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ChangeLog
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ChangeLog
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2008-02-20 Jan Aerts <jandot@bioruby.org>
* lib/bio/db/fasta.rb
* lib/bio/db/fasta/format.erb
* test/unit/bio/db/test_fasta.rb
Renamed #to_seq to #to_biosequence to reflect that same method in
embl.rb, genbank.rb and others.
2008-02-20 Jan Aerts <jandot@bioruby.org>
* lib/bio.rb
* lib/bio/db/embl/common.rb
* lib/bio/db/embl/embl.rb
* lib/bio/db/embl/format.erb
* lib/bio/sequence/common.rb
* lib/bio/sequence/format.rb
* test/unit/bio/db/embl/test_embl_to_bioseq.rb
Fixed some bugs in importing EMBL files and added functionality to
export a Bio::Sequence to EMBL format.
2008-02-18 Jan Aerts <jandot@bioruby.org>
* lib/bio/reference.rb
Added export method to EMBL format.
2008-02-12 Naohisa Goto <ng@bioruby.org>
* 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 <k@bioruby.org>
* 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 <k@bioruby.org>
* lib/bio/io/hinv.rb
Bio::Hinv to access the H-invitational DB (http://h-invitational.jp/)
web service in REST mode is added.
2007-12-30 Toshiaki Katayama <k@bioruby.org>
* BioRuby 1.2.1 released
This version is not Ruby 1.9 (released few days ago) compliant yet.
2007-12-28 Naohisa Goto <ng@bioruby.org>
* 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 <ng@bioruby.org>
* 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
variables.
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 <k@bioruby.org>
* lib/bio/db/medline.rb
Added doi and pii methods to extract DOI and PII number from AID field
2007-12-18 Naohisa Goto <ng@bioruby.org>
* 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 <k@bioruby.org>
* 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 <ng@bioruby.org>
* 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 <k@bioruby.org>
* 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
compatibility).
2007-07-19 Toshiaki Katayama <k@bioruby.org>
* BioRuby 1.1.0 released
2007-07-17 Toshiaki Katayama <k@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@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
* 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 <k@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@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@bioruby.org>
* 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@bioruby.org>
* lib/bio/io/flatfile.rb
Bio::FlatFile.foreach is added (which is suggested by IO.foreach).
2007-06-28 Toshiaki Katayama <k@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@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@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@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@corevx.com>
* License headers are completely rewrited to Ruby's.
2007-04-02 Naohisa Goto <ng@bioruby.org>
* 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@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@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@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@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@bioruby.org>
* 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@bioruby.org>
* 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@bioruby.org>
* lib/bio/io/flatfile.rb
Added support for KEGG EGENES.
2007-02-02 Trevor Wennblom <trevor@corevx.com>
* lib/bio/util/restriction_enzyme*
Bio::RestrictionEnzyme stabilized.
2007-02-02 Trevor Wennblom <trevor@corevx.com>
* lib/bio/db/lasergene.rb
Bio::Lasergene Interface for DNAStar Lasergene sequence file format
2007-02-02 Trevor Wennblom <trevor@corevx.com>
* lib/bio/db/soft.rb
Bio::SOFT for reading SOFT formatted NCBI GEO files.
2007-01-16 Toshiaki Katayama <k@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@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@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
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
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@burnham.org>
* lib/bio/db/nexus.rb
Bio::Nexus is newly developed during the Phyloinformatics hackathon.
2006-12-16 Toshiaki Katayama <k@birouby.org>
* lib/bio/io/sql.rb
Updated to follow recent BioSQL schema contributed by
Raoul Jean Pierre Bonnal.
2006-12-15 Mitsuteru Nakao <n@bioruby.org>
* lib/bio/appl/iprscan/report.rb
Bio::Iprscan::Report for InterProScan output is newly added.
2006-12-15 Naohisa Goto <ng@bioruby.org>
* 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 <ng@bioruby.org>
* 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
Bio::Alignment::Output.
* 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 <ng@bioruby.org>
* 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 <k@bioruby.org>
* doc/Desing.rd.ja, doc/TODO.rd.ja, doc/BioRuby.rd.ja are obsoletd.
2006-10-05 Naohisa Goto <ng@bioruby.org>
* 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 <k@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@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@bioruby.org>
* 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 <ng@bioruby.org>
* 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 <ng@bioruby.org>
* 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 <ng@bioruby.org>
* lib/bio/io/flatfile.rb
Bug fix: Bio::FlatFile.open(klass, filename) didn't work.
2006-05-30 Toshiaki Katayama <k@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@bioruby.org>
* lib/bio/appl/pts1.rb
Bio::PTS1 first commit.
2006-04-30 Naohisa Goto <ng@bioruby.org>
* 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 <n@bioruby.org>
* lib/bio/io/ensembl.rb
Bio::Ensembl first commit. It is a client class for Ensembl Genome
Browser.
2006-03-22 Naohisa Goto <ng@bioruby.org>
* 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 <k@bioruby.org>
* BioRuby 1.0.0 released
2006-02-10 Toshiaki Katayama <k@bioruby.org>
* 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 <k@bioruby.org>
* License to be changed to Ruby's (not yet completed).
2006-02-01 Trevor Wennblom <trevor@corevx.com>
* Bio::RestrictionEnzyme first commit for comments.
* See lib/bio/util/restriction_enzyme.rb and
test/unit/bio/util/restriction_enzyme
2006-01-28 Toshiaki Katayama <k@bioruby.org>
* 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 <k@bioruby.org>
* 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 <k@bioruby.org>
* BioRuby 0.7.1 is released.
2006-01-12 Toshiaki Katayama <k@bioruby.org>
* 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 <ng@bioruby.org>
* Bio::PDB is refactored. See doc/Changes-0.7 for more details.
2005-12-19 Toshiaki Katayama <k@bioruby.org>
* BioRuby 0.7.0 is released.
See doc/Changes-0.7.rd file for major and incompatible changes.
2005-12-19 Naohisa Goto <ng@bioruby.org>
* 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
Bio::PDB::DataType.
* 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
Bio::PDB::Record::HETATM.
2005-12-02 Naohisa Goto <ng:bioruby.org>
* lib/bio/alignment.rb
* Old Bio::Alignment class is renamed to
Bio::Alignment::OriginalAlignment.
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 <k@bioruby.org>
* lib/bio/sequence.rb
Bio::Sequence.auto(str) 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.