Path: | RELEASE_NOTES.rdoc |
Last Update: | Sun Dec 04 02:16:41 +0000 2011 |
A lot of changes have been made to the BioRuby 1.4.2 after the version 1.4.1 is released. This document describes important and/or incompatible changes since the BioRuby 1.4.1 release.
For known problems, see KNOWN_ISSUES.rdoc.
The running speed of Bio::RestrictionEnzyme::Analysis.cut is significantly increased. The new code is 50 to 80 fold faster than the previous code when cutting 1Mbp sequence running on Ruby 1.9.2p180. The code is written by Tomoaki NISHIYAMA and Naohisa Goto.
For DDBJ Web API for Biology (WABI) web service, in additon to SOAP, REST (REpresentational State Transfer) interface is added as Bio::DDBJ::REST. Currently, only selected APIs are implemented.
Bio::Blast with remote DDBJ server uses REST instead of SOAP, because Soap4r (SOAP library for Ruby) does not work well with Ruby 1.9. We can now use remote DDBJ BLAST server with Ruby 1.9.
The Tutorial.rd is updated by Pjotr Prins and Michael O‘Keefe.
Added many unit tests for Bio::GenBank, Bio::GenPept, Bio::NBRF, Bio::PDB and so on. Most of them are developed by Kazuhiro Hayashi during the Google Summer of Code 2010.
In Fastq output formatter, default width value is changed from 70 to nil. The nil means "without wrapping". The new default behavior without wrapping is generally good with many recent applications that read fastq.
In the return value of Bio::SPTR#cc(‘WEB RESOURCE’), "NAME" and "NOTE" are now renamed to "Name" and "Note", respectively. The change is due to the UniProt format change since UniProtKB release 12.2 of 11-Sep-2007. (See www.uniprot.org/docs/sp_news.htm#rel12.2 for details.) Note that "Name" and "Note" are used even when parsing older format. The change would also affect Marshal.dump (and YAML.dump) data.
When executing remote BLAST with "genomenet" server, options "-b" and "-v" are now correctly used to limit the number of hits to be reported. In 1.4.1 and before, "-B" and "-V" were mistakenly used for the purpose.
Bio::Blast with remote DDBJ server uses REST instead of SOAP.
Due to the speedup, internal data structure of the following classes are changed: Bio::RestrictionEnzyme::Range::SequenceRange, Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts, Bio::RestrictionEnzyme::Range::SequenceRange::Fragment. This indicates that Marshal.dump (and YAML.dump) data generated by older versions cannot be loaded by the new version, and vice versa, although public APIs of the classes keep compatibility.
The following issues are added or updated. See KNOWN_ISSUES.rdoc for other already known issues.