[Bioperl-guts-l] [bioperl/bioperl-live] 2eca6f: updated FASTA result parsing for version 3.6; FAST...

Mon Nov 8 17:01:14 EST 2010

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

Commit: 2eca6fcfbde3c8639941805670e93a68baef1c97
    https://github.com/bioperl/bioperl-live/commit/2eca6fcfbde3c8639941805670e93a68baef1c97
Author: Aaron J. Mackey <amackey at virginia.edu>
Date:   2010-09-21 (Tue, 21 Sep 2010)

Changed paths:
  M Bio/Search/HSP/FastaHSP.pm
  M Bio/SearchIO/fasta.pm

Log Message:
-----------
updated FASTA result parsing for version 3.6; FASTA hits may now include more than one HSP, and report E2() expectations via \$hsp->evalue2()

Commit: 0ae94bafb9ec919a477ecc5b20024ec9482afbe4
    https://github.com/bioperl/bioperl-live/commit/0ae94bafb9ec919a477ecc5b20024ec9482afbe4
Author: Naama Menda <nm249 at cornell.edu>
Date:   2010-09-22 (Wed, 22 Sep 2010)

Changed paths:
  M t/Ontology/IO/obo.t
  A t/data/sp_subset.obo

Log Message:
-----------
added tests for obo.pm parsing secondary ids

Commit: 6285ff0f21df957cb702fd210daa06454390f56a
    https://github.com/bioperl/bioperl-live/commit/6285ff0f21df957cb702fd210daa06454390f56a
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-09-22 (Wed, 22 Sep 2010)

Changed paths:
  M MANIFEST

Log Message:
-----------
update manifest

Commit: f4a2731cb2e9d83f1c317cea2acf598db676ecc4
    https://github.com/bioperl/bioperl-live/commit/f4a2731cb2e9d83f1c317cea2acf598db676ecc4
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-09-22 (Wed, 22 Sep 2010)

Changed paths:
  M MANIFEST.SKIP

Log Message:
-----------
update MANIFEST.SKIP

Commit: fb5c8bb0f5d3e2367e52bc37f638ec21f69667bf
    https://github.com/bioperl/bioperl-live/commit/fb5c8bb0f5d3e2367e52bc37f638ec21f69667bf
Author: Jonathan "Duke" Leto <jonathan at leto.net>
Date:   2010-09-26 (Sun, 26 Sep 2010)

Changed paths:
  M t/Ontology/IO/obo.t
  A t/data/sp_subset.obo

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

Commit: 52b69943dc5fb8d9eafbd38748776e42a63ec366
    https://github.com/bioperl/bioperl-live/commit/52b69943dc5fb8d9eafbd38748776e42a63ec366
Author: Jonathan "Duke" Leto <jonathan at leto.net>
Date:   2010-09-27 (Mon, 27 Sep 2010)

Changed paths:
  M Changes

Log Message:
-----------
Add note to Changes about new OBO parsing features

Commit: 18b0fd2233cc6a7b359b1ab7a6902159e373b7f4
    https://github.com/bioperl/bioperl-live/commit/18b0fd2233cc6a7b359b1ab7a6902159e373b7f4
Author: Dave Messina <online at davemessina.com>
Date:   2010-09-28 (Tue, 28 Sep 2010)

Changed paths:
  M examples/make_primers.pl

Log Message:
-----------
typo in docs

Commit: 5d928aee0d2a8963939615d4fedeedb867769425
    https://github.com/bioperl/bioperl-live/commit/5d928aee0d2a8963939615d4fedeedb867769425
Author: Kai Blin <kai.blin at biotech.uni-tuebingen.de>
Date:   2010-10-06 (Wed, 06 Oct 2010)

Changed paths:
  M Bio/SearchIO/hmmer3.pm
  M t/SearchIO/hmmer3.t

Log Message:
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Bio::SearchIO::hmmer3: Fix the hmm and query start/stop positions

While writing the tests I misunderstood the values in the hmmer output. Fixed the tests to test for the correct values, fixed the parser to report the correct values.

Commit: 002d1e64e69437ea20b022ac42c2c8a27c49ba29
    https://github.com/bioperl/bioperl-live/commit/002d1e64e69437ea20b022ac42c2c8a27c49ba29
Author: Kai Blin <kai.blin at biotech.uni-tuebingen.de>
Date:   2010-10-06 (Wed, 06 Oct 2010)

Changed paths:
  M Bio/SearchIO/hmmer3.pm
  M t/SearchIO/hmmer3.t

Log Message:
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SearchIO::hmmer3: Correctly parse out aligments

The hmmer3 parser failed to correctly parse out the hit sequence, the
conservation sequence and the query sequence from alignments.

Fixed bug #3136

Commit: 7a0b8512bfc07203de13fd810224ef017dd5c814
    https://github.com/bioperl/bioperl-live/commit/7a0b8512bfc07203de13fd810224ef017dd5c814
Author: Kai Blin <kai.blin at biotech.uni-tuebingen.de>
Date:   2010-10-07 (Thu, 07 Oct 2010)

Changed paths:
  M Bio/SearchIO/hmmer3.pm
  M t/SearchIO/hmmer3.t
  A t/data/hmmscan_sec_struct.out

Log Message:
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Bio::SearchIO::hmmer3: Deal with possible model track

Some hmmer3 result files have a line giving a secondary structure model.
Deal with these results while not breaking the existing files.

Commit: f642bfad8996f4a17e69da3cfabb758bcd1315be
    https://github.com/bioperl/bioperl-live/commit/f642bfad8996f4a17e69da3cfabb758bcd1315be
Author: Kai Blin <kai.blin at biotech.uni-tuebingen.de>
Date:   2010-10-07 (Thu, 07 Oct 2010)

Changed paths:
  M Bio/SearchIO/hmmer3.pm
  M t/SearchIO/hmmer3.t
  M t/data/hmmscan_sec_struct.out

Log Message:
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Bio::SearchIO::hmmer3: Model file indicator is at end of line

Forgot a $ in the regext for the secondary structure mode line detection
regex, so that regex misdetected alignments containing Cys-Ser AAs.

Add a test case, fix the bug.

Commit: b8687ba4295c141fc28eb4766bcb759623ec3944
    https://github.com/bioperl/bioperl-live/commit/b8687ba4295c141fc28eb4766bcb759623ec3944
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-10-11 (Mon, 11 Oct 2010)

Changed paths:
  M Bio/SearchIO/axt.pm
  A t/SearchIO/axt.t
  A t/data/test_data.axt

Log Message:
-----------
[bug 3145] fix courtesy Aaron Goodman.  AXT parsing was also missing tests, so added minimal tests and data

Commit: 6e3a9768a91a662b063b8237a2597de7213ad59b
    https://github.com/bioperl/bioperl-live/commit/6e3a9768a91a662b063b8237a2597de7213ad59b
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-10-11 (Mon, 11 Oct 2010)

Changed paths:
  M Bio/SeqIO/fastq.pm

Log Message:
-----------
[bug 3133] add some ducmentation on the quality_header() flag, which prints out the (redudant) header for the quality line if set

Commit: ed246bc622e75ba56844e2fe78609a039e03d37c
    https://github.com/bioperl/bioperl-live/commit/ed246bc622e75ba56844e2fe78609a039e03d37c
Author: Jonathan "Duke" Leto <jonathan at leto.net>
Date:   2010-10-13 (Wed, 13 Oct 2010)

Changed paths:
  M Bio/Ontology/SimpleOntologyEngine.pm
  M Bio/OntologyIO/Handlers/InterProHandler.pm
  M t/Ontology/Ontology.t
  A t/data/interpro_relationship.xml

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

Commit: be285e28341f265cb628ea0d8922499bf443a778
    https://github.com/bioperl/bioperl-live/commit/be285e28341f265cb628ea0d8922499bf443a778
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-10-13 (Wed, 13 Oct 2010)

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

Log Message:
-----------
catch using simple string instead of array ref for id param, so one doesn't have to do []; this broke recently when adding code allowing the use of POST for large requests

Commit: 7990837e8bd0266759a144d8277a38e1a2c11931
    https://github.com/bioperl/bioperl-live/commit/7990837e8bd0266759a144d8277a38e1a2c11931
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-10-15 (Fri, 15 Oct 2010)

Changed paths:
  M Bio/Tools/EUtilities.pm
  M Bio/Tools/EUtilities/Summary/ItemContainerI.pm
  M t/RemoteDB/EUtilities.t

Log Message:
-----------
fix get_count so it returns the actual number of IDs returned if no actual count is set

Commit: b266b538bc2c3cd9512fe58f8b7d720fd5c59578
    https://github.com/bioperl/bioperl-live/commit/b266b538bc2c3cd9512fe58f8b7d720fd5c59578
Author: Dave Messina <online at davemessina.com>
Date:   2010-10-17 (Sun, 17 Oct 2010)

Changed paths:
  M Bio/DB/GenBank.pm

Log Message:
-----------
clarify documentation on what's returned from new()

Commit: b49db38d75ad47091928828e18234b1d922cbdf9
    https://github.com/bioperl/bioperl-live/commit/b49db38d75ad47091928828e18234b1d922cbdf9
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-10-24 (Sun, 24 Oct 2010)

Changed paths:
  M Bio/DB/SwissProt.pm

Log Message:
-----------
[bug 3148] switch default to "expasy" until we can work out REST service interface

Commit: f078d3ac493a9e4e2b558aa9721a9fce80f4639c
    https://github.com/bioperl/bioperl-live/commit/f078d3ac493a9e4e2b558aa9721a9fce80f4639c
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-10-26 (Tue, 26 Oct 2010)

Changed paths:
  M Bio/DB/SwissProt.pm

Log Message:
-----------
[bug 3148] URL change at DBFetch was the culprit; default back to EBI

Commit: 008214f69a50e5e47a300eb1c314bce326be37f9
    https://github.com/bioperl/bioperl-live/commit/008214f69a50e5e47a300eb1c314bce326be37f9
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-10-26 (Tue, 26 Oct 2010)

Changed paths:
  M Bio/DB/BioFetch.pm

Log Message:
-----------
URL changed for DBFetch

Commit: ce7df8e3986693760ca2b51c141950445ee56a39
    https://github.com/bioperl/bioperl-live/commit/ce7df8e3986693760ca2b51c141950445ee56a39
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-10-26 (Tue, 26 Oct 2010)

Changed paths:
  M t/RemoteDB/EMBL.t

Log Message:
-----------
future-proof a test

Commit: 8e7666cc06c67c19fd2bb22ba1fbae1101876cd8
    https://github.com/bioperl/bioperl-live/commit/8e7666cc06c67c19fd2bb22ba1fbae1101876cd8
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-10-27 (Wed, 27 Oct 2010)

Changed paths:
  M Bio/DB/Biblio/biofetch.pm
  M Bio/DB/EMBL.pm
  M Bio/DB/RefSeq.pm

Log Message:
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more DBFetch URL changes (might be nice to centralize this, but I digress....)

Commit: 11b87613fbe77070682850a68a7304bd18b55e3a
    https://github.com/bioperl/bioperl-live/commit/11b87613fbe77070682850a68a7304bd18b55e3a
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-10-27 (Wed, 27 Oct 2010)

Changed paths:
  M Bio/DB/Biblio/biofetch.pm
  M Bio/DB/BioFetch.pm
  M Bio/DB/EMBL.pm
  M Bio/DB/RefSeq.pm
  M examples/db/dbfetch
  M scripts/DB/biofetch_genbank_proxy.PLS

Log Message:
-----------
even more DBFetch changes, yay!

Commit: a9d6712b04b907d938f84eb001bb8494ddefdb32
    https://github.com/bioperl/bioperl-live/commit/a9d6712b04b907d938f84eb001bb8494ddefdb32
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-11-03 (Wed, 03 Nov 2010)

Changed paths:
  M Bio/SeqFeature/Lite.pm

Log Message:
-----------
display_name should be settable, like name()

Commit: 7c64e8410d291dbd7097b2cd8fc948d95063d153
    https://github.com/bioperl/bioperl-live/commit/7c64e8410d291dbd7097b2cd8fc948d95063d153
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-11-04 (Thu, 04 Nov 2010)

Changed paths:
  M Bio/DB/Biblio/eutils.pm

Log Message:
-----------
check for definedness prior to calling methods

Commit: 651bfbe989f4231bf90410896b5904d6a01110fc
    https://github.com/bioperl/bioperl-live/commit/651bfbe989f4231bf90410896b5904d6a01110fc
Author: Chris Fields <cjfields at bioperl.org>
Date:   2010-11-08 (Mon, 08 Nov 2010)

Changed paths:
  M Bio/Tree/NodeNHX.pm
  M Bio/Tree/Tree.pm
  M Bio/Tree/TreeFunctionsI.pm
  M Bio/TreeIO.pm
  A Bio/TreeIO/NewickParser.pm
  M Bio/TreeIO/TreeEventBuilder.pm
  M Bio/TreeIO/newick.pm
  M Bio/TreeIO/nhx.pm
  M t/Tree/Node.t
  M t/Tree/TreeIO.t
  M t/Tree/TreeIO/newick.t
  M t/Tree/TreeIO/nhx.t
  A t/data/biorecipe.nhx
  A t/data/ex1.nucl.nhx
  A t/data/nhx-bacteria.nhx
  A t/data/tol-2010-02-18.nhx
  A t/data/wellcome_tol.nhx

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