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ChangeLog
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ChangeLog
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2003-07-16 KATAYAMA Toshiaki <k@bioruby.org>
* BioRuby version 0.5.1 released.
* lib/bio/sequence.rb: some methods (using 'rna?' internally) were
temporally unusable by the changes in 0.5.0 is fixed.
* lib/bio/io/flatfile.rb: autodetection failure of the fasta entry
without sequence is fixed. FlatFile.auto method is added.
* lib/bio/db.rb: sugtag2array fixed. DB.open now accepts IO/ARGF.
* lib/bio/db/embl.rb: references method is added.
2003-06-25 KATAYAMA Toshiaki <k@bioruby.org>
* BioRuby version 0.5.0 released.
* lib/bio/appl/blast/report.rb:
Refactored from xmlparser.rb, rexml.rb, and format8.rb files.
Formats are auto detected and parsers are automatically
selected by checking whether XMLParser or REXML are installed.
You can call simply as
Bio::Blast::Report.new(blastoutput)
or you can choose parsers/format explicitly by
Bio::Blast::Report.xmlparser(format7blastoutput)
Bio::Blast::Report.rexml(fomat7blastoutput)
Bio::Blast::Report.tab(format8blastoutput)
You can also use newly added class method reports for multiple
xml blast output.
Bio::Blast.reports(output) # output can be IO or String
* lib/bio/appl/fasta/report.rb:
Refactored from format10.rb, format6.rb and sample/* files.
* lib/bio/appl/hmmer/report.rb:
Bug fix and clean up.
* bin/biogetseq:
Newly added OBDA (BioRegistry) entry retrieval command.
* etc/bioinformatics/seqdatabase.ini, lib/bio/io/registry.rb:
Updated for new OBDA spec (Singapore version).
Including config file versioning and changes in tag names,
support for OBDA_SEARCH_PATH environmental variable.
* lib/bio/io/keggapi.rb:
Newly added KEGG API client library.
<http://www.genome.ad.jp/kegg/soap/>
* lib/bio/io/ddbjxml.rb:
Newly added DDBJ XML client library (test needed).
<http://xml.nig.ac.jp/>
* lib/bio/io/das.rb:
Newly added BioDAS client library.
* lib/bio/db/gff.rb:
Newly added GFF format parser/store library.
* lib/bio/appl/tmhmm/report.rb:
Newly added TMHMM report parser.
<http://www.cbs.dtu.dk/services/TMHMM/>
* lib/bio/appl/targetp/report.rb:
Newly added TargetP report parser.
<http://www.cbs.dtu.dk/services/TargetP/>
* lib/bio/appl/sosui/report.rb:
Newly added SOSUI report parser.
<http://sosui.proteome.bio.tuat.ac.jp/cgi-bin/sosui.cgi>
* lib/bio/appl/psort/report.rb:
Newly added PSORT report parser.
<http://www.psort.org/>, <http://psort.ims.u-tokyo.ac.jp/>
* lib/bio/appl/genscan/report.rb:
Newly added GENSCAN report parser.
<http://genes.mit.edu/GENSCAN.html>
* lib/bio/db/prosite.rb: bug fix in ps2re method.
* lib/bio/db/fantom.rb:
Newly added FANTOM database parser (XML).
<http://fantom2.gsc.riken.go.jp/>
* lib/bio/db/go.rb:
Newly added GO parser.
<http://www.geneontology.org/>
* lib/bio/feature.rb:
'each' method now accepts an argument to select specific feature.
* lib/bio/db/fasta.rb: definition=, data= to change comment line.
* lib/bio/db/genbank.rb:
References and features now accept a block. 'acc_version' method
is added to return the Accsession.Version string.
'accession' method now returns Accession part of the acc_version.
'version' method now returns Version part of the acc_version as
an integer.
* lib/bio/db/keggtab.rb:
Rewrited for bug fix and clean up (note: some methods renamed!)
* gsub('abrev', 'abbrev') in method names
* db_path_by_keggorg is changed to db_path_by_abbrev
* @bio_root is changed to @bioroot (ENV['BIOROOT'] overrides)
* Bio::KEGG::DBname is changed to Bio::KEGG::Keggtab::DB
* @database is added (a hash with its key db_abbreb)
* database, name, path methods added with its argument db_abbreb
* lib/bio/io/flatfile.rb:
Enumerable mix-in is included.
* lib/bio/io/flatfile/indexer.rb:
Indexing of the FASTA format file is now supported with various
type of definition line.
* bin/dbget:
Removed (moved under sample directory because the port of the
dbget server is now closed).
* install.rb:
Changed to use setup 3.1.4 to avoid installing CVS/ directory.
* sample/goslim.rb:
Added a sample to generate histogram from GO slim.
* sample/tdiary.rb:
Added for tDiary <http://www.tdiary.org/> users. have fun. :)
2003-01-28 KATAYAMA Toshiaki <k@bioruby.org>
* BioRuby version 0.4.0 released.
* bin/bioflat:
* newly added for the BioFlat indexing
* lib/bio/io/flatfile.rb, flatfile/{indexer.rb,index.rb,bdb.rb}:
* flatfile indexing is supported by N. Goto
* lib/bio/db/genbank.rb: changed to contain common methods only
* lib/bio/db/genbank/genbank.rb
* lib/bio/db/genbank/genpept.rb
* lib/bio/db/genbank/refseq.rb
* lib/bio/db/genbank/ddbj.rb
* lib/bio/db/embl.rb: changed to contain common methods only
* lib/bio/db/embl/embl.rb
* lib/bio/db/embl/sptr.rb
* lib/bio/db/embl/swissprot.rb
* lib/bio/db/embl/trembl.rb
* lib/bio/appl/emboss.rb:
* added - just a generic wrapper, no specific parsers yet.
* lib/bio/appl/hmmer.rb:
* added - execution wrapper
* lib/bio/appl/hmmer/report.rb:
* added - parsers for hmmsearch, hmmpfam contributed by H. Suga
* lib/bio/db.rb: open method added for easy use of flatfile.
* lib/bio/db/kegg/genes.rb:
* fixed bug in codon_usage method in the case of long sequence >999
* eclinks, splinks, pathways, gbposition, chromosome methods added
* lib/bio/db/aaindex.rb:
* adapted for the new AAindex2 format (release >= 6.0).
* lib/bio/db/fasta.rb: entry_id is changed to return first word only
* lib/bio/data/na.rb, aa.rb, keggorg.rb:
* moved under class NucleicAcid, AminoAcid, KEGG (!)
* in the test codes, DBGET is replaced by BioFetch
2002-08-30 Yoshinori K. Okuji <okuji@enbug.org>
* lib/bio/matrix.rb: Removed.
* lib/bio/db/aaindex.rb: Require matrix instead of bio/matrix.
* lib/bio/db/transfac.rb: Likewise.
* lib/bio/pathway.rb: Likewise.
(Pathway#dump_matrix): Don't use Matrix#dump.
2002-07-30 KATAYAMA Toshiaki <k@bioruby.org>
* BioRuby version 0.3.9 released.
* lib/bio/location.rb:
* Locations#length (size) methods added (contributed by N. Goto)
* Locations#relative method added (contributed by N. Goto)
* Locations#absolute method is renamed from offset
* Locations#offset, offset_aa methods removed
* use absolute/relative(n, :aa) for _aa
* Locations#[], range methods added
* Location#range method added
* lib/bio/db/embl.rb:
* fix accession method.
* lib/bio/db/genpept.rb:
* temporally added - in the next release, we will make refactoring.
* lib/bio/reference.rb:
* in bibtex and bibitem format, "PMIDnum" is changed to "PMID:num".
* lib/bio/io/pubmed.rb:
* esearch, efetch methods are added.
* lib/bio/db/aaindex.rb:
* fix serious bug in the index method to support negative values.
* lib/bio/db.rb:
* fix fetch method to cut tag without fail.
* lib/bio/extend.rb:
* added first_line_only option for the prefix in fill method.
* doc/Tutorial.rd.ja:
* added docs on BibTeX etc.
2002-06-26 KATAYAMA Toshiaki <k@bioruby.org>
* BioRuby version 0.3.8 released.
* lib/bio/sequence.rb:
* normalize! method added for clean up the object itself.
* 'to_seq' method was renamed to 'seq' (!)
* to_xxxx should be used when the class of the object changes.
* lib/bio/appl/blast/xmparser.rb:
* each_iteration, each_hit, each, hits, statistics, message methods
are added in Report class.
* statistics, message methods are added in Iteration class.
* methods compatible with Fasta::Report::Hit are added in Hit class.
* lib/bio/appl/blast/rexml.rb:
* many APIs were changed to follow the xmlparser.rb's. (!)
* lib/bio/appl/{blast.rb,fasta.rb]:
* class method parser() is added for loading specified Report class.
* etc/bioinformatics/seqdatabase.ini: added for OBDA (!)
* sample setup for BioRegistry - Open Bio Sequence Database Access.
* lib/bio/extend.rb: added (!)
* This module adds some functionarity to the existing classes and
not loaded by default. User should require specifically if needed.
* lib/bio/util/*: removed and merged into lib/bio/extend.rb (!)
* lib/bio/id.rb: removed (!)
* lib/bio/db/{embl.rb,sptr.rb,transfac.rb}: added entry_id
* lib/bio/data/keggorg.rb: updated
* sample/genes2* sample/genome2*: updated
* doc/Tutrial.rd.ja: updated
2002-06-19 KATAYAMA Toshiaki <k@bioruby.org>
* BioRuby version 0.3.7 released.
* lib/bio/sequence.rb: Sequence inherits String again (!)
* lib/bio/db.rb, db/embl.rb, db/sptr.rb: moved EMBL specific methods
2002-06-18 KATAYAMA Toshiaki <k@bioruby.org>
* lib/bio/feature.rb: Bio::Feature#[] method added
* doc/Tutrial.rd.ja: changed to use Feature class
2002-05-28 KATAYAMA Toshiaki <k@bioruby.org>
* lib/bio/appl/fasta.rb: parser separated, API renewal (!)
* lib/bio/appl/fasta/format10.rb: moved from fasta.rb
* lib/bio/appl/blast.rb: parser separated, API renewal (!)
* lib/bio/appl/blast/format8.rb: newly added
* lib/bio/appl/blast/rexml.rb: newly added
* lib/bio/appl/blast/xmlparser.rb: moved from blast.rb
2002-05-16 KATAYAMA Toshiaki <k@bioruby.org>
* lib/bio/sequence.rb: added alias 'Seq' for class Sequence
* lib/bio/db/fasta.rb: entry method added
2002-05-15 KATAYAMA Toshiaki <k@bioruby.org>
* lib/bio/io/dbget.rb: bug fixed for pfam (was wrongly skip # lines)
* lib/bio/location.rb: offset method added, eased range check
2002-04-26 KATAYAMA Toshiaki <k@bioruby.org>
* sample/biofetch.rb: new 'info=' option added
2002-04-22 KATAYAMA Toshiaki <k@bioruby.org>
* lib/bio/appl/fasta.rb: follow changes made at fasta.genome.ad.jp
* sample/gb2tab.rb: fixed to use authors.inspect for reference
2002-04-15 KATAYAMA Toshiaki <k@bioruby.org>
* sample/gb2fasta.rb: changed to follow new genbank.rb spec.
* sample/gt2fasta.rb: changed to follow new genbank.rb spec.
* sample/gbtab2mysql.rb: added for loading tab delimited data.
2002/04/08
* version 0.3.6 released -k
* fixed inconsistency among db.rb, genbank.rb, genome.rb -k
* lib/bio/db/genbank.rb : serious bug fixed in locus method -k
* lib/bio/feature.rb : method name 'type' has changed -k
2002/03/27
* sample/gb2tab.rb changed to follow new genbank.rb w/ new schema -k
2002/03/26
* sample/gb2tab.rb use ruby instead of perl in the example -o
* sample/gb2fasta.rb updated -o
2002/03/11
* version 0.3.5 released -k
2002/03/04
* lib/bio/sequence.rb to_a, to_ary methods renamed to names, codes -k
* sample/biofetch.rb added for BioFetch server -k
* bin/biofetch added for BioFetch client -k
* lib/bio/io/fetch.rb added for BioFetch library -k
* lib/bio/io/sql.rb added for BioSQL -k
* lib/bio/io/registry.rb added for BioDirectory/Registry -k
* lib/bio/feature.rb added for BioSQL, GenBank, EMBL etc. -k
* lib/bio/db/genbank.rb rewrited to use Features, References -k
* lib/bio/db/{genes,genome}.rb clean up -k
* lib/bio/reference.rb added class References -k
2002/02/05
* changed to use 'cgi' instead of 'cgi-lib' -n,k
2002/01/31
* version 0.3.4 released -k
* lib/bio/db/genbank.rb -k
* fix for multiple 'allele' in the feature key. (thanx Lixin)
2002/01/07
* lib/bio/appl/blast.rb -n
* remote blast support etc.
2001/12/18
* lib/bio/id.rb -k
* newly created
* lib/bio/io/brdb.rb -k
* newly created
* lib/bio/db.rb -k
* template methods are deleted
* detailed docuement added
* lib/bio/sequence.rb -k
* to_fasta, complement, translate fixed (due to the changes made
in 0.3.3)
* Sequence::NA#initialize doesn't replace 'u' with 't' any longer
* gc_percent, complement, translate, to_re, molecular_weight
methods are adapted to this change
* molecular_weight changed to calculate more precisely
* test code added
* lib/bio.rb -k
* rescue for require 'bio/appl/blast' is deleted
2001/12/15
* lib/bio/sequence.rb -o
* Sequence#to_str added
2001/12/15
* version 0.3.3 released -k