BioRuby 1.4.1 RELEASE NOTES¶ ↑

A lot of changes have been made to the BioRuby 1.4.1 after the version 1.4.0 is released. This document describes important and/or incompatible changes since the BioRuby 1.4.0 release.

For known problems, see KNOWN_ISSUES.rdoc.

New features¶ ↑

PAML Codeml support is significantly improved¶ ↑

PAML Codeml result parser is completely rewritten and is significantly improved. The code is developed by Pjotr Prins.

KEGG PATHWAY and KEGG MODULE parser¶ ↑

Parsers for KEGG PATHWAY and KEGG MODULE data are added. The code is developed by Kozo Nishida and Toshiaki Katayama.

Bio::KEGG improvements¶ ↑

Following new methods are added.

• Bio::KEGG::GENES#keggclass, keggclasses, names_as_array, names, motifs_as_strings, motifs_as_hash, motifs

• Bio::KEGG::GENOME#original_databases

Test codes are added and improved.¶ ↑

Test codes are added and improved. Tney are developed by Kazuhiro Hayashi, Kozo Nishida, John Prince, and Naohisa Goto.

Other new methods¶ ↑

• Bio::Fastq#mask

• Bio::Sequence#output_fasta

• Bio::ClustalW::Report#get_sequence

• Bio::Reference#==

• Bio::Location#==

• Bio::Locations#==

• Bio::FastaNumericFormat#to_biosequence

Bug fixes¶ ↑

Bio::Tree¶ ↑

Following methods did not work correctly.

• Bio::Tree#collect_edge!

• Bio::Tree#remove_edge_if

Bio::KEGG::GENES and Bio::KEGG::GENOME¶ ↑

• Fixed bugs in Bio::KEGG::GENES#pathway.

• Fixed parser errors due to the format changes of KEGG GENES and KEGG GENOME.

Other bug fixes¶ ↑

• In Bio::Command, changed not to call fork(2) on platforms that do not support it.

• Bio::MEDLINE#initialize should handle continuation of lines.

• Typo and a missing field in Bio::GO::GeneAssociation#to_str.

• Bug fix of Bio::FastaNumericFormat#to_biosequence.

• Fixed UniProt GN parsing issue in Bio::SPTR.

Incompatible changes¶ ↑

Bio::PAML::Codeml::Report¶ ↑

The code is completely rewritten. See the RDoc for details.

Bio::KEGG::ORTHOLOGY¶ ↑

Bio::KEGG::ORTHOLOGY#pathways is changed to return a hash. The old pathway method is renamed to pathways_in_keggclass for compatibility.

Bio::AAindex2¶ ↑

Bio::AAindex2 now copies each symmetric element for lower triangular matrix to the upper right part, because the Matrix class in Ruby 1.9.2 no longer accepts any dimension mismatches. We think the previous behavior is a bug.

Bio::MEDLINE¶ ↑

Bio::MEDLINE#reference no longer puts empty values in the returned Bio::Reference object. We think the previous behavior is a bug. We also think the effect is very small.

Known issues¶ ↑

The following issues are added or updated. See KNOWN_ISSUES.rdoc for other already known issues.

String escaping of command-line arguments in Ruby 1.9.X on Windows¶ ↑

After BioRuby 1.4.1, in Ruby 1.9.X running on Windows, escaping of command-line arguments are processed by the Ruby interpreter. Before BioRuby 1.4.0, the escaping is executed in Bio::Command#escape_shell_windows, and the behavior is different from the Ruby interpreter’s one.

Curreltly, due to the change, test/functional/bio/test_command.rb may fail on Windows with Ruby 1.9.X.