* Updated tutorial (original commit id: 7b91086 and some preceding commits)
* New methods Bio::NCBI::REST::EFetch.nucleotide and protein, to get data from "nucleotide" and "protein" database respectively. Because NCBI changed not to accept "gb" format for the database "sequence", the two new methods are added for convenience. * In BioRuby Shell, efetch method uses the above new methods.
* New method Bio::Fastq#to_s. Thanks to Tomoaki NISHIYAMA who wrote a patch. (#37)
* Bio::DDBJ::REST::*: new classes for DDBJ REST web services (WABI). Currently not all services are covered. (lib/bio/io/ddbjrest.rb) * autoload of the above (lib/bio/db/genbank/ddbj.rb, lib/bio.rb) * Tests for the above (but still incomplete) (test/functional/bio/io/test_ddbjrest.rb) * Remote BLAST using DDBJ server now uses REST interface instead of SOAP, for Ruby 1.9.x support. (lib/bio/appl/blast/ddbj.rb)
* In Bio::Sequence#output(:fastq) (Fastq output formatter), default width value is changed from 70 to nil, which means "without wrapping". close [Feature #3191] (https://redmine.open-bio.org/issues/3191)
* Bug fix: Bio::SPTR follow-up of UniProtKB format changes. * Tests are added about the fix. * Bug fix: Bio::SPTR#cc_web_resource should be private. * Incompatible changes in Bio::SPTR#cc("WEB RESOURCE") is documented in RELEASE_NOTES.rdoc. * KNOWN_ISSUES.rdoc: description about incompleteness of the fix. * Thanks to Nicholas Letourneau who reports the issue. (#36)
* Test bug fix: FuncTestCommandQuery: use sort command in PATH. Thanks to Tomoaki Nishiyama who reports the issue. (#13)
* README.rdoc: now Ruby 1.8.6 or later is required. * README.rdoc: removed old obsolete descriptions. * README.rdoc: modified about RubyGems. * KNOWN_ISSUES.rdoc: moved descriptions about older RubyGems and CVS from README.rdoc. * KNOWN_ISSUES.rdoc: modified about end-of-life Ruby versions.
* Speedup of Bio::RestrictionEnzyme::Analysis.cut. The new code is 50 to 80 fold faster than the previous code when cutting 1Mbp sequence running on Ruby 1.9.2p180. * Thanks to Tomoaki NISHIYAMA who wrote the first version of the patch. Thanks to ray1729 (on GitHub) who reports the issue. (#10)
* New classes Bio::RestrictionEnzyme::SortedNumArray and Bio::RestrictionEnzyme::DenseIntArray. Both of them are for Bio::RestrictionEnzyme internal use only. They will be used for the speedup of restriction enzyme analysis.
* Added a test for Bio::FastaFormat#entry_overrun. * Removed a void test class.
* Bug fix: Bio::FastaFormat#query passes nil to the given factory object. Thanks to Philipp Comans who reports the bug. (#35) * Test method for Bio::FastaFormat#query is added.
* Changed database name in the example. Thanks to Philipp Comans who reports the issue.
* Bug fix: changed GenomeNet remote BLAST host name and path. Thanks to Philipp Comans who reports the bug. ( #34 )
* Added a comment for rubydoctest * Changed example Ruby version representation * This is part of commit ba5b9c2 and modified to merge with the current HEAD.