at leto.net>
Date:   2010-07-21 (Wed, 21 Jul 2010)

Changed paths:
  M t/Ontology/IO/interpro.t

Log Message:
-----------
Add a test to show that there is a bug with get_dbxrefs on InterPro terms



From bugzilla-daemon at portal.open-bio.org  Thu Jul 22 09:40:15 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 22 Jul 2010 09:40:15 -0400
Subject: [Bioperl-guts-l] [Bug 3122] New: Bio::SeqIO ignores first line of
	piped Fasta sequence when no format parameter is set
Message-ID: <bug-3122-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3122

           Summary: Bio::SeqIO ignores first line of piped Fasta sequence
                    when no format parameter is set
           Product: BioPerl
           Version: unspecified
          Platform: PC
        OS/Version: Windows
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Bio::SeqIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: roy.chaudhuri at gmail.com


See discussion here:
http://lists.open-bio.org/pipermail/bioperl-l/2010-July/033683.html

When reading in a piped Fasta sequence, if the format is not specified, the
first line is ignored, and the first line of the sequence is used as the id.


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From bugzilla-daemon at portal.open-bio.org  Thu Jul 22 10:40:27 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 22 Jul 2010 10:40:27 -0400
Subject: [Bioperl-guts-l] [Bug 3122] Bio::SeqIO ignores first line of piped
	Fasta sequence when no format parameter is set
In-Reply-To: <bug-3122-25@http.bugzilla.open-bio.org/>
Message-ID: <201007221440.o6MEeRrV029223@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3122


kirovs at gmail.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |kirovs at gmail.com




------- Comment #1 from kirovs at gmail.com  2010-07-22 10:40 EST -------
The culprit is Bio/Tools//GuessSeqFormat.pm.
I propose that in the block:
if (defined $self->{-file}) {
        # Close the file we opened.
        close($fh);
    } elsif (ref $fh eq 'GLOB') {
        # Try seeking to the start position.
        seek($fh, $start_pos, 0);
    } elsif (defined $fh && $fh->can('setpos')) {
        # Seek to the start position.
        $fh->setpos($start_pos);
    }

there should be changes-
seek($fh, $start_pos, 0) || $self->throw("Failed resetting the filehandle; IO
error occurred");

Also if input is STDIN, format is mandatory.

The reason for all this is seek fails on STDIN (pointer is read only?).


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From bugzilla-daemon at portal.open-bio.org  Thu Jul 22 10:45:47 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 22 Jul 2010 10:45:47 -0400
Subject: [Bioperl-guts-l] [Bug 3122] Bio::SeqIO ignores first line of piped
	Fasta sequence when no format parameter is set
In-Reply-To: <bug-3122-25@http.bugzilla.open-bio.org/>
Message-ID: <201007221445.o6MEjlZw029570@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3122


kirovs at gmail.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
         OS/Version|Windows                     |All




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From bugzilla-daemon at portal.open-bio.org  Thu Jul 22 11:06:07 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 22 Jul 2010 11:06:07 -0400
Subject: [Bioperl-guts-l] [Bug 3122] Bio::SeqIO ignores first line of piped
	Fasta sequence when no format parameter is set
In-Reply-To: <bug-3122-25@http.bugzilla.open-bio.org/>
Message-ID: <201007221506.o6MF67Vq030486@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3122





------- Comment #2 from kirovs at gmail.com  2010-07-22 11:06 EST -------
Update on seek and pipes:
http://www.perlmonks.org/?node_id=637267
Claim is you cannot seek in pipes.
One workaround would be to write a temp file?


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From bugzilla-daemon at portal.open-bio.org  Thu Jul 22 11:16:23 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 22 Jul 2010 11:16:23 -0400
Subject: [Bioperl-guts-l] [Bug 3123] New: get_dbxrefs does not work on
	InterPro terms
Message-ID: <bug-3123-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3123

           Summary: get_dbxrefs does not work on InterPro terms
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: jonathan at leto.net


It seems that get_dbxrefs always returns undef on Inter:

I wrote a test that shows the problem on this github branch:

http://github.com/bioperl/bioperl-live/tree/topic/leto_interpro_get_dbxref


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From bugzilla-daemon at portal.open-bio.org  Thu Jul 22 11:33:54 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 22 Jul 2010 11:33:54 -0400
Subject: [Bioperl-guts-l] [Bug 3123] get_dbxrefs does not work on InterPro
	terms
In-Reply-To: <bug-3123-25@http.bugzilla.open-bio.org/>
Message-ID: <201007221533.o6MFXs8B031797@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3123


cjfields at bioperl.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED




------- Comment #1 from cjfields at bioperl.org  2010-07-22 11:33 EST -------
Ick.  This is likely due to my ripping out a bunch of code a few years back
that hadn't been completely implemented, related to features and annotation. 
I'll look into it.


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From noreply at github.com  Thu Jul 22 12:27:50 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 22 Jul 2010 09:27:50 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 19d5b7: Refactor some tests
	in t/Ontology/IO/interpro.t
Message-ID: <20100722162750.ECADC42193@smtp1.rs.github.com>

Branch: refs/heads/topic/eutils_carryover
Home:   http://github.com/bioperl/bioperl-live

Commit: 19d5b75172cf69b7b406826d0edac30edbc79967
    http://github.com/bioperl/bioperl-live/commit/19d5b75172cf69b7b406826d0edac30edbc79967
Author: Duke Leto <jonathan at leto.net>
Date:   2010-07-20 (Tue, 20 Jul 2010)

Changed paths:
  M t/Ontology/IO/interpro.t

Log Message:
-----------
Refactor some tests in t/Ontology/IO/interpro.t


Commit: 7314afb87a294043cd2c8d7b9861b96186019cb8
    http://github.com/bioperl/bioperl-live/commit/7314afb87a294043cd2c8d7b9861b96186019cb8
Author: Duke Leto <jonathan at leto.net>
Date:   2010-07-20 (Tue, 20 Jul 2010)

Changed paths:
  M Bio/OntologyIO/Handlers/InterProHandler.pm
  M t/Ontology/IO/interpro.t
  M t/data/interpro.xml

Log Message:
-----------
Add Conserved_site as an InterPro root term and update relevant tests



From noreply at github.com  Thu Jul 22 12:27:52 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 22 Jul 2010 09:27:52 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 505452: squash warnings
	popping up with uninit data; marke...
Message-ID: <20100722162752.45A05422EA@smtp1.rs.github.com>

Branch: refs/heads/topic/leto_interpro_get_dbxref
Home:   http://github.com/bioperl/bioperl-live

Commit: 50545289aa5be39ee8fec2834a9389f78c80caaf
    http://github.com/bioperl/bioperl-live/commit/50545289aa5be39ee8fec2834a9389f78c80caaf
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-22 (Thu, 22 Jul 2010)

Changed paths:
  M Bio/OntologyIO/Handlers/InterProHandler.pm

Log Message:
-----------
squash warnings popping up with uninit data; marked as a TODO (is this supposed to be an error?)



From noreply at github.com  Thu Jul 22 16:04:17 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 22 Jul 2010 13:04:17 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 09f5f0: Add a test for each
	kind of InterPro dbxref contex...
Message-ID: <20100722200417.8DD87421AE@smtp1.rs.github.com>

Branch: refs/heads/topic/leto_interpro_get_dbxref
Home:   http://github.com/bioperl/bioperl-live

Commit: 09f5f0e4525dc4e68de29fba890dd2388f7882d8
    http://github.com/bioperl/bioperl-live/commit/09f5f0e4525dc4e68de29fba890dd2388f7882d8
Author: Jonathan "Duke" Leto <jonathan at leto.net>
Date:   2010-07-22 (Thu, 22 Jul 2010)

Changed paths:
  M t/Ontology/IO/interpro.t

Log Message:
-----------
Add a test for each kind of InterPro dbxref context



From noreply at github.com  Thu Jul 22 16:56:55 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 22 Jul 2010 13:56:55 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 09f5f0: Add a test for each
	kind of InterPro dbxref contex...
Message-ID: <20100722205655.79E3D4217B@smtp1.rs.github.com>

Branch: refs/heads/topic/cjfields_interpro_get_dbxref
Home:   http://github.com/bioperl/bioperl-live

Commit: 09f5f0e4525dc4e68de29fba890dd2388f7882d8
    http://github.com/bioperl/bioperl-live/commit/09f5f0e4525dc4e68de29fba890dd2388f7882d8
Author: Jonathan "Duke" Leto <jonathan at leto.net>
Date:   2010-07-22 (Thu, 22 Jul 2010)

Changed paths:
  M t/Ontology/IO/interpro.t

Log Message:
-----------
Add a test for each kind of InterPro dbxref context



From noreply at github.com  Thu Jul 22 17:00:13 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 22 Jul 2010 14:00:13 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 22c410: reimplement various
	methods in terms of get_dbxref...
Message-ID: <20100722210013.B73024208F@smtp1.rs.github.com>

Branch: refs/heads/topic/cjfields_interpro_get_dbxref
Home:   http://github.com/bioperl/bioperl-live

Commit: 22c410869b9c97d6660c2631d060c351b3c0008e
    http://github.com/bioperl/bioperl-live/commit/22c410869b9c97d6660c2631d060c351b3c0008e
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-22 (Thu, 22 Jul 2010)

Changed paths:
  M Bio/Ontology/InterProTerm.pm

Log Message:
-----------
reimplement various methods in terms of get_dbxrefs, for consistency


Commit: 5fb02a92b79022b17f5e50f4f59701a9cb88a636
    http://github.com/bioperl/bioperl-live/commit/5fb02a92b79022b17f5e50f4f59701a9cb88a636
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-22 (Thu, 22 Jul 2010)

Changed paths:
  M Bio/OntologyIO/Handlers/InterProHandler.pm

Log Message:
-----------
use add_dbxrefs with contexts instead of the various methods (could revert back, but this is more direct)



From noreply at github.com  Thu Jul 22 17:35:19 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 22 Jul 2010 14:35:19 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 3a817b: Add some tests for
	get_members and protein_count a...
Message-ID: <20100722213519.4F2F3422EF@smtp1.rs.github.com>

Branch: refs/heads/topic/leto_interpro_get_dbxref
Home:   http://github.com/bioperl/bioperl-live

Commit: 3a817b6abc818cb55799d9cb0419af62da50f1db
    http://github.com/bioperl/bioperl-live/commit/3a817b6abc818cb55799d9cb0419af62da50f1db
Author: Jonathan "Duke" Leto <jonathan at leto.net>
Date:   2010-07-22 (Thu, 22 Jul 2010)

Changed paths:
  M t/Ontology/IO/interpro.t

Log Message:
-----------
Add some tests for get_members and protein_count and refactor tests for get_dbxrefs



From noreply at github.com  Thu Jul 22 17:42:08 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 22 Jul 2010 14:42:08 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 6c2c95: Add tests for
	class_list, get_examples and get_ext...
Message-ID: <20100722214208.CAB814202F@smtp1.rs.github.com>

Branch: refs/heads/topic/leto_interpro_get_dbxref
Home:   http://github.com/bioperl/bioperl-live

Commit: 6c2c9546b6622f629d06219b4c97cf740eb30582
    http://github.com/bioperl/bioperl-live/commit/6c2c9546b6622f629d06219b4c97cf740eb30582
Author: Jonathan "Duke" Leto <jonathan at leto.net>
Date:   2010-07-22 (Thu, 22 Jul 2010)

Changed paths:
  M t/Ontology/IO/interpro.t

Log Message:
-----------
Add tests for class_list, get_examples and get_external_documents



From noreply at github.com  Thu Jul 22 17:57:24 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 22 Jul 2010 14:57:24 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] c495ed: Add a test for
	get_references and to_string
Message-ID: <20100722215724.465DC422E2@smtp1.rs.github.com>

Branch: refs/heads/topic/leto_interpro_get_dbxref
Home:   http://github.com/bioperl/bioperl-live

Commit: c495ed104461c3dfad303665229233dd167c446e
    http://github.com/bioperl/bioperl-live/commit/c495ed104461c3dfad303665229233dd167c446e
Author: Jonathan "Duke" Leto <jonathan at leto.net>
Date:   2010-07-22 (Thu, 22 Jul 2010)

Changed paths:
  M t/Ontology/IO/interpro.t

Log Message:
-----------
Add a test for get_references and to_string



From noreply at github.com  Thu Jul 22 18:27:18 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 22 Jul 2010 15:27:18 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 846480: a bit o' debugging;
	alias add_dbxrefs to add_dbxre...
Message-ID: <20100722222718.D6D2C422C7@smtp1.rs.github.com>

Branch: refs/heads/topic/cjfields_interpro_get_dbxref
Home:   http://github.com/bioperl/bioperl-live

Commit: 846480ab85e6f0334228cd4a7558bc7100488f98
    http://github.com/bioperl/bioperl-live/commit/846480ab85e6f0334228cd4a7558bc7100488f98
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-22 (Thu, 22 Jul 2010)

Changed paths:
  M Bio/Ontology/Term.pm

Log Message:
-----------
a bit o' debugging; alias add_dbxrefs to add_dbxref


Commit: e867641900b8ebfb261f493ba214d2a7f0394c2b
    http://github.com/bioperl/bioperl-live/commit/e867641900b8ebfb261f493ba214d2a7f0394c2b
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-22 (Thu, 22 Jul 2010)

Changed paths:
  M Bio/Ontology/Term.pm
  M Bio/OntologyIO/Handlers/InterProHandler.pm

Log Message:
-----------
pinpointing the problem, perhaps, paint me perplexed



From noreply at github.com  Thu Jul 22 22:21:29 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 22 Jul 2010 19:21:29 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 42712c: Add some tests for
	get_members and protein_count a...
Message-ID: <20100723022129.2F874421B6@smtp1.rs.github.com>

Branch: refs/heads/topic/cjfields_interpro_get_dbxref
Home:   http://github.com/bioperl/bioperl-live

Commit: 42712cb91cd27c9cb53a4801bc2f07857c96fc8e
    http://github.com/bioperl/bioperl-live/commit/42712cb91cd27c9cb53a4801bc2f07857c96fc8e
Author: Jonathan "Duke" Leto <jonathan at leto.net>
Date:   2010-07-22 (Thu, 22 Jul 2010)

Changed paths:
  M t/Ontology/IO/interpro.t

Log Message:
-----------
Add some tests for get_members and protein_count and refactor tests for get_dbxrefs


Commit: 5b72ea0f61c759d4dda9bae624e26a74555f5890
    http://github.com/bioperl/bioperl-live/commit/5b72ea0f61c759d4dda9bae624e26a74555f5890
Author: Jonathan "Duke" Leto <jonathan at leto.net>
Date:   2010-07-22 (Thu, 22 Jul 2010)

Changed paths:
  M t/Ontology/IO/interpro.t

Log Message:
-----------
Add tests for class_list, get_examples and get_external_documents


Commit: 2a7e75fafed01305c70570f942dbc46e858d5cd3
    http://github.com/bioperl/bioperl-live/commit/2a7e75fafed01305c70570f942dbc46e858d5cd3
Author: Jonathan "Duke" Leto <jonathan at leto.net>
Date:   2010-07-22 (Thu, 22 Jul 2010)

Changed paths:
  M t/Ontology/IO/interpro.t

Log Message:
-----------
Add a test for get_references and to_string


Commit: 70501acef697144663043c0eb2d9e559d191ec78
    http://github.com/bioperl/bioperl-live/commit/70501acef697144663043c0eb2d9e559d191ec78
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-22 (Thu, 22 Jul 2010)

Changed paths:
  M Bio/Ontology/InterProTerm.pm

Log Message:
-----------
more fixes for warnings; tests are passing



From bugzilla-daemon at portal.open-bio.org  Thu Jul 22 22:29:25 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 22 Jul 2010 22:29:25 -0400
Subject: [Bioperl-guts-l] [Bug 3123] get_dbxrefs does not work on InterPro
	terms
In-Reply-To: <bug-3123-25@http.bugzilla.open-bio.org/>
Message-ID: <201007230229.o6N2TPl8023081@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3123





------- Comment #2 from cjfields at bioperl.org  2010-07-22 22:29 EST -------
After the work on IRC, I merged your changes in to my branch and everything is
passing:  

http://github.com/bioperl/bioperl-live/tree/topic/cjfields_interpro_get_dbxref

If the fixes work for you and it's adequate/correct for the dbxrefs to be on
the leaf terms, then we can merge to master and close everything out.


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From noreply at github.com  Fri Jul 23 11:26:40 2010
From: noreply at github.com (noreply at github.com)
Date: Fri, 23 Jul 2010 08:26:40 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] aee9fe: move
	Bio::Assembly::IO tests into their own direct...
Message-ID: <20100723152640.B9D37422F3@smtp1.rs.github.com>

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

Commit: aee9fe22fab799449799472274f12ba26836abb5
    http://github.com/bioperl/bioperl-live/commit/aee9fe22fab799449799472274f12ba26836abb5
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-23 (Fri, 23 Jul 2010)

Changed paths:
  R t/Assembly/10_core.t
  R t/Assembly/20_bowtie.t
  R t/Assembly/30_sam.t
  A t/Assembly/IO/bowtie.t
  A t/Assembly/IO/sam.t
  A t/Assembly/core.t

Log Message:
-----------
move Bio::Assembly::IO tests into their own directory for consistency; we're not following the 10/20/30 system for tests



From noreply at github.com  Fri Jul 23 11:34:10 2010
From: noreply at github.com (noreply at github.com)
Date: Fri, 23 Jul 2010 08:34:10 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] a30498: cleanup tests,
	passing but file cleanup not in pla...
Message-ID: <20100723153410.60CBC42193@smtp1.rs.github.com>

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

Commit: a30498a180daeae225097de0ba18f4db97847b16
    http://github.com/bioperl/bioperl-live/commit/a30498a180daeae225097de0ba18f4db97847b16
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-23 (Fri, 23 Jul 2010)

Changed paths:
  M t/Assembly/IO/bowtie.t
  M t/Assembly/IO/sam.t
  M t/Assembly/core.t

Log Message:
-----------
cleanup tests, passing but file cleanup not in place yet



From noreply at github.com  Fri Jul 23 13:09:44 2010
From: noreply at github.com (noreply at github.com)
Date: Fri, 23 Jul 2010 10:09:44 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] a7be37: clean up generated
	index files
Message-ID: <20100723170944.79BE44204F@smtp1.rs.github.com>

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

Commit: a7be3795df0e37a6743c479b7ff58d82e743aadb
    http://github.com/bioperl/bioperl-live/commit/a7be3795df0e37a6743c479b7ff58d82e743aadb
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-23 (Fri, 23 Jul 2010)

Changed paths:
  M t/Assembly/IO/sam.t

Log Message:
-----------
clean up generated index files



From noreply at github.com  Fri Jul 23 13:16:01 2010
From: noreply at github.com (noreply at github.com)
Date: Fri, 23 Jul 2010 10:16:01 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 8a8d14: test count off on
	skip (ID mapper appears to be ha...
Message-ID: <20100723171601.0E57B42304@smtp1.rs.github.com>

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

Commit: 8a8d142e204d2b0808aaa073da4d01d86a0fa780
    http://github.com/bioperl/bioperl-live/commit/8a8d142e204d2b0808aaa073da4d01d86a0fa780
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-23 (Fri, 23 Jul 2010)

Changed paths:
  M t/RemoteDB/SwissProt.t

Log Message:
-----------
test count off on skip (ID mapper appears to be having some issues)



From noreply at github.com  Fri Jul 23 13:19:01 2010
From: noreply at github.com (noreply at github.com)
Date: Fri, 23 Jul 2010 10:19:01 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 424905: remote db ID change
	causing fail
Message-ID: <20100723171901.23BF742303@smtp1.rs.github.com>

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

Commit: 4249053c21b2ed1d152b27cfab9efe0d205b40da
    http://github.com/bioperl/bioperl-live/commit/4249053c21b2ed1d152b27cfab9efe0d205b40da
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-23 (Fri, 23 Jul 2010)

Changed paths:
  M t/RemoteDB/GenPept.t

Log Message:
-----------
remote db ID change causing fail



From bugzilla-daemon at portal.open-bio.org  Fri Jul 23 14:16:59 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 23 Jul 2010 14:16:59 -0400
Subject: [Bioperl-guts-l] [Bug 3123] get_dbxrefs does not work on InterPro
	terms
In-Reply-To: <bug-3123-25@http.bugzilla.open-bio.org/>
Message-ID: <201007231816.o6NIGxXb001905@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3123





------- Comment #3 from jonathan at leto.net  2010-07-23 14:16 EST -------
Everthing looks good to me. I will let you merge to master.

Nice work!


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From noreply at github.com  Fri Jul 23 15:44:05 2010
From: noreply at github.com (noreply at github.com)
Date: Fri, 23 Jul 2010 12:44:05 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 605c9d: Merge branch
	'topic/cjfields_interpro_get_dbxref'
Message-ID: <20100723194405.0CF2B42326@smtp1.rs.github.com>

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

Commit: 605c9dda01eb900281899d4032d6d44e04945fa4
    http://github.com/bioperl/bioperl-live/commit/605c9dda01eb900281899d4032d6d44e04945fa4
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-23 (Fri, 23 Jul 2010)

Changed paths:
  M Bio/Ontology/InterProTerm.pm
  M Bio/Ontology/Term.pm
  M Bio/OntologyIO/Handlers/InterProHandler.pm
  M t/Ontology/IO/interpro.t

Log Message:
-----------
Merge branch 'topic/cjfields_interpro_get_dbxref'


Commit: da9d58434396c658c65176cd8e142a1183728d6c
    http://github.com/bioperl/bioperl-live/commit/da9d58434396c658c65176cd8e142a1183728d6c
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-23 (Fri, 23 Jul 2010)

Changed paths:
  M MANIFEST
  M MANIFEST.SKIP
  M maintenance/symlink_script.pl

Log Message:
-----------
[RT 54702] patch symlink_script.pl, thanks to Curtis Jewell, and update MANIFEST/MANIFEST.SKIP



From noreply at github.com  Fri Jul 23 16:02:50 2010
From: noreply at github.com (noreply at github.com)
Date: Fri, 23 Jul 2010 13:02:50 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-run] d58682: [RT 58464] patching
	to allow file names with space...
Message-ID: <20100723200250.A0EBA42315@smtp1.rs.github.com>

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

Commit: d586822725e8cd6aadff9e15e2d8659f2f162bb8
    http://github.com/bioperl/bioperl-run/commit/d586822725e8cd6aadff9e15e2d8659f2f162bb8
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-23 (Fri, 23 Jul 2010)

Changed paths:
  M lib/Bio/Tools/Run/Alignment/Clustalw.pm
  M lib/Bio/Tools/Run/Primer3.pm

Log Message:
-----------
[RT 58464] patching to allow file names with spaces


Commit: 4024088741080a3c4e7408f91757fb14fc3a8a5b
    http://github.com/bioperl/bioperl-run/commit/4024088741080a3c4e7408f91757fb14fc3a8a5b
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-23 (Fri, 23 Jul 2010)

Changed paths:
  M lib/Bio/Tools/Run/Alignment/Blat.pm
  A lib/Bio/Tools/Run/Alignment/Clustalw.pm.orig
  A lib/Bio/Tools/Run/Alignment/Clustalw.pm.rej

Log Message:
-----------
add dots param


Commit: 0205676d4192ac107b9d7721a97c65753bfe5cb0
    http://github.com/bioperl/bioperl-run/commit/0205676d4192ac107b9d7721a97c65753bfe5cb0
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-23 (Fri, 23 Jul 2010)

Changed paths:
  M lib/Bio/Tools/Run/Alignment/Blat.pm
  R lib/Bio/Tools/Run/Alignment/Clustalw.pm.orig
  R lib/Bio/Tools/Run/Alignment/Clustalw.pm.rej

Log Message:
-----------
Revert "add dots param"

This reverts commit 4b82f66543326d8afd13cd4a585e9552eca2ab5b.



From noreply at github.com  Fri Jul 23 16:04:53 2010
From: noreply at github.com (noreply at github.com)
Date: Fri, 23 Jul 2010 13:04:53 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 2bfc2c: [RT 58464] patching
	to allow file names with space...
Message-ID: <20100723200453.2A5A742315@smtp1.rs.github.com>

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

Commit: 2bfc2c93e13edc560d1e156d2b278404eb6d9006
    http://github.com/bioperl/bioperl-live/commit/2bfc2c93e13edc560d1e156d2b278404eb6d9006
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-23 (Fri, 23 Jul 2010)

Changed paths:
  M Bio/Tools/Run/WrapperBase.pm

Log Message:
-----------
[RT 58464] patching to allow file names with spaces



From noreply at github.com  Fri Jul 23 16:15:41 2010
From: noreply at github.com (noreply at github.com)
Date: Fri, 23 Jul 2010 13:15:41 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-db] 98d2a0: [RT 44466] remove
	corba-related scripts, now obsol...
Message-ID: <20100723201541.1F9194232E@smtp1.rs.github.com>

Branch: refs/heads/master
Home:   http://github.com/bioperl/bioperl-db

Commit: 98d2a0fed2d9b7e7437b15abc6bd829b32afe777
    http://github.com/bioperl/bioperl-db/commit/98d2a0fed2d9b7e7437b15abc6bd829b32afe777
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-23 (Fri, 23 Jul 2010)

Changed paths:
  R scripts/corba/bioenv_server.pl
  R scripts/corba/caching_corba_server.pl
  R scripts/corba/test_bioenv.pl

Log Message:
-----------
[RT 44466] remove corba-related scripts, now obsolete



From bugzilla-daemon at portal.open-bio.org  Sat Jul 24 12:39:00 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sat, 24 Jul 2010 12:39:00 -0400
Subject: [Bioperl-guts-l] [Bug 3123] get_dbxrefs does not work on InterPro
	terms
In-Reply-To: <bug-3123-25@http.bugzilla.open-bio.org/>
Message-ID: <201007241639.o6OGd0Vb019526@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3123


cjfields at bioperl.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|ASSIGNED                    |RESOLVED
         Resolution|                            |FIXED




------- Comment #4 from cjfields at bioperl.org  2010-07-24 12:38 EST -------
Agreed!  Merged back to master, so closing out.


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From noreply at github.com  Sun Jul 25 15:06:25 2010
From: noreply at github.com (noreply at github.com)
Date: Sun, 25 Jul 2010 12:06:25 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 3a03b2: silence exception
	that happens with -y option
Message-ID: <20100725190625.B1D5842345@smtp1.rs.github.com>

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

Commit: 3a03b239d3cfcc1cf6b6d7828898186e6f797ae1
    http://github.com/bioperl/bioperl-live/commit/3a03b239d3cfcc1cf6b6d7828898186e6f797ae1
Author: John SJ Anderson <genehack at genehack.org>
Date:   2010-07-25 (Sun, 25 Jul 2010)

Changed paths:
  M scripts/Bio-DB-GFF/genbank2gff3.PLS

Log Message:
-----------
silence exception that happens with -y option



From noreply at github.com  Mon Jul 26 07:19:11 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 26 Jul 2010 04:19:11 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] f63896: added interval
	stats support to pg - untested
Message-ID: <20100726111911.E7701422E0@smtp1.rs.github.com>

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

Commit: f638961c340067ab44e9725cf240febb5999ed76
    http://github.com/bioperl/bioperl-live/commit/f638961c340067ab44e9725cf240febb5999ed76
Author: Lincoln Stein <lincoln.stein at gmail.com>
Date:   2010-07-26 (Mon, 26 Jul 2010)

Changed paths:
  M Bio/DB/SeqFeature/Store/DBI/Pg.pm

Log Message:
-----------
added interval stats support to pg - untested



From noreply at github.com  Mon Jul 26 17:36:44 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 26 Jul 2010 14:36:44 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] fb68a0: whitespace cleanup
	in WrapperBase.pm code
Message-ID: <20100726213644.82965422E4@smtp1.rs.github.com>

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

Commit: fb68a052cd5adfa5b6822a60545869535a3d01d0
    http://github.com/bioperl/bioperl-live/commit/fb68a052cd5adfa5b6822a60545869535a3d01d0
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-26 (Mon, 26 Jul 2010)

Changed paths:
  M Bio/Tools/Run/WrapperBase.pm

Log Message:
-----------
whitespace cleanup in WrapperBase.pm code



From noreply at github.com  Mon Jul 26 17:42:55 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 26 Jul 2010 14:42:55 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 3997d7: StandAloneBlast.t
	should allow different types of ...
Message-ID: <20100726214255.B35B4422C6@smtp1.rs.github.com>

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

Commit: 3997d706cd1b6b5526c5ece2c7974177a339c975
    http://github.com/bioperl/bioperl-live/commit/3997d706cd1b6b5526c5ece2c7974177a339c975
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-26 (Mon, 26 Jul 2010)

Changed paths:
  M t/Tools/Run/StandAloneBlast.t

Log Message:
-----------
StandAloneBlast.t should allow different types of quoting



From noreply at github.com  Mon Jul 26 18:32:00 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 26 Jul 2010 15:32:00 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 95f860: Add a failing test
	for <cite> elements in term def...
Message-ID: <20100726223200.90895422D5@smtp1.rs.github.com>

Branch: refs/heads/topic/leto_interpro_cite
Home:   http://github.com/bioperl/bioperl-live

Commit: 95f860a9b288bd88ed0a22e64a0b089d75059139
    http://github.com/bioperl/bioperl-live/commit/95f860a9b288bd88ed0a22e64a0b089d75059139
Author: Jonathan "Duke" Leto <jonathan at leto.net>
Date:   2010-07-26 (Mon, 26 Jul 2010)

Changed paths:
  M t/Ontology/IO/interpro.t

Log Message:
-----------
Add a failing test for <cite> elements in term definitions



From noreply at github.com  Mon Jul 26 19:53:15 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 26 Jul 2010 16:53:15 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] ffb03e: phiX174 sequence,
	for is_circular SF tests
Message-ID: <20100726235315.EDB9E422E1@smtp1.rs.github.com>

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

Commit: ffb03eb6fe094a1b72398ebe42bc9b8861513570
    http://github.com/bioperl/bioperl-live/commit/ffb03eb6fe094a1b72398ebe42bc9b8861513570
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-26 (Mon, 26 Jul 2010)

Changed paths:
  A t/data/PX1CG.gb

Log Message:
-----------
phiX174 sequence, for is_circular SF tests


Commit: 6213d4afc6b9d8341194a27bffc1d74fc135305e
    http://github.com/bioperl/bioperl-live/commit/6213d4afc6b9d8341194a27bffc1d74fc135305e
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-26 (Mon, 26 Jul 2010)

Changed paths:
  M Bio/SeqIO/genbank.pm

Log Message:
-----------
ss-DNA is legit



From noreply at github.com  Tue Jul 27 00:04:26 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 26 Jul 2010 21:04:26 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 589130: * add tests for
	circular sequences
Message-ID: <20100727040426.04703422E9@smtp1.rs.github.com>

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

Commit: 5891306ee783160e6bc8705b25f090add51f8a32
    http://github.com/bioperl/bioperl-live/commit/5891306ee783160e6bc8705b25f090add51f8a32
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-26 (Mon, 26 Jul 2010)

Changed paths:
  M t/SeqFeature/SeqFeature.t

Log Message:
-----------
* add tests for circular sequences
* Splicing, strandedness, round-trip of FT string work
* start, end, length are wrong



From noreply at github.com  Tue Jul 27 00:13:28 2010
From: noreply at github.com (noreply at github.com)
Date: Mon, 26 Jul 2010 21:13:28 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] ffb03e: phiX174 sequence,
	for is_circular SF tests
Message-ID: <20100727041328.D045A422C6@smtp1.rs.github.com>

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

Commit: ffb03eb6fe094a1b72398ebe42bc9b8861513570
    http://github.com/bioperl/bioperl-live/commit/ffb03eb6fe094a1b72398ebe42bc9b8861513570
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-26 (Mon, 26 Jul 2010)

Changed paths:
  A t/data/PX1CG.gb

Log Message:
-----------
phiX174 sequence, for is_circular SF tests


Commit: 6213d4afc6b9d8341194a27bffc1d74fc135305e
    http://github.com/bioperl/bioperl-live/commit/6213d4afc6b9d8341194a27bffc1d74fc135305e
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-26 (Mon, 26 Jul 2010)

Changed paths:
  M Bio/SeqIO/genbank.pm

Log Message:
-----------
ss-DNA is legit


Commit: 5891306ee783160e6bc8705b25f090add51f8a32
    http://github.com/bioperl/bioperl-live/commit/5891306ee783160e6bc8705b25f090add51f8a32
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-26 (Mon, 26 Jul 2010)

Changed paths:
  M t/SeqFeature/SeqFeature.t

Log Message:
-----------
* add tests for circular sequences
* Splicing, strandedness, round-trip of FT string work
* start, end, length are wrong



From noreply at github.com  Tue Jul 27 12:19:56 2010
From: noreply at github.com (noreply at github.com)
Date: Tue, 27 Jul 2010 09:19:56 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] d752a4: allow looping
	ranges for circular genomes. See Re...
Message-ID: <20100727161956.96E41422B6@smtp1.rs.github.com>

Branch: refs/heads/circular
Home:   http://github.com/bioperl/bioperl-live

Commit: d752a4cb5168d1bb01f8c80247a57f66b2bd9daf
    http://github.com/bioperl/bioperl-live/commit/d752a4cb5168d1bb01f8c80247a57f66b2bd9daf
Author: Chris Mungall <cjm at berkeleybop.org>
Date:   2010-07-27 (Tue, 27 Jul 2010)

Changed paths:
  M Bio/SeqFeature/Tools/Unflattener.pm

Log Message:
-----------
allow looping ranges for circular genomes. See  Re: [Gmod-ajax] flatfile-to-json.pl error with GFF



From noreply at github.com  Tue Jul 27 18:12:12 2010
From: noreply at github.com (noreply at github.com)
Date: Tue, 27 Jul 2010 15:12:12 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 6672d9: more informative
	err msf
Message-ID: <20100727221212.E0AFC422F0@smtp1.rs.github.com>

Branch: refs/heads/circular
Home:   http://github.com/bioperl/bioperl-live

Commit: 6672d91f12fbc8224a377ac6a5e11e10cf1f7c41
    http://github.com/bioperl/bioperl-live/commit/6672d91f12fbc8224a377ac6a5e11e10cf1f7c41
Author: Chris Mungall <cjm at berkeleybop.org>
Date:   2010-07-27 (Tue, 27 Jul 2010)

Changed paths:
  M Bio/SeqFeature/Tools/TypeMapper.pm

Log Message:
-----------
more informative err msf



From bugzilla-daemon at portal.open-bio.org  Wed Jul 28 09:05:16 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 28 Jul 2010 09:05:16 -0400
Subject: [Bioperl-guts-l] [Bug 3125] New: bioperl-run LVB.pm and LVB.t
	require updates for LVB version 2.3
Message-ID: <bug-3125-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3125

           Summary: bioperl-run LVB.pm and LVB.t require updates for LVB
                    version 2.3
           Product: BioPerl
           Version: main-trunk
          Platform: All
               URL: http://biology.st-andrews.ac.uk/cegg/lvb.aspx
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bioperl-run
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: db60 at st-andrews.ac.uk


The user interface to LVB has changed. From LVB 2.3, the user is no longer
asked whether the analysis should be 'fast' or 'slow'.

This change is not yet reflected in "lib/Bio/Tools/Run/Phylo/LVB.pm". The
DURATION parameter (and its action) should be removed. "t/LVB.t" will also
require minor change.

Would someone like to make these changes? I just tried to update things myself,
from trunk ("svn checkout http://svn.github.com/bioperl/bioperl-run.git").
However, even the previous version (LVB 2.2) fails tests, before I've modified
anything. Last time I looked - some years ago - LVB 2.2 passed all its tests.
Probably I'm doing something wrong.

Thank you very much,

Daniel


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From noreply at github.com  Wed Jul 28 12:33:30 2010
From: noreply at github.com (noreply at github.com)
Date: Wed, 28 Jul 2010 09:33:30 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 14cccb: fixed interval
	stats table for postgres--used with...
Message-ID: <20100728163330.63BEB422D1@smtp1.rs.github.com>

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

Commit: 14cccbb1c525cc60215f6a111824c4dd3f7df681
    http://github.com/bioperl/bioperl-live/commit/14cccbb1c525cc60215f6a111824c4dd3f7df681
Author: Scott Cain <scott+git at scottcain.net>
Date:   2010-07-28 (Wed, 28 Jul 2010)

Changed paths:
  M Bio/DB/SeqFeature/Store/DBI/Pg.pm

Log Message:
-----------
fixed interval stats table for postgres--used with GBrowse's summary view.



From bugzilla-daemon at portal.open-bio.org  Wed Jul 28 12:44:59 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 28 Jul 2010 12:44:59 -0400
Subject: [Bioperl-guts-l] [Bug 3126] New: description() method returns
	nothing in Bio::DB::Fasta
Message-ID: <bug-3126-25@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3126

           Summary: description() method returns nothing in Bio::DB::Fasta
           Product: BioPerl
           Version: unspecified
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bioperl-run
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: tab00547 at nifty.com


description() method of a Bio::Seq object generated through using 
Bio::DB:Fasta returns null:  the descriptions following the ID in the FASTA
header are not returned.  
I think this is caused by a bug in Bio/DB/Fasta.pm as indicated by the
following patch output:

--- Fasta.pm.org        2010-07-28 03:27:26.000000000 +0900
+++ Fasta.pm    2010-07-28 03:51:11.000000000 +0900
@@ -1146,7 +1146,7 @@
     my $self = shift;
     my $header = $self->{'db'}->header($self->{id});
     # remove the id from the header
-    return (split(/\s+/,$header,2))[2];
+    return (split(/\s+/,$header,2))[1];
 }

 *desc = \&description;


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From bugzilla-daemon at portal.open-bio.org  Wed Jul 28 12:48:05 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 28 Jul 2010 12:48:05 -0400
Subject: [Bioperl-guts-l] [Bug 3126] description() method returns nothing in
	Bio::DB::Fasta
In-Reply-To: <bug-3126-25@http.bugzilla.open-bio.org/>
Message-ID: <201007281648.o6SGm5Qi019581@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3126





------- Comment #1 from tab00547 at nifty.com  2010-07-28 12:48 EST -------
Created an attachment (id=1531)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1531&action=view)
proposed patch for Bio/DB/Fasta.pm


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From noreply at github.com  Thu Jul 29 07:10:00 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 29 Jul 2010 04:10:00 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 6ded08: Fixed sql syntax
	error in creation of interval_sta...
Message-ID: <20100729110959.F15294230E@smtp1.rs.github.com>

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

Commit: 6ded0828bff9c9eb891515f5449e5014232891f9
    http://github.com/bioperl/bioperl-live/commit/6ded0828bff9c9eb891515f5449e5014232891f9
Author: Lincoln Stein <lincoln.stein at gmail.com>
Date:   2010-07-28 (Wed, 28 Jul 2010)

Changed paths:
  M Bio/DB/SeqFeature/Store/DBI/Pg.pm

Log Message:
-----------
Fixed sql syntax error in creation of interval_stats table


Commit: 2faecfaa45a0f4cf01dea536a20df63e3a13e6a9
    http://github.com/bioperl/bioperl-live/commit/2faecfaa45a0f4cf01dea536a20df63e3a13e6a9
Author: Lincoln Stein <lincoln.stein at gmail.com>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M Bio/DB/SeqFeature/Store/DBI/Pg.pm
  M Bio/SeqIO/genbank.pm
  M Bio/Tools/Run/WrapperBase.pm
  M t/SeqFeature/SeqFeature.t
  M t/Tools/Run/StandAloneBlast.t
  A t/data/PX1CG.gb

Log Message:
-----------
merge



From noreply at github.com  Thu Jul 29 11:26:24 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 29 Jul 2010 08:26:24 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 34a985: fixed a problem
	where the loader tried to create t...
Message-ID: <20100729152624.317B7422E5@smtp1.rs.github.com>

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

Commit: 34a985742749d581c6377dc5e3e0abea20965f40
    http://github.com/bioperl/bioperl-live/commit/34a985742749d581c6377dc5e3e0abea20965f40
Author: Scott Cain <scott+git at scottcain.net>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M Bio/DB/SeqFeature/Store/DBI/Pg.pm

Log Message:
-----------
fixed a problem where the loader tried to create the summary stats table twice



From noreply at github.com  Thu Jul 29 14:08:21 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 29 Jul 2010 11:08:21 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] a3ee8b: Introspect feature
	objects and call apporpriate GF...
Message-ID: <20100729180821.C3FCC4234E@smtp1.rs.github.com>

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

Commit: a3ee8b9c7dfb10b3601cfc8f0d851287832efdb1
    http://github.com/bioperl/bioperl-live/commit/a3ee8b9c7dfb10b3601cfc8f0d851287832efdb1
Author: John SJ Anderson <genehack at genehack.org>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS

Log Message:
-----------
Introspect feature objects and call apporpriate GFF output method

Depending on how the database was built, next_seq() may return
something that supports gff3_string() or someting that supports
gff_string(). Introspect on the feature object to figure out which of
these two methods are supported, and call the appropriate one:
gff3_string() if it exists, gff_string() otherwise.

If neither method exists on the feature object, thrown an exception
with a stack trace.


Commit: f63c4dba999c88f9481be9f173cb7c3005236329
    http://github.com/bioperl/bioperl-live/commit/f63c4dba999c88f9481be9f173cb7c3005236329
Author: John SJ Anderson <genehack at genehack.org>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M Bio/DB/SeqFeature/Store/DBI/mysql.pm

Log Message:
-----------
Expand how sequence features are rebuilt when objects are _NOT_ stored in the database

When an object is being rebuilt by _rebuild_object(), if we don't have all of:

  * start
  * end
  * typeid
  * db_seqid
  * strand

then pull that information out of the database and override any
missing information when instantiating the new object.



From noreply at github.com  Thu Jul 29 16:40:21 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 29 Jul 2010 13:40:21 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 40eb18: Merge branch
	'master' into branch-1-6
Message-ID: <20100729204021.3D9B04230E@smtp1.rs.github.com>

Branch: refs/heads/branch-1-6
Home:   http://github.com/bioperl/bioperl-live

Commit: 40eb18fe391c64d3ddbc4491c55e425c83f51eda
    http://github.com/bioperl/bioperl-live/commit/40eb18fe391c64d3ddbc4491c55e425c83f51eda
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M Bio/DB/SeqFeature/Store/DBI/Pg.pm
  M Bio/DB/SeqFeature/Store/DBI/mysql.pm
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
  M t/SeqFeature/SeqFeature.t

Log Message:
-----------
Merge branch 'master' into branch-1-6



From noreply at github.com  Thu Jul 29 16:51:05 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 29 Jul 2010 13:51:05 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 4b125a: first alpha
Message-ID: <20100729205105.9E30142317@smtp1.rs.github.com>

Branch: refs/heads/branch-1-6
Home:   http://github.com/bioperl/bioperl-live

Commit: 4b125a50afb8319f13a0839e73e29bf3741999ff
    http://github.com/bioperl/bioperl-live/commit/4b125a50afb8319f13a0839e73e29bf3741999ff
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-29 (Thu, 29 Jul 2010)

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

Log Message:
-----------
first alpha



From noreply at github.com  Thu Jul 29 17:26:16 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 29 Jul 2010 14:26:16 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] f69a78: domain flag borking
	the request; fix courtesy John...
Message-ID: <20100729212616.5A1E04234F@smtp1.rs.github.com>

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

Commit: f69a78932e59f5810aaebf7cbefa500ccc714dbd
    http://github.com/bioperl/bioperl-live/commit/f69a78932e59f5810aaebf7cbefa500ccc714dbd
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M Bio/Tools/Analysis/Protein/Scansite.pm

Log Message:
-----------
domain flag borking the request; fix courtesy John Obenauer



From noreply at github.com  Thu Jul 29 17:28:04 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 29 Jul 2010 14:28:04 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] a6d919: strip keyword
	substitution from perl modules
Message-ID: <20100729212804.402544234F@smtp1.rs.github.com>

Branch: refs/heads/topic/strip_vc_interp_tags
Home:   http://github.com/bioperl/bioperl-live

Commit: a6d919137717e7178ae8d1624c283adcdc23b6db
    http://github.com/bioperl/bioperl-live/commit/a6d919137717e7178ae8d1624c283adcdc23b6db
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M Bio/Align/AlignI.pm
  M Bio/Align/DNAStatistics.pm
  M Bio/Align/PairwiseStatistics.pm
  M Bio/Align/ProteinStatistics.pm
  M Bio/Align/StatisticsI.pm
  M Bio/Align/Utilities.pm
  M Bio/AlignIO.pm
  M Bio/AlignIO/arp.pm
  M Bio/AlignIO/bl2seq.pm
  M Bio/AlignIO/clustalw.pm
  M Bio/AlignIO/emboss.pm
  M Bio/AlignIO/fasta.pm
  M Bio/AlignIO/maf.pm
  M Bio/AlignIO/mase.pm
  M Bio/AlignIO/mega.pm
  M Bio/AlignIO/meme.pm
  M Bio/AlignIO/metafasta.pm
  M Bio/AlignIO/msf.pm
  M Bio/AlignIO/nexml.pm
  M Bio/AlignIO/nexus.pm
  M Bio/AlignIO/pfam.pm
  M Bio/AlignIO/phylip.pm
  M Bio/AlignIO/proda.pm
  M Bio/AlignIO/prodom.pm
  M Bio/AlignIO/psi.pm
  M Bio/AlignIO/selex.pm
  M Bio/AlignIO/stockholm.pm
  M Bio/AlignIO/xmfa.pm
  M Bio/AnalysisI.pm
  M Bio/AnalysisParserI.pm
  M Bio/AnalysisResultI.pm
  M Bio/AnnotatableI.pm
  M Bio/Annotation/AnnotationFactory.pm
  M Bio/Annotation/Collection.pm
  M Bio/Annotation/Comment.pm
  M Bio/Annotation/DBLink.pm
  M Bio/Annotation/OntologyTerm.pm
  M Bio/Annotation/Reference.pm
  M Bio/Annotation/SimpleValue.pm
  M Bio/Annotation/StructuredValue.pm
  M Bio/Annotation/Target.pm
  M Bio/Annotation/TypeManager.pm
  M Bio/AnnotationCollectionI.pm
  M Bio/AnnotationI.pm
  M Bio/Assembly/Contig.pm
  M Bio/Assembly/ContigAnalysis.pm
  M Bio/Assembly/IO/bowtie.pm
  M Bio/Assembly/IO/maq.pm
  M Bio/Assembly/IO/phrap.pm
  M Bio/Assembly/IO/sam.pm
  M Bio/Assembly/IO/tigr.pm
  M Bio/Assembly/Scaffold.pm
  M Bio/Assembly/ScaffoldI.pm
  M Bio/Assembly/Singlet.pm
  M Bio/Biblio.pm
  M Bio/Biblio/Article.pm
  M Bio/Biblio/BiblioBase.pm
  M Bio/Biblio/Book.pm
  M Bio/Biblio/BookArticle.pm
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  M Bio/Tools/Prediction/Exon.pm
  M Bio/Tools/Prediction/Gene.pm
  M Bio/Tools/Primer/Assessor/Base.pm
  M Bio/Tools/Primer/AssessorI.pm
  M Bio/Tools/Primer/Feature.pm
  M Bio/Tools/Primer/Pair.pm
  M Bio/Tools/Primer3.pm
  M Bio/Tools/Prints.pm
  M Bio/Tools/Profile.pm
  M Bio/Tools/Promoterwise.pm
  M Bio/Tools/Protparam.pm
  M Bio/Tools/Pseudowise.pm
  M Bio/Tools/QRNA.pm
  M Bio/Tools/RNAMotif.pm
  M Bio/Tools/RandomDistFunctions.pm
  M Bio/Tools/RepeatMasker.pm
  M Bio/Tools/Run/GenericParameters.pm
  M Bio/Tools/Run/ParametersI.pm
  M Bio/Tools/Run/RemoteBlast.pm
  M Bio/Tools/Run/StandAloneBlast.pm
  M Bio/Tools/Run/StandAloneNCBIBlast.pm
  M Bio/Tools/Run/StandAloneWUBlast.pm
  M Bio/Tools/Run/WrapperBase.pm
  M Bio/Tools/Run/WrapperBase/CommandExts.pm
  M Bio/Tools/Seg.pm
  M Bio/Tools/SeqPattern.pm
  M Bio/Tools/SeqStats.pm
  M Bio/Tools/SeqWords.pm
  M Bio/Tools/SiRNA.pm
  M Bio/Tools/Sigcleave.pm
  M Bio/Tools/Signalp.pm
  M Bio/Tools/Signalp/ExtendedSignalp.pm
  M Bio/Tools/Sim4/Exon.pm
  M Bio/Tools/Sim4/Results.pm
  M Bio/Tools/Spidey/Exon.pm
  M Bio/Tools/Spidey/Results.pm
  M Bio/Tools/TargetP.pm
  M Bio/Tools/Tmhmm.pm
  M Bio/Tools/dpAlign.pm
  M Bio/Tools/ipcress.pm
  M Bio/Tools/isPcr.pm
  M Bio/Tools/pICalculator.pm
  M Bio/Tools/pSW.pm
  M Bio/Tools/tRNAscanSE.pm
  M Bio/Tree/AlleleNode.pm
  M Bio/Tree/Compatible.pm
  M Bio/Tree/DistanceFactory.pm
  M Bio/Tree/Draw/Cladogram.pm
  M Bio/Tree/Node.pm
  M Bio/Tree/NodeI.pm
  M Bio/Tree/NodeNHX.pm
  M Bio/Tree/RandomFactory.pm
  M Bio/Tree/Statistics.pm
  M Bio/Tree/Tree.pm
  M Bio/Tree/TreeFunctionsI.pm
  M Bio/Tree/TreeI.pm
  M Bio/TreeIO.pm
  M Bio/TreeIO/TreeEventBuilder.pm
  M Bio/TreeIO/cluster.pm
  M Bio/TreeIO/lintree.pm
  M Bio/TreeIO/newick.pm
  M Bio/TreeIO/nexml.pm
  M Bio/TreeIO/nexus.pm
  M Bio/TreeIO/nhx.pm
  M Bio/TreeIO/pag.pm
  M Bio/TreeIO/tabtree.pm
  M Bio/UpdateableSeqI.pm
  M Bio/Variation/AAChange.pm
  M Bio/Variation/AAReverseMutate.pm
  M Bio/Variation/Allele.pm
  M Bio/Variation/DNAMutation.pm
  M Bio/Variation/IO.pm
  M Bio/Variation/IO/flat.pm
  M Bio/Variation/IO/xml.pm
  M Bio/Variation/RNAChange.pm
  M Bio/Variation/SNP.pm
  M Bio/Variation/SeqDiff.pm
  M Bio/Variation/VariantI.pm
  M Bio/WebAgent.pm
  M t/lib/Array/Compare.pm

Log Message:
-----------
strip keyword substitution from perl modules


Commit: ebe37d53b211768b08bca23b4a94248f767ae597
    http://github.com/bioperl/bioperl-live/commit/ebe37d53b211768b08bca23b4a94248f767ae597
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M examples/align/aligntutorial.pl
  M examples/align/clustalw.pl
  M examples/align/simplealign.pl
  M examples/biblio/biblio-eutils-example.pl
  M examples/biblio/biblio-soap-example.pl
  M examples/contributed/nmrpdb_parse.pl
  M examples/contributed/prosite2perl.pl
  M examples/liveseq/change_gene.pl
  M examples/make_primers.pl
  M examples/popgen/parse_calc_stats.pl
  M examples/rev_and_trans.pl
  M examples/root/exceptions1.pl
  M examples/root/exceptions2.pl
  M examples/root/exceptions3.pl
  M examples/root/exceptions4.pl
  M examples/searchio/custom_writer.pl
  M examples/searchio/hitwriter.pl
  M examples/searchio/hspwriter.pl
  M examples/searchio/htmlwriter.pl
  M examples/searchio/psiblast_features.pl
  M examples/searchio/psiblast_iterations.pl
  M examples/searchio/rawwriter.pl
  M examples/searchio/resultwriter.pl
  M examples/tools/extract_genes.pl
  M examples/tools/psw.pl
  M examples/tools/reverse-translate.pl
  M examples/tools/run_primer3.pl
  M examples/tools/seq_pattern.pl
  M examples/tools/standaloneblast.pl
  M maintenance/authors.pl
  M maintenance/cvs2cl_by_file.pl
  M maintenance/modules.pl
  M maintenance/pod.pl
  M maintenance/version.pl
  M scripts/Bio-DB-GFF/bulk_load_gff.PLS
  M scripts/Bio-DB-GFF/fast_load_gff.PLS
  M scripts/Bio-DB-GFF/genbank2gff.PLS
  M scripts/Bio-DB-GFF/generate_histogram.PLS
  M scripts/Bio-DB-GFF/process_sgd.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
  M scripts/DB/biofetch_genbank_proxy.PLS
  M scripts/DB/biogetseq.PLS
  M scripts/DB/flanks.PLS
  M scripts/biblio/biblio.PLS
  M scripts/das/das_server.pl
  M scripts/index/bp_seqret.PLS
  M scripts/popgen/composite_LD.PLS
  M scripts/popgen/heterogeneity_test.PLS
  M scripts/searchio/filter_search.PLS
  M scripts/searchio/parse_hmmsearch.PLS
  M scripts/seq/extract_feature_seq.PLS
  M scripts/seq/make_mrna_protein.PLS
  M scripts/seq/seqconvert.PLS
  M scripts/seq/seqretsplit.PLS
  M scripts/seq/split_seq.PLS
  M scripts/seq/translate_seq.PLS
  M scripts/seq/unflatten_seq.PLS
  M scripts/seqstats/aacomp.PLS
  M scripts/seqstats/chaos_plot.PLS
  M scripts/seqstats/gccalc.PLS
  M scripts/seqstats/oligo_count.PLS
  M scripts/taxa/classify_hits_kingdom.PLS
  M scripts/utilities/bp_mrtrans.PLS
  M scripts/utilities/bp_nrdb.PLS
  M scripts/utilities/mask_by_search.PLS
  M scripts/utilities/pairwise_kaks.PLS
  M scripts/utilities/remote_blast.PLS
  M scripts/utilities/revtrans-motif.PLS
  M scripts/utilities/search2BSML.PLS
  M scripts/utilities/search2alnblocks.PLS
  M scripts/utilities/search2gff.PLS
  M scripts/utilities/search2tribe.PLS

Log Message:
-----------
strip keyword substitution from perl scripts



From noreply at github.com  Thu Jul 29 17:51:38 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 29 Jul 2010 14:51:38 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 1d4985: strip keyword
	substitution from perl modules
Message-ID: <20100729215138.D7E5042177@smtp1.rs.github.com>

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

Commit: 1d4985cf8a721df8db3db8381b7c810cf0d328dc
    http://github.com/bioperl/bioperl-live/commit/1d4985cf8a721df8db3db8381b7c810cf0d328dc
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M Bio/Align/AlignI.pm
  M Bio/Align/DNAStatistics.pm
  M Bio/Align/PairwiseStatistics.pm
  M Bio/Align/ProteinStatistics.pm
  M Bio/Align/StatisticsI.pm
  M Bio/Align/Utilities.pm
  M Bio/AlignIO.pm
  M Bio/AlignIO/arp.pm
  M Bio/AlignIO/bl2seq.pm
  M Bio/AlignIO/clustalw.pm
  M Bio/AlignIO/emboss.pm
  M Bio/AlignIO/fasta.pm
  M Bio/AlignIO/maf.pm
  M Bio/AlignIO/mase.pm
  M Bio/AlignIO/mega.pm
  M Bio/AlignIO/meme.pm
  M Bio/AlignIO/metafasta.pm
  M Bio/AlignIO/msf.pm
  M Bio/AlignIO/nexml.pm
  M Bio/AlignIO/nexus.pm
  M Bio/AlignIO/pfam.pm
  M Bio/AlignIO/phylip.pm
  M Bio/AlignIO/proda.pm
  M Bio/AlignIO/prodom.pm
  M Bio/AlignIO/psi.pm
  M Bio/AlignIO/selex.pm
  M Bio/AlignIO/stockholm.pm
  M Bio/AlignIO/xmfa.pm
  M Bio/AnalysisI.pm
  M Bio/AnalysisParserI.pm
  M Bio/AnalysisResultI.pm
  M Bio/AnnotatableI.pm
  M Bio/Annotation/AnnotationFactory.pm
  M Bio/Annotation/Collection.pm
  M Bio/Annotation/Comment.pm
  M Bio/Annotation/DBLink.pm
  M Bio/Annotation/OntologyTerm.pm
  M Bio/Annotation/Reference.pm
  M Bio/Annotation/SimpleValue.pm
  M Bio/Annotation/StructuredValue.pm
  M Bio/Annotation/Target.pm
  M Bio/Annotation/TypeManager.pm
  M Bio/AnnotationCollectionI.pm
  M Bio/AnnotationI.pm
  M Bio/Assembly/Contig.pm
  M Bio/Assembly/ContigAnalysis.pm
  M Bio/Assembly/IO/bowtie.pm
  M Bio/Assembly/IO/maq.pm
  M Bio/Assembly/IO/phrap.pm
  M Bio/Assembly/IO/sam.pm
  M Bio/Assembly/IO/tigr.pm
  M Bio/Assembly/Scaffold.pm
  M Bio/Assembly/ScaffoldI.pm
  M Bio/Assembly/Singlet.pm
  M Bio/Biblio.pm
  M Bio/Biblio/Article.pm
  M Bio/Biblio/BiblioBase.pm
  M Bio/Biblio/Book.pm
  M Bio/Biblio/BookArticle.pm
  M Bio/Biblio/IO.pm
  M Bio/Biblio/IO/medline2ref.pm
  M Bio/Biblio/IO/medlinexml.pm
  M Bio/Biblio/IO/pubmed2ref.pm
  M Bio/Biblio/IO/pubmedxml.pm
  M Bio/Biblio/Journal.pm
  M Bio/Biblio/JournalArticle.pm
  M Bio/Biblio/MedlineArticle.pm
  M Bio/Biblio/MedlineBook.pm
  M Bio/Biblio/MedlineBookArticle.pm
  M Bio/Biblio/MedlineJournal.pm
  M Bio/Biblio/MedlineJournalArticle.pm
  M Bio/Biblio/Organisation.pm
  M Bio/Biblio/Patent.pm
  M Bio/Biblio/Person.pm
  M Bio/Biblio/Proceeding.pm
  M Bio/Biblio/Provider.pm
  M Bio/Biblio/PubmedArticle.pm
  M Bio/Biblio/PubmedBookArticle.pm
  M Bio/Biblio/PubmedJournalArticle.pm
  M Bio/Biblio/Ref.pm
  M Bio/Biblio/Service.pm
  M Bio/Biblio/TechReport.pm
  M Bio/Biblio/Thesis.pm
  M Bio/Biblio/WebResource.pm
  M Bio/Cluster/ClusterFactory.pm
  M Bio/Cluster/SequenceFamily.pm
  M Bio/Cluster/UniGene.pm
  M Bio/Cluster/UniGeneI.pm
  M Bio/ClusterI.pm
  M Bio/ClusterIO.pm
  M Bio/ClusterIO/dbsnp.pm
  M Bio/ClusterIO/unigene.pm
  M Bio/CodonUsage/IO.pm
  M Bio/CodonUsage/Table.pm
  M Bio/Coordinate/Chain.pm
  M Bio/Coordinate/Collection.pm
  M Bio/Coordinate/ExtrapolatingPair.pm
  M Bio/Coordinate/GeneMapper.pm
  M Bio/Coordinate/Graph.pm
  M Bio/Coordinate/MapperI.pm
  M Bio/Coordinate/Pair.pm
  M Bio/Coordinate/Result.pm
  M Bio/Coordinate/Result/Gap.pm
  M Bio/Coordinate/Result/Match.pm
  M Bio/Coordinate/ResultI.pm
  M Bio/Coordinate/Utils.pm
  M Bio/DB/Ace.pm
  M Bio/DB/Biblio/biofetch.pm
  M Bio/DB/Biblio/eutils.pm
  M Bio/DB/Biblio/soap.pm
  M Bio/DB/BiblioI.pm
  M Bio/DB/BioFetch.pm
  M Bio/DB/CUTG.pm
  M Bio/DB/DBFetch.pm
  M Bio/DB/EMBL.pm
  M Bio/DB/EUtilities.pm
  M Bio/DB/EntrezGene.pm
  M Bio/DB/Expression.pm
  M Bio/DB/Failover.pm
  M Bio/DB/Fasta.pm
  M Bio/DB/FileCache.pm
  M Bio/DB/Flat.pm
  M Bio/DB/Flat/BDB.pm
  M Bio/DB/Flat/BDB/embl.pm
  M Bio/DB/Flat/BDB/fasta.pm
  M Bio/DB/Flat/BDB/genbank.pm
  M Bio/DB/Flat/BDB/swiss.pm
  M Bio/DB/Flat/BinarySearch.pm
  M Bio/DB/GFF.pm
  M Bio/DB/GFF/Adaptor/berkeleydb.pm
  M Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
  M Bio/DB/GFF/Adaptor/dbi.pm
  M Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
  M Bio/DB/GFF/Adaptor/memory.pm
  M Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
  M Bio/DB/GFF/Adaptor/memory/iterator.pm
  M Bio/DB/GenBank.pm
  M Bio/DB/GenPept.pm
  M Bio/DB/GenericWebAgent.pm
  M Bio/DB/InMemoryCache.pm
  M Bio/DB/LocationI.pm
  M Bio/DB/MeSH.pm
  M Bio/DB/NCBIHelper.pm
  M Bio/DB/Qual.pm
  M Bio/DB/Query/GenBank.pm
  M Bio/DB/Query/WebQuery.pm
  M Bio/DB/QueryI.pm
  M Bio/DB/RandomAccessI.pm
  M Bio/DB/RefSeq.pm
  M Bio/DB/ReferenceI.pm
  M Bio/DB/Registry.pm
  M Bio/DB/SeqFeature.pm
  M Bio/DB/SeqFeature/NormalizedFeature.pm
  M Bio/DB/SeqFeature/NormalizedFeatureI.pm
  M Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
  M Bio/DB/SeqFeature/Segment.pm
  M Bio/DB/SeqFeature/Store.pm
  M Bio/DB/SeqFeature/Store/DBI/Iterator.pm
  M Bio/DB/SeqFeature/Store/DBI/mysql.pm
  M Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
  M Bio/DB/SeqFeature/Store/GFF3Loader.pm
  M Bio/DB/SeqFeature/Store/LoadHelper.pm
  M Bio/DB/SeqFeature/Store/Loader.pm
  M Bio/DB/SeqFeature/Store/bdb.pm
  M Bio/DB/SeqFeature/Store/berkeleydb.pm
  M Bio/DB/SeqFeature/Store/memory.pm
  M Bio/DB/SeqI.pm
  M Bio/DB/SeqVersion.pm
  M Bio/DB/SeqVersion/gi.pm
  M Bio/DB/SwissProt.pm
  M Bio/DB/Taxonomy.pm
  M Bio/DB/Taxonomy/entrez.pm
  M Bio/DB/Taxonomy/flatfile.pm
  M Bio/DB/Taxonomy/list.pm
  M Bio/DB/UpdateableSeqI.pm
  M Bio/DB/WebDBSeqI.pm
  M Bio/DBLinkContainerI.pm
  M Bio/Das/FeatureTypeI.pm
  M Bio/Das/SegmentI.pm
  M Bio/DasI.pm
  M Bio/DescribableI.pm
  M Bio/Event/EventGeneratorI.pm
  M Bio/Event/EventHandlerI.pm
  M Bio/Factory/AnalysisI.pm
  M Bio/Factory/ApplicationFactoryI.pm
  M Bio/Factory/DriverFactory.pm
  M Bio/Factory/FTLocationFactory.pm
  M Bio/Factory/LocationFactoryI.pm
  M Bio/Factory/MapFactoryI.pm
  M Bio/Factory/ObjectBuilderI.pm
  M Bio/Factory/ObjectFactory.pm
  M Bio/Factory/ObjectFactoryI.pm
  M Bio/Factory/SeqAnalysisParserFactory.pm
  M Bio/Factory/SeqAnalysisParserFactoryI.pm
  M Bio/Factory/SequenceFactoryI.pm
  M Bio/Factory/SequenceProcessorI.pm
  M Bio/Factory/SequenceStreamI.pm
  M Bio/Factory/TreeFactoryI.pm
  M Bio/FeatureHolderI.pm
  M Bio/FeatureIO.pm
  M Bio/FeatureIO/gtf.pm
  M Bio/HandlerBaseI.pm
  M Bio/IdCollectionI.pm
  M Bio/IdentifiableI.pm
  M Bio/Index/Abstract.pm
  M Bio/Index/AbstractSeq.pm
  M Bio/Index/Blast.pm
  M Bio/Index/BlastTable.pm
  M Bio/Index/EMBL.pm
  M Bio/Index/Fasta.pm
  M Bio/Index/GenBank.pm
  M Bio/Index/Qual.pm
  M Bio/Index/Stockholm.pm
  M Bio/Index/SwissPfam.pm
  M Bio/Index/Swissprot.pm
  M Bio/LiveSeq/AARange.pm
  M Bio/LiveSeq/Chain.pm
  M Bio/LiveSeq/ChainI.pm
  M Bio/LiveSeq/DNA.pm
  M Bio/LiveSeq/Exon.pm
  M Bio/LiveSeq/Gene.pm
  M Bio/LiveSeq/IO/BioPerl.pm
  M Bio/LiveSeq/IO/Loader.pm
  M Bio/LiveSeq/Intron.pm
  M Bio/LiveSeq/Mutation.pm
  M Bio/LiveSeq/Mutator.pm
  M Bio/LiveSeq/Prim_Transcript.pm
  M Bio/LiveSeq/Range.pm
  M Bio/LiveSeq/Repeat_Region.pm
  M Bio/LiveSeq/Repeat_Unit.pm
  M Bio/LiveSeq/SeqI.pm
  M Bio/LiveSeq/Transcript.pm
  M Bio/LiveSeq/Translation.pm
  M Bio/LocatableSeq.pm
  M Bio/Location/Atomic.pm
  M Bio/Location/AvWithinCoordPolicy.pm
  M Bio/Location/CoordinatePolicyI.pm
  M Bio/Location/Fuzzy.pm
  M Bio/Location/FuzzyLocationI.pm
  M Bio/Location/NarrowestCoordPolicy.pm
  M Bio/Location/Simple.pm
  M Bio/Location/Split.pm
  M Bio/Location/SplitLocationI.pm
  M Bio/Location/WidestCoordPolicy.pm
  M Bio/LocationI.pm
  M Bio/Map/Clone.pm
  M Bio/Map/Contig.pm
  M Bio/Map/CytoMap.pm
  M Bio/Map/CytoMarker.pm
  M Bio/Map/CytoPosition.pm
  M Bio/Map/EntityI.pm
  M Bio/Map/FPCMarker.pm
  M Bio/Map/MapI.pm
  M Bio/Map/Mappable.pm
  M Bio/Map/MappableI.pm
  M Bio/Map/Marker.pm
  M Bio/Map/MarkerI.pm
  M Bio/Map/Physical.pm
  M Bio/Map/Position.pm
  M Bio/Map/PositionHandler.pm
  M Bio/Map/PositionHandlerI.pm
  M Bio/Map/PositionI.pm
  M Bio/Map/Relative.pm
  M Bio/Map/RelativeI.pm
  M Bio/Map/SimpleMap.pm
  M Bio/MapIO.pm
  M Bio/MapIO/mapmaker.pm
  M Bio/Matrix/Generic.pm
  M Bio/Matrix/IO.pm
  M Bio/Matrix/IO/mlagan.pm
  M Bio/Matrix/IO/phylip.pm
  M Bio/Matrix/IO/scoring.pm
  M Bio/Matrix/Mlagan.pm
  M Bio/Matrix/PSM/IO.pm
  M Bio/Matrix/PSM/IO/mast.pm
  M Bio/Matrix/PSM/IO/masta.pm
  M Bio/Matrix/PSM/IO/meme.pm
  M Bio/Matrix/PSM/IO/psiblast.pm
  M Bio/Matrix/PSM/IO/transfac.pm
  M Bio/Matrix/PSM/InstanceSite.pm
  M Bio/Matrix/PSM/InstanceSiteI.pm
  M Bio/Matrix/PSM/ProtMatrix.pm
  M Bio/Matrix/PSM/ProtPsm.pm
  M Bio/Matrix/PSM/Psm.pm
  M Bio/Matrix/PSM/PsmHeader.pm
  M Bio/Matrix/PSM/PsmHeaderI.pm
  M Bio/Matrix/PSM/PsmI.pm
  M Bio/Matrix/PSM/SiteMatrix.pm
  M Bio/Matrix/PSM/SiteMatrixI.pm
  M Bio/Matrix/PhylipDist.pm
  M Bio/Matrix/Scoring.pm
  M Bio/MolEvol/CodonModel.pm
  M Bio/Ontology/DocumentRegistry.pm
  M Bio/Ontology/GOterm.pm
  M Bio/Ontology/InterProTerm.pm
  M Bio/Ontology/OBOEngine.pm
  M Bio/Ontology/OBOterm.pm
  M Bio/Ontology/Ontology.pm
  M Bio/Ontology/OntologyEngineI.pm
  M Bio/Ontology/OntologyI.pm
  M Bio/Ontology/OntologyStore.pm
  M Bio/Ontology/Path.pm
  M Bio/Ontology/PathI.pm
  M Bio/Ontology/Relationship.pm
  M Bio/Ontology/RelationshipFactory.pm
  M Bio/Ontology/RelationshipI.pm
  M Bio/Ontology/RelationshipType.pm
  M Bio/Ontology/SimpleOntologyEngine.pm
  M Bio/Ontology/Term.pm
  M Bio/Ontology/TermFactory.pm
  M Bio/Ontology/TermI.pm
  M Bio/OntologyIO.pm
  M Bio/OntologyIO/Handlers/BaseSAXHandler.pm
  M Bio/OntologyIO/Handlers/InterProHandler.pm
  M Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
  M Bio/OntologyIO/InterProParser.pm
  M Bio/OntologyIO/dagflat.pm
  M Bio/OntologyIO/goflat.pm
  M Bio/OntologyIO/obo.pm
  M Bio/OntologyIO/simplehierarchy.pm
  M Bio/OntologyIO/soflat.pm
  M Bio/ParameterBaseI.pm
  M Bio/Perl.pm
  M Bio/Phenotype/Correlate.pm
  M Bio/Phenotype/MeSH/Term.pm
  M Bio/Phenotype/MeSH/Twig.pm
  M Bio/Phenotype/Measure.pm
  M Bio/Phenotype/OMIM/MiniMIMentry.pm
  M Bio/Phenotype/OMIM/OMIMentry.pm
  M Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
  M Bio/Phenotype/OMIM/OMIMparser.pm
  M Bio/Phenotype/Phenotype.pm
  M Bio/Phenotype/PhenotypeI.pm
  M Bio/PhyloNetwork.pm
  M Bio/PhyloNetwork/Factory.pm
  M Bio/PhyloNetwork/FactoryX.pm
  M Bio/PhyloNetwork/GraphViz.pm
  M Bio/PhyloNetwork/RandomFactory.pm
  M Bio/PhyloNetwork/TreeFactory.pm
  M Bio/PhyloNetwork/TreeFactoryMulti.pm
  M Bio/PhyloNetwork/TreeFactoryX.pm
  M Bio/PhyloNetwork/muVector.pm
  M Bio/PopGen/Genotype.pm
  M Bio/PopGen/IO.pm
  M Bio/PopGen/IO/csv.pm
  M Bio/PopGen/IO/hapmap.pm
  M Bio/PopGen/IO/phase.pm
  M Bio/PopGen/IO/prettybase.pm
  M Bio/PopGen/Individual.pm
  M Bio/PopGen/Marker.pm
  M Bio/PopGen/PopStats.pm
  M Bio/PopGen/Population.pm
  M Bio/PopGen/PopulationI.pm
  M Bio/PopGen/Simulation/Coalescent.pm
  M Bio/PopGen/Simulation/GeneticDrift.pm
  M Bio/PopGen/Statistics.pm
  M Bio/PopGen/Utilities.pm
  M Bio/PrimarySeq.pm
  M Bio/PrimarySeqI.pm
  M Bio/PullParserI.pm
  M Bio/Range.pm
  M Bio/RangeI.pm
  M Bio/Restriction/Analysis.pm
  M Bio/Restriction/Enzyme.pm
  M Bio/Restriction/Enzyme/MultiCut.pm
  M Bio/Restriction/Enzyme/MultiSite.pm
  M Bio/Restriction/EnzymeCollection.pm
  M Bio/Restriction/EnzymeI.pm
  M Bio/Restriction/IO.pm
  M Bio/Restriction/IO/bairoch.pm
  M Bio/Restriction/IO/base.pm
  M Bio/Restriction/IO/itype2.pm
  M Bio/Restriction/IO/prototype.pm
  M Bio/Restriction/IO/withrefm.pm
  M Bio/Root/Build.pm
  M Bio/Root/Exception.pm
  M Bio/Root/HTTPget.pm
  M Bio/Root/IO.pm
  M Bio/Root/Root.pm
  M Bio/Root/RootI.pm
  M Bio/Root/Storable.pm
  M Bio/Root/Test.pm
  M Bio/Root/Test/Warn.pm
  M Bio/Root/Utilities.pm
  M Bio/Root/Version.pm
  M Bio/Search/DatabaseI.pm
  M Bio/Search/GenericDatabase.pm
  M Bio/Search/HSP/BlastHSP.pm
  M Bio/Search/HSP/BlastPullHSP.pm
  M Bio/Search/HSP/FastaHSP.pm
  M Bio/Search/HSP/GenericHSP.pm
  M Bio/Search/HSP/HMMERHSP.pm
  M Bio/Search/HSP/HSPFactory.pm
  M Bio/Search/HSP/HSPI.pm
  M Bio/Search/HSP/HmmpfamHSP.pm
  M Bio/Search/HSP/ModelHSP.pm
  M Bio/Search/HSP/PSLHSP.pm
  M Bio/Search/HSP/PsiBlastHSP.pm
  M Bio/Search/HSP/PullHSPI.pm
  M Bio/Search/HSP/WABAHSP.pm
  M Bio/Search/Hit/BlastHit.pm
  M Bio/Search/Hit/BlastPullHit.pm
  M Bio/Search/Hit/Fasta.pm
  M Bio/Search/Hit/GenericHit.pm
  M Bio/Search/Hit/HMMERHit.pm
  M Bio/Search/Hit/HitFactory.pm
  M Bio/Search/Hit/HitI.pm
  M Bio/Search/Hit/HmmpfamHit.pm
  M Bio/Search/Hit/ModelHit.pm
  M Bio/Search/Hit/PsiBlastHit.pm
  M Bio/Search/Hit/PullHitI.pm
  M Bio/Search/Iteration/GenericIteration.pm
  M Bio/Search/Iteration/IterationI.pm
  M Bio/Search/Result/BlastPullResult.pm
  M Bio/Search/Result/BlastResult.pm
  M Bio/Search/Result/CrossMatchResult.pm
  M Bio/Search/Result/GenericResult.pm
  M Bio/Search/Result/HMMERResult.pm
  M Bio/Search/Result/HmmpfamResult.pm
  M Bio/Search/Result/PullResultI.pm
  M Bio/Search/Result/ResultFactory.pm
  M Bio/Search/Result/ResultI.pm
  M Bio/Search/Result/WABAResult.pm
  M Bio/Search/Tiling/MapTiling.pm
  M Bio/Search/Tiling/TilingI.pm
  M Bio/SearchDist.pm
  M Bio/SearchIO.pm
  M Bio/SearchIO/EventHandlerI.pm
  M Bio/SearchIO/FastHitEventBuilder.pm
  M Bio/SearchIO/IteratedSearchResultEventBuilder.pm
  M Bio/SearchIO/SearchResultEventBuilder.pm
  M Bio/SearchIO/SearchWriterI.pm
  M Bio/SearchIO/Writer/BSMLResultWriter.pm
  M Bio/SearchIO/Writer/GbrowseGFF.pm
  M Bio/SearchIO/Writer/HSPTableWriter.pm
  M Bio/SearchIO/Writer/HTMLResultWriter.pm
  M Bio/SearchIO/Writer/HitTableWriter.pm
  M Bio/SearchIO/Writer/ResultTableWriter.pm
  M Bio/SearchIO/Writer/TextResultWriter.pm
  M Bio/SearchIO/XML/BlastHandler.pm
  M Bio/SearchIO/XML/PsiBlastHandler.pm
  M Bio/SearchIO/axt.pm
  M Bio/SearchIO/blast.pm
  M Bio/SearchIO/blast_pull.pm
  M Bio/SearchIO/blasttable.pm
  M Bio/SearchIO/blastxml.pm
  M Bio/SearchIO/cross_match.pm
  M Bio/SearchIO/erpin.pm
  M Bio/SearchIO/exonerate.pm
  M Bio/SearchIO/fasta.pm
  M Bio/SearchIO/hmmer.pm
  M Bio/SearchIO/hmmer_pull.pm
  M Bio/SearchIO/infernal.pm
  M Bio/SearchIO/megablast.pm
  M Bio/SearchIO/psl.pm
  M Bio/SearchIO/rnamotif.pm
  M Bio/SearchIO/sim4.pm
  M Bio/SearchIO/waba.pm
  M Bio/SearchIO/wise.pm
  M Bio/Seq.pm
  M Bio/Seq/BaseSeqProcessor.pm
  M Bio/Seq/EncodedSeq.pm
  M Bio/Seq/LargePrimarySeq.pm
  M Bio/Seq/LargeSeq.pm
  M Bio/Seq/LargeSeqI.pm
  M Bio/Seq/Meta.pm
  M Bio/Seq/Meta/Array.pm
  M Bio/Seq/MetaI.pm
  M Bio/Seq/PrimaryQual.pm
  M Bio/Seq/PrimedSeq.pm
  M Bio/Seq/QualI.pm
  M Bio/Seq/Quality.pm
  M Bio/Seq/RichSeq.pm
  M Bio/Seq/RichSeqI.pm
  M Bio/Seq/SeqBuilder.pm
  M Bio/Seq/SeqFactory.pm
  M Bio/Seq/SeqFastaSpeedFactory.pm
  M Bio/Seq/SeqWithQuality.pm
  M Bio/Seq/SequenceTrace.pm
  M Bio/SeqAnalysisParserI.pm
  M Bio/SeqEvolution/DNAPoint.pm
  M Bio/SeqEvolution/EvolutionI.pm
  M Bio/SeqEvolution/Factory.pm
  M Bio/SeqFeature/Annotated.pm
  M Bio/SeqFeature/AnnotationAdaptor.pm
  M Bio/SeqFeature/Collection.pm
  M Bio/SeqFeature/CollectionI.pm
  M Bio/SeqFeature/Computation.pm
  M Bio/SeqFeature/FeaturePair.pm
  M Bio/SeqFeature/Gene/Exon.pm
  M Bio/SeqFeature/Gene/ExonI.pm
  M Bio/SeqFeature/Gene/GeneStructure.pm
  M Bio/SeqFeature/Gene/GeneStructureI.pm
  M Bio/SeqFeature/Gene/Intron.pm
  M Bio/SeqFeature/Gene/NC_Feature.pm
  M Bio/SeqFeature/Gene/Poly_A_site.pm
  M Bio/SeqFeature/Gene/Promoter.pm
  M Bio/SeqFeature/Gene/Transcript.pm
  M Bio/SeqFeature/Gene/TranscriptI.pm
  M Bio/SeqFeature/Gene/UTR.pm
  M Bio/SeqFeature/Generic.pm
  M Bio/SeqFeature/PositionProxy.pm
  M Bio/SeqFeature/Primer.pm
  M Bio/SeqFeature/SiRNA/Oligo.pm
  M Bio/SeqFeature/SiRNA/Pair.pm
  M Bio/SeqFeature/Similarity.pm
  M Bio/SeqFeature/SimilarityPair.pm
  M Bio/SeqFeature/Tools/FeatureNamer.pm
  M Bio/SeqFeature/Tools/IDHandler.pm
  M Bio/SeqFeature/Tools/TypeMapper.pm
  M Bio/SeqFeature/Tools/Unflattener.pm
  M Bio/SeqFeature/TypedSeqFeatureI.pm
  M Bio/SeqFeatureI.pm
  M Bio/SeqI.pm
  M Bio/SeqIO.pm
  M Bio/SeqIO/FTHelper.pm
  M Bio/SeqIO/Handler/GenericRichSeqHandler.pm
  M Bio/SeqIO/MultiFile.pm
  M Bio/SeqIO/abi.pm
  M Bio/SeqIO/ace.pm
  M Bio/SeqIO/alf.pm
  M Bio/SeqIO/asciitree.pm
  M Bio/SeqIO/bsml_sax.pm
  M Bio/SeqIO/chadoxml.pm
  M Bio/SeqIO/chaos.pm
  M Bio/SeqIO/chaosxml.pm
  M Bio/SeqIO/ctf.pm
  M Bio/SeqIO/embl.pm
  M Bio/SeqIO/embldriver.pm
  M Bio/SeqIO/entrezgene.pm
  M Bio/SeqIO/excel.pm
  M Bio/SeqIO/exp.pm
  M Bio/SeqIO/fasta.pm
  M Bio/SeqIO/flybase_chadoxml.pm
  M Bio/SeqIO/game.pm
  M Bio/SeqIO/game/featHandler.pm
  M Bio/SeqIO/game/gameSubs.pm
  M Bio/SeqIO/game/gameWriter.pm
  M Bio/SeqIO/game/seqHandler.pm
  M Bio/SeqIO/gbdriver.pm
  M Bio/SeqIO/gcg.pm
  M Bio/SeqIO/genbank.pm
  M Bio/SeqIO/interpro.pm
  M Bio/SeqIO/kegg.pm
  M Bio/SeqIO/largefasta.pm
  M Bio/SeqIO/lasergene.pm
  M Bio/SeqIO/locuslink.pm
  M Bio/SeqIO/metafasta.pm
  M Bio/SeqIO/nexml.pm
  M Bio/SeqIO/phd.pm
  M Bio/SeqIO/pir.pm
  M Bio/SeqIO/pln.pm
  M Bio/SeqIO/qual.pm
  M Bio/SeqIO/raw.pm
  M Bio/SeqIO/scf.pm
  M Bio/SeqIO/seqxml.pm
  M Bio/SeqIO/strider.pm
  M Bio/SeqIO/swiss.pm
  M Bio/SeqIO/swissdriver.pm
  M Bio/SeqIO/tab.pm
  M Bio/SeqIO/table.pm
  M Bio/SeqIO/tigr.pm
  M Bio/SeqIO/tigrxml.pm
  M Bio/SeqIO/ztr.pm
  M Bio/SeqUtils.pm
  M Bio/SimpleAlign.pm
  M Bio/SimpleAnalysisI.pm
  M Bio/Species.pm
  M Bio/Structure/Atom.pm
  M Bio/Structure/Chain.pm
  M Bio/Structure/Entry.pm
  M Bio/Structure/IO.pm
  M Bio/Structure/IO/pdb.pm
  M Bio/Structure/Model.pm
  M Bio/Structure/Residue.pm
  M Bio/Structure/StructureI.pm
  M Bio/Symbol/Alphabet.pm
  M Bio/Symbol/AlphabetI.pm
  M Bio/Symbol/DNAAlphabet.pm
  M Bio/Symbol/ProteinAlphabet.pm
  M Bio/Symbol/Symbol.pm
  M Bio/Symbol/SymbolI.pm
  M Bio/Taxon.pm
  M Bio/Taxonomy.pm
  M Bio/Taxonomy/Node.pm
  M Bio/Taxonomy/Taxon.pm
  M Bio/Taxonomy/Tree.pm
  M Bio/Tools/AlignFactory.pm
  M Bio/Tools/Alignment/Consed.pm
  M Bio/Tools/Alignment/Trim.pm
  M Bio/Tools/Analysis/DNA/ESEfinder.pm
  M Bio/Tools/Analysis/Protein/ELM.pm
  M Bio/Tools/Analysis/Protein/NetPhos.pm
  M Bio/Tools/Analysis/Protein/Scansite.pm
  M Bio/Tools/Analysis/SimpleAnalysisBase.pm
  M Bio/Tools/AnalysisResult.pm
  M Bio/Tools/Blat.pm
  M Bio/Tools/CodonTable.pm
  M Bio/Tools/Coil.pm
  M Bio/Tools/ECnumber.pm
  M Bio/Tools/EMBOSS/Palindrome.pm
  M Bio/Tools/EPCR.pm
  M Bio/Tools/ERPIN.pm
  M Bio/Tools/ESTScan.pm
  M Bio/Tools/EUtilities/Cookie.pm
  M Bio/Tools/EUtilities/History.pm
  M Bio/Tools/EUtilities/Info.pm
  M Bio/Tools/EUtilities/Info/FieldInfo.pm
  M Bio/Tools/EUtilities/Info/LinkInfo.pm
  M Bio/Tools/EUtilities/Query/GlobalQuery.pm
  M Bio/Tools/EUtilities/Summary/DocSum.pm
  M Bio/Tools/EUtilities/Summary/Item.pm
  M Bio/Tools/EUtilities/Summary/ItemContainerI.pm
  M Bio/Tools/Eponine.pm
  M Bio/Tools/Est2Genome.pm
  M Bio/Tools/Fgenesh.pm
  M Bio/Tools/FootPrinter.pm
  M Bio/Tools/GFF.pm
  M Bio/Tools/Gel.pm
  M Bio/Tools/Geneid.pm
  M Bio/Tools/Genemark.pm
  M Bio/Tools/Genewise.pm
  M Bio/Tools/Genomewise.pm
  M Bio/Tools/Genscan.pm
  M Bio/Tools/Glimmer.pm
  M Bio/Tools/Grail.pm
  M Bio/Tools/GuessSeqFormat.pm
  M Bio/Tools/HMMER/Domain.pm
  M Bio/Tools/HMMER/Results.pm
  M Bio/Tools/HMMER/Set.pm
  M Bio/Tools/Hmmpfam.pm
  M Bio/Tools/IUPAC.pm
  M Bio/Tools/Infernal.pm
  M Bio/Tools/Lucy.pm
  M Bio/Tools/MZEF.pm
  M Bio/Tools/Phylo/Gumby.pm
  M Bio/Tools/Phylo/Molphy.pm
  M Bio/Tools/Phylo/Molphy/Result.pm
  M Bio/Tools/Phylo/PAML.pm
  M Bio/Tools/Phylo/PAML/Codeml.pm
  M Bio/Tools/Phylo/PAML/ModelResult.pm
  M Bio/Tools/Phylo/PAML/Result.pm
  M Bio/Tools/Phylo/Phylip/ProtDist.pm
  M Bio/Tools/Prediction/Exon.pm
  M Bio/Tools/Prediction/Gene.pm
  M Bio/Tools/Primer/Assessor/Base.pm
  M Bio/Tools/Primer/AssessorI.pm
  M Bio/Tools/Primer/Feature.pm
  M Bio/Tools/Primer/Pair.pm
  M Bio/Tools/Primer3.pm
  M Bio/Tools/Prints.pm
  M Bio/Tools/Profile.pm
  M Bio/Tools/Promoterwise.pm
  M Bio/Tools/Protparam.pm
  M Bio/Tools/Pseudowise.pm
  M Bio/Tools/QRNA.pm
  M Bio/Tools/RNAMotif.pm
  M Bio/Tools/RandomDistFunctions.pm
  M Bio/Tools/RepeatMasker.pm
  M Bio/Tools/Run/GenericParameters.pm
  M Bio/Tools/Run/ParametersI.pm
  M Bio/Tools/Run/RemoteBlast.pm
  M Bio/Tools/Run/StandAloneBlast.pm
  M Bio/Tools/Run/StandAloneNCBIBlast.pm
  M Bio/Tools/Run/StandAloneWUBlast.pm
  M Bio/Tools/Run/WrapperBase.pm
  M Bio/Tools/Run/WrapperBase/CommandExts.pm
  M Bio/Tools/Seg.pm
  M Bio/Tools/SeqPattern.pm
  M Bio/Tools/SeqStats.pm
  M Bio/Tools/SeqWords.pm
  M Bio/Tools/SiRNA.pm
  M Bio/Tools/Sigcleave.pm
  M Bio/Tools/Signalp.pm
  M Bio/Tools/Signalp/ExtendedSignalp.pm
  M Bio/Tools/Sim4/Exon.pm
  M Bio/Tools/Sim4/Results.pm
  M Bio/Tools/Spidey/Exon.pm
  M Bio/Tools/Spidey/Results.pm
  M Bio/Tools/TargetP.pm
  M Bio/Tools/Tmhmm.pm
  M Bio/Tools/dpAlign.pm
  M Bio/Tools/ipcress.pm
  M Bio/Tools/isPcr.pm
  M Bio/Tools/pICalculator.pm
  M Bio/Tools/pSW.pm
  M Bio/Tools/tRNAscanSE.pm
  M Bio/Tree/AlleleNode.pm
  M Bio/Tree/Compatible.pm
  M Bio/Tree/DistanceFactory.pm
  M Bio/Tree/Draw/Cladogram.pm
  M Bio/Tree/Node.pm
  M Bio/Tree/NodeI.pm
  M Bio/Tree/NodeNHX.pm
  M Bio/Tree/RandomFactory.pm
  M Bio/Tree/Statistics.pm
  M Bio/Tree/Tree.pm
  M Bio/Tree/TreeFunctionsI.pm
  M Bio/Tree/TreeI.pm
  M Bio/TreeIO.pm
  M Bio/TreeIO/TreeEventBuilder.pm
  M Bio/TreeIO/cluster.pm
  M Bio/TreeIO/lintree.pm
  M Bio/TreeIO/newick.pm
  M Bio/TreeIO/nexml.pm
  M Bio/TreeIO/nexus.pm
  M Bio/TreeIO/nhx.pm
  M Bio/TreeIO/pag.pm
  M Bio/TreeIO/tabtree.pm
  M Bio/UpdateableSeqI.pm
  M Bio/Variation/AAChange.pm
  M Bio/Variation/AAReverseMutate.pm
  M Bio/Variation/Allele.pm
  M Bio/Variation/DNAMutation.pm
  M Bio/Variation/IO.pm
  M Bio/Variation/IO/flat.pm
  M Bio/Variation/IO/xml.pm
  M Bio/Variation/RNAChange.pm
  M Bio/Variation/SNP.pm
  M Bio/Variation/SeqDiff.pm
  M Bio/Variation/VariantI.pm
  M Bio/WebAgent.pm
  M t/lib/Array/Compare.pm

Log Message:
-----------
strip keyword substitution from perl modules


Commit: 4017a483d2e5c15d5a95a63b4d19fd1ba23f679a
    http://github.com/bioperl/bioperl-live/commit/4017a483d2e5c15d5a95a63b4d19fd1ba23f679a
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M examples/align/aligntutorial.pl
  M examples/align/clustalw.pl
  M examples/align/simplealign.pl
  M examples/biblio/biblio-eutils-example.pl
  M examples/biblio/biblio-soap-example.pl
  M examples/contributed/nmrpdb_parse.pl
  M examples/contributed/prosite2perl.pl
  M examples/liveseq/change_gene.pl
  M examples/make_primers.pl
  M examples/popgen/parse_calc_stats.pl
  M examples/rev_and_trans.pl
  M examples/root/exceptions1.pl
  M examples/root/exceptions2.pl
  M examples/root/exceptions3.pl
  M examples/root/exceptions4.pl
  M examples/searchio/custom_writer.pl
  M examples/searchio/hitwriter.pl
  M examples/searchio/hspwriter.pl
  M examples/searchio/htmlwriter.pl
  M examples/searchio/psiblast_features.pl
  M examples/searchio/psiblast_iterations.pl
  M examples/searchio/rawwriter.pl
  M examples/searchio/resultwriter.pl
  M examples/tools/extract_genes.pl
  M examples/tools/psw.pl
  M examples/tools/reverse-translate.pl
  M examples/tools/run_primer3.pl
  M examples/tools/seq_pattern.pl
  M examples/tools/standaloneblast.pl
  M maintenance/authors.pl
  M maintenance/cvs2cl_by_file.pl
  M maintenance/modules.pl
  M maintenance/pod.pl
  M maintenance/version.pl
  M scripts/Bio-DB-GFF/bulk_load_gff.PLS
  M scripts/Bio-DB-GFF/fast_load_gff.PLS
  M scripts/Bio-DB-GFF/genbank2gff.PLS
  M scripts/Bio-DB-GFF/generate_histogram.PLS
  M scripts/Bio-DB-GFF/process_sgd.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
  M scripts/DB/biofetch_genbank_proxy.PLS
  M scripts/DB/biogetseq.PLS
  M scripts/DB/flanks.PLS
  M scripts/biblio/biblio.PLS
  M scripts/das/das_server.pl
  M scripts/index/bp_seqret.PLS
  M scripts/popgen/composite_LD.PLS
  M scripts/popgen/heterogeneity_test.PLS
  M scripts/searchio/filter_search.PLS
  M scripts/searchio/parse_hmmsearch.PLS
  M scripts/seq/extract_feature_seq.PLS
  M scripts/seq/make_mrna_protein.PLS
  M scripts/seq/seqconvert.PLS
  M scripts/seq/seqretsplit.PLS
  M scripts/seq/split_seq.PLS
  M scripts/seq/translate_seq.PLS
  M scripts/seq/unflatten_seq.PLS
  M scripts/seqstats/aacomp.PLS
  M scripts/seqstats/chaos_plot.PLS
  M scripts/seqstats/gccalc.PLS
  M scripts/seqstats/oligo_count.PLS
  M scripts/taxa/classify_hits_kingdom.PLS
  M scripts/utilities/bp_mrtrans.PLS
  M scripts/utilities/bp_nrdb.PLS
  M scripts/utilities/mask_by_search.PLS
  M scripts/utilities/pairwise_kaks.PLS
  M scripts/utilities/remote_blast.PLS
  M scripts/utilities/revtrans-motif.PLS
  M scripts/utilities/search2BSML.PLS
  M scripts/utilities/search2alnblocks.PLS
  M scripts/utilities/search2gff.PLS
  M scripts/utilities/search2tribe.PLS

Log Message:
-----------
strip keyword substitution from perl scripts



From noreply at github.com  Thu Jul 29 17:56:44 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 29 Jul 2010 14:56:44 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] f69a78: domain flag borking
	the request; fix courtesy John...
Message-ID: <20100729215645.0B278422DF@smtp1.rs.github.com>

Branch: refs/heads/branch-1-6
Home:   http://github.com/bioperl/bioperl-live

Commit: f69a78932e59f5810aaebf7cbefa500ccc714dbd
    http://github.com/bioperl/bioperl-live/commit/f69a78932e59f5810aaebf7cbefa500ccc714dbd
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M Bio/Tools/Analysis/Protein/Scansite.pm

Log Message:
-----------
domain flag borking the request; fix courtesy John Obenauer


Commit: 1d4985cf8a721df8db3db8381b7c810cf0d328dc
    http://github.com/bioperl/bioperl-live/commit/1d4985cf8a721df8db3db8381b7c810cf0d328dc
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M Bio/Align/AlignI.pm
  M Bio/Align/DNAStatistics.pm
  M Bio/Align/PairwiseStatistics.pm
  M Bio/Align/ProteinStatistics.pm
  M Bio/Align/StatisticsI.pm
  M Bio/Align/Utilities.pm
  M Bio/AlignIO.pm
  M Bio/AlignIO/arp.pm
  M Bio/AlignIO/bl2seq.pm
  M Bio/AlignIO/clustalw.pm
  M Bio/AlignIO/emboss.pm
  M Bio/AlignIO/fasta.pm
  M Bio/AlignIO/maf.pm
  M Bio/AlignIO/mase.pm
  M Bio/AlignIO/mega.pm
  M Bio/AlignIO/meme.pm
  M Bio/AlignIO/metafasta.pm
  M Bio/AlignIO/msf.pm
  M Bio/AlignIO/nexml.pm
  M Bio/AlignIO/nexus.pm
  M Bio/AlignIO/pfam.pm
  M Bio/AlignIO/phylip.pm
  M Bio/AlignIO/proda.pm
  M Bio/AlignIO/prodom.pm
  M Bio/AlignIO/psi.pm
  M Bio/AlignIO/selex.pm
  M Bio/AlignIO/stockholm.pm
  M Bio/AlignIO/xmfa.pm
  M Bio/AnalysisI.pm
  M Bio/AnalysisParserI.pm
  M Bio/AnalysisResultI.pm
  M Bio/AnnotatableI.pm
  M Bio/Annotation/AnnotationFactory.pm
  M Bio/Annotation/Collection.pm
  M Bio/Annotation/Comment.pm
  M Bio/Annotation/DBLink.pm
  M Bio/Annotation/OntologyTerm.pm
  M Bio/Annotation/Reference.pm
  M Bio/Annotation/SimpleValue.pm
  M Bio/Annotation/StructuredValue.pm
  M Bio/Annotation/Target.pm
  M Bio/Annotation/TypeManager.pm
  M Bio/AnnotationCollectionI.pm
  M Bio/AnnotationI.pm
  M Bio/Assembly/Contig.pm
  M Bio/Assembly/ContigAnalysis.pm
  M Bio/Assembly/IO/bowtie.pm
  M Bio/Assembly/IO/maq.pm
  M Bio/Assembly/IO/phrap.pm
  M Bio/Assembly/IO/sam.pm
  M Bio/Assembly/IO/tigr.pm
  M Bio/Assembly/Scaffold.pm
  M Bio/Assembly/ScaffoldI.pm
  M Bio/Assembly/Singlet.pm
  M Bio/Biblio.pm
  M Bio/Biblio/Article.pm
  M Bio/Biblio/BiblioBase.pm
  M Bio/Biblio/Book.pm
  M Bio/Biblio/BookArticle.pm
  M Bio/Biblio/IO.pm
  M Bio/Biblio/IO/medline2ref.pm
  M Bio/Biblio/IO/medlinexml.pm
  M Bio/Biblio/IO/pubmed2ref.pm
  M Bio/Biblio/IO/pubmedxml.pm
  M Bio/Biblio/Journal.pm
  M Bio/Biblio/JournalArticle.pm
  M Bio/Biblio/MedlineArticle.pm
  M Bio/Biblio/MedlineBook.pm
  M Bio/Biblio/MedlineBookArticle.pm
  M Bio/Biblio/MedlineJournal.pm
  M Bio/Biblio/MedlineJournalArticle.pm
  M Bio/Biblio/Organisation.pm
  M Bio/Biblio/Patent.pm
  M Bio/Biblio/Person.pm
  M Bio/Biblio/Proceeding.pm
  M Bio/Biblio/Provider.pm
  M Bio/Biblio/PubmedArticle.pm
  M Bio/Biblio/PubmedBookArticle.pm
  M Bio/Biblio/PubmedJournalArticle.pm
  M Bio/Biblio/Ref.pm
  M Bio/Biblio/Service.pm
  M Bio/Biblio/TechReport.pm
  M Bio/Biblio/Thesis.pm
  M Bio/Biblio/WebResource.pm
  M Bio/Cluster/ClusterFactory.pm
  M Bio/Cluster/SequenceFamily.pm
  M Bio/Cluster/UniGene.pm
  M Bio/Cluster/UniGeneI.pm
  M Bio/ClusterI.pm
  M Bio/ClusterIO.pm
  M Bio/ClusterIO/dbsnp.pm
  M Bio/ClusterIO/unigene.pm
  M Bio/CodonUsage/IO.pm
  M Bio/CodonUsage/Table.pm
  M Bio/Coordinate/Chain.pm
  M Bio/Coordinate/Collection.pm
  M Bio/Coordinate/ExtrapolatingPair.pm
  M Bio/Coordinate/GeneMapper.pm
  M Bio/Coordinate/Graph.pm
  M Bio/Coordinate/MapperI.pm
  M Bio/Coordinate/Pair.pm
  M Bio/Coordinate/Result.pm
  M Bio/Coordinate/Result/Gap.pm
  M Bio/Coordinate/Result/Match.pm
  M Bio/Coordinate/ResultI.pm
  M Bio/Coordinate/Utils.pm
  M Bio/DB/Ace.pm
  M Bio/DB/Biblio/biofetch.pm
  M Bio/DB/Biblio/eutils.pm
  M Bio/DB/Biblio/soap.pm
  M Bio/DB/BiblioI.pm
  M Bio/DB/BioFetch.pm
  M Bio/DB/CUTG.pm
  M Bio/DB/DBFetch.pm
  M Bio/DB/EMBL.pm
  M Bio/DB/EUtilities.pm
  M Bio/DB/EntrezGene.pm
  M Bio/DB/Expression.pm
  M Bio/DB/Failover.pm
  M Bio/DB/Fasta.pm
  M Bio/DB/FileCache.pm
  M Bio/DB/Flat.pm
  M Bio/DB/Flat/BDB.pm
  M Bio/DB/Flat/BDB/embl.pm
  M Bio/DB/Flat/BDB/fasta.pm
  M Bio/DB/Flat/BDB/genbank.pm
  M Bio/DB/Flat/BDB/swiss.pm
  M Bio/DB/Flat/BinarySearch.pm
  M Bio/DB/GFF.pm
  M Bio/DB/GFF/Adaptor/berkeleydb.pm
  M Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
  M Bio/DB/GFF/Adaptor/dbi.pm
  M Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
  M Bio/DB/GFF/Adaptor/memory.pm
  M Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
  M Bio/DB/GFF/Adaptor/memory/iterator.pm
  M Bio/DB/GenBank.pm
  M Bio/DB/GenPept.pm
  M Bio/DB/GenericWebAgent.pm
  M Bio/DB/InMemoryCache.pm
  M Bio/DB/LocationI.pm
  M Bio/DB/MeSH.pm
  M Bio/DB/NCBIHelper.pm
  M Bio/DB/Qual.pm
  M Bio/DB/Query/GenBank.pm
  M Bio/DB/Query/WebQuery.pm
  M Bio/DB/QueryI.pm
  M Bio/DB/RandomAccessI.pm
  M Bio/DB/RefSeq.pm
  M Bio/DB/ReferenceI.pm
  M Bio/DB/Registry.pm
  M Bio/DB/SeqFeature.pm
  M Bio/DB/SeqFeature/NormalizedFeature.pm
  M Bio/DB/SeqFeature/NormalizedFeatureI.pm
  M Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
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  M Bio/Root/Build.pm
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  M Bio/SeqFeature/Gene/Promoter.pm
  M Bio/SeqFeature/Gene/Transcript.pm
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  M Bio/SeqFeature/Gene/UTR.pm
  M Bio/SeqFeature/Generic.pm
  M Bio/SeqFeature/PositionProxy.pm
  M Bio/SeqFeature/Primer.pm
  M Bio/SeqFeature/SiRNA/Oligo.pm
  M Bio/SeqFeature/SiRNA/Pair.pm
  M Bio/SeqFeature/Similarity.pm
  M Bio/SeqFeature/SimilarityPair.pm
  M Bio/SeqFeature/Tools/FeatureNamer.pm
  M Bio/SeqFeature/Tools/IDHandler.pm
  M Bio/SeqFeature/Tools/TypeMapper.pm
  M Bio/SeqFeature/Tools/Unflattener.pm
  M Bio/SeqFeature/TypedSeqFeatureI.pm
  M Bio/SeqFeatureI.pm
  M Bio/SeqI.pm
  M Bio/SeqIO.pm
  M Bio/SeqIO/FTHelper.pm
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  M Bio/SeqIO/MultiFile.pm
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  M Bio/SeqIO/chaosxml.pm
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  M Bio/SeqIO/entrezgene.pm
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  M Bio/SeqIO/fasta.pm
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  M Bio/SeqIO/game.pm
  M Bio/SeqIO/game/featHandler.pm
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  M Bio/SeqIO/game/gameWriter.pm
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  M Bio/SeqIO/gbdriver.pm
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  M Bio/Symbol/ProteinAlphabet.pm
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  M Bio/Taxon.pm
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  M Bio/Taxonomy/Node.pm
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  M Bio/Taxonomy/Tree.pm
  M Bio/Tools/AlignFactory.pm
  M Bio/Tools/Alignment/Consed.pm
  M Bio/Tools/Alignment/Trim.pm
  M Bio/Tools/Analysis/DNA/ESEfinder.pm
  M Bio/Tools/Analysis/Protein/ELM.pm
  M Bio/Tools/Analysis/Protein/NetPhos.pm
  M Bio/Tools/Analysis/Protein/Scansite.pm
  M Bio/Tools/Analysis/SimpleAnalysisBase.pm
  M Bio/Tools/AnalysisResult.pm
  M Bio/Tools/Blat.pm
  M Bio/Tools/CodonTable.pm
  M Bio/Tools/Coil.pm
  M Bio/Tools/ECnumber.pm
  M Bio/Tools/EMBOSS/Palindrome.pm
  M Bio/Tools/EPCR.pm
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  M Bio/Tools/EUtilities/Info.pm
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  M Bio/Tools/EUtilities/Query/GlobalQuery.pm
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  M Bio/Tools/Glimmer.pm
  M Bio/Tools/Grail.pm
  M Bio/Tools/GuessSeqFormat.pm
  M Bio/Tools/HMMER/Domain.pm
  M Bio/Tools/HMMER/Results.pm
  M Bio/Tools/HMMER/Set.pm
  M Bio/Tools/Hmmpfam.pm
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  M Bio/Tools/Lucy.pm
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  M Bio/Tools/Phylo/PAML.pm
  M Bio/Tools/Phylo/PAML/Codeml.pm
  M Bio/Tools/Phylo/PAML/ModelResult.pm
  M Bio/Tools/Phylo/PAML/Result.pm
  M Bio/Tools/Phylo/Phylip/ProtDist.pm
  M Bio/Tools/Prediction/Exon.pm
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  M Bio/Tools/Primer/Assessor/Base.pm
  M Bio/Tools/Primer/AssessorI.pm
  M Bio/Tools/Primer/Feature.pm
  M Bio/Tools/Primer/Pair.pm
  M Bio/Tools/Primer3.pm
  M Bio/Tools/Prints.pm
  M Bio/Tools/Profile.pm
  M Bio/Tools/Promoterwise.pm
  M Bio/Tools/Protparam.pm
  M Bio/Tools/Pseudowise.pm
  M Bio/Tools/QRNA.pm
  M Bio/Tools/RNAMotif.pm
  M Bio/Tools/RandomDistFunctions.pm
  M Bio/Tools/RepeatMasker.pm
  M Bio/Tools/Run/GenericParameters.pm
  M Bio/Tools/Run/ParametersI.pm
  M Bio/Tools/Run/RemoteBlast.pm
  M Bio/Tools/Run/StandAloneBlast.pm
  M Bio/Tools/Run/StandAloneNCBIBlast.pm
  M Bio/Tools/Run/StandAloneWUBlast.pm
  M Bio/Tools/Run/WrapperBase.pm
  M Bio/Tools/Run/WrapperBase/CommandExts.pm
  M Bio/Tools/Seg.pm
  M Bio/Tools/SeqPattern.pm
  M Bio/Tools/SeqStats.pm
  M Bio/Tools/SeqWords.pm
  M Bio/Tools/SiRNA.pm
  M Bio/Tools/Sigcleave.pm
  M Bio/Tools/Signalp.pm
  M Bio/Tools/Signalp/ExtendedSignalp.pm
  M Bio/Tools/Sim4/Exon.pm
  M Bio/Tools/Sim4/Results.pm
  M Bio/Tools/Spidey/Exon.pm
  M Bio/Tools/Spidey/Results.pm
  M Bio/Tools/TargetP.pm
  M Bio/Tools/Tmhmm.pm
  M Bio/Tools/dpAlign.pm
  M Bio/Tools/ipcress.pm
  M Bio/Tools/isPcr.pm
  M Bio/Tools/pICalculator.pm
  M Bio/Tools/pSW.pm
  M Bio/Tools/tRNAscanSE.pm
  M Bio/Tree/AlleleNode.pm
  M Bio/Tree/Compatible.pm
  M Bio/Tree/DistanceFactory.pm
  M Bio/Tree/Draw/Cladogram.pm
  M Bio/Tree/Node.pm
  M Bio/Tree/NodeI.pm
  M Bio/Tree/NodeNHX.pm
  M Bio/Tree/RandomFactory.pm
  M Bio/Tree/Statistics.pm
  M Bio/Tree/Tree.pm
  M Bio/Tree/TreeFunctionsI.pm
  M Bio/Tree/TreeI.pm
  M Bio/TreeIO.pm
  M Bio/TreeIO/TreeEventBuilder.pm
  M Bio/TreeIO/cluster.pm
  M Bio/TreeIO/lintree.pm
  M Bio/TreeIO/newick.pm
  M Bio/TreeIO/nexml.pm
  M Bio/TreeIO/nexus.pm
  M Bio/TreeIO/nhx.pm
  M Bio/TreeIO/pag.pm
  M Bio/TreeIO/tabtree.pm
  M Bio/UpdateableSeqI.pm
  M Bio/Variation/AAChange.pm
  M Bio/Variation/AAReverseMutate.pm
  M Bio/Variation/Allele.pm
  M Bio/Variation/DNAMutation.pm
  M Bio/Variation/IO.pm
  M Bio/Variation/IO/flat.pm
  M Bio/Variation/IO/xml.pm
  M Bio/Variation/RNAChange.pm
  M Bio/Variation/SNP.pm
  M Bio/Variation/SeqDiff.pm
  M Bio/Variation/VariantI.pm
  M Bio/WebAgent.pm
  M t/lib/Array/Compare.pm

Log Message:
-----------
strip keyword substitution from perl modules


Commit: 4017a483d2e5c15d5a95a63b4d19fd1ba23f679a
    http://github.com/bioperl/bioperl-live/commit/4017a483d2e5c15d5a95a63b4d19fd1ba23f679a
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M examples/align/aligntutorial.pl
  M examples/align/clustalw.pl
  M examples/align/simplealign.pl
  M examples/biblio/biblio-eutils-example.pl
  M examples/biblio/biblio-soap-example.pl
  M examples/contributed/nmrpdb_parse.pl
  M examples/contributed/prosite2perl.pl
  M examples/liveseq/change_gene.pl
  M examples/make_primers.pl
  M examples/popgen/parse_calc_stats.pl
  M examples/rev_and_trans.pl
  M examples/root/exceptions1.pl
  M examples/root/exceptions2.pl
  M examples/root/exceptions3.pl
  M examples/root/exceptions4.pl
  M examples/searchio/custom_writer.pl
  M examples/searchio/hitwriter.pl
  M examples/searchio/hspwriter.pl
  M examples/searchio/htmlwriter.pl
  M examples/searchio/psiblast_features.pl
  M examples/searchio/psiblast_iterations.pl
  M examples/searchio/rawwriter.pl
  M examples/searchio/resultwriter.pl
  M examples/tools/extract_genes.pl
  M examples/tools/psw.pl
  M examples/tools/reverse-translate.pl
  M examples/tools/run_primer3.pl
  M examples/tools/seq_pattern.pl
  M examples/tools/standaloneblast.pl
  M maintenance/authors.pl
  M maintenance/cvs2cl_by_file.pl
  M maintenance/modules.pl
  M maintenance/pod.pl
  M maintenance/version.pl
  M scripts/Bio-DB-GFF/bulk_load_gff.PLS
  M scripts/Bio-DB-GFF/fast_load_gff.PLS
  M scripts/Bio-DB-GFF/genbank2gff.PLS
  M scripts/Bio-DB-GFF/generate_histogram.PLS
  M scripts/Bio-DB-GFF/process_sgd.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
  M scripts/DB/biofetch_genbank_proxy.PLS
  M scripts/DB/biogetseq.PLS
  M scripts/DB/flanks.PLS
  M scripts/biblio/biblio.PLS
  M scripts/das/das_server.pl
  M scripts/index/bp_seqret.PLS
  M scripts/popgen/composite_LD.PLS
  M scripts/popgen/heterogeneity_test.PLS
  M scripts/searchio/filter_search.PLS
  M scripts/searchio/parse_hmmsearch.PLS
  M scripts/seq/extract_feature_seq.PLS
  M scripts/seq/make_mrna_protein.PLS
  M scripts/seq/seqconvert.PLS
  M scripts/seq/seqretsplit.PLS
  M scripts/seq/split_seq.PLS
  M scripts/seq/translate_seq.PLS
  M scripts/seq/unflatten_seq.PLS
  M scripts/seqstats/aacomp.PLS
  M scripts/seqstats/chaos_plot.PLS
  M scripts/seqstats/gccalc.PLS
  M scripts/seqstats/oligo_count.PLS
  M scripts/taxa/classify_hits_kingdom.PLS
  M scripts/utilities/bp_mrtrans.PLS
  M scripts/utilities/bp_nrdb.PLS
  M scripts/utilities/mask_by_search.PLS
  M scripts/utilities/pairwise_kaks.PLS
  M scripts/utilities/remote_blast.PLS
  M scripts/utilities/revtrans-motif.PLS
  M scripts/utilities/search2BSML.PLS
  M scripts/utilities/search2alnblocks.PLS
  M scripts/utilities/search2gff.PLS
  M scripts/utilities/search2tribe.PLS

Log Message:
-----------
strip keyword substitution from perl scripts


Commit: 81582e43542ff22c9dd05de66a38f492217b54e8
    http://github.com/bioperl/bioperl-live/commit/81582e43542ff22c9dd05de66a38f492217b54e8
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M Bio/Align/AlignI.pm
  M Bio/Align/DNAStatistics.pm
  M Bio/Align/PairwiseStatistics.pm
  M Bio/Align/ProteinStatistics.pm
  M Bio/Align/StatisticsI.pm
  M Bio/Align/Utilities.pm
  M Bio/AlignIO.pm
  M Bio/AlignIO/arp.pm
  M Bio/AlignIO/bl2seq.pm
  M Bio/AlignIO/clustalw.pm
  M Bio/AlignIO/emboss.pm
  M Bio/AlignIO/fasta.pm
  M Bio/AlignIO/maf.pm
  M Bio/AlignIO/mase.pm
  M Bio/AlignIO/mega.pm
  M Bio/AlignIO/meme.pm
  M Bio/AlignIO/metafasta.pm
  M Bio/AlignIO/msf.pm
  M Bio/AlignIO/nexml.pm
  M Bio/AlignIO/nexus.pm
  M Bio/AlignIO/pfam.pm
  M Bio/AlignIO/phylip.pm
  M Bio/AlignIO/proda.pm
  M Bio/AlignIO/prodom.pm
  M Bio/AlignIO/psi.pm
  M Bio/AlignIO/selex.pm
  M Bio/AlignIO/stockholm.pm
  M Bio/AlignIO/xmfa.pm
  M Bio/AnalysisI.pm
  M Bio/AnalysisParserI.pm
  M Bio/AnalysisResultI.pm
  M Bio/AnnotatableI.pm
  M Bio/Annotation/AnnotationFactory.pm
  M Bio/Annotation/Collection.pm
  M Bio/Annotation/Comment.pm
  M Bio/Annotation/DBLink.pm
  M Bio/Annotation/OntologyTerm.pm
  M Bio/Annotation/Reference.pm
  M Bio/Annotation/SimpleValue.pm
  M Bio/Annotation/StructuredValue.pm
  M Bio/Annotation/Target.pm
  M Bio/Annotation/TypeManager.pm
  M Bio/AnnotationCollectionI.pm
  M Bio/AnnotationI.pm
  M Bio/Assembly/Contig.pm
  M Bio/Assembly/ContigAnalysis.pm
  M Bio/Assembly/IO/bowtie.pm
  M Bio/Assembly/IO/maq.pm
  M Bio/Assembly/IO/phrap.pm
  M Bio/Assembly/IO/sam.pm
  M Bio/Assembly/IO/tigr.pm
  M Bio/Assembly/Scaffold.pm
  M Bio/Assembly/ScaffoldI.pm
  M Bio/Assembly/Singlet.pm
  M Bio/Biblio.pm
  M Bio/Biblio/Article.pm
  M Bio/Biblio/BiblioBase.pm
  M Bio/Biblio/Book.pm
  M Bio/Biblio/BookArticle.pm
  M Bio/Biblio/IO.pm
  M Bio/Biblio/IO/medline2ref.pm
  M Bio/Biblio/IO/medlinexml.pm
  M Bio/Biblio/IO/pubmed2ref.pm
  M Bio/Biblio/IO/pubmedxml.pm
  M Bio/Biblio/Journal.pm
  M Bio/Biblio/JournalArticle.pm
  M Bio/Biblio/MedlineArticle.pm
  M Bio/Biblio/MedlineBook.pm
  M Bio/Biblio/MedlineBookArticle.pm
  M Bio/Biblio/MedlineJournal.pm
  M Bio/Biblio/MedlineJournalArticle.pm
  M Bio/Biblio/Organisation.pm
  M Bio/Biblio/Patent.pm
  M Bio/Biblio/Person.pm
  M Bio/Biblio/Proceeding.pm
  M Bio/Biblio/Provider.pm
  M Bio/Biblio/PubmedArticle.pm
  M Bio/Biblio/PubmedBookArticle.pm
  M Bio/Biblio/PubmedJournalArticle.pm
  M Bio/Biblio/Ref.pm
  M Bio/Biblio/Service.pm
  M Bio/Biblio/TechReport.pm
  M Bio/Biblio/Thesis.pm
  M Bio/Biblio/WebResource.pm
  M Bio/Cluster/ClusterFactory.pm
  M Bio/Cluster/SequenceFamily.pm
  M Bio/Cluster/UniGene.pm
  M Bio/Cluster/UniGeneI.pm
  M Bio/ClusterI.pm
  M Bio/ClusterIO.pm
  M Bio/ClusterIO/dbsnp.pm
  M Bio/ClusterIO/unigene.pm
  M Bio/CodonUsage/IO.pm
  M Bio/CodonUsage/Table.pm
  M Bio/Coordinate/Chain.pm
  M Bio/Coordinate/Collection.pm
  M Bio/Coordinate/ExtrapolatingPair.pm
  M Bio/Coordinate/GeneMapper.pm
  M Bio/Coordinate/Graph.pm
  M Bio/Coordinate/MapperI.pm
  M Bio/Coordinate/Pair.pm
  M Bio/Coordinate/Result.pm
  M Bio/Coordinate/Result/Gap.pm
  M Bio/Coordinate/Result/Match.pm
  M Bio/Coordinate/ResultI.pm
  M Bio/Coordinate/Utils.pm
  M Bio/DB/Ace.pm
  M Bio/DB/Biblio/biofetch.pm
  M Bio/DB/Biblio/eutils.pm
  M Bio/DB/Biblio/soap.pm
  M Bio/DB/BiblioI.pm
  M Bio/DB/BioFetch.pm
  M Bio/DB/CUTG.pm
  M Bio/DB/DBFetch.pm
  M Bio/DB/EMBL.pm
  M Bio/DB/EUtilities.pm
  M Bio/DB/EntrezGene.pm
  M Bio/DB/Expression.pm
  M Bio/DB/Failover.pm
  M Bio/DB/Fasta.pm
  M Bio/DB/FileCache.pm
  M Bio/DB/Flat.pm
  M Bio/DB/Flat/BDB.pm
  M Bio/DB/Flat/BDB/embl.pm
  M Bio/DB/Flat/BDB/fasta.pm
  M Bio/DB/Flat/BDB/genbank.pm
  M Bio/DB/Flat/BDB/swiss.pm
  M Bio/DB/Flat/BinarySearch.pm
  M Bio/DB/GFF.pm
  M Bio/DB/GFF/Adaptor/berkeleydb.pm
  M Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
  M Bio/DB/GFF/Adaptor/dbi.pm
  M Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
  M Bio/DB/GFF/Adaptor/memory.pm
  M Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
  M Bio/DB/GFF/Adaptor/memory/iterator.pm
  M Bio/DB/GenBank.pm
  M Bio/DB/GenPept.pm
  M Bio/DB/GenericWebAgent.pm
  M Bio/DB/InMemoryCache.pm
  M Bio/DB/LocationI.pm
  M Bio/DB/MeSH.pm
  M Bio/DB/NCBIHelper.pm
  M Bio/DB/Qual.pm
  M Bio/DB/Query/GenBank.pm
  M Bio/DB/Query/WebQuery.pm
  M Bio/DB/QueryI.pm
  M Bio/DB/RandomAccessI.pm
  M Bio/DB/RefSeq.pm
  M Bio/DB/ReferenceI.pm
  M Bio/DB/Registry.pm
  M Bio/DB/SeqFeature.pm
  M Bio/DB/SeqFeature/NormalizedFeature.pm
  M Bio/DB/SeqFeature/NormalizedFeatureI.pm
  M Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
  M Bio/DB/SeqFeature/Segment.pm
  M Bio/DB/SeqFeature/Store.pm
  M Bio/DB/SeqFeature/Store/DBI/Iterator.pm
  M Bio/DB/SeqFeature/Store/DBI/mysql.pm
  M Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
  M Bio/DB/SeqFeature/Store/GFF3Loader.pm
  M Bio/DB/SeqFeature/Store/LoadHelper.pm
  M Bio/DB/SeqFeature/Store/Loader.pm
  M Bio/DB/SeqFeature/Store/bdb.pm
  M Bio/DB/SeqFeature/Store/berkeleydb.pm
  M Bio/DB/SeqFeature/Store/memory.pm
  M Bio/DB/SeqI.pm
  M Bio/DB/SeqVersion.pm
  M Bio/DB/SeqVersion/gi.pm
  M Bio/DB/SwissProt.pm
  M Bio/DB/Taxonomy.pm
  M Bio/DB/Taxonomy/entrez.pm
  M Bio/DB/Taxonomy/flatfile.pm
  M Bio/DB/Taxonomy/list.pm
  M Bio/DB/UpdateableSeqI.pm
  M Bio/DB/WebDBSeqI.pm
  M Bio/DBLinkContainerI.pm
  M Bio/Das/FeatureTypeI.pm
  M Bio/Das/SegmentI.pm
  M Bio/DasI.pm
  M Bio/DescribableI.pm
  M Bio/Event/EventGeneratorI.pm
  M Bio/Event/EventHandlerI.pm
  M Bio/Factory/AnalysisI.pm
  M Bio/Factory/ApplicationFactoryI.pm
  M Bio/Factory/DriverFactory.pm
  M Bio/Factory/FTLocationFactory.pm
  M Bio/Factory/LocationFactoryI.pm
  M Bio/Factory/MapFactoryI.pm
  M Bio/Factory/ObjectBuilderI.pm
  M Bio/Factory/ObjectFactory.pm
  M Bio/Factory/ObjectFactoryI.pm
  M Bio/Factory/SeqAnalysisParserFactory.pm
  M Bio/Factory/SeqAnalysisParserFactoryI.pm
  M Bio/Factory/SequenceFactoryI.pm
  M Bio/Factory/SequenceProcessorI.pm
  M Bio/Factory/SequenceStreamI.pm
  M Bio/Factory/TreeFactoryI.pm
  M Bio/FeatureHolderI.pm
  M Bio/FeatureIO.pm
  M Bio/FeatureIO/gtf.pm
  M Bio/HandlerBaseI.pm
  M Bio/IdCollectionI.pm
  M Bio/IdentifiableI.pm
  M Bio/Index/Abstract.pm
  M Bio/Index/AbstractSeq.pm
  M Bio/Index/Blast.pm
  M Bio/Index/BlastTable.pm
  M Bio/Index/EMBL.pm
  M Bio/Index/Fasta.pm
  M Bio/Index/GenBank.pm
  M Bio/Index/Qual.pm
  M Bio/Index/Stockholm.pm
  M Bio/Index/SwissPfam.pm
  M Bio/Index/Swissprot.pm
  M Bio/LiveSeq/AARange.pm
  M Bio/LiveSeq/Chain.pm
  M Bio/LiveSeq/ChainI.pm
  M Bio/LiveSeq/DNA.pm
  M Bio/LiveSeq/Exon.pm
  M Bio/LiveSeq/Gene.pm
  M Bio/LiveSeq/IO/BioPerl.pm
  M Bio/LiveSeq/IO/Loader.pm
  M Bio/LiveSeq/Intron.pm
  M Bio/LiveSeq/Mutation.pm
  M Bio/LiveSeq/Mutator.pm
  M Bio/LiveSeq/Prim_Transcript.pm
  M Bio/LiveSeq/Range.pm
  M Bio/LiveSeq/Repeat_Region.pm
  M Bio/LiveSeq/Repeat_Unit.pm
  M Bio/LiveSeq/SeqI.pm
  M Bio/LiveSeq/Transcript.pm
  M Bio/LiveSeq/Translation.pm
  M Bio/LocatableSeq.pm
  M Bio/Location/Atomic.pm
  M Bio/Location/AvWithinCoordPolicy.pm
  M Bio/Location/CoordinatePolicyI.pm
  M Bio/Location/Fuzzy.pm
  M Bio/Location/FuzzyLocationI.pm
  M Bio/Location/NarrowestCoordPolicy.pm
  M Bio/Location/Simple.pm
  M Bio/Location/Split.pm
  M Bio/Location/SplitLocationI.pm
  M Bio/Location/WidestCoordPolicy.pm
  M Bio/LocationI.pm
  M Bio/Map/Clone.pm
  M Bio/Map/Contig.pm
  M Bio/Map/CytoMap.pm
  M Bio/Map/CytoMarker.pm
  M Bio/Map/CytoPosition.pm
  M Bio/Map/EntityI.pm
  M Bio/Map/FPCMarker.pm
  M Bio/Map/MapI.pm
  M Bio/Map/Mappable.pm
  M Bio/Map/MappableI.pm
  M Bio/Map/Marker.pm
  M Bio/Map/MarkerI.pm
  M Bio/Map/Physical.pm
  M Bio/Map/Position.pm
  M Bio/Map/PositionHandler.pm
  M Bio/Map/PositionHandlerI.pm
  M Bio/Map/PositionI.pm
  M Bio/Map/Relative.pm
  M Bio/Map/RelativeI.pm
  M Bio/Map/SimpleMap.pm
  M Bio/MapIO.pm
  M Bio/MapIO/mapmaker.pm
  M Bio/Matrix/Generic.pm
  M Bio/Matrix/IO.pm
  M Bio/Matrix/IO/mlagan.pm
  M Bio/Matrix/IO/phylip.pm
  M Bio/Matrix/IO/scoring.pm
  M Bio/Matrix/Mlagan.pm
  M Bio/Matrix/PSM/IO.pm
  M Bio/Matrix/PSM/IO/mast.pm
  M Bio/Matrix/PSM/IO/masta.pm
  M Bio/Matrix/PSM/IO/meme.pm
  M Bio/Matrix/PSM/IO/psiblast.pm
  M Bio/Matrix/PSM/IO/transfac.pm
  M Bio/Matrix/PSM/InstanceSite.pm
  M Bio/Matrix/PSM/InstanceSiteI.pm
  M Bio/Matrix/PSM/ProtMatrix.pm
  M Bio/Matrix/PSM/ProtPsm.pm
  M Bio/Matrix/PSM/Psm.pm
  M Bio/Matrix/PSM/PsmHeader.pm
  M Bio/Matrix/PSM/PsmHeaderI.pm
  M Bio/Matrix/PSM/PsmI.pm
  M Bio/Matrix/PSM/SiteMatrix.pm
  M Bio/Matrix/PSM/SiteMatrixI.pm
  M Bio/Matrix/PhylipDist.pm
  M Bio/Matrix/Scoring.pm
  M Bio/MolEvol/CodonModel.pm
  M Bio/Ontology/DocumentRegistry.pm
  M Bio/Ontology/GOterm.pm
  M Bio/Ontology/InterProTerm.pm
  M Bio/Ontology/OBOEngine.pm
  M Bio/Ontology/OBOterm.pm
  M Bio/Ontology/Ontology.pm
  M Bio/Ontology/OntologyEngineI.pm
  M Bio/Ontology/OntologyI.pm
  M Bio/Ontology/OntologyStore.pm
  M Bio/Ontology/Path.pm
  M Bio/Ontology/PathI.pm
  M Bio/Ontology/Relationship.pm
  M Bio/Ontology/RelationshipFactory.pm
  M Bio/Ontology/RelationshipI.pm
  M Bio/Ontology/RelationshipType.pm
  M Bio/Ontology/SimpleOntologyEngine.pm
  M Bio/Ontology/Term.pm
  M Bio/Ontology/TermFactory.pm
  M Bio/Ontology/TermI.pm
  M Bio/OntologyIO.pm
  M Bio/OntologyIO/Handlers/BaseSAXHandler.pm
  M Bio/OntologyIO/Handlers/InterProHandler.pm
  M Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
  M Bio/OntologyIO/InterProParser.pm
  M Bio/OntologyIO/dagflat.pm
  M Bio/OntologyIO/goflat.pm
  M Bio/OntologyIO/obo.pm
  M Bio/OntologyIO/simplehierarchy.pm
  M Bio/OntologyIO/soflat.pm
  M Bio/ParameterBaseI.pm
  M Bio/Perl.pm
  M Bio/Phenotype/Correlate.pm
  M Bio/Phenotype/MeSH/Term.pm
  M Bio/Phenotype/MeSH/Twig.pm
  M Bio/Phenotype/Measure.pm
  M Bio/Phenotype/OMIM/MiniMIMentry.pm
  M Bio/Phenotype/OMIM/OMIMentry.pm
  M Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
  M Bio/Phenotype/OMIM/OMIMparser.pm
  M Bio/Phenotype/Phenotype.pm
  M Bio/Phenotype/PhenotypeI.pm
  M Bio/PhyloNetwork.pm
  M Bio/PhyloNetwork/Factory.pm
  M Bio/PhyloNetwork/FactoryX.pm
  M Bio/PhyloNetwork/GraphViz.pm
  M Bio/PhyloNetwork/RandomFactory.pm
  M Bio/PhyloNetwork/TreeFactory.pm
  M Bio/PhyloNetwork/TreeFactoryMulti.pm
  M Bio/PhyloNetwork/TreeFactoryX.pm
  M Bio/PhyloNetwork/muVector.pm
  M Bio/PopGen/Genotype.pm
  M Bio/PopGen/IO.pm
  M Bio/PopGen/IO/csv.pm
  M Bio/PopGen/IO/hapmap.pm
  M Bio/PopGen/IO/phase.pm
  M Bio/PopGen/IO/prettybase.pm
  M Bio/PopGen/Individual.pm
  M Bio/PopGen/Marker.pm
  M Bio/PopGen/PopStats.pm
  M Bio/PopGen/Population.pm
  M Bio/PopGen/PopulationI.pm
  M Bio/PopGen/Simulation/Coalescent.pm
  M Bio/PopGen/Simulation/GeneticDrift.pm
  M Bio/PopGen/Statistics.pm
  M Bio/PopGen/Utilities.pm
  M Bio/PrimarySeq.pm
  M Bio/PrimarySeqI.pm
  M Bio/PullParserI.pm
  M Bio/Range.pm
  M Bio/RangeI.pm
  M Bio/Restriction/Analysis.pm
  M Bio/Restriction/Enzyme.pm
  M Bio/Restriction/Enzyme/MultiCut.pm
  M Bio/Restriction/Enzyme/MultiSite.pm
  M Bio/Restriction/EnzymeCollection.pm
  M Bio/Restriction/EnzymeI.pm
  M Bio/Restriction/IO.pm
  M Bio/Restriction/IO/bairoch.pm
  M Bio/Restriction/IO/base.pm
  M Bio/Restriction/IO/itype2.pm
  M Bio/Restriction/IO/prototype.pm
  M Bio/Restriction/IO/withrefm.pm
  M Bio/Root/Build.pm
  M Bio/Root/Exception.pm
  M Bio/Root/HTTPget.pm
  M Bio/Root/IO.pm
  M Bio/Root/Root.pm
  M Bio/Root/RootI.pm
  M Bio/Root/Storable.pm
  M Bio/Root/Test.pm
  M Bio/Root/Test/Warn.pm
  M Bio/Root/Utilities.pm
  M Bio/Root/Version.pm
  M Bio/Search/DatabaseI.pm
  M Bio/Search/GenericDatabase.pm
  M Bio/Search/HSP/BlastHSP.pm
  M Bio/Search/HSP/BlastPullHSP.pm
  M Bio/Search/HSP/FastaHSP.pm
  M Bio/Search/HSP/GenericHSP.pm
  M Bio/Search/HSP/HMMERHSP.pm
  M Bio/Search/HSP/HSPFactory.pm
  M Bio/Search/HSP/HSPI.pm
  M Bio/Search/HSP/HmmpfamHSP.pm
  M Bio/Search/HSP/ModelHSP.pm
  M Bio/Search/HSP/PSLHSP.pm
  M Bio/Search/HSP/PsiBlastHSP.pm
  M Bio/Search/HSP/PullHSPI.pm
  M Bio/Search/HSP/WABAHSP.pm
  M Bio/Search/Hit/BlastHit.pm
  M Bio/Search/Hit/BlastPullHit.pm
  M Bio/Search/Hit/Fasta.pm
  M Bio/Search/Hit/GenericHit.pm
  M Bio/Search/Hit/HMMERHit.pm
  M Bio/Search/Hit/HitFactory.pm
  M Bio/Search/Hit/HitI.pm
  M Bio/Search/Hit/HmmpfamHit.pm
  M Bio/Search/Hit/ModelHit.pm
  M Bio/Search/Hit/PsiBlastHit.pm
  M Bio/Search/Hit/PullHitI.pm
  M Bio/Search/Iteration/GenericIteration.pm
  M Bio/Search/Iteration/IterationI.pm
  M Bio/Search/Result/BlastPullResult.pm
  M Bio/Search/Result/BlastResult.pm
  M Bio/Search/Result/CrossMatchResult.pm
  M Bio/Search/Result/GenericResult.pm
  M Bio/Search/Result/HMMERResult.pm
  M Bio/Search/Result/HmmpfamResult.pm
  M Bio/Search/Result/PullResultI.pm
  M Bio/Search/Result/ResultFactory.pm
  M Bio/Search/Result/ResultI.pm
  M Bio/Search/Result/WABAResult.pm
  M Bio/Search/Tiling/MapTiling.pm
  M Bio/Search/Tiling/TilingI.pm
  M Bio/SearchDist.pm
  M Bio/SearchIO.pm
  M Bio/SearchIO/EventHandlerI.pm
  M Bio/SearchIO/FastHitEventBuilder.pm
  M Bio/SearchIO/IteratedSearchResultEventBuilder.pm
  M Bio/SearchIO/SearchResultEventBuilder.pm
  M Bio/SearchIO/SearchWriterI.pm
  M Bio/SearchIO/Writer/BSMLResultWriter.pm
  M Bio/SearchIO/Writer/GbrowseGFF.pm
  M Bio/SearchIO/Writer/HSPTableWriter.pm
  M Bio/SearchIO/Writer/HTMLResultWriter.pm
  M Bio/SearchIO/Writer/HitTableWriter.pm
  M Bio/SearchIO/Writer/ResultTableWriter.pm
  M Bio/SearchIO/Writer/TextResultWriter.pm
  M Bio/SearchIO/XML/BlastHandler.pm
  M Bio/SearchIO/XML/PsiBlastHandler.pm
  M Bio/SearchIO/axt.pm
  M Bio/SearchIO/blast.pm
  M Bio/SearchIO/blast_pull.pm
  M Bio/SearchIO/blasttable.pm
  M Bio/SearchIO/blastxml.pm
  M Bio/SearchIO/cross_match.pm
  M Bio/SearchIO/erpin.pm
  M Bio/SearchIO/exonerate.pm
  M Bio/SearchIO/fasta.pm
  M Bio/SearchIO/hmmer.pm
  M Bio/SearchIO/hmmer_pull.pm
  M Bio/SearchIO/infernal.pm
  M Bio/SearchIO/megablast.pm
  M Bio/SearchIO/psl.pm
  M Bio/SearchIO/rnamotif.pm
  M Bio/SearchIO/sim4.pm
  M Bio/SearchIO/waba.pm
  M Bio/SearchIO/wise.pm
  M Bio/Seq.pm
  M Bio/Seq/BaseSeqProcessor.pm
  M Bio/Seq/EncodedSeq.pm
  M Bio/Seq/LargePrimarySeq.pm
  M Bio/Seq/LargeSeq.pm
  M Bio/Seq/LargeSeqI.pm
  M Bio/Seq/Meta.pm
  M Bio/Seq/Meta/Array.pm
  M Bio/Seq/MetaI.pm
  M Bio/Seq/PrimaryQual.pm
  M Bio/Seq/PrimedSeq.pm
  M Bio/Seq/QualI.pm
  M Bio/Seq/Quality.pm
  M Bio/Seq/RichSeq.pm
  M Bio/Seq/RichSeqI.pm
  M Bio/Seq/SeqBuilder.pm
  M Bio/Seq/SeqFactory.pm
  M Bio/Seq/SeqFastaSpeedFactory.pm
  M Bio/Seq/SeqWithQuality.pm
  M Bio/Seq/SequenceTrace.pm
  M Bio/SeqAnalysisParserI.pm
  M Bio/SeqEvolution/DNAPoint.pm
  M Bio/SeqEvolution/EvolutionI.pm
  M Bio/SeqEvolution/Factory.pm
  M Bio/SeqFeature/Annotated.pm
  M Bio/SeqFeature/AnnotationAdaptor.pm
  M Bio/SeqFeature/Collection.pm
  M Bio/SeqFeature/CollectionI.pm
  M Bio/SeqFeature/Computation.pm
  M Bio/SeqFeature/FeaturePair.pm
  M Bio/SeqFeature/Gene/Exon.pm
  M Bio/SeqFeature/Gene/ExonI.pm
  M Bio/SeqFeature/Gene/GeneStructure.pm
  M Bio/SeqFeature/Gene/GeneStructureI.pm
  M Bio/SeqFeature/Gene/Intron.pm
  M Bio/SeqFeature/Gene/NC_Feature.pm
  M Bio/SeqFeature/Gene/Poly_A_site.pm
  M Bio/SeqFeature/Gene/Promoter.pm
  M Bio/SeqFeature/Gene/Transcript.pm
  M Bio/SeqFeature/Gene/TranscriptI.pm
  M Bio/SeqFeature/Gene/UTR.pm
  M Bio/SeqFeature/Generic.pm
  M Bio/SeqFeature/PositionProxy.pm
  M Bio/SeqFeature/Primer.pm
  M Bio/SeqFeature/SiRNA/Oligo.pm
  M Bio/SeqFeature/SiRNA/Pair.pm
  M Bio/SeqFeature/Similarity.pm
  M Bio/SeqFeature/SimilarityPair.pm
  M Bio/SeqFeature/Tools/FeatureNamer.pm
  M Bio/SeqFeature/Tools/IDHandler.pm
  M Bio/SeqFeature/Tools/TypeMapper.pm
  M Bio/SeqFeature/Tools/Unflattener.pm
  M Bio/SeqFeature/TypedSeqFeatureI.pm
  M Bio/SeqFeatureI.pm
  M Bio/SeqI.pm
  M Bio/SeqIO.pm
  M Bio/SeqIO/FTHelper.pm
  M Bio/SeqIO/Handler/GenericRichSeqHandler.pm
  M Bio/SeqIO/MultiFile.pm
  M Bio/SeqIO/abi.pm
  M Bio/SeqIO/ace.pm
  M Bio/SeqIO/alf.pm
  M Bio/SeqIO/asciitree.pm
  M Bio/SeqIO/bsml_sax.pm
  M Bio/SeqIO/chadoxml.pm
  M Bio/SeqIO/chaos.pm
  M Bio/SeqIO/chaosxml.pm
  M Bio/SeqIO/ctf.pm
  M Bio/SeqIO/embl.pm
  M Bio/SeqIO/embldriver.pm
  M Bio/SeqIO/entrezgene.pm
  M Bio/SeqIO/excel.pm
  M Bio/SeqIO/exp.pm
  M Bio/SeqIO/fasta.pm
  M Bio/SeqIO/flybase_chadoxml.pm
  M Bio/SeqIO/game.pm
  M Bio/SeqIO/game/featHandler.pm
  M Bio/SeqIO/game/gameSubs.pm
  M Bio/SeqIO/game/gameWriter.pm
  M Bio/SeqIO/game/seqHandler.pm
  M Bio/SeqIO/gbdriver.pm
  M Bio/SeqIO/gcg.pm
  M Bio/SeqIO/genbank.pm
  M Bio/SeqIO/interpro.pm
  M Bio/SeqIO/kegg.pm
  M Bio/SeqIO/largefasta.pm
  M Bio/SeqIO/lasergene.pm
  M Bio/SeqIO/locuslink.pm
  M Bio/SeqIO/metafasta.pm
  M Bio/SeqIO/nexml.pm
  M Bio/SeqIO/phd.pm
  M Bio/SeqIO/pir.pm
  M Bio/SeqIO/pln.pm
  M Bio/SeqIO/qual.pm
  M Bio/SeqIO/raw.pm
  M Bio/SeqIO/scf.pm
  M Bio/SeqIO/seqxml.pm
  M Bio/SeqIO/strider.pm
  M Bio/SeqIO/swiss.pm
  M Bio/SeqIO/swissdriver.pm
  M Bio/SeqIO/tab.pm
  M Bio/SeqIO/table.pm
  M Bio/SeqIO/tigr.pm
  M Bio/SeqIO/tigrxml.pm
  M Bio/SeqIO/ztr.pm
  M Bio/SeqUtils.pm
  M Bio/SimpleAlign.pm
  M Bio/SimpleAnalysisI.pm
  M Bio/Species.pm
  M Bio/Structure/Atom.pm
  M Bio/Structure/Chain.pm
  M Bio/Structure/Entry.pm
  M Bio/Structure/IO.pm
  M Bio/Structure/IO/pdb.pm
  M Bio/Structure/Model.pm
  M Bio/Structure/Residue.pm
  M Bio/Structure/StructureI.pm
  M Bio/Symbol/Alphabet.pm
  M Bio/Symbol/AlphabetI.pm
  M Bio/Symbol/DNAAlphabet.pm
  M Bio/Symbol/ProteinAlphabet.pm
  M Bio/Symbol/Symbol.pm
  M Bio/Symbol/SymbolI.pm
  M Bio/Taxon.pm
  M Bio/Taxonomy.pm
  M Bio/Taxonomy/Node.pm
  M Bio/Taxonomy/Taxon.pm
  M Bio/Taxonomy/Tree.pm
  M Bio/Tools/AlignFactory.pm
  M Bio/Tools/Alignment/Consed.pm
  M Bio/Tools/Alignment/Trim.pm
  M Bio/Tools/Analysis/DNA/ESEfinder.pm
  M Bio/Tools/Analysis/Protein/ELM.pm
  M Bio/Tools/Analysis/Protein/NetPhos.pm
  M Bio/Tools/Analysis/Protein/Scansite.pm
  M Bio/Tools/Analysis/SimpleAnalysisBase.pm
  M Bio/Tools/AnalysisResult.pm
  M Bio/Tools/Blat.pm
  M Bio/Tools/CodonTable.pm
  M Bio/Tools/Coil.pm
  M Bio/Tools/ECnumber.pm
  M Bio/Tools/EMBOSS/Palindrome.pm
  M Bio/Tools/EPCR.pm
  M Bio/Tools/ERPIN.pm
  M Bio/Tools/ESTScan.pm
  M Bio/Tools/EUtilities/Cookie.pm
  M Bio/Tools/EUtilities/History.pm
  M Bio/Tools/EUtilities/Info.pm
  M Bio/Tools/EUtilities/Info/FieldInfo.pm
  M Bio/Tools/EUtilities/Info/LinkInfo.pm
  M Bio/Tools/EUtilities/Query/GlobalQuery.pm
  M Bio/Tools/EUtilities/Summary/DocSum.pm
  M Bio/Tools/EUtilities/Summary/Item.pm
  M Bio/Tools/EUtilities/Summary/ItemContainerI.pm
  M Bio/Tools/Eponine.pm
  M Bio/Tools/Est2Genome.pm
  M Bio/Tools/Fgenesh.pm
  M Bio/Tools/FootPrinter.pm
  M Bio/Tools/GFF.pm
  M Bio/Tools/Gel.pm
  M Bio/Tools/Geneid.pm
  M Bio/Tools/Genemark.pm
  M Bio/Tools/Genewise.pm
  M Bio/Tools/Genomewise.pm
  M Bio/Tools/Genscan.pm
  M Bio/Tools/Glimmer.pm
  M Bio/Tools/Grail.pm
  M Bio/Tools/GuessSeqFormat.pm
  M Bio/Tools/HMMER/Domain.pm
  M Bio/Tools/HMMER/Results.pm
  M Bio/Tools/HMMER/Set.pm
  M Bio/Tools/Hmmpfam.pm
  M Bio/Tools/IUPAC.pm
  M Bio/Tools/Infernal.pm
  M Bio/Tools/Lucy.pm
  M Bio/Tools/MZEF.pm
  M Bio/Tools/Phylo/Gumby.pm
  M Bio/Tools/Phylo/Molphy.pm
  M Bio/Tools/Phylo/Molphy/Result.pm
  M Bio/Tools/Phylo/PAML.pm
  M Bio/Tools/Phylo/PAML/Codeml.pm
  M Bio/Tools/Phylo/PAML/ModelResult.pm
  M Bio/Tools/Phylo/PAML/Result.pm
  M Bio/Tools/Phylo/Phylip/ProtDist.pm
  M Bio/Tools/Prediction/Exon.pm
  M Bio/Tools/Prediction/Gene.pm
  M Bio/Tools/Primer/Assessor/Base.pm
  M Bio/Tools/Primer/AssessorI.pm
  M Bio/Tools/Primer/Feature.pm
  M Bio/Tools/Primer/Pair.pm
  M Bio/Tools/Primer3.pm
  M Bio/Tools/Prints.pm
  M Bio/Tools/Profile.pm
  M Bio/Tools/Promoterwise.pm
  M Bio/Tools/Protparam.pm
  M Bio/Tools/Pseudowise.pm
  M Bio/Tools/QRNA.pm
  M Bio/Tools/RNAMotif.pm
  M Bio/Tools/RandomDistFunctions.pm
  M Bio/Tools/RepeatMasker.pm
  M Bio/Tools/Run/GenericParameters.pm
  M Bio/Tools/Run/ParametersI.pm
  M Bio/Tools/Run/RemoteBlast.pm
  M Bio/Tools/Run/StandAloneBlast.pm
  M Bio/Tools/Run/StandAloneNCBIBlast.pm
  M Bio/Tools/Run/StandAloneWUBlast.pm
  M Bio/Tools/Run/WrapperBase.pm
  M Bio/Tools/Run/WrapperBase/CommandExts.pm
  M Bio/Tools/Seg.pm
  M Bio/Tools/SeqPattern.pm
  M Bio/Tools/SeqStats.pm
  M Bio/Tools/SeqWords.pm
  M Bio/Tools/SiRNA.pm
  M Bio/Tools/Sigcleave.pm
  M Bio/Tools/Signalp.pm
  M Bio/Tools/Signalp/ExtendedSignalp.pm
  M Bio/Tools/Sim4/Exon.pm
  M Bio/Tools/Sim4/Results.pm
  M Bio/Tools/Spidey/Exon.pm
  M Bio/Tools/Spidey/Results.pm
  M Bio/Tools/TargetP.pm
  M Bio/Tools/Tmhmm.pm
  M Bio/Tools/dpAlign.pm
  M Bio/Tools/ipcress.pm
  M Bio/Tools/isPcr.pm
  M Bio/Tools/pICalculator.pm
  M Bio/Tools/pSW.pm
  M Bio/Tools/tRNAscanSE.pm
  M Bio/Tree/AlleleNode.pm
  M Bio/Tree/Compatible.pm
  M Bio/Tree/DistanceFactory.pm
  M Bio/Tree/Draw/Cladogram.pm
  M Bio/Tree/Node.pm
  M Bio/Tree/NodeI.pm
  M Bio/Tree/NodeNHX.pm
  M Bio/Tree/RandomFactory.pm
  M Bio/Tree/Statistics.pm
  M Bio/Tree/Tree.pm
  M Bio/Tree/TreeFunctionsI.pm
  M Bio/Tree/TreeI.pm
  M Bio/TreeIO.pm
  M Bio/TreeIO/TreeEventBuilder.pm
  M Bio/TreeIO/cluster.pm
  M Bio/TreeIO/lintree.pm
  M Bio/TreeIO/newick.pm
  M Bio/TreeIO/nexml.pm
  M Bio/TreeIO/nexus.pm
  M Bio/TreeIO/nhx.pm
  M Bio/TreeIO/pag.pm
  M Bio/TreeIO/tabtree.pm
  M Bio/UpdateableSeqI.pm
  M Bio/Variation/AAChange.pm
  M Bio/Variation/AAReverseMutate.pm
  M Bio/Variation/Allele.pm
  M Bio/Variation/DNAMutation.pm
  M Bio/Variation/IO.pm
  M Bio/Variation/IO/flat.pm
  M Bio/Variation/IO/xml.pm
  M Bio/Variation/RNAChange.pm
  M Bio/Variation/SNP.pm
  M Bio/Variation/SeqDiff.pm
  M Bio/Variation/VariantI.pm
  M Bio/WebAgent.pm
  M examples/align/aligntutorial.pl
  M examples/align/clustalw.pl
  M examples/align/simplealign.pl
  M examples/biblio/biblio-eutils-example.pl
  M examples/biblio/biblio-soap-example.pl
  M examples/contributed/nmrpdb_parse.pl
  M examples/contributed/prosite2perl.pl
  M examples/liveseq/change_gene.pl
  M examples/make_primers.pl
  M examples/popgen/parse_calc_stats.pl
  M examples/rev_and_trans.pl
  M examples/root/exceptions1.pl
  M examples/root/exceptions2.pl
  M examples/root/exceptions3.pl
  M examples/root/exceptions4.pl
  M examples/searchio/custom_writer.pl
  M examples/searchio/hitwriter.pl
  M examples/searchio/hspwriter.pl
  M examples/searchio/htmlwriter.pl
  M examples/searchio/psiblast_features.pl
  M examples/searchio/psiblast_iterations.pl
  M examples/searchio/rawwriter.pl
  M examples/searchio/resultwriter.pl
  M examples/tools/extract_genes.pl
  M examples/tools/psw.pl
  M examples/tools/reverse-translate.pl
  M examples/tools/run_primer3.pl
  M examples/tools/seq_pattern.pl
  M examples/tools/standaloneblast.pl
  M maintenance/authors.pl
  M maintenance/cvs2cl_by_file.pl
  M maintenance/modules.pl
  M maintenance/pod.pl
  M maintenance/version.pl
  M scripts/Bio-DB-GFF/bulk_load_gff.PLS
  M scripts/Bio-DB-GFF/fast_load_gff.PLS
  M scripts/Bio-DB-GFF/genbank2gff.PLS
  M scripts/Bio-DB-GFF/generate_histogram.PLS
  M scripts/Bio-DB-GFF/process_sgd.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
  M scripts/DB/biofetch_genbank_proxy.PLS
  M scripts/DB/biogetseq.PLS
  M scripts/DB/flanks.PLS
  M scripts/biblio/biblio.PLS
  M scripts/das/das_server.pl
  M scripts/index/bp_seqret.PLS
  M scripts/popgen/composite_LD.PLS
  M scripts/popgen/heterogeneity_test.PLS
  M scripts/searchio/filter_search.PLS
  M scripts/searchio/parse_hmmsearch.PLS
  M scripts/seq/extract_feature_seq.PLS
  M scripts/seq/make_mrna_protein.PLS
  M scripts/seq/seqconvert.PLS
  M scripts/seq/seqretsplit.PLS
  M scripts/seq/split_seq.PLS
  M scripts/seq/translate_seq.PLS
  M scripts/seq/unflatten_seq.PLS
  M scripts/seqstats/aacomp.PLS
  M scripts/seqstats/chaos_plot.PLS
  M scripts/seqstats/gccalc.PLS
  M scripts/seqstats/oligo_count.PLS
  M scripts/taxa/classify_hits_kingdom.PLS
  M scripts/utilities/bp_mrtrans.PLS
  M scripts/utilities/bp_nrdb.PLS
  M scripts/utilities/mask_by_search.PLS
  M scripts/utilities/pairwise_kaks.PLS
  M scripts/utilities/remote_blast.PLS
  M scripts/utilities/revtrans-motif.PLS
  M scripts/utilities/search2BSML.PLS
  M scripts/utilities/search2alnblocks.PLS
  M scripts/utilities/search2gff.PLS
  M scripts/utilities/search2tribe.PLS
  M t/lib/Array/Compare.pm

Log Message:
-----------
Merge branch 'master' into branch-1-6



From noreply at github.com  Fri Jul 30 00:27:12 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 29 Jul 2010 21:27:12 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 4ee526: [bug 3122] catch
	seek calls on the unseekable (tha...
Message-ID: <20100730042712.E60DB4233F@smtp1.rs.github.com>

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

Commit: 4ee526b24557ae40c39a0090ef95a5d42d186c48
    http://github.com/bioperl/bioperl-live/commit/4ee526b24557ae40c39a0090ef95a5d42d186c48
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M Bio/Tools/GuessSeqFormat.pm
  M Changes

Log Message:
-----------
[bug 3122] catch seek calls on the unseekable (thanks to Stefan and Roy)



From bugzilla-daemon at portal.open-bio.org  Fri Jul 30 00:28:46 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Jul 2010 00:28:46 -0400
Subject: [Bioperl-guts-l] [Bug 3122] Bio::SeqIO ignores first line of piped
	Fasta sequence when no format parameter is set
In-Reply-To: <bug-3122-25@http.bugzilla.open-bio.org/>
Message-ID: <201007300428.o6U4SkIa032225@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3122


cjfields at bioperl.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #3 from cjfields at bioperl.org  2010-07-30 00:28 EST -------
Fixed on master branch, to appear in 1.6.2 alpha1.  Thanks all!


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From bugzilla-daemon at portal.open-bio.org  Fri Jul 30 00:31:19 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Jul 2010 00:31:19 -0400
Subject: [Bioperl-guts-l] [Bug 3125] bioperl-run LVB.pm and LVB.t require
	updates for LVB version 2.3
In-Reply-To: <bug-3125-25@http.bugzilla.open-bio.org/>
Message-ID: <201007300431.o6U4VJwr001731@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3125





------- Comment #1 from cjfields at bioperl.org  2010-07-30 00:31 EST -------
Not sure when we can get to this; all depends on how difficult it will be to
update it. 


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From noreply at github.com  Fri Jul 30 00:47:52 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 29 Jul 2010 21:47:52 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] b31f53: [bug 3126] catch
	description (patch courtesy Toshi...
Message-ID: <20100730044752.37E9642360@smtp1.rs.github.com>

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

Commit: b31f53500ff6e58c44a51d6e299ed5bef75f5a6a
    http://github.com/bioperl/bioperl-live/commit/b31f53500ff6e58c44a51d6e299ed5bef75f5a6a
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M Bio/DB/Fasta.pm
  M Changes
  M t/LocalDB/DBFasta.t
  M t/data/dbfa/1.fa

Log Message:
-----------
[bug 3126] catch description (patch courtesy Toshihiko Akiba); test added



From bugzilla-daemon at portal.open-bio.org  Fri Jul 30 00:48:07 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Jul 2010 00:48:07 -0400
Subject: [Bioperl-guts-l] [Bug 3126] description() method returns nothing in
	Bio::DB::Fasta
In-Reply-To: <bug-3126-25@http.bugzilla.open-bio.org/>
Message-ID: <201007300448.o6U4m7m8003614@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3126


cjfields at bioperl.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #2 from cjfields at bioperl.org  2010-07-30 00:48 EST -------
Patch committed, thanks!


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From bugzilla-daemon at portal.open-bio.org  Fri Jul 30 00:50:40 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Jul 2010 00:50:40 -0400
Subject: [Bioperl-guts-l] [Bug 3028] Bio::TreeIO::nexus Fails to correctly
	output FigTree Formatting tags
In-Reply-To: <bug-3028-25@http.bugzilla.open-bio.org/>
Message-ID: <201007300450.o6U4oeLr003676@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3028


cjfields at bioperl.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|REOPENED                    |RESOLVED
         Resolution|                            |FIXED




------- Comment #6 from cjfields at bioperl.org  2010-07-30 00:50 EST -------
No reply.  Closing, unfortunately w/o tests.


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From noreply at github.com  Fri Jul 30 01:02:23 2010
From: noreply at github.com (noreply at github.com)
Date: Thu, 29 Jul 2010 22:02:23 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 15aad7: [bug 3039] added
	Dave's changes to a branch; these...
Message-ID: <20100730050223.80C3742340@smtp1.rs.github.com>

Branch: refs/heads/topic/bug3039
Home:   http://github.com/bioperl/bioperl-live

Commit: 15aad7e8f7079d7dd7e92e05de1ed9d56d367ce6
    http://github.com/bioperl/bioperl-live/commit/15aad7e8f7079d7dd7e92e05de1ed9d56d367ce6
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M Bio/TreeIO/newick.pm
  M t/Tree/TreeIO/newick.t

Log Message:
-----------
[bug 3039] added Dave's changes to a branch; these are causing test failures outside of t/newick.t, unfortunately, so needs investigating



From bugzilla-daemon at portal.open-bio.org  Fri Jul 30 01:04:36 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Jul 2010 01:04:36 -0400
Subject: [Bioperl-guts-l] [Bug 3039] TreeIO::newick writes root node branch
	length incorrectly
In-Reply-To: <bug-3039-25@http.bugzilla.open-bio.org/>
Message-ID: <201007300504.o6U54aYT007275@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3039





------- Comment #4 from cjfields at bioperl.org  2010-07-30 01:04 EST -------
Dave, these are causing failures with other tests.  I think it's close, though
(some of the failures may be due to bad test data, so need a look from someone
with newick experience).  

Within t/Tree:

t/Tree/Compatible.t .................. ok   
t/Tree/Node.t ........................ 1/40 Argument "fake" isn't numeric in
numeric eq (==) at Bio/TreeIO/newick.pm line 357, <GEN0> line 1.

#   Failed test 'after reroot on fake node'
#   at t/Tree/Node.t line 100.
#          got: '(B:23,(C:50,(A:52,D:70)68:11):23):fake;
# '
#     expected: '(B:23,(C:50,(A:52,D:70)68:11):23)fake;
# '
Argument "B" isn't numeric in numeric eq (==) at Bio/TreeIO/newick.pm line 357,
<GEN0> line 1.

#   Failed test 'reroot on B'
#   at t/Tree/Node.t line 103.
#          got: '(((C:50,(A:52,D:70)68:11):23)fake:23):B;
# '
#     expected: '(((C:50,(A:52,D:70)68:11):23)fake:23)B;
# '
# Looks like you failed 2 tests of 40.
t/Tree/Node.t ........................ Dubious, test returned 2 (wstat 512,
0x200)
Failed 2/40 subtests 
t/Tree/PhyloNetwork/Factory.t ........ ok     
t/Tree/PhyloNetwork/GraphViz.t ....... ok   
t/Tree/PhyloNetwork/MuVector.t ....... ok   
t/Tree/PhyloNetwork/PhyloNetwork.t ... ok     
t/Tree/PhyloNetwork/RandomFactory.t .. 1/70 Argument "Node4" isn't numeric in
numeric eq (==) at Bio/TreeIO/newick.pm line 357.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Graph is not DAG:#H1-l1,Node3-#H1,Node3-l2,T1-#H1,T1-Node3,T1-T1,T1-l3
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
STACK: Bio::PhyloNetwork::recompute Bio/PhyloNetwork.pm:597
STACK: Bio::PhyloNetwork::build_from_graph Bio/PhyloNetwork.pm:373
STACK: Bio::PhyloNetwork::do_attack Bio/PhyloNetwork.pm:652
STACK: Bio::PhyloNetwork::RandomFactory::random_attack
Bio/PhyloNetwork/RandomFactory.pm:181
STACK: Bio::PhyloNetwork::RandomFactory::next_network
Bio/PhyloNetwork/RandomFactory.pm:155
STACK: t/Tree/PhyloNetwork/RandomFactory.t:22
-----------------------------------------------------------
# Looks like you planned 70 tests but ran 2.
# Looks like your test exited with 255 just after 2.
t/Tree/PhyloNetwork/RandomFactory.t .. Dubious, test returned 255 (wstat 65280,
0xff00)
Failed 68/70 subtests 
t/Tree/PhyloNetwork/TreeFactory.t .... ok     
t/Tree/RandomTreeFactory.t ........... 1/5 Argument "Node8" isn't numeric in
numeric eq (==) at Bio/TreeIO/newick.pm line 357.
t/Tree/RandomTreeFactory.t ........... ok   
t/Tree/Tree.t ........................ ok     
t/Tree/TreeIO.t ...................... ok     
t/Tree/TreeIO/lintree.t .............. ok     
t/Tree/TreeIO/newick.t ............... 1/27 Odd number of elements in hash
assignment at Bio/TreeIO.pm line 128.
Use of uninitialized value within @_ in list assignment at Bio/Root/Root.pm
line 261.
Use of uninitialized value within @_ in list assignment at Bio/Root/Root.pm
line 261.
t/Tree/TreeIO/newick.t ............... ok     
t/Tree/TreeIO/nexml.t ................ 1/46 # Begin tests for writing tree
files
t/Tree/TreeIO/nexml.t ................ ok     
t/Tree/TreeIO/nexus.t ................ ok     
t/Tree/TreeIO/nhx.t .................. ok   
t/Tree/TreeIO/phyloxml.t ............. ok     
t/Tree/TreeIO/svggraph.t ............. ok   
t/Tree/TreeIO/tabtree.t .............. ok     
t/Tree/TreeStatistics.t .............. ok  


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From bugzilla-daemon at portal.open-bio.org  Fri Jul 30 01:05:59 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Jul 2010 01:05:59 -0400
Subject: [Bioperl-guts-l] [Bug 3039] TreeIO::newick writes root node branch
	length incorrectly
In-Reply-To: <bug-3039-25@http.bugzilla.open-bio.org/>
Message-ID: <201007300505.o6U55xU6007323@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3039





------- Comment #5 from cjfields at bioperl.org  2010-07-30 01:05 EST -------
Forgot to mention, these are in the branch 'topic/bug3039' on github.


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From bugzilla-daemon at portal.open-bio.org  Fri Jul 30 01:09:04 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Jul 2010 01:09:04 -0400
Subject: [Bioperl-guts-l] [Bug 3056] Bio::Tools::Run::Primer3 has not
	updated for Primer3 versions 2 and above
In-Reply-To: <bug-3056-25@http.bugzilla.open-bio.org/>
Message-ID: <201007300509.o6U594Fd007425@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3056





------- Comment #2 from cjfields at bioperl.org  2010-07-30 01:09 EST -------
Addendum : code is now in GitHub.

(In reply to comment #1)
> Won't fix.  We have an experimental Primer3 reimplementation in bioperl-dev
> that you are welcome to try, called Bio::Tools::Primer3Redux (it has a
> different API, hence the name).  
> 
> You can checkout the latest code using svn.  I'll leave this open in the
> meantime, as it still needs tests.


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From noreply at github.com  Fri Jul 30 12:01:47 2010
From: noreply at github.com (noreply at github.com)
Date: Fri, 30 Jul 2010 09:01:47 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] b0b52c: dir in maint for
	working on dynamiting the monolit...
Message-ID: <20100730160147.AAD61422FE@smtp1.rs.github.com>

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

Commit: b0b52cc1eebeef12f5704cbf10a99e231c3a7856
    http://github.com/bioperl/bioperl-live/commit/b0b52cc1eebeef12f5704cbf10a99e231c3a7856
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-30 (Fri, 30 Jul 2010)

Changed paths:
  A maintenance/big_split/file_classification.csv
  A maintenance/big_split/rbuels_notes.txt

Log Message:
-----------
dir in maint for working on dynamiting the monolith



From bugzilla-daemon at portal.open-bio.org  Fri Jul 30 12:16:56 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Jul 2010 12:16:56 -0400
Subject: [Bioperl-guts-l] [Bug 3125] bioperl-run LVB.pm and LVB.t require
	updates for LVB version 2.3
In-Reply-To: <bug-3125-25@http.bugzilla.open-bio.org/>
Message-ID: <201007301616.o6UGGu2l000776@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3125





------- Comment #2 from db60 at st-andrews.ac.uk  2010-07-30 12:16 EST -------
(In reply to comment #1)

Dear Chris,

Thank you for your rapid reply.

> Not sure when we can get to this; all depends on how difficult it will be to
> update it.

If someone were able to get the tests passing for LVB 2.2 again (or I am doing
something wrong that makes them fail?), I could adapt them to LVB 2.3.
Alternatively: would you be able to remove LVB.pm and LVB.t from BioPerl?

The old version of LVB required stdin as follows:

i|s
u|f
integer 0 to 900000000 | blank line
f|s
integer 1 to 1000000 | blank line

The new version requires one less line:

i|s
u|f
integer 0 to 0 to 900000000 or blank line
integer 1 to 1000000 or blank line

For example, this would be valid stdin for LVB 2.2:

===begin quote===
i
u

s

===end quote===

The corresponding stdin for LVB 2.3 would be:

===begin quote===
i
u


===end quote===

Best wishes,

Daniel


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From noreply at github.com  Fri Jul 30 13:01:20 2010
From: noreply at github.com (noreply at github.com)
Date: Fri, 30 Jul 2010 10:01:20 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] c1abbd: Force ID field for
	all gb files converted to gff3
Message-ID: <20100730170120.2614A42331@smtp1.rs.github.com>

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

Commit: c1abbd13a50eff41f9fc5d3780765e6a89ead83a
    http://github.com/bioperl/bioperl-live/commit/c1abbd13a50eff41f9fc5d3780765e6a89ead83a
Author: Nathan Liles <nml5566 at dev.open-bio.org>
Date:   2010-07-30 (Fri, 30 Jul 2010)

Changed paths:
  M Bio/Tools/GFF.pm
  M Build.PL

Log Message:
-----------
Force ID field for all gb files converted to gff3



From noreply at github.com  Fri Jul 30 13:24:40 2010
From: noreply at github.com (noreply at github.com)
Date: Fri, 30 Jul 2010 10:24:40 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 4ee526: [bug 3122] catch
	seek calls on the unseekable (tha...
Message-ID: <20100730172440.9F8E84233C@smtp1.rs.github.com>

Branch: refs/heads/branch-1-6
Home:   http://github.com/bioperl/bioperl-live

Commit: 4ee526b24557ae40c39a0090ef95a5d42d186c48
    http://github.com/bioperl/bioperl-live/commit/4ee526b24557ae40c39a0090ef95a5d42d186c48
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M Bio/Tools/GuessSeqFormat.pm
  M Changes

Log Message:
-----------
[bug 3122] catch seek calls on the unseekable (thanks to Stefan and Roy)


Commit: b31f53500ff6e58c44a51d6e299ed5bef75f5a6a
    http://github.com/bioperl/bioperl-live/commit/b31f53500ff6e58c44a51d6e299ed5bef75f5a6a
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-29 (Thu, 29 Jul 2010)

Changed paths:
  M Bio/DB/Fasta.pm
  M Changes
  M t/LocalDB/DBFasta.t
  M t/data/dbfa/1.fa

Log Message:
-----------
[bug 3126] catch description (patch courtesy Toshihiko Akiba); test added


Commit: b0b52cc1eebeef12f5704cbf10a99e231c3a7856
    http://github.com/bioperl/bioperl-live/commit/b0b52cc1eebeef12f5704cbf10a99e231c3a7856
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2010-07-30 (Fri, 30 Jul 2010)

Changed paths:
  A maintenance/big_split/file_classification.csv
  A maintenance/big_split/rbuels_notes.txt

Log Message:
-----------
dir in maint for working on dynamiting the monolith


Commit: c1abbd13a50eff41f9fc5d3780765e6a89ead83a
    http://github.com/bioperl/bioperl-live/commit/c1abbd13a50eff41f9fc5d3780765e6a89ead83a
Author: Nathan Liles <nml5566 at dev.open-bio.org>
Date:   2010-07-30 (Fri, 30 Jul 2010)

Changed paths:
  M Bio/Tools/GFF.pm
  M Build.PL

Log Message:
-----------
Force ID field for all gb files converted to gff3


Commit: 7f6ac0bcf4da43b157452793cd734eae0858fc39
    http://github.com/bioperl/bioperl-live/commit/7f6ac0bcf4da43b157452793cd734eae0858fc39
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-30 (Fri, 30 Jul 2010)

Changed paths:
  M ide/bioperl-mode/dist/bioperl-mode-xemacs.tar
  M ide/bioperl-mode/dist/bioperl-mode.tar

Log Message:
-----------
sync tars over from master


Commit: 1766d4ede599f6ffcb3bd4c2334674e849414369
    http://github.com/bioperl/bioperl-live/commit/1766d4ede599f6ffcb3bd4c2334674e849414369
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-30 (Fri, 30 Jul 2010)

Changed paths:
  M Bio/DB/Fasta.pm
  M Bio/Tools/GFF.pm
  M Bio/Tools/GuessSeqFormat.pm
  M Build.PL
  M Changes
  A maintenance/big_split/file_classification.csv
  A maintenance/big_split/rbuels_notes.txt
  M t/LocalDB/DBFasta.t
  M t/data/dbfa/1.fa

Log Message:
-----------
Merge branch 'master' into branch-1-6



From noreply at github.com  Fri Jul 30 15:58:51 2010
From: noreply at github.com (noreply at github.com)
Date: Fri, 30 Jul 2010 12:58:51 -0700
Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 56ba53: return the first
	note (scalar context of array, wa...
Message-ID: <20100730195851.58FC94234F@smtp1.rs.github.com>

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

Commit: 56ba5382b9df6583417bb2c82253b122644542ab
    http://github.com/bioperl/bioperl-live/commit/56ba5382b9df6583417bb2c82253b122644542ab
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-07-30 (Fri, 30 Jul 2010)

Changed paths:
  M Bio/SeqFeature/Lite.pm

Log Message:
-----------
return the first note (scalar context of array, was returning number of notes)



From bugzilla-daemon at portal.open-bio.org  Sat Jul 31 00:34:25 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sat, 31 Jul 2010 00:34:25 -0400
Subject: [Bioperl-guts-l] [Bug 3108] Bio::SearchIO
In-Reply-To: <bug-3108-25@http.bugzilla.open-bio.org/>
Message-ID: <201007310434.o6V4YPlp014629@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3108


cjfields at bioperl.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |INVALID




------- Comment #3 from cjfields at bioperl.org  2010-07-31 00:34 EST -------
Ruling invalid based on lack of response.  Feel free to reopen if you have a
specific BLAST report example demonstrating the bug.


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From bugzilla-daemon at portal.open-bio.org  Sat Jul 31 16:43:53 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sat, 31 Jul 2010 16:43:53 -0400
Subject: [Bioperl-guts-l] [Bug 2691] Bio::Microarray::Tools::ReseqChip
	depends on CPAN module Statistics::Frequency
In-Reply-To: <bug-2691-25@http.bugzilla.open-bio.org/>
Message-ID: <201007312043.o6VKhr2M000715@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2691


cjfields at bioperl.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #9 from cjfields at bioperl.org  2010-07-31 16:43 EST -------
Moved to a separate distribution (Bio-Microarray), the dependencies are
localized with that distribution now.  Closing out.


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From bugzilla-daemon at portal.open-bio.org  Sat Jul 31 16:44:51 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sat, 31 Jul 2010 16:44:51 -0400
Subject: [Bioperl-guts-l] [Bug 2332] Software for analysis of redundant
	fragments of affys human mitochip v2
In-Reply-To: <bug-2332-25@http.bugzilla.open-bio.org/>
Message-ID: <201007312044.o6VKipo3000762@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2332


cjfields at bioperl.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|ASSIGNED                    |RESOLVED
         Resolution|                            |FIXED




------- Comment #20 from cjfields at bioperl.org  2010-07-31 16:44 EST -------
Now in the Bio-Microarray distribution on github.  Closing out.


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From bugzilla-daemon at portal.open-bio.org  Sat Jul 31 16:44:53 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sat, 31 Jul 2010 16:44:53 -0400
Subject: [Bioperl-guts-l] [Bug 2691] Bio::Microarray::Tools::ReseqChip
	depends on CPAN module Statistics::Frequency
In-Reply-To: <bug-2691-25@http.bugzilla.open-bio.org/>
Message-ID: <201007312044.o6VKirmV000774@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2691


Bug 2691 depends on bug 2332, which changed state.

Bug 2332 Summary: Software for analysis of redundant fragments of affys human mitochip v2
http://bugzilla.open-bio.org/show_bug.cgi?id=2332

           What    |Old Value                   |New Value
----------------------------------------------------------------------------
             Status|ASSIGNED                    |RESOLVED
         Resolution|                            |FIXED



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From bugzilla-daemon at portal.open-bio.org  Sat Jul 31 16:59:39 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sat, 31 Jul 2010 16:59:39 -0400
Subject: [Bioperl-guts-l] [Bug 2673] original fields not inherited by seq
	objects in alignment slices
In-Reply-To: <bug-2673-25@http.bugzilla.open-bio.org/>
Message-ID: <201007312059.o6VKxdm8012023@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2673


cjfields at bioperl.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|ASSIGNED                    |RESOLVED
         Resolution|                            |FIXED




------- Comment #10 from cjfields at bioperl.org  2010-07-31 16:59 EST -------
Per the last reply, I think we have this functionality covered.  Closing out.


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From bugzilla-daemon at portal.open-bio.org  Sat Jul 31 16:59:41 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sat, 31 Jul 2010 16:59:41 -0400
Subject: [Bioperl-guts-l] [Bug 2775] is_circular not maintained through
	->revcom
In-Reply-To: <bug-2775-25@http.bugzilla.open-bio.org/>
Message-ID: <201007312059.o6VKxfLw012052@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2775


cjfields at bioperl.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
   Target Milestone|1.6.1 point release         |1.6.3 point release

Bug 2775 depends on bug 2673, which changed state.

Bug 2673 Summary: original fields not inherited by seq objects in alignment slices
http://bugzilla.open-bio.org/show_bug.cgi?id=2673

           What    |Old Value                   |New Value
----------------------------------------------------------------------------
             Status|ASSIGNED                    |RESOLVED
         Resolution|                            |FIXED



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