[BioRuby-cvs] bioruby ChangeLog,1.66,1.67
Katayama Toshiaki
k at dev.open-bio.org
Wed Jul 18 08:20:51 UTC 2007
Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv27890
Modified Files:
ChangeLog
Log Message:
* Added changes made by Katayama over the past year
Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.66
retrieving revision 1.67
diff -C2 -d -r1.66 -r1.67
*** ChangeLog 16 Jul 2007 12:44:04 -0000 1.66
--- ChangeLog 18 Jul 2007 08:20:48 -0000 1.67
***************
*** 1,16 ****
2007-07-16 Naohisa Goto <ng at bioruby.org>
* lib/bio/mafft/report.rb
! For generic multi-fasta formatted sequence alignment,
! Bio::Alignment::MultiFastaFormat is newly added based on
! Bio::MAFFT::Report class, and Bio::MAFFT::Report is
! changed to inherit the new class.
! Tests are added in test/unit/bio/appl/mafft/test_report.rb.
* lib/bio/alignment.rb
! New modules and classes Bio::Alignment::FactoryTemplate::* are added.
! They are used by following three new classes.
* lib/bio/appl/muscle.rb
--- 1,23 ----
+ 2007-07-17 Toshiaki Katayama <k at bioruby.org>
+
+ * lib/bio/io/das.rb
+
+ Fixed that mapmaster method to return correct value (mapmaseter's
+ URL). This bug is reported and fixed by Dave Thorne.
+
2007-07-16 Naohisa Goto <ng at bioruby.org>
* lib/bio/mafft/report.rb
! For generic multi-fasta formatted sequence alignment,
! Bio::Alignment::MultiFastaFormat is newly added based on
! Bio::MAFFT::Report class, and Bio::MAFFT::Report is
! changed to inherit the new class.
! Tests are added in test/unit/bio/appl/mafft/test_report.rb.
* lib/bio/alignment.rb
! New modules and classes Bio::Alignment::FactoryTemplate::* are added.
! They are used by following three new classes.
* lib/bio/appl/muscle.rb
***************
*** 18,31 ****
* lib/bio/appl/tcoffee.rb
! New classess Bio::Muscle, Bio::Probcons, and Bio::Tcoffee are added
! for MUSCLE, ProbCons, and T-Coffee multiple alignment programs.
! Contributed by Jeffrey Blakeslee and colleagues.
* lib/bio/appl/clustalw.rb
* lib/bio/appl/mafft.rb
! Interfaces of Bio::ClustalW and Bio::MAFFT are added/modified
! to follow Bio::Alignment::FactoryTemplate (but not yet changed to
! use it).
2007-07-09 Naohisa Goto <ng at bioruby.org>
--- 25,65 ----
* lib/bio/appl/tcoffee.rb
! New classess Bio::Muscle, Bio::Probcons, and Bio::Tcoffee are added
! for MUSCLE, ProbCons, and T-Coffee multiple alignment programs.
! Contributed by Jeffrey Blakeslee and colleagues.
* lib/bio/appl/clustalw.rb
* lib/bio/appl/mafft.rb
! Interfaces of Bio::ClustalW and Bio::MAFFT are added/modified
! to follow Bio::Alignment::FactoryTemplate (but not yet changed to
! use it).
!
! 2007-07-09 Toshiaki Katayama <k at bioruby.org>
!
! * BioRuby shell on Rails has new CSS theme
!
! Completely new design for BioRuby shell on Rails translated from
! the 'DibdoltRed' theme on www.openwebdesign.org which is created by
! Darjan Panic and Brian Green as a public domain work!
!
! 2007-07-09 Toshiaki Katayama <k at bioruby.org>
!
! * lib/bio/db/kegg/taxonomy.rb
!
! Newly added KEGG taxonomy file parser which treats taxonomic tree
! structure of the KEGG organisms. The file is available at
! ftp://ftp.genome.jp/pub/kegg/genes/taxonomy
! and is a replacement of the previously used keggtab file (obsoleted).
!
! * lib/bio/db/kegg/keggtab.rb
!
! Bio::KEGG::Keggtab is obsoleted as the file is no longer provided.
! Use Bio::KEGG::Taxonomy (lib/bio/db/kegg/taxonomy.rb) instead.
!
! * lib/bio/shell/plugin/soap.rb
!
! Newly added web service plugins for BioRuby shell which supports
! NCBI SOAP, EBI SOAP and DDBJ XML in addition to the KEGG API.
2007-07-09 Naohisa Goto <ng at bioruby.org>
***************
*** 33,49 ****
* lib/bio/db/pdb/pdb.rb
! Pdb_LString.new is changed not to raise error for nil.
! Fixed a bug when below records does not exist in a PDB entry:
! REMARK (remark), JRNL (jrnl), HELIX (helix),
! TURN (turn), SHEET (sheet), SSBOND (ssbond), SEQRES (seqres),
! DBREF (dbref), KEYWDS (keywords), AUTHOR (authors),
! HEADER (entry_id, accession, classification),
! TITLE (definition), and REVDAT (version) records (methods).
! Incompatible change: Bio::PDB#record is changed to return
! an empty array for nonexistent record.
! (reported by Mikael Borg)
2007-07-09 Naohisa Goto <ng at bioruby.org>
--- 67,83 ----
* lib/bio/db/pdb/pdb.rb
! Pdb_LString.new is changed not to raise error for nil.
! Fixed a bug when below records does not exist in a PDB entry:
! REMARK (remark), JRNL (jrnl), HELIX (helix),
! TURN (turn), SHEET (sheet), SSBOND (ssbond), SEQRES (seqres),
! DBREF (dbref), KEYWDS (keywords), AUTHOR (authors),
! HEADER (entry_id, accession, classification),
! TITLE (definition), and REVDAT (version) records (methods).
! Incompatible change: Bio::PDB#record is changed to return
! an empty array for nonexistent record.
! (reported by Mikael Borg)
2007-07-09 Naohisa Goto <ng at bioruby.org>
***************
*** 51,55 ****
* lib/bio/io/flatfile.rb
! Bio::FlatFile.foreach is added (which is suggested by IO.foreach).
2007-04-02 Naohisa Goto <ng at bioruby.org>
--- 85,214 ----
* lib/bio/io/flatfile.rb
! Bio::FlatFile.foreach is added (which is suggested by IO.foreach).
!
! 2007-06-28 Toshiaki Katayama <k at bioruby.org>
!
! * lib/bio/shell/setup.rb, core.rb
!
! Changed not to use Dir.chdir by caching full path of the save
! directory at a start up time, so that user can freely change
! the work directory without affecting object/history saving
! functionality.
!
! Bio::Shell.cache[:savedir] stores the session saving directory
! (session means shell/session/{config,history,object} files),
! Bio::Shell.cache[:workdir] stores the working directory at a start
! up time (can be same directory with the :savedir) and both are
! converted and stored as full path allowing user to use Dir.chdir
! in the shell session).
!
! If --rails (-r) option is applied, 'bioruby' command will run in
! the Rails server mode, and the server will start in the :savedir.
!
! (A) IRB mode
!
! 1. run in the current directory and the session will be saved
! in the ~/.bioruby directory
!
! % bioruby
!
! 2. run in the current directory and the session will be saved
! in the foo/bar directory
!
! % bioruby foo/bar
!
! 3. run in the current directory and the session will be saved
! in the /tmp/foo/bar directory
!
! % bioruby /tmp/foo/bar
!
! (B) Rails mode
!
! 4. run in the ~/.bioruby directory and the session will also be saved
! in the ~/.bioruby directory
!
! % bioruby -r
!
! 5. run in the foo/bar directory and the session will also be saved
! in the foo/bar directory
!
! % bioruby -r foo/bar
!
! 6. run in the /tmp/foo/bar directory and the session will also be
! saved in the /tmp/foo/bar directory
!
! % bioruby -r /tmp/foo/bar
!
! (C) Script mode
!
! 7. run in the current directory using the session saved
! in the ~/.bioruby directory
!
! % bioruby ~/.bioruby/shell/script.rb
!
! 8. run in the current directory using the session saved
! in the foo/bar directory
!
! % bioruby foo/bar/shell/script.rb
!
! 9. run in the current directory using the session saved
! in the /tmp/foo/bar directory
!
! % bioruby /tmp/foo/bar/shell/script.rb
!
! 2007-06-21 Toshiaki Katayama <k at bioruby.org>
!
! * lib/bio/shell/setup.rb
!
! If no directory is specified to the bioruby command,
! use ~/.bioruby directory as the default save directory
! instead of the current directory, as suggested by Jun Sese.
!
! User can use 'bioruby' command without botherd by directories
! and files previously created by the 'bioruby' command
! in the current directory even when not needed.
!
! 2007-05-19 Toshiaki Katayama <k at bioruby.org>
!
! * lib/bio/appl/fasta.rb
!
! Bug fixed that exec_local fails to exec when @ktup is nil.
! This problem is reported and fixed by Fredrik Johansson.
!
! * lib/bio/db/gff.rb
!
! parser_attributes method in GFF3 class is modified to use
! '=' char as a separator instead of ' ' (which is used in
! GFF2 spec).
!
! 2007-04-06 Toshiaki Katayama <k at bioruby.org>
!
! * COPYING, COPYING.LIB are removed
!
! BioRuby is now distributed under the same terms as Ruby.
!
! On behalf of the BioRuby developer, I have asked all authors of
! the BioRuby code to change BioRuby's license from LGPL to Ruby's.
! And we have finished to change license of all modules in the BioRuby
! library. This means that Ruby user can freely use BioRuby library
! without being annoyed by licensing issues.
!
! * lib/bio/db/kegg/ko.rb is renamed to lib/bio/db/kegg/ortholog.rb
!
! KEGG KO database is renamed to KEGG ORTHOLOG database, thus we
! follow the change. Bio::KEGG::KO is renamed to Bio::KEGG::ORTHOLOG.
!
! Bio::KEGG::ORTHOLOG#genes, dblinks methods are rewrited to use
! lines_fetch method.
!
! * lib/bio/data/aa.rb
!
! to_re method is changed that the generated regexp to include
! ambiguous amino acid itself - replacement of amino acid X should
! include X itself.
!
! 2007-04-05 Trevor Wennblom <trevor at corevx.com>
!
! * License headers are completely rewrited to Ruby's.
2007-04-02 Naohisa Goto <ng at bioruby.org>
***************
*** 57,64 ****
* lib/bio/appl/mafft.rb
! Incompatible change: Bio::MAFFT#output is changed to return
! a string of multi-fasta formmatted text. To get an array of
! Bio::FastaFormat objects (as of 1.0 or before), please use
! report.data instead.
2007-03-27 Naohisa Goto <ng at bioruby.org>
--- 216,302 ----
* lib/bio/appl/mafft.rb
! Incompatible change: Bio::MAFFT#output is changed to return
! a string of multi-fasta formmatted text. To get an array of
! Bio::FastaFormat objects (as of 1.0 or before), please use
! report.data instead.
!
! 2007-03-29 Toshiaki Katayama <k at bioruby.org>
!
! * lib/bio/db/kegg/cell.rb
!
! Obsoleted as the KEGG CELL database is not publically available
! any more.
!
! 2007-03-28 Toshiaki Katayama <k at bioruby.org>
!
! * lib/bio/shell/rails/.../bioruby_controller.rb
!
! BioRuby shell on Rails access is changed to be limited only from
! the localhost for security reason (if local_request?).
!
! * lib/bio/command.rb
!
! The post_form method is modified to accept URL as a string and
! extended to accept params as
! array of string
! array of hash
! array of array
! or
! string
! in addition to hash (also can be ommited if not needed - defaults
! to nil).
!
! Keys and parameters of params are forced to use to_s for sure.
!
! * lib/bio/io/ensembl.rb
!
! Re-designed to allows user to use Bio::Ensembl.new without
! creating inherited sub class.
!
! Changed to use Bio::Command.post_form
!
! * lib/bio/das.rb
!
! Changed to use Bio::Command
!
! * lib/bio/shell/plugin/das.rb
!
! Newly added BioDAS client plugin for BioRuby shell.
!
! das.list_sequences
! das.dna
! das.features
!
! 2007-03-15 Toshiaki Katayama <k at bioruby.org>
!
! * lib/bio/shell/irb.rb
!
! Changed to load Rails environment when bioruby shell is invoked
! in the Rails project directory. This means that user can use
! 'bioruby' command as a better './script/console' which has
! persistent objects and shared history.
!
! 2007-03-08 Toshiaki Katayama <k at bioruby.org>
!
! * lib/bio/db/kegg/drug.rb
!
! Newly added KEGG DRUG database parser.
!
! * lib/bio/db/kegg/glycan.rb
!
! Bio::KEGG::GLYCAN#bindings method is removed.
! Bio::KEGG::GLYCAN#comment, remarks methods are added.
! Bio::KEGG::GLYCAN#orthologs and dblinks methods are changed to use
! lines_fetch method.
!
! * lib/bio/kegg/compound.rb
!
! Bio::KEGG::COMPOUND#glycans method is added
! Bio::KEGG::COMPOUND#names method is changed to return an array
! of stripped strings.
!
! * lib/bio/db/kegg/genes.rb
!
! Bio::KEGG::GENES#orthologs method is added.
2007-03-27 Naohisa Goto <ng at bioruby.org>
***************
*** 66,76 ****
* lib/bio/command.rb
! Bio::Command.call_command_fork and query_command_fork methods
! are changed to handle all Ruby exceptions in the child process.
* lib/bio/io/flatfile.rb
! UniProt format autodetection was changed to follow the change of
! UniProtKB release 9.0 of 31-Oct-2006.
2007-02-12 Naohisa Goto <ng at bioruby.org>
--- 304,314 ----
* lib/bio/command.rb
! Bio::Command.call_command_fork and query_command_fork methods
! are changed to handle all Ruby exceptions in the child process.
* lib/bio/io/flatfile.rb
! UniProt format autodetection was changed to follow the change of
! UniProtKB release 9.0 of 31-Oct-2006.
2007-02-12 Naohisa Goto <ng at bioruby.org>
***************
*** 78,84 ****
* lib/bio/io/flatfile.rb
! Exception class UnknownDataFormatError is added.
! It will be raised before reading data from IO when data format
! hasn't been specified due to failure of file format autodetection.
2007-02-02 Trevor Wennblom <trevor at corevx.com>
--- 316,328 ----
* lib/bio/io/flatfile.rb
! Exception class UnknownDataFormatError is added.
! It will be raised before reading data from IO when data format
! hasn't been specified due to failure of file format autodetection.
!
! 2007-02-12 Toshiaki Katayama <k at bioruby.org>
!
! * lib/bio/io/flatfile.rb
!
! Added support for KEGG EGENES.
2007-02-02 Trevor Wennblom <trevor at corevx.com>
***************
*** 100,106 ****
--- 344,404 ----
Bio::SOFT for reading SOFT formatted NCBI GEO files.
+ 2007-01-16 Toshiaki Katayama <k at bioruby.org>
+
+ * BioRuby shell on Rails new features and fixes
+
+ New features:
+ * Input [#] is linked to action for filling textarea from history
+ * [methods] is separated into columns for readability
+
+ Fixes and improvements:
+ * HIDE_VARIABLES is moved from helper to controller to avoid warning
+ "already initialized constant - HIDE_VARIABLES" repeated on reload.
+ * <div id="evaluate"> is renamed to "log_#" with number for future
+ extention.
+ * <div id="log_#"> are inserted in the <div id="logs">
+
+ 2007-01-15 Toshiaki Katayama <k at bioruby.org>
+
+ * lib/bio/db.rb
+
+ lines_fetch method (internally used various bio/db/*.rb modules)
+ is rewrited to concatenate indented sub field.
+
+ * lib/bio/db/kegg/compound.rb
+
+ Bio::KEGG::COMPOUND#comment method which returns contents of
+ the COMMENT line is added
+
+ * lib/bio/db/kegg/enzyme.rb
+
+ Bio::KEGG::ENZYME#entry_id is changed to return EC number only.
+ Previous version of entry_id method is renamed to entry method
+ which returns a "EC x.x.x.x Enzyme" style string.
+
+ Bio::KEGG::ENZYME#obsolete? method is added which returns boolean
+ value (true or false) according to the ENTRY line contains
+ a string 'Obsolete' or not.
+
+ Bio::KEGG::ENZYME#all_reac, iubmb_reactions, kegg_reactions methods
+ are added to support newly added ALL_REAC field.
+
+ Bio::KEGG::ENZYME#inhibitors and orthologs methods are added.
+
+ Bio::KEGG::ENZYME#substrates, products, inhibitors, cofactors,
+ pathways, orthologs, diseases, motifs methods are rewrited to
+ utilizes new lines_fetch method in db.rb to process continuous
+ sub field.
+
+ * lib/bio/db/kegg/genome.rb
+
+ Bio::KEGG::GENOME#scaffolds, gc, genomemap methods are obsoleted.
+ Bio::KEGG::GENOME#distance, data_source, original_db methods are
+ added.
+
2006-12-24 Toshiaki Katayama <k at bioruby.org>
* bin/bioruby, lib/bio/shell/, lib/bio/shell/rails/
+ (lib/bio/shell/rails/vendor/plugins/generators/)
Web functionallity of the BioRuby shell is completely rewrited
***************
*** 113,116 ****
--- 411,433 ----
visual effects.
+ * lib/bio/.rb
+
+ Extended to have Bio.command where command can be any BioRuby
+ shell methods.
+ ex. puts Bio.getseq("atgc" * 10).randomize.translate
+
+ * lib/bio/shell/plugin/entry.rb, seq.rb
+
+ seq, ent, obj commands are renamed to getseq, getent, getobj
+ respectively. This getseq is also changed to return Bio::Sequence
+ with @moltype = Bio::Sequence::NA object instead of Bio::Sequence::NA
+ object.
+
+ * lib/bio/db/kegg/kgml.rb
+
+ Some method names are changed to avoid confusion:
+ * entry_type is renamed to category (<entry type="">)
+ * map is renamed to pathway (<entry map="">)
+
2006-12-19 Christian Zmasek <czmasek at burnham.org>
***************
*** 177,180 ****
--- 494,501 ----
NHX (New Hampshire eXtended) parser/writer support are added.
+ 2006-12-13 Toshiaki Katayama <k at bioruby.org>
+
+ * doc/Desing.rd.ja, doc/TODO.rd.ja, doc/BioRuby.rd.ja are obsoletd.
+
2006-10-05 Naohisa Goto <ng at bioruby.org>
***************
*** 189,192 ****
--- 510,610 ----
is newly added.
+ 2006-09-19 Toshiaki Katayama <k at bioruby.org>
+
+ * lib/bio/io/soapwsdl.rb
+ * lib/bio/io/ebisoap.rb
+ * lib/bio/io/ncbisoap.rb
+
+ Newly added web service modules.
+
+ * lib/bio/db/kegg/kgml.rb
+
+ Accessor for the <component> attribute is added.
+
+ * lib/bio/shell/plugin/codon.rb
+
+ Support for Pyrrolysine and Selenocysteine are added in the
+ BioRuby shell.
+
+ * lib/bio/sshell/plugin/seq.rb
+
+ sixtrans, skip, step methods are added in the BioRuby shell.
+ bioruby> seqtrans(seq)
+
+ bioruby> seq.step(window_size) {|subseq|
+ # do something on subseq
+ }
+
+ bioruby> seq.skip(window_sizep, step_size) {|subseq|
+ # do something on subseq
+ }
+
+ 2006-07-26 Toshiaki Katayama <k at bioruby.org>
+
+ * lib/bio/data/aa.rb
+
+ Amino acids J (Xle: I/L), O (Pyl: pyrrolysine) and X (unknown)
+ are added (now we have consumed 26 alphabets!).
+
+ * lib/bio/io/fastacmd.rb
+
+ Fixed that new version of fastacmd (in BLAST package) changed
+ the option from '-D T' to '-D 1', contributed by the author
+ of this module Shuji Shigenobu.
+
+ * lib/bio/shell/plugin/psort.rb
+
+ Newly added BioRuby shell plugin for PSORT
+
+ * lib/bio/shell/plugin/blast.rb
+
+ Newly added BioRuby shell plugin for BLAST search against KEGG GENES
+
+ * lib/bio/db/prosite.rb
+
+ PROSITE#re instance method is added to translate PATTERN of
+ the entry to Regexp using PROSITE.pa2re class method.
+
+ * lib/bio/db/kegg/genes.rb
+
+ Bio::KEGG::GENES#keggclass method is renamed to pathway
+ Bio::KEGG::GENES#splinks method is removed
+ Bio::KEGG::GENES#motifs method is added
+ these reflect changes made in the original KEGG GENES database.
+
+ Bio::KEGG::GENES#locations method is added to return Bio::Locations
+ Bio::KEGG::GENES#codon_usage is renamed cu_list (returns as Array)
+ Bio::KEGG::GENES#cu is renamed to codon_usage (returns as Hash)
+ Bio::KEGG::GENES#aalen, nalen methods are changed to return
+ the number written in the entry (use seq.length to obtain calculated
+ number as before).
+
+ * lib/bio/db/kegg/kgml.rb
+
+ Names of some accessors have been changed (including bug fixes)
+ and instance variable @dom is obsoleted. Here's a list of
+ incompatible attribute names with KGML tags by this change:
+ <entry>
+ :id -> :entry_id
+ :type -> :entry_type
+ names()
+ <graphics>
+ :name -> :label
+ :type -> :shape
+ <relation>
+ :entry1 -> :node1
+ :entry2 -> :node2
+ :type -> :rel
+ <subtype>
+ edge()
+ <reaction>
+ :name -> :entry_id
+ :type -> :direction
+
+ * lib/bio/io/das.rb
+
+ Bug fixed that the value of segment.stop was overwritten by
+ segment.orientation.
+
2006-07-14 Naohisa Goto <ng at bioruby.org>
***************
*** 235,238 ****
--- 653,663 ----
Bug fix: Bio::FlatFile.open(klass, filename) didn't work.
+ 2006-05-30 Toshiaki Katayama <k at bioruby.org>
+
+ * lib/bio/io/soapwsdl.rb
+
+ Generic list_methods method which extracts web service methods
+ defined in the WSDL file is added.
+
2006-05-02 Mitsuteru Nakao <n at bioruby.org>
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