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Commits on Apr 27, 2016
  1. @cjfields

    Merge pull request #145 from jogoodma/obodef

    cjfields committed Apr 27, 2016
    Fix for the Disease Ontology OBO file 'def' lines
Commits on Apr 26, 2016
  1. @jogoodma
Commits on Apr 10, 2016
  1. @bosborne
  2. @bosborne
  3. @bosborne

    URLify

    bosborne committed Apr 10, 2016
Commits on Apr 5, 2016
  1. @cjfields

    Merge pull request #142 from hdevillers/master

    cjfields committed Apr 5, 2016
    Fixed issue #126: Parsing DT lines from embl files
Commits on Mar 29, 2016
  1. @cjfields

    Merge pull request #143 from bioperl#131

    cjfields committed Mar 29, 2016
    Added support for Infernal 1.1
Commits on Mar 18, 2016
  1. @pcantalupo

    updating Changes

    pcantalupo committed Mar 17, 2016
Commits on Mar 12, 2016
  1. @pcantalupo
Commits on Feb 23, 2016
  1. @hdevillers

    Fixed issue #126: Parsing DT lines from embl files

    hdevillers committed Feb 23, 2016
    From the issue #126: in embl.pm, lines 305 and 311, the two regex that parse the DT lines are always false do to the use of the modifier x without escaping white-space in regex. Thus 'creation_release', 'update_release' and 'update_version' are always missing. I proposed to remove the x modifiers.
    
    This fix revealed an other issue while writing Bio::Seq into an embl file. The call of the thee above values is wrong and the output display the ref type of the variables instead of the values. To fix it, I simply add a call to the method ->value(), to get the value.
  2. @hdevillers

    Delete embl.pm

    hdevillers committed Feb 23, 2016
Commits on Feb 22, 2016
  1. @hdevillers

    Fixed issue #126: Parsing DT lines from embl files

    hdevillers committed Feb 22, 2016
    From the issue #126: in embl.pm, lines 305 and 311, the two regex that parse the DT lines are always false do to the use of the modifier x without escaping white-space in regex. Thus 'creation_release', 'update_release' and 'update_version' are always missing. I proposed to remove the x modifiers.
    
    This fix revealed an other issue while writing Bio::Seq into an embl file. The call of the thee above values is wrong and the output display the ref type of the variables instead of the values. To fix it, I simply add a call to the method ->value(), to get the value.
Commits on Feb 20, 2016
  1. @cjfields

    Merge pull request #138 from sillitoe/master

    cjfields committed Feb 20, 2016
    Allow SearchIO::hmmer3 to parse output from phmmer
Commits on Feb 16, 2016
  1. @hyphaltip

    Merge pull request #140 from bioperl/issue-137-patch-1

    hyphaltip committed Feb 16, 2016
    fix IDs per Issue #137 when making DNAaln objects
  2. @hyphaltip

    add tests for Issue #137

    hyphaltip committed Feb 16, 2016
  3. @hyphaltip

    fix IDs per Issue #137 when making DNAaln objects

    hyphaltip committed Feb 16, 2016
    for aa_to_dna_aln - use the display id for to the DNAseq object not the key in the hash which links proteins to DNA when making then new DNA (well CDS) alignment object.
  4. @hyphaltip

    Merge pull request #139 from northeyt/master

    hyphaltip committed Feb 16, 2016
    remove my redeclaration that fails with perl 5.23.2
  5. @northeyt
Commits on Feb 4, 2016
  1. @sillitoe
  2. @cjfields

    Merge pull request #128 from dk/master

    cjfields committed Feb 3, 2016
    don't hang on parsing fasta36 -m 9 output
  3. @cjfields

    Merge pull request #79 from Buuntu/master

    cjfields committed Feb 3, 2016
    Added script to extract DNA sequences (as well as 5' or 3' regions if specified) from a FASTA file using a BLAST output file
Commits on Jan 27, 2016
  1. @cjfields

    don't enforce strict line length for FASTA, it's good practice but no…

    cjfields committed Jan 26, 2016
    …t canonical and breaks things
Commits on Jan 8, 2016
  1. @bosborne
  2. @bosborne
Commits on Dec 30, 2015
  1. @pcantalupo
  2. @majensen

    Merge pull request #136 from bioperl/feat-travis-containers

    majensen committed Dec 30, 2015
    Feat travis containers (#135)
  3. feat(travis-containers) : whitelist master again

    Mark A. Jensen committed Dec 30, 2015
  4. feat(travis-containers) : mods for containers

    Mark A. Jensen committed Dec 30, 2015
    Used addons.apt.packages to bring in reqd pkgs without
    sudo.
    
    Mod whitelist to run on this branch only.
  5. @majensen

    fix #134 : do apt-get **update** first

    majensen committed Dec 30, 2015
    Crap, I'm not Chuck.
  6. @majensen

    fix #134 : do apt-get update first

    majensen committed Dec 30, 2015
    Trying a Chuck Norris fix (but I tried it on a fork and it worked)
Commits on Dec 22, 2015
  1. @majensen

    Update README.md

    majensen committed Dec 22, 2015
Commits on Dec 21, 2015
  1. @fjossandon
  2. @fjossandon
  3. @bosborne
  4. @bosborne

    Remove ctrl M

    bosborne committed Dec 21, 2015
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