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Commits on Nov 14, 2014
  1. Naohisa Goto

    add FastaFormat#first_name method

    Ben J. Woodcroft authored ngoto committed
  2. Naohisa Goto

    fix typo

    ngoto authored
     * fix typo. Thanks to Iain Barnett who reported the bug in
       #93
       (c4843d6)
  3. Naohisa Goto
Commits on Nov 13, 2014
  1. Naohisa Goto

    Add tests for Bio::PubMed#search, query, pmfetch

    ngoto authored
     * Add tests for Bio::PubMed#search, query, pmfetch, although
       they will be deprecated in the future.
     * This commit and commit bfe4292
       are inspired by #76
       (though the pull request have not been merged), and the commits
       fix the issue #75.
       Thanks to Paul Leader who reported the issue and the pull request.
  2. Naohisa Goto

    Change default tool and email values

    ngoto authored
     * Default "tool" and "email" values are changed to "bioruby" and
       "staff@bioruby.org" respectively. Now, the author of a script
       do not need to set his/her email address unless the script makes
       excess traffic to NCBI.
     * Update RDoc documentation
  3. Naohisa Goto

    Bug fix: use NCBI E-Utilities instead of old deprecated API

    ngoto authored
     * Bio::PubMed#search, query, pmfetch: remove old code using deprecated
       and/or unofficial web API, and change use esearch or efetch methods
       which use NCBI E-utilities. These methods will be deprecated in the
       future. To indicate this, show warning message if $VERBOSE is true.
     * Update RDoc documentation
Commits on Nov 11, 2014
  1. Naohisa Goto

    remove unused $Id:$ line

    ngoto authored
  2. Naohisa Goto

    Change default server to EBI Dbfetch server; remove BioRuby BioFetch …

    ngoto authored
    …server
    
     * Change default server to EBI Dbfetch server.
     * The BioRuby BioFetch server is removed. When "-r" option (force to use
       BioRuby server) is specified, warning message is shown, and the program
       exits with code 1 (abnormal exit).
     * Usage message is also changed.
  3. Naohisa Goto
  4. Naohisa Goto
  5. Naohisa Goto

    Issue about Bio::Fetch and BioRuby BioFetch server is resolved

    ngoto authored
     * Issue about Bio::Fetch is resolved by recent commits.
    
     * The BioRuby BioFetch server is deprecated. There is no hope to restart
       the service again. EBI Dbfetch server is an alternative.
  6. Naohisa Goto
  7. Naohisa Goto

    Incompatibile change: remove Bio::Fetch.query; add Bio::Fetch::EBI.query

    ngoto authored
     * Incompatible change: remove a class method Bio::Fetch.query because
       default server URL in Bio::Fetch is deprecated.
    
     * New class method: Bio::Fetch::EBI.query. This can be used as an
       alternative method of deprecated Bio::Fetch.query method.
  8. Naohisa Goto

    Incompatible change: Default server in Bio::Fetch.new is deperecated

    ngoto authored
     * Incompatible change: Default server URL in Bio::Fetch.new is deprecated.
       Users must explicitly specify the URL. Alternatively, users must change
       their code to use Bio::Fetch::EBI.
    
     * New class Bio::Fetch::EBI, EBI Dbfetch client. This acts the same as
       Bio::Fetch.new(Bio::Fetch::EBI::URL) with default database name
       "ena_sequence".
  9. Naohisa Goto

    removed unused variables

    ngoto authored
  10. Naohisa Goto

    Updated URL of EMBL-EBI Dbfetch

    ngoto authored
  11. Naohisa Goto

    Update lib/bio/io/fetch.rb

    Jose Irizarry authored ngoto committed
    Use EBI's dbfetch endpoint as default since BioRuby's endpoint has been disabled for a while now.
Commits on Oct 21, 2014
  1. Naohisa Goto

    Doc bug fix: wrong sample code

    ngoto authored
  2. Naohisa Goto

    Prevent to repeat calculations of total bases

    ngoto authored
     * Bio::Sequence::NA#gc_content, at_content, gc_skew, at_skew: Prevent to
       repeat calculations of total bases.
  3. Naohisa Goto

    Documentation bug fix: Return value is Rational or Float.

    ngoto authored
     * Bio::Sequence::NA#gc_content, at_content, gc_skew, at_skew: Return value
       is Rational or Float in recent versions of Ruby. Documentation added for
       the treatment of "u" and to return 0.0 if there are no bases.
       Reported by ctSkennerton (#73 ).
Commits on Aug 11, 2014
  1. Naohisa Goto
Commits on Aug 5, 2014
  1. Naohisa Goto

    Update URIs

    ngoto authored
     * Update URIs.
     * Remove links to RubyForge and RAA which have already been closed.
     * Add some words for Ruby 1.9 or later.
Commits on May 16, 2014
  1. Iain Barnett Naohisa Goto
  2. Iain Barnett Naohisa Goto

    Fixed the stack level too deep errors by using Hash#invert.

    yb66 authored ngoto committed
  3. Iain Barnett Naohisa Goto

    Refactored to shorten, remove rescues, and clarify.

    yb66 authored ngoto committed
Commits on Mar 19, 2014
  1. Naohisa Goto

    Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008)

    ngoto authored
    * Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008).
      Thanks to a researcher who reports the patch via email.
Commits on Jan 17, 2014
  1. Naohisa Goto
  2. Naohisa Goto

    gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci

    ngoto authored
     * gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci
     * .travis.yml is modified to use gemfile/Gemfile.travis-rbx for rbx.
  3. Naohisa Goto

    .travis.yml: fix mistakes

    ngoto authored
  4. Naohisa Goto

    Ruby 2.1 workaround: Array#uniq does not always choose the first item

    ngoto authored
     * Ruby 2.1 workaround: Array#uniq does not always choose the first item.
       Thanks to Andrew Grimm who reported the issue.
       (#92 )
       Note that the behavior change is also regarded as a bug in Ruby and
       is fixed. (https://bugs.ruby-lang.org/issues/9340 )
  5. Naohisa Goto

    .travis.yml: workaround to avoid error in Ruby 1.8.7 and jruby-18mode

    ngoto authored
     * workaround to avoid error in Ruby 1.8.7 and jruby-18mode
       (reference: rubygems/rubygems#763 )
  6. Naohisa Goto

    .travis.yml: rbx version is changed to 2.2.3

    ngoto authored
     * rbx version is changed to 2.2.3
     * add dependent gems for rbx platforms, described in
       http://docs.travis-ci.com/user/languages/ruby/
Commits on Jan 10, 2014
  1. Naohisa Goto

    .travis.yml: change ruby versions for tar and gem integration tests

    ngoto authored
     * In tar and gem integration tests, Ruby versions are changed to
       MRI 2.0.0 and jruby-19mode.
     * Add jruby-18mode
     * Add rbx-2.1.1
Commits on Jan 8, 2014
  1. Naohisa Goto

    .travis.yml: Add 2.1.0 and 2.0.0, remove rbx-XXmode

    ngoto authored
     * Add 2.1.0 and 2.0.0
     * Remove rbx-18mode and rbx-19mode
     * 1.9.2 is moved from "include" to "rvm".
     * 1.8.7 is moved from "rvm" to "include", and remove
       "gemfiles/Gemfile.travis-ruby1.8" line from "gemfile".
     * Remove "exclude" and simplify build matrix.
     * Suggested by agrimm in #91
Commits on Dec 10, 2013
  1. Brynjar Smári Bjarnason Naohisa Goto

    Bug fix: Only do gsub on bio_ref.reference.authors if it exists.

    binnisb authored ngoto committed
     * Bug fix: Only do gsub on bio_ref.reference.authors if it exists.
       Fix #89
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