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Commits on Jun 24, 2016
  1. @fjossandon

    Merge pull request #159 from jkeenan/sirna-left-brace

    Avoid "Unescaped left brace in regex is deprecated" warning.
    fjossandon committed on GitHub Jun 23, 2016
Commits on Jun 23, 2016
  1. @jkeenan

    Avoid "Unescaped left brace in regex is deprecated" warning.

    In Perl 5.24.0, when running t/Tools/SiRNA.t, we were getting the warning
    above on two consecutive lines.  The underlying reason for the warnings was
    that pattern in question never really was a regex quantifier.
    
    This patch silences those warnings and
    prevents the module from failing on future versions of perl.
    
    The test suite was never exercising the code in question.  Now it will
    exercise the code in question, but that will mean different numbers of pairs
    to be expected in t/Tools/SiRNA.t.
    jkeenan committed Jun 22, 2016
Commits on Jun 11, 2016
  1. @cjfields

    git Bugs link

    cjfields committed Jun 11, 2016
Commits on Jun 5, 2016
  1. @cjfields
  2. @cjfields
  3. @cjfields

    Fix for #154, per @stuartrbaker

    cjfields committed Jun 5, 2016
Commits on May 16, 2016
  1. @cjfields

    Merge pull request #150 from jkeenan/missing_manifest

    Restore missing MANIFEST.
    cjfields committed May 16, 2016
  2. @cjfields

    Merge pull request #149 from lskatz/master

    Updated assess_bootstrap documentation
    cjfields committed May 16, 2016
Commits on May 15, 2016
  1. @jkeenan

    Restore missing MANIFEST.

    When running ./BUILD on source code checked out from github.com, got warning
    about missing or corrupt MANIFEST.  Followed instruction to run ./Build
    manifest.
    jkeenan committed May 15, 2016
Commits on May 10, 2016
  1. @lskatz

    Updated assess_bootstrap documentation

    * added a missing parameter `$guide_tree` in usage
    * added guide tree in `Args`
    lskatz committed May 10, 2016
Commits on May 9, 2016
  1. @bosborne

    Merge pull request #148 from bioperl/phylip-alignio-fix

    Phylip alignio fix
    bosborne committed May 9, 2016
Commits on May 7, 2016
  1. @bosborne
  2. @bosborne
Commits on Apr 27, 2016
  1. @cjfields

    Merge pull request #145 from jogoodma/obodef

    Fix for the Disease Ontology OBO file 'def' lines
    cjfields committed Apr 27, 2016
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

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

    Merge pull request #143 from bioperl#131

    Added support for Infernal 1.1
    cjfields committed Mar 29, 2016
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

    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.
    hdevillers committed Feb 23, 2016
  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

    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.
    hdevillers committed Feb 22, 2016
Commits on Feb 20, 2016
  1. @cjfields

    Merge pull request #138 from sillitoe/master

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

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

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

    add tests for Issue #137

    hyphaltip committed Feb 16, 2016
  3. @hyphaltip

    fix IDs per Issue #137 when making DNAaln objects

    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.
    hyphaltip committed Feb 16, 2016
  4. @hyphaltip

    Merge pull request #139 from northeyt/master

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

    Merge pull request #128 from dk/master

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

    Merge pull request #79 from Buuntu/master

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

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

    …t canonical and breaks things
    cjfields committed Jan 26, 2016
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