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2008-02-12 Naohisa Goto <>
* lib/bio/appl/blast/format0.rb
Fixed bugs: Failed to parse query length for long query
(>= 10000 letters) as comma is inserted for digit separator
by blastall; Failed to parse e-value for some BLASTX results.
Thanks to Shuji Shigenobu who reported the bugs and sent patches.
2008-02-02 Toshiaki Katayama <>
* lib/bio/shell/rails/vendor/plugins/
The 'generators' directory is moved under the 'bioruby' subdirectory
so that 'bioruby --rails' command can work with Rails 2.x series
in addition to the Rails 1.2.x series.
2008-01-10 Toshiaki Katayama <>
* lib/bio/io/hinv.rb
Bio::Hinv to access the H-invitational DB (
web service in REST mode is added.
2007-12-30 Toshiaki Katayama <>
* BioRuby 1.2.1 released
This version is not Ruby 1.9 (released few days ago) compliant yet.
2007-12-28 Naohisa Goto <>
* lib/bio/appl/blast/report/format0.rb
Fixed parse error when compisition-based statistics were enabled.
In addition, Bio::Blast::Default::Report#references and
Bio::Blast::Default::Report::HSP#stat_method methods are added.
In NCBI BLAST 2.2.17, default option of composition-based
statistics for blastp or tblastn are changed to be enabled
by default.
* lib/bio/appl/blast/report/wublast.rb
Changed to follow the above changes in format0.rb.
* lib/bio/sequence/common.rb
Ruby 1.9 compliant: in window_search method, a local variable name
outside the iterator loop is changed not to be shadowed by the
iterator variable.
* lib/bio/db/pdb/pdb.rb
Ruby 1.9 compliant: changed to avoid "RuntimeError: implicit
argument passing of super from method defined by define_method()
is not supported. Specify all arguments explicitly." error.
Ruby 1.9 compliant: Bio::PDB::Record.get_record_class and
Bio::PDB::Record.create_definition_hash (Note: they should only
be internally used by PDB parser and users should not call them)
are changed to follow the change of Module#constants which
returns an array of Symbol instead of String.
2007-12-26 Naohisa Goto <>
* lib/bio/alignment.rb
Ruby 1.9 compliant: in EnumerableExtension#each_window and
OriginalAlignment#index methods, local variable names outside the
iterator loops are changed not to be shadowed by iterator
Warning messages for uninitialized instance variables of
@gap_regexp, @gap_char, @missing_char, and @seqclass
are suppressed.
* test/unit/bio/test_alignment.rb
Ruby 1.9 compliant: Ruby 1.9 compliant: The last comma in Array.[]
is no longer allowed. (For example,
class A < Array; end; A[ 1, 2, 3, ]
raises syntax error in Ruby 1.9.)
2007-12-21 Toshiaki Katayama <>
* lib/bio/db/medline.rb
Added doi and pii methods to extract DOI and PII number from AID field
2007-12-18 Naohisa Goto <>
* lib/bio/db/pdb/pdb.rb
Bio::PDB#inspect is added to prevent memory exhaust problem.
([BioRuby] Parse big PDB use up all memory)
* lib/bio/db/pdb/model.rb
Bio::PDB::Model#inspect is added.
* lib/bio/db/pdb/chain.rb
Bio::PDB::Chain#inspect is added.
* lib/bio/db/pdb/residue.rb
Bio::PDB::Residue#inspect is added.
This also affects Bio::PDB::Heterogen#inspect.
2007-12-15 Toshiaki Katayama <>
* BioRuby 1.2.0 released
* BioRuby shell is improved
* file save functionality is fixed
* deprecated require_gem is changed to gem to suppress warnings
* deprecated end_form_tag is rewrited to suppress warnings
* images for Rails shell are separated to the bioruby directory
* spinner is shown during the evaluation
* background image in the textarea is removed for the visibility
* Bio::Blast is fixed to parse -m 8 formatted result correctly
* Bio::PubMed is rewrited to enhance its functionality
* e.g. 'rettype' => 'count' and 'retmode' => 'xml' are available
* Bio::FlatFile is improved to accept recent MEDLINE format
* Bio::KEGG::COMPOUND is enhanced to utilize REMARK field
* Bio::KEGG::API is fixed to skip filter when the value is Fixnum
* A number of minor bug fixes
2007-12-12 Naohisa Goto <>
* lib/bio/db/newick.rb:
Changed to be compliant with the Gary Olsen's Interpretation of
the "Newick's 8:45" Tree Format Standard.
* test/unit/bio/db/test_newick.rb
More tests are added.
* lib/bio/io/flatfile/indexer.rb
Fixed a misspelling in Bio::FlatFileIndex.formatstring2class.
2007-11-28 Toshiaki Katayama <>
* lib/bio/io/pubmed.rb:
Fixed search, query methods (but use of esearch and efetch is
strongly recommended).
efetch method is enhanced to accept any PubMed search options
as a hash (to retrieve in XML format etc.)
Changed to wait 3 seconds among each access by default to be
compliant with the NCBI terms (Make no more than one request
every 3 seconds).
All Bio::PubMed.* class methods are changed to instance methods
(interface as the class methods are remained for the backward
2007-07-19 Toshiaki Katayama <>
* BioRuby 1.1.0 released
2007-07-17 Toshiaki Katayama <>
* 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 <>
* 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
* lib/bio/appl/probcons.rb
* 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 <>
* BioRuby shell on Rails has new CSS theme
Completely new design for BioRuby shell on Rails translated from
the 'DibdoltRed' theme on which is created by
Darjan Panic and Brian Green as a public domain work!
2007-07-09 Toshiaki Katayama <>
* 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
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 <>
* lib/bio/db/pdb/pdb.rb 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 <>
* lib/bio/io/flatfile.rb
Bio::FlatFile.foreach is added (which is suggested by IO.foreach).
2007-06-28 Toshiaki Katayama <>
* 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
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 <>
* 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 <>
* 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 <>
* 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 <>
* License headers are completely rewrited to Ruby's.
2007-04-02 Naohisa Goto <>
* 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 instead.
2007-03-29 Toshiaki Katayama <>
* lib/bio/db/kegg/cell.rb
Obsoleted as the KEGG CELL database is not publically available
any more.
2007-03-28 Toshiaki Katayama <>
* 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
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 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.
2007-03-15 Toshiaki Katayama <>
* 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 <>
* 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 <>
* 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 <>
* 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 <>
* lib/bio/io/flatfile.rb
Added support for KEGG EGENES.
2007-02-02 Trevor Wennblom <>
* lib/bio/util/restriction_enzyme*
Bio::RestrictionEnzyme stabilized.
2007-02-02 Trevor Wennblom <>
* lib/bio/db/lasergene.rb
Bio::Lasergene Interface for DNAStar Lasergene sequence file format
2007-02-02 Trevor Wennblom <>
* lib/bio/db/soft.rb
Bio::SOFT for reading SOFT formatted NCBI GEO files.
2007-01-16 Toshiaki Katayama <>
* 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
* <div id="log_#"> are inserted in the <div id="logs">
2007-01-15 Toshiaki Katayama <>
* 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
2006-12-24 Toshiaki Katayama <>
* bin/bioruby, lib/bio/shell/, lib/bio/shell/rails/
Web functionallity of the BioRuby shell is completely rewrited
to utilize generator of the Ruby on Rails. This means we don't
need to have a copy of the rails installation in our code base
any more. The shell now run in threads so user does not need
to run 2 processes as before (drb and webrick). Most importantly,
the shell is extended to have textarea to input any code and
the evaluated result is returned with AJAX having various neat
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
* 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 <>
* lib/bio/db/nexus.rb
Bio::Nexus is newly developed during the Phyloinformatics hackathon.
2006-12-16 Toshiaki Katayama <>
* lib/bio/io/sql.rb
Updated to follow recent BioSQL schema contributed by
Raoul Jean Pierre Bonnal.
2006-12-15 Mitsuteru Nakao <>
* lib/bio/appl/iprscan/report.rb
Bio::Iprscan::Report for InterProScan output is newly added.
2006-12-15 Naohisa Goto <>
* lib/bio/appl/mafft/report.rb
Bio::MAFFT::Report#initialize is changed to get a string of
multi-fasta formmatted text instead of Array.
2006-12-14 Naohisa Goto <>
* lib/bio/appl/phylip/alignment.rb
Phylip format multiple sequence alignment parser class
Bio::Phylip::PhylipFormat is newly added.
* lib/bio/appl/phylip/distance_matrix.rb
Bio::Phylip::DistanceMatrix, a parser for phylip distance matrix
(generated by dnadist/protdist/restdist programs) is newly added.
* lib/bio/appl/gcg/msf.rb, lib/bio/appl/gcg/seq.rb
Bio::GCG::Msf in lib/bio/appl/gcg/msf.rb for GCG MSF multiple
sequence alignment format parser, and Bio::GCG::Seq in
lib/bio/appl/gcg/seq.rb for GCG sequence format parser are
newly added.
* lib/bio/alignment.rb
Output of Phylip interleaved/non-interleaved format (.phy),
Molphy alignment format (.mol), and GCG MSF format (.msf)
are supported. Bio::Alignment::ClustalWFormatter is removed
and methods in the module are renamed and moved to
* lib/bio/appl/clustalw.rb, lib/bio/appl/mafft.rb, lib/bio/appl/sim4.rb
Changed to use Bio::Command instead of Open3.popen3.
2006-12-13 Naohisa Goto <>
* lib/bio/tree.rb, lib/bio/db/newick.rb
Bio::PhylogeneticTree is renamed to Bio::Tree, and
lib/bio/phylogenetictree.rb is renamed to lib/bio/tree.rb.
NHX (New Hampshire eXtended) parser/writer support are added.
2006-12-13 Toshiaki Katayama <>
* doc/Desing.rd.ja, doc/TODO.rd.ja, doc/BioRuby.rd.ja are obsoletd.
2006-10-05 Naohisa Goto <>
* lib/bio/db/newick.rb
Bio::Newick for Newick standard phylogenetic tree parser is
newly added (contributed by Daniel Amelang).
* lib/bio/phylogenetictree.rb
Bio::PhylogeneticTree for phylogenetic tree data structure
is newly added.
2006-09-19 Toshiaki Katayama <>
* 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 <>
* 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:
:id -> :entry_id
:type -> :entry_type
:name -> :label
:type -> :shape
:entry1 -> :node1
:entry2 -> :node2
:type -> :rel
:name -> :entry_id
:type -> :direction
* lib/bio/io/das.rb
Bug fixed that the value of segment.stop was overwritten by
2006-07-14 Naohisa Goto <>
* lib/bio/command.rb
Bio::Command::Tools and Bio::Command::NetTools are combined
and re-constructed into a new Bio::Command module.
lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb,
lib/bio/appl/emboss.rb, lib/bio/appl/psort.rb,
lib/bio/appl/hmmer.rb, lib/bio/db/fantom.rb,
lib/bio/io/fastacmd.rb, lib/bio/io/fetch.rb,
lib/bio/io/keggapi.rb, lib/bio/io/pubmed.rb, and
lib/bio/io/registry.rb are changed to use the new Bio::Command
instead of old Bio::Command or Net::HTTP.
2006-06-29 Naohisa Goto <>
* lib/bio/appl/blat/report.rb
Bio::BLAT::Report::Hit#milli_bad, #percent_identity, #protein?,
#score, and #psl_version methods/attributes are newly added,
and psl files without headers are supported (discussed in
bioruby-ja ML).
2006-06-27 Naohisa Goto <>
* lib/bio/sequence/na.rb
Bio::Sequence::NA#gc_content, #at_content, #gc_skew, #at_skew
are newly added. Bio::Sequence::NA#gc_percent are changed
not to raise ZeroDivisionError and returns 0 when given sequence
is empty.
* lib/bio/db/pdb/pdb.rb
Bio::PDB::ATOM#name, #resName, #iCode, #chaarge, #segID, and
#element are changed to strip whitespaces when initializing.
Bio::PDB::HETATM is also subject to the above changes.
(suggested by Mikael Borg)
2006-06-12 Naohisa Goto <>
* lib/bio/io/flatfile.rb
Bug fix:, filename) didn't work.
2006-05-30 Toshiaki Katayama <>
* 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 <>
* lib/bio/appl/pts1.rb
Bio::PTS1 first commit.
2006-04-30 Naohisa Goto <>
* lib/bio/appl/blast/format0.rb
Bug fix: parse error for hits whose database sequence names
contain 'Score', and subsequent hits after them would lost
(reported by Tomoaki NISHIYAMA).
2006-04-14 Mitsuteru Nakao <>
* lib/bio/io/ensembl.rb
Bio::Ensembl first commit. It is a client class for Ensembl Genome
2006-03-22 Naohisa Goto <>
* lib/bio/io/flatfile.rb
Bug fix: Bio::FlatFile raises error for pipes, ARGF, etc.
The bug also affects bio/appl/mafft.rb, bio/appl/clustalw.rb,
bio/appl/blast.rb, bio/io/fastacmd.rb, and so on.
Bio::FlatFile#entry_start_pos and #entry_ended_pos are
changed to be enabled only when Bio::FlatFile#entry_pos_flag
is true.
2006-02-27 Toshiaki Katayama <>
* BioRuby 1.0.0 released
2006-02-10 Toshiaki Katayama <>
* BioRuby shell is changed to use session/ directory under the current
or specified directory to store the session information instead of
./.bioruby directory.
2006-02-05 Toshiaki Katayama <>
* License to be changed to Ruby's (not yet completed).
2006-02-01 Trevor Wennblom <>
* Bio::RestrictionEnzyme first commit for comments.
* See lib/bio/util/restriction_enzyme.rb and
2006-01-28 Toshiaki Katayama <>
* lib/bio/appl/emboss.rb
EMBOSS USA format is now accepted via seqret/entret commands
and also utilized in the BioRuby shell (lib/bio/shell.rb,
plugin/entry.rb, plugin/emboss.rb).
* lib/bio/io/brdb.rb is removed - unused Bio::BRDB (BioRuby DB)
2006-01-23 Toshiaki Katayama <>
* lib/bio/sequence.rb
Bio::Sequence is refactored to be a container class for
any sequence annotations. Functionality is separared into
several files under the lib/bio/sequence/ direcotry as
common.rb, compat.rb, aa.rb, na.rb, format.rb
2006-01-20 Toshiaki Katayama <>
* BioRuby 0.7.1 is released.
2006-01-12 Toshiaki Katayama <>
* lib/bio/db.ra: fixed a bug of the tag_cut method introduced in 0.7.0
(reported by Alex Gutteridge)
2006-01-04 Naohisa Goto <>
* Bio::PDB is refactored. See doc/Changes-0.7 for more details.
2005-12-19 Toshiaki Katayama <>
* BioRuby 0.7.0 is released.
See doc/Changes-0.7.rd file for major and incompatible changes.
2005-12-19 Naohisa Goto <>
* lib/bio/db/pdb.rb, lib/bio/db/pdb/pdb.rb, lib/bio/db/pdb/*.rb
* Many changes have been made.
* Bio::PDB::FieldDef is removed and Bio::PDB::Record is completely
changed. Now, Record is changed from hash to Struct, and
method_missing is no longer used.
* In the "MODEL" record, model_serial is changed to serial.
* In any records, record_type is changed to record_name.
* In most records contains real numbers, changed to return
float values instead of strings.
* Pdb_AChar, Pdb_Atom, Pdb_Character, Pdb_Continuation,
Pdb_Date, Pdb_IDcode, Pdb_Integer, Pdb_LString, Pdb_List,
Pdb_Real, Pdb_Residue_name, Pdb_SList, Pdb_Specification_list,
Pdb_String, Pdb_StringRJ and Pdb_SymOP are moved under
* There are more and more changes to be written...
* lib/bio/db/pdb/atom.rb
* Bio::PDB::Atom is removed.
Instead, please use Bio::PDB::Record::ATOM and
2005-12-02 Naohisa Goto <>
* lib/bio/alignment.rb
* Old Bio::Alignment class is renamed to
Now, new Bio::Alignment is a module. However,
you don't mind so much because most of the class methods
previously existed are defined to delegate to the new
Bio::Alignment::OriginalAlignment class,
for keeping backward compatibility.
* New classes and modules are introduced. Please refer RDoc.
* each_site and some methods changed to return Bio::Alignment::Site,
which inherits Array (previously returned Array).
* consensus_iupac now returns only standard bases
'a', 'c', 'g', 't', 'm', 'r', 'w', 's', 'y', 'k', 'v',
'h', 'd', 'b', 'n', or nil (in SiteMethods#consensus_iupac) or
'?' (or missing_char, in EnumerableExtension#consensus_iupac).
Note that consensus_iupac now does not return u and invalid
letters not defined in IUPAC standard even if all bases
are equal.
* There are more and more changes to be written...
2005-11-05 Toshiaki Katayama <>
* lib/bio/sequence.rb method is added which auto detect the
molecular type of the string and then returns the
Bio::Sequence::NA or Bio::Sequence::AA object.
Bio::Sequence#blast and Bio::Sequence#fasta methods are removed.
* lib/bio/shell/plugin/codon.rb
Newly added plugin to treat codon table.
ColoredCodonTable is ported from the codontable.rb
2005-11-01 Toshiaki Katayama <>
* bin/bioruby, lib/bio/shell/
All methods are changed to private methods to avoid adding them
in top level binding, which caused many unexpected behaviors,
as adviced by Koichi Sasada.
The MIDI plugin is now able to select musical scales.
2005-10-23 Toshiaki Katayama <>
* lib/bio/util/color_scheme
Newly contributed Bio::ColorScheme
* lib/bio/db/kegg/kgml.rb
Newly added KEGG KGML parser.
2005-10-05 Toshiaki Katayama <>
* lib/bio/shell/plugin/midi.rb
Sequcne to MIDI plugin is contributed by Natsuhiro Ichinose
2005-09-25 Toshiaki Katayama <>
Newly added guideline document for the contributors.
Updated and added instructions on RubyGems.
2005-09-23 Toshiaki Katayama <>
* bin/bioruby, lib/bio/shell.rb, lib/bio/shell/core.rb,
lib/bio/shell/session.rb, lib/bio/shell/plugin/seq.rb,
lib/bio/shell/flatfile.rb, lib/bio/shell/obda.rb
Newly added BioRuby shell, the command line user interface.
Try 'bioruby' command in your terminal.
* doc/Changes-0.7.rd
Newly added document describing incompatible and important
changes between the BioRuby 0.6 and 0.7 versions.
* lib/bio/sequence.rb
Bio::Sequence.guess, Bio::Sequence#guess methods are added
which guess the sequence type by following fomula (default
value for the threshold is 0.9).
number of ATGC
--------------------------------------- > threshold
number of other chars - number of N
2005-09-10 Naohisa Goto <>
* lib/bio.rb, lib/bio/appl/blast.rb, lib/bio/appl/blast/format0.rb,
lib/bio/appl/blast/report.rb, lib/bio/appl/clustalw.rb,
lib/bio/appl/fasta.rb, lib/bio/appl/fasta/format10.rb,
lib/bio/appl/hmmer.rb, lib/bio/appl/hmmer/report.rb,
lib/bio/appl/mafft.rb, lib/bio/appl/psort.rb,
lib/bio/appl/psort/report.rb, lib/bio/appl/sim4.rb,
lib/bio/db/genbank/ddbj.rb, lib/bio/io/flatfile/bdb.rb,
lib/bio/io/flatfile/index.rb, lib/bio/io/flatfile/indexer.rb
fixed autoload problem
* lib/bio/appl/blast.rb, lib/bio/appl/blast/report.rb
Bio::Blast.reports method was moved from lib/bio/appl/blast/report.rb
to lib/bio/appl/blast.rb for autoload.
2005-08-31 Toshiaki Katayama <>
* BioRuby 0.6.4 is released.
* doc/KEGG_API.rd
Newly added English version of the KEGG API manual.
* lib/bio/aa.rb
the 'one2name' method introduced in 0.6.3 is fixed and added 'one'
and 'three' methods as aliases for 'to_1' and 'to_3' methods.
2005-08-31 Naohisa Goto <>
* removed unused file lib/bio/appl/factory.rb
(the functionality had been integrated into lib/bio/command.rb)
* doc/Tutorial.rd
Newly added an English translation of the Japanese tutorial.
2005-08-16 Naohisa Goto <>
* lib/bio/command.rb
Newly added Bio::Command::Tools module.
Bio::Command::Tools is a collection of useful methods
for execution of external commands.
* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb,
lib/bio/appl/hmmer.rb, lib/bio/io/fastacmd.rb
For security reason, shell special characters are escaped.
* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb, lib/bio/appl/hmmer.rb
Options are stored with an array (@options).
#options and #opions= methods are added.
* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb
Bio::Blast.remote and Bio::Fasta.remote is fixed to work
with the recent change of the GenomeNet.
2005-08-11 Toshiaki Katayama <>
* Sequence#to_re method to have compatibility with 0.6.2 for RNA
* Fixed Bio::Fastacmd#fetch to work
* Bio::Fastacmd and Bio::Bl2seq classes (introduced in 0.6.3) are
renamed to Bio::Blast::Fastacmd, Bio::Blast::Bl2seq respectively.
2005-08-09 Toshiaki Katayama <>
* BioRuby 0.6.3 is released.
This version would be the final release to support Ruby 1.6 series
(as long as no serious bug is found:).
* lib/bio/util/sirna.rb:
Newly added method for desing of siRNA, contributed by
Itoshi Nikaido. The lib/bio/util/ directory if reserved
for bioinfomatics algorithms implemented by pure Ruby.
* lib/bio/io/fastacmd.rb:
Newly added wrapper for NCBI fastacmd program, contributed by
Shinji Shigenobu.
* lib/bio/appl/hmmer/report.rb:
Bug fixed by Masashi Fujita when the position of sequence
rarely becomes '-' instead of digits.
2005-08-08 Mitsuteru Nakao <>
* lib/bio/db/embl/sptr.rb:
Added Bio::SPTR#protein_name and Bio::SPTR#synoyms methods.
contributed by Luca Pireddu.
Changed Bio::SPTR#gn, Bio::SPTR#gene_name and
Bio::SPTR#gene_names methods. contributed by Luca Pireddu.
2005-08-08 Naohisa Goto <>
* lib/bio/appl/bl2seq/report.rb:
Newly added bl2seq (BLAST 2 sequences) output parser.
* lib/bio/appl/blast/format0.rb:
Added `self.class::` before for bl2seq/report.rb
2005-08-07 Toshiaki Katayama <>
* lib/bio/sequence.rb, lib/bio/data/na.rb, lib/bio/data/aa.rb:
Bio::NucleicAcid, Bio::AminoAcid classes are refactored to have
Data module, and this module is included and extended to make
all methods as both of instance methods and class methods.
Bio::Sequence::NA and AA classes are rewrited (molecular_weight,
to_re methods) to use Bio::NucleicAcid.
Bio::Sequence::NA#molecular_weight method is fixed to subtract
two hydrogens per each base.
* lib/bio/db/medline.rb: publication_type (pt) method is added.
2005-08-07 Naohisa Goto <>
* lib/bio/db/genbank/common.rb:
Avoid NoMethodError (private method `chomp` called for nil:NilClass)
when parsing features of
2005-07-11 Toshiaki Katayama <>
* bin/br_pmfetch.rb:
Added sort by page option (--sort page)
* lib/io/higet.rb:
Newly added Bio::HGC::HiGet class for HiGet SOAP service.
2005-06-28 Toshiaki Katayama <>
* gemspec.rb: newly added RubyGems spec file.
2005-06-21 Naohisa Goto <>
* lib/bio/appl/blast/report.rb:
Newly added support for reading BLAST -m 7 result files
through Bio::FlatFile by adding
DELIMITER = "</BlastOutput>\n" to Bio::Blast::Report class.
(Note that tab-delimited format (-m 8 and -m 9) are not yet
supported by Bio::FlatFile)
* lib/bio/io/flatfile.rb:
Added file format autodetection of BLAST XML format.
2005-06-20 Naohisa Goto <>
* lib/bio/appl/blast/format0.rb: added 'to_s' to store original entry
2005-04-04 Mitsuteru Nakao <>
* lib/bio/db/go.rb:
Newly added Bio::GO::External2go class for parsing external2go file.
2005-03-10 Naohisa Goto <>
* lib/bio/io/flatfile.rb:
Added file format autodetection of Spidey (Bio::Spidey::Report).
2005-03-10 Naohisa Goto <>
* lib/bio/io/flatfile.rb:
Added file format autodetection for Bio::KEGG::KO,
Bio::KEGG::GLYCAN, Bio::KEGG::REACTION, Bio::Blat::Report
and Bio::Sim4::Report.
In order to distinguish Bio::KEGG::REACTION and
Bio::KEGG::COMPOUND, autodetection regexp. of
Bio::KEGG::COMPOUND were modified.
2005-02-09 KATAYAMA Toshiaki <>
* lib/bio/db/kegg/genes.rb:
Added cu method which returns codon usage in Hash for the
convenience (codon_usage method returns in Array or Fixnum).
2004-12-13 KATAYAMA Toshiaki <>
* BioRuby 0.6.2 released.
* test/all_tests.rb:
Unit tests for some classes are newly incorporated by
Moses Hohman. You can try it by 'ruby install.rb test'
* lib/bio/appl/spidey/report.rb:
Newly added Spidey result parser class.
* lib/bio/appl/blat/report.rb:
Newly added BLAT result parser class.
* fixes and improvements:
* lib/bio/appl/blast/blast/format0.rb
* minor fix for the Blast default format parser
* lib/bio/alignment.rb
* Alignment class
* lib/bio/db/prosite.rb
* bug reported by Rolv Seehuus is fixed
* some methods are added
2004-10-25 KATAYAMA Toshiaki <>
* lib/bio/db/{compound.rb,reaction.rb,glycan.rb}:
Newly added parser for KEGG REACTION and KEGG GLYCAN database
entries, fix for KEGG COMPOUND parser to support the new format.
2004-10-09 GOTO Naohisa <>
* lib/bio/appl/sim4.rb
Newly added sim4 wrapper class.
This is test version, specs would be changed frequently.
* lib/bio/appl/sim4/report.rb
Newly added sim4 result parser class.
2004-08-25 KATAYAMA Toshiaki <>
* BioRuby 0.6.1 released.
* fix for the packaging miss of 0.6.0
* bin/*.rb are renamed to bin/br_*.rb (similar to the BioPerl's
convention: bp_*.pl)
2004-08-24 KATAYAMA Toshiaki <>
* BioRuby 0.6.0 released.
* many fixes for Ruby 1.8
* updated for -> transition
* lib/bio/db/pdb.rb
Newly added parser for PDB contributed by Alex Gutteridge (EBI).
* lib/bio/data/codontable.rb
Bio::CodonTable is rewrited to be a class instead of static variable.
Now it can hold table definition, start codons, stop codons and
added methods to detect start/stop codons and reverse translation.
Also includes sample code to show codon table in ANSI colored
ascii art, have fun.
* lib/bio/sequence.rb
Bio::Sequence::NA#translate is rewrited to accept an user defined
codon table as a Bio::CodonTable object and any character can be
specified for the unknown codon. This method runs about 30% faster
than ever before.
Bio::Sequence::AA#to_re method is added for the symmetry.
Bio::Seq will be changed to hold generic rich sequence features.
This means Bio::Seq is no longer an alias of Bio::Sequence but
is a sequence object model, something like contents of a GenBank
entry, common in BioPerl, BioJava etc.
* lib/bio/io/soapwsdl.rb
Newly added common interface for SOAP/WSDL in BioRuby
used by keggapi.rb, ddbjxml.rb.
* lib/bio/io/keggapi.rb
Completely rewrited to support KEGG API v3.0
* lib/bio/io/esoap.rb
Newly added client library for Entrez Utilities SOAP interface.
* lib/bio/db/genbank, lib/bio/db/embl
Refactored to use common.rb as a common module.
* bin/pmfetch.rb
Newly added command to search PubMed.
* bin/biofetch.rb, flatfile.rb, biogetseq.rb
Renamed to have .rb suffix.
* sample/biofetch.rb
Rewrited to use KEGG API instead of DBGET
2003-10-13 KATAYAMA Toshiaki <>
* BioRuby 0.5.3 released.
Fixed bugs in Blast XML parsers: xmlparser.rb is fixed not to
omit the string after ' and " in sequence definitions,
rexml.rb is fixed not to raise NoMethodError as "undefined
method `each_element_with_text' for nil:NilClass".
2003-10-07 GOTO Naohisa <>
* lib/bio/db/nbrf.rb
Newly added NBRF/PIR flatfile sequence format class.
2003-09-30 GOTO Naohisa <>
* lib/bio/db/pdb.rb
Newly added PDB database flatfile format class.
This is pre-alpha version, specs shall be changed frequently.
2003-08-22 KATAYAMA Toshiaki <>
* BioRuby 0.5.2 released.
Fixed to be loaded in Ruby 1.8.0 without warnings.
* doc/KEGG_API.rd.ja
Newly added a Japanese document on the KEGG API.
2003-08-12 GOTO Naohisa <>
* lib/bio/appl/blast/format0.rb
Newly added NCBI BLAST default (-m 0) output parser,
which may be 5-10x faster than BioPerl's parser.
This is alpha version, specs may be frequently changed.
PHI-BLAST support is still incomplete.
Ruby 1.8 recommended. In ruby 1.6, you need strscan.
* lib/bio/appl/blast/wublast.rb
Newly added WU-BLAST default output parser.
This is alpha version, specs may be frequently changed.
Support for parameters and statistics are still incomplete.
Ruby 1.8 recommended. In ruby 1.6, you need strscan.
2003-07-25 GOTO Naohisa <>
* lib/bio/alignment.rb:
Newly added multiple sequence alignment class.
* lib/bio/appl/alignfactory.rb:
Newly added template class for multiple alignment software.
* lib/bio/appl/clustalw.rb:
Newly added CLUSTAL W wrapper.
* lib/bio/appl/clustalw/report.rb:
Newly added CLUSTAL W result data (*.aln file) parser.
* lib/bio/appl/mafft.rb, lib/bio/appl/mafft/report.rb:
Newly added MAFFT wrapper and report parser.
(MAFFT is a multiple sequence alignment program based on FFT.)
2003-07-16 KATAYAMA Toshiaki <>
* 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. method is added.
* lib/bio/db.rb: sugtag2array fixed. now accepts IO/ARGF.
* lib/bio/db/embl.rb: references method is added.
2003-06-25 KATAYAMA Toshiaki <>
* 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
or you can choose parsers/format explicitly by
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.
* lib/bio/io/ddbjxml.rb:
Newly added DDBJ XML client library (test needed).
* 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.
* lib/bio/appl/targetp/report.rb:
Newly added TargetP report parser.
* lib/bio/appl/sosui/report.rb:
Newly added SOSUI report parser.
* lib/bio/appl/psort/report.rb:
Newly added PSORT report parser.
<>, <>
* lib/bio/appl/genscan/report.rb:
Newly added GENSCAN report parser.
* lib/bio/db/prosite.rb: bug fix in ps2re method.
* lib/bio/db/fantom.rb:
Newly added FANTOM database parser (XML).
* lib/bio/db/go.rb:
Newly added GO parser.
* 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 <> users. have fun. :)
2003-01-28 KATAYAMA Toshiaki <>
* 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 <>
* 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 <>
* 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 <>
* 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 <>
* 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 <>
* lib/bio/feature.rb: Bio::Feature#[] method added
* doc/Tutrial.rd.ja: changed to use Feature class
2002-05-28 KATAYAMA Toshiaki <>
* 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 <>
* lib/bio/sequence.rb: added alias 'Seq' for class Sequence
* lib/bio/db/fasta.rb: entry method added
2002-05-15 KATAYAMA Toshiaki <>
* 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 <>
* sample/biofetch.rb: new 'info=' option added
2002-04-22 KATAYAMA Toshiaki <>
* lib/bio/appl/fasta.rb: follow changes made at
* sample/gb2tab.rb: fixed to use authors.inspect for reference
2002-04-15 KATAYAMA Toshiaki <>
* 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.
* 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
* sample/gb2tab.rb changed to follow new genbank.rb w/ new schema -k
* sample/gb2tab.rb use ruby instead of perl in the example -o
* sample/gb2fasta.rb updated -o
* version 0.3.5 released -k
* 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
* changed to use 'cgi' instead of 'cgi-lib' -n,k
* version 0.3.4 released -k
* lib/bio/db/genbank.rb -k
* fix for multiple 'allele' in the feature key. (thanx Lixin)
* lib/bio/appl/blast.rb -n
* remote blast support etc.
* 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
* lib/bio/sequence.rb -o
* Sequence#to_str added
* version 0.3.3 released -k
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