ngoto-bio 1.2.9.9501 → 1.3.0
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- data/ChangeLog +201 -4
- data/KNOWN_ISSUES.rdoc +24 -2
- data/README.rdoc +29 -0
- data/Rakefile +44 -5
- data/bin/br_pmfetch.rb +4 -3
- data/bioruby.gemspec +11 -3
- data/bioruby.gemspec.erb +40 -5
- data/doc/Changes-0.7.rd +7 -0
- data/doc/Changes-1.3.rdoc +17 -0
- data/doc/Tutorial.rd.html +1031 -0
- data/doc/Tutorial.rd.ja +111 -45
- data/doc/Tutorial.rd.ja.html +2225 -0
- data/doc/bioruby.css +281 -0
- data/lib/bio/appl/blast/format0.rb +7 -2
- data/lib/bio/db/gff.rb +2 -2
- data/lib/bio/db/lasergene.rb +3 -3
- data/lib/bio/db/soft.rb +3 -3
- data/lib/bio/io/togows.rb +458 -0
- data/lib/bio/shell/core.rb +2 -2
- data/lib/bio/shell/plugin/entry.rb +27 -4
- data/lib/bio/shell/plugin/ncbirest.rb +27 -29
- data/lib/bio/shell/plugin/togows.rb +40 -0
- data/lib/bio/shell.rb +1 -0
- data/lib/bio/util/color_scheme.rb +2 -2
- data/lib/bio/util/contingency_table.rb +2 -2
- data/lib/bio/util/restriction_enzyme.rb +2 -2
- data/lib/bio/version.rb +25 -0
- data/lib/bio.rb +4 -1
- data/test/functional/bio/io/test_togows.rb +267 -0
- data/test/runner.rb +7 -0
- data/test/unit/bio/db/test_gff.rb +63 -0
- data/test/unit/bio/io/test_togows.rb +161 -0
- metadata +11 -3
data/ChangeLog
CHANGED
@@ -1,3 +1,196 @@
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2009-02-20 Naohisa Goto <ng@bioruby.org>
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* BioRuby 1.3.0 is released.
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2009-02-19 Naohisa Goto <ng@bioruby.org>
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* lib/bio/version.rb
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Preparation for bioruby-1.3.0 release.
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(commit fd7fc9f78bc5f4d9a10b3c0d457d9781c9ec2e49)
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* bioruby.gemspec.erb
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Fixed a logic to determine whether in git repository, and file
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lists are changed to be sorted.
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(commit ede0c0d7aeab078b6183c4e0e7c74faec32739f7)
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2009-02-18 Naohisa Goto <ng@bioruby.org>
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* README.rdoc
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Added list of document files bundled in the BioRuby distribution.
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(commit 92748f848e4708766e44c22b2f02ac662491971f)
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2009-02-10 Naohisa Goto <ng@bioruby.org>
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* KNOWN_ISSUES.rdoc
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Added details about the text mode issue on mswin32/mingw32/bccwin32
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and about non-UNIX/Windows systems.
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(commit 342a167a23d3b078bd77b3f16f0ceb1aa071df66)
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2009-02-09 Naohisa Goto <ng@bioruby.org>
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* test/unit/bio/db/test_gff.rb
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Test bug fix: test_gff.rb failed in some environment (e.g. Windows)
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because the default formatting rule of Float#to_s depends on the
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libc implementation.
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(commit f39bf88ed6a41bd328372ee7de7a23902235f833)
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2009-02-06 Naohisa Goto <ng@bioruby.org>
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* lib/bio/db/gff.rb, test/unit/bio/db/test_gff.rb
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* Bug fix: Bio::GFF::GFF3::Record#id and #id= should be changed
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to follow the previous incompatible change of @attributes.
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Thanks to Tomoaki NISHIYAMA who reports the bug ([BioRuby]
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GFF3 status (possible bug?)).
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* Unit tests are added.
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(commit 5258d88ef98a12fd7829eb86aa8664a18a672a43)
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(commit c0c7708b3e91b0d2f2d0d50a4a0ba36928057cc8)
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2009-02-05 Naohisa Goto <ng@bioruby.org>
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* Rakefile
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New task "tutorial2html" to generate html from doc/Tutorial.rd
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and doc/Tutorial.rd.ja.
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(commit 8d66fae59477f01f12b2fa3509ea34c371102725)
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* doc/Tutorial.rd.html, doc/Tutorial.rd.ja.html
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Automatically generated tutorial html from RD formatted documents.
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(commit 90c4a23eea08b06dd758aaa0a53bea789602d252)
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* doc/bioruby.css
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Newly added stylesheet for the tutorial html files. The bioruby.css
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have been used in http://bioruby.org/ and have been maintained by
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Toshiaki Katayama.
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(commit b69dc243787525de065bdf2e6b7da68d6079ab91)
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* test/runner.rb
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Added workaroud for test-unit-2.0.x.
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(commit 475ac6a6b38e8df30de3d9bf4c7e810759ab023d)
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2009-02-04 Naohisa Goto <ng@bioruby.org>
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* lib/bio/appl/blast/format0.rb
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Bug fix: a null line can be inserted after query name lines.
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(commit bea9ce35b4177f407575ed0752c36bba8a50f502)
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2009-02-03 Naohisa Goto <ng@bioruby.org>
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* Tutorial.rd.ja
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* Document bug: BioRuby shell commands seq, ent, obj were renamed to
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getseq, getent, getobj, respectively. Thanks to Hiroyuki Mishima
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who reports the issue ([BioRuby-ja]).
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* Changes of returned value of getseq are also reflected to the
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document.
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* Recommended Ruby version and installation procedure are also
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changed.
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(commit 916e96ca549db71a550e7a5d3bd49a3149614313)
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* doc/Changes-0.7.rd
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Documentation forgotten in 1.1.0: rename of BioRuby shell commands.
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(commit 64113314caac3453b4cc3b80ece9b5fb5841e069)
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2009-01-30 Naohisa Goto <ng@bioruby.org>
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* lib/bio/appl/blast/format0.rb
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Bug fix: incorrect parsing of hit sequence's whole length.
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(commit 98e6f57630b2c3394a9403f58e76b102346c56ef)
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Bug fix: Whole length of a hit sequence is mistakenly parsed when
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it contains ",". WU-BLAST parser is also affected in addition to
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NCBI BLAST parser.
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* lib/bio/db/lasergene.rb, lib/bio/db/soft.rb,
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lib/bio/util/color_scheme.rb, lib/bio/util/contingency_table.rb,
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lib/bio/util/restriction_enzyme.rb
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Removed ":nodoc:" in in "module Bio" which prevents RDoc of the
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Bio module.
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(commit 458db79b467d40ed02db0d085218f611e7dd5e04)
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2009-01-29 Naohisa Goto <ng@bioruby.org>
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* doc/Changes-1.3.rdoc
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Added documents about Bio::TogoWS and Bio::BIORUBY_VERSION.
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* lib/bio/shell/plugin/entry.rb
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getent (BioRuby shell command) is changed to use EBI Dbfetch or
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TogoWS in addition to NCBI or KEGG API.
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(commit 0e172590f60dd5a5f27a24ecd230037a7909224c)
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* lib/bio/shell/plugin/togows.rb, lib/bio/shell.rb
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Added new shell plugin providing accesses to TogoWS REST services.
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(commit 03f6720b90e90703c23536a11b3f12c8155550ff)
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* lib/bio.rb
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Added autoload of Bio::TogoWS.
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(commit f8605e1234164a7aa7f236b4e96a4299229753d7)
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* test/functional/bio/io/test_togows.rb,
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test/unit/bio/io/test_togows.rb
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Newly added functional and unit tests for Bio::TogoWS::REST.
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(commit f04152b80d07f44f146fa3fa0729facede865aac)
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* lib/bio/io/togows.rb
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New class Bio::TogoWS::REST, a REST client for the TogoWS web
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service (http://togows.dbcls.jp/site/en/rest.html).
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(commit 652d2534163675182b9ce30cbb1dd5efff45cd60)
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* bin/br_pmfetch.rb
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Changed to use Bio::BIORUBY_VERSION_ID instead of CVS version ID.
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(commit f69d538ffa9ded00eb68dd306e65505d03b6c656)
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* lib/bio/shell/core.rb
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Changed to use BIORUBY_VERSION_ID.
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(commit 4ce11656a205e85cae64eca27cef7cd94eb80930)
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* bioruby.gemspec.erb
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Gem version is now determined from lib/bio/version.rb or
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BIORUBY_GEM_VERSION environment variable.
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(commit 1811e845e60bc2847ea5717ef936bad93f9f2c87)
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* Rakefile
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* Changed to use lib/bio/version.rb.
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* Environment variable BIORUBY_EXTRAVERSION is renamed to
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BIORUBY_EXTRA_VERSION.
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* Added dependency on lib/bio/version.rb to bioruby.gemspec.
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(commit fb27eaa584cda1bb4cb75e10085996503361c98a)
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* lib/bio.rb, lib/bio/version.rb
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Bio::BIORUBY_VERSION is split into lib/bio/version.rb.
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(commit 9779398c3fa0e9405a875b754a5243e0d6922c32)
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* New file lib/bio/version.rb contains BioRuby version information.
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* New constants: Bio::BIORUBY_EXTRA_VERSION stores extra version
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string (e.g. "-pre1") and Bio::BIORUBY_VERSION_ID stores BioRuby
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version string (e.g. "1.3.0-pre1").
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* Bio::BIORUBY_VERSION is changed to be frozen. Above two constants
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also store frozen values.
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2009-01-26 Naohisa Goto <ng@bioruby.org>
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* KNOWN_ISSUES.rdoc
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@@ -5,21 +198,25 @@
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Newly added KNOWN_ISSUES.rdoc that describes known issues and
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bugs in current BioRuby.
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(commit 06b10262be0bf797a3b133e4697e9b0955408944)
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(commit a65ad8b42613e46b0b4bb0650d6301da0dcc88c9)
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* lib/bio/shell/plugin/ncbirest.rb, lib/bio/shell.rb
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New shell plugin lib/bio/shell/plugin/ncbirest.rb, providing
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"efetch", "einfo", "esearch", and "esearch_count" methods.
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They act the same as those defined in Bio::NCBI::REST, except
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that efetch
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-
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that "efetch" fetches entries with pre-defined databases
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depending on arguments.
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(commit c482e1864aa0dbca3727b1059d4fe3d0aefb3917)
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(commit 3360b8905fdbcd4ca050470fdb2f02a7387e8bb9)
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* lib/bio/shell/plugin/entry.rb
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-
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-
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Shell commands "getent" and "getseq" are changed to use
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"efetch" method when "gb" or some variant is specified as
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the database.
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(commit c482e1864aa0dbca3727b1059d4fe3d0aefb3917)
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(commit 3360b8905fdbcd4ca050470fdb2f02a7387e8bb9)
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* bioruby.gemspec.erb, bioruby.gemspec
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data/KNOWN_ISSUES.rdoc
CHANGED
@@ -38,20 +38,42 @@ SOAP4R (SOAP and WSDL implementation) is no longer bundled with Ruby 1.9.
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In addition, because of the API changes in recent SOAP4R, some
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classes/modules using SOAP4R may not work.
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=== Problem with REXML DoS vulnerability patch before 09-Nov-2008
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(WONT_FIX) If you have applied a patch taken from
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http://www.ruby-lang.org/en/news/2008/08/23/dos-vulnerability-in-rexml/
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before 09 Nov 2008 12:40 +0900, because of the bug in the patch,
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parsing of Blast XML results with REXML parser may fail. The bug is already
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fixed and new patch is available on the above URL. Note that some Linux
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distributions would have incorporated the patch in their manners, and may
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have the same problem.
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== 2. OS and/or architecture-dependent issues
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=== Microsoft Windows
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-
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-
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==== Text mode issues
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Following 4 tests failed on mswin32 (and maybe on mingw32 and bccwin32)
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because of the conversion of line feed codes in the text mode.
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* test_ended_pos and test_start_pos in test/unit/bio/io/test_flatfile.rb
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* test_pos in test/unit/bio/io/flatfile/test_buffer.rb
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* test_entry_pos in test/unit/bio/appl/blast/test_rpsblast.rb
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This indicates that br_bioflat.rb and Bio::FlatFileIndex may create
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incorrect indexes on mswin32, mingw32, and bccwin32. In addition,
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Bio::FlatFile may return incorrect data.
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==== Windows 95/98/98SE/ME
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(WONT_FIX) Some methods that call external programs may not work in
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Windows 95/98/98SE/ME because of the limitation of COMMAND.COM.
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=== OpenVMS, BeOS, OS/2, djgpp, Windows CE
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(WONT_FIX) BioRuby may not work on these platforms.
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== 3. Known issues and bugs in BioRuby
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=== Bio::Ensembl
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data/README.rdoc
CHANGED
@@ -35,6 +35,35 @@ services including KEGG API can be easily utilized by BioRuby.
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== FOR MORE INFORMATION
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=== Documents in this distribution
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==== General information
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README.rdoc:: This file. General information and installation procedure.
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KNOWN_ISSUES.rdoc:: Known issues and bugs in BioRuby.
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doc/Changes-1.3.rdoc:: News and incompatible changes from 1.2.1 to 1.3.0.
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doc/Changes-0.7.rd:: News and incompatible changes from 0.6.4 to 1.2.1.
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==== Tutorials and other useful information
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doc/Tutorial.rd:: BioRuby Tutorial.
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doc/Tutorial.rd.html:: HTML version of Tutorial.rd.
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doc/KEGG_API.rd:: Documents about KEGG API, including usage of Bio::KEGG::API.
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==== BioRuby development
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ChangeLog:: History of changes.
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README_DEV.rdoc:: Describes ways to contribute to the BioRuby project, including coding styles and documentation guidelines.
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==== Documents written in Japanese
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doc/Tutorial.rd.ja:: BioRuby Tutorial written in Japanese.
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doc/Tutorial.rd.ja.html:: HTML version of Tutorial.rd.ja.
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doc/KEGG_API.rd.ja:: Japanese translation of KEGG_API.rd.
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=== WWW
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BioRuby's official website is at http://bioruby.org/.
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You will find links to related resources including downloads,
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mailing lists, Wiki documentation etc. in the top page.
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data/Rakefile
CHANGED
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require 'rake/packagetask'
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require 'rake/gempackagetask'
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require 'rake/rdoctask'
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-
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|
15
|
+
load "./lib/bio/version.rb"
|
16
|
+
BIO_VERSION_RB_LOADED = true
|
15
17
|
|
16
18
|
# Version string for tar.gz, tar.bz2, or zip archive.
|
17
19
|
# If nil, use the value in lib/bio.rb
|
18
20
|
# Note that gem version is always determined from bioruby.gemspec.erb.
|
19
21
|
version = ENV['BIORUBY_VERSION'] || Bio::BIORUBY_VERSION.join(".")
|
20
22
|
version = nil if version.to_s.empty?
|
21
|
-
extraversion = ENV['
|
23
|
+
extraversion = ENV['BIORUBY_EXTRA_VERSION'] || Bio::BIORUBY_EXTRA_VERSION
|
22
24
|
extraversion = nil if extraversion.to_s.empty?
|
23
|
-
version += extraversion.to_s if version and extraversion
|
24
25
|
BIORUBY_VERSION = version
|
26
|
+
BIORUBY_EXTRA_VERSION = extraversion
|
25
27
|
|
26
28
|
task :default => "test"
|
27
29
|
|
@@ -63,7 +65,8 @@ task :regemspec do
|
|
63
65
|
end
|
64
66
|
|
65
67
|
desc "Update #{GEM_SPEC_FILE}"
|
66
|
-
file GEM_SPEC_FILE => [ GEM_SPEC_TEMPLATE_FILE, 'Rakefile'
|
68
|
+
file GEM_SPEC_FILE => [ GEM_SPEC_TEMPLATE_FILE, 'Rakefile',
|
69
|
+
'lib/bio/version.rb' ] do |t|
|
67
70
|
puts "creates #{GEM_SPEC_FILE}"
|
68
71
|
File.open(t.name, 'w') do |w|
|
69
72
|
w.print gem_spec_string
|
@@ -79,7 +82,7 @@ Rake::PackageTask.new("bioruby") do |pkg|
|
|
79
82
|
pkg.need_tar_gz = true
|
80
83
|
pkg.package_files.import(spec.files)
|
81
84
|
pkg.package_files.include(*tar_additional_files)
|
82
|
-
pkg.version = BIORUBY_VERSION || spec.version
|
85
|
+
pkg.version = (BIORUBY_VERSION || spec.version) + BIORUBY_EXTRA_VERSION.to_s
|
83
86
|
end
|
84
87
|
|
85
88
|
Rake::GemPackageTask.new(spec) do |pkg|
|
@@ -102,3 +105,39 @@ Rake::RDocTask.new do |r|
|
|
102
105
|
r.main = main
|
103
106
|
r.options = opts
|
104
107
|
end
|
108
|
+
|
109
|
+
# Tutorial files
|
110
|
+
TUTORIAL_RD = 'doc/Tutorial.rd'
|
111
|
+
TUTORIAL_RD_JA = 'doc/Tutorial.rd.ja'
|
112
|
+
|
113
|
+
TUTORIAL_RD_HTML = TUTORIAL_RD + '.html'
|
114
|
+
TUTORIAL_RD_JA_HTML = TUTORIAL_RD_JA + '.html'
|
115
|
+
|
116
|
+
HTMLFILES_TUTORIAL = [ TUTORIAL_RD_HTML, TUTORIAL_RD_JA_HTML ]
|
117
|
+
|
118
|
+
# Formatting RD to html.
|
119
|
+
def rd2html(src, dst)
|
120
|
+
sh "rd2 -r rd/rd2html-lib.rb --with-css=bioruby.css #{src} > #{dst}"
|
121
|
+
end
|
122
|
+
|
123
|
+
# Tutorial.rd to Tutorial.rd.html
|
124
|
+
file TUTORIAL_RD_HTML => TUTORIAL_RD do |t|
|
125
|
+
rd2html(t.prerequisites[0], t.name)
|
126
|
+
end
|
127
|
+
|
128
|
+
# Tutorial.rd.ja to Tutorial.html.ja
|
129
|
+
file TUTORIAL_RD_JA_HTML => TUTORIAL_RD_JA do |t|
|
130
|
+
rd2html(t.prerequisites[0], t.name)
|
131
|
+
end
|
132
|
+
|
133
|
+
desc "Update doc/Tutorial*.html"
|
134
|
+
task :tutorial2html => HTMLFILES_TUTORIAL
|
135
|
+
|
136
|
+
desc "Force update doc/Tutorial*.html"
|
137
|
+
task :retutorial2html do
|
138
|
+
# safe_unlink HTMLFILES_TUTORIAL
|
139
|
+
HTMLFILES_TUTORIAL.each do |x|
|
140
|
+
Rake::Task[x].execute
|
141
|
+
end
|
142
|
+
end
|
143
|
+
|
data/bin/br_pmfetch.rb
CHANGED
@@ -6,15 +6,16 @@
|
|
6
6
|
# Toshiaki Katayama <k@bioruby.org>
|
7
7
|
# License:: The Ruby License
|
8
8
|
#
|
9
|
-
# $Id
|
9
|
+
# $Id:$
|
10
10
|
#
|
11
11
|
|
12
|
-
|
12
|
+
require 'bio'
|
13
|
+
|
14
|
+
PROG_VER = "Powered by BioRuby #{Bio::BIORUBY_VERSION_ID}"
|
13
15
|
PROG_NAME = File.basename($0)
|
14
16
|
|
15
17
|
|
16
18
|
require 'getoptlong'
|
17
|
-
require 'bio'
|
18
19
|
|
19
20
|
|
20
21
|
### formatting
|
data/bioruby.gemspec
CHANGED
@@ -3,7 +3,7 @@
|
|
3
3
|
#
|
4
4
|
Gem::Specification.new do |s|
|
5
5
|
s.name = 'bio'
|
6
|
-
s.version = "1.
|
6
|
+
s.version = "1.3.0"
|
7
7
|
|
8
8
|
s.author = "BioRuby project"
|
9
9
|
s.email = "staff@bioruby.org"
|
@@ -31,7 +31,10 @@ Gem::Specification.new do |s|
|
|
31
31
|
"doc/KEGG_API.rd",
|
32
32
|
"doc/KEGG_API.rd.ja",
|
33
33
|
"doc/Tutorial.rd",
|
34
|
+
"doc/Tutorial.rd.html",
|
34
35
|
"doc/Tutorial.rd.ja",
|
36
|
+
"doc/Tutorial.rd.ja.html",
|
37
|
+
"doc/bioruby.css",
|
35
38
|
"etc/bioinformatics/seqdatabase.ini",
|
36
39
|
"extconf.rb",
|
37
40
|
"lib/bio.rb",
|
@@ -202,6 +205,7 @@ Gem::Specification.new do |s|
|
|
202
205
|
"lib/bio/io/registry.rb",
|
203
206
|
"lib/bio/io/soapwsdl.rb",
|
204
207
|
"lib/bio/io/sql.rb",
|
208
|
+
"lib/bio/io/togows.rb",
|
205
209
|
"lib/bio/location.rb",
|
206
210
|
"lib/bio/map.rb",
|
207
211
|
"lib/bio/pathway.rb",
|
@@ -235,6 +239,7 @@ Gem::Specification.new do |s|
|
|
235
239
|
"lib/bio/shell/plugin/psort.rb",
|
236
240
|
"lib/bio/shell/plugin/seq.rb",
|
237
241
|
"lib/bio/shell/plugin/soap.rb",
|
242
|
+
"lib/bio/shell/plugin/togows.rb",
|
238
243
|
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb",
|
239
244
|
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml",
|
240
245
|
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml",
|
@@ -290,6 +295,7 @@ Gem::Specification.new do |s|
|
|
290
295
|
"lib/bio/util/restriction_enzyme/single_strand_complement.rb",
|
291
296
|
"lib/bio/util/restriction_enzyme/string_formatting.rb",
|
292
297
|
"lib/bio/util/sirna.rb",
|
298
|
+
"lib/bio/version.rb",
|
293
299
|
"rdoc.zsh",
|
294
300
|
"sample/any2fasta.rb",
|
295
301
|
"sample/biofetch.rb",
|
@@ -354,6 +360,7 @@ Gem::Specification.new do |s|
|
|
354
360
|
"test/functional/bio/appl/test_pts1.rb",
|
355
361
|
"test/functional/bio/io/test_ensembl.rb",
|
356
362
|
"test/functional/bio/io/test_soapwsdl.rb",
|
363
|
+
"test/functional/bio/io/test_togows.rb",
|
357
364
|
"test/functional/bio/sequence/test_output_embl.rb",
|
358
365
|
"test/functional/bio/test_command.rb",
|
359
366
|
"test/runner.rb",
|
@@ -403,6 +410,7 @@ Gem::Specification.new do |s|
|
|
403
410
|
"test/unit/bio/io/test_fastacmd.rb",
|
404
411
|
"test/unit/bio/io/test_flatfile.rb",
|
405
412
|
"test/unit/bio/io/test_soapwsdl.rb",
|
413
|
+
"test/unit/bio/io/test_togows.rb",
|
406
414
|
"test/unit/bio/sequence/test_aa.rb",
|
407
415
|
"test/unit/bio/sequence/test_common.rb",
|
408
416
|
"test/unit/bio/sequence/test_compat.rb",
|
@@ -443,11 +451,11 @@ Gem::Specification.new do |s|
|
|
443
451
|
|
444
452
|
s.has_rdoc = true
|
445
453
|
s.extra_rdoc_files = [
|
454
|
+
"ChangeLog",
|
446
455
|
"KNOWN_ISSUES.rdoc",
|
447
456
|
"README.rdoc",
|
448
457
|
"README_DEV.rdoc",
|
449
|
-
"doc/Changes-1.3.rdoc"
|
450
|
-
"ChangeLog"
|
458
|
+
"doc/Changes-1.3.rdoc"
|
451
459
|
]
|
452
460
|
s.rdoc_options << '--main' << 'README.rdoc'
|
453
461
|
s.rdoc_options << '--title' << 'BioRuby API documentation'
|
data/bioruby.gemspec.erb
CHANGED
@@ -1,6 +1,41 @@
|
|
1
1
|
Gem::Specification.new do |s|
|
2
2
|
s.name = 'bio'
|
3
|
-
s.version = "
|
3
|
+
s.version = "<% ###### Below is executed in ERB environment ######
|
4
|
+
# Version can be specified by the environment variable
|
5
|
+
env_ver = ENV['BIORUBY_GEM_VERSION']
|
6
|
+
env_ver = nil if env_ver.to_s.strip.empty?
|
7
|
+
|
8
|
+
# By default, determined from lib/bio/version.rb
|
9
|
+
load "./lib/bio/version.rb" unless defined?(BIO_VERSION_RB_LOADED)
|
10
|
+
case Bio::BIORUBY_EXTRA_VERSION
|
11
|
+
when nil
|
12
|
+
suffix = nil
|
13
|
+
when /\A\.(\d+)\z/
|
14
|
+
suffix = $1
|
15
|
+
when /\-alpha(\d+)/
|
16
|
+
decrement = true
|
17
|
+
suffix = 9000 + $1.to_i
|
18
|
+
when /\-pre(\d+)/
|
19
|
+
decrement = true
|
20
|
+
suffix = 9500 + $1.to_i
|
21
|
+
when /\-rc(\d+)/
|
22
|
+
decrement = true
|
23
|
+
suffix = 9900 + $1.to_i
|
24
|
+
else
|
25
|
+
suffix = "0000"
|
26
|
+
end
|
27
|
+
ver = Bio::BIORUBY_VERSION.reverse.collect do |i|
|
28
|
+
if decrement then
|
29
|
+
i -= 1
|
30
|
+
i < 0 ? (i += 10) : decrement = false
|
31
|
+
end
|
32
|
+
i
|
33
|
+
end.reverse
|
34
|
+
ver.push suffix if suffix
|
35
|
+
%><%=
|
36
|
+
(env_ver || ver.join('.'))
|
37
|
+
###### Above is executed in ERB environment ######
|
38
|
+
%>"
|
4
39
|
|
5
40
|
s.author = "BioRuby project"
|
6
41
|
s.email = "staff@bioruby.org"
|
@@ -16,7 +51,7 @@ Gem::Specification.new do |s|
|
|
16
51
|
files = (`git ls-files` rescue nil).to_s.split(/\r?\n/)
|
17
52
|
files.delete_if { |x| x.empty? }
|
18
53
|
# When git-ls-files isn't available, creates a list from current files.
|
19
|
-
|
54
|
+
if !($?.success?) or files.size <= 0 then
|
20
55
|
files =
|
21
56
|
[ "README.rdoc", "README_DEV.rdoc",
|
22
57
|
"ChangeLog", "KNOWN_ISSUES.rdoc",
|
@@ -33,7 +68,7 @@ Gem::Specification.new do |s|
|
|
33
68
|
end
|
34
69
|
end
|
35
70
|
%><%=
|
36
|
-
files.collect { |x| x.dump }.join(",\n ")
|
71
|
+
files.sort.collect { |x| x.dump }.join(",\n ")
|
37
72
|
###### Above is executed in ERB environment ######
|
38
73
|
%>
|
39
74
|
]
|
@@ -49,7 +84,7 @@ Gem::Specification.new do |s|
|
|
49
84
|
'doc/Changes-1.3.rdoc' ]
|
50
85
|
end
|
51
86
|
rdoc_files.push "ChangeLog" unless rdoc_files.include?("ChangeLog")
|
52
|
-
rdoc_files.collect { |x| x.dump }.join(",\n ")
|
87
|
+
rdoc_files.sort.collect { |x| x.dump }.join(",\n ")
|
53
88
|
###### Above is executed in ERB environment ######
|
54
89
|
%>
|
55
90
|
]
|
@@ -74,7 +109,7 @@ Gem::Specification.new do |s|
|
|
74
109
|
if exec_files.empty? then
|
75
110
|
exec_files = [ "bioruby", "br_biofetch.rb", "br_biogetseq.rb", "br_bioflat.rb", "br_pmfetch.rb" ]
|
76
111
|
end
|
77
|
-
exec_files.collect { |x| x.dump }.join(",\n ")
|
112
|
+
exec_files.sort.collect { |x| x.dump }.join(",\n ")
|
78
113
|
###### Above is executed in ERB environment ######
|
79
114
|
%>
|
80
115
|
]
|
data/doc/Changes-0.7.rd
CHANGED
@@ -338,6 +338,13 @@ In 1.1.0:
|
|
338
338
|
instead of a string or nil: score, percent_identity, percent_positive,
|
339
339
|
percent_gaps.
|
340
340
|
|
341
|
+
--- BioRuby Shell
|
342
|
+
|
343
|
+
In 1.1.0:
|
344
|
+
|
345
|
+
* Shell commands seq, ent, obj are renamed to getseq, getent, getobj,
|
346
|
+
respectively.
|
347
|
+
|
341
348
|
=== Deleted files
|
342
349
|
|
343
350
|
: lib/bio/db/genbank.rb
|
data/doc/Changes-1.3.rdoc
CHANGED
@@ -58,6 +58,11 @@ particular use cases.
|
|
58
58
|
|
59
59
|
New method Bio::Locations#to_s is added to support output of features.
|
60
60
|
|
61
|
+
=== Bio::TogoWS::REST
|
62
|
+
|
63
|
+
TogoWS REST client class is newly added. Information about TogoWS REST service
|
64
|
+
can be found on http://togows.dbcls.jp/site/en/rest.html.
|
65
|
+
|
61
66
|
== Deprecated classes
|
62
67
|
|
63
68
|
=== Bio::Features
|
@@ -74,6 +79,18 @@ will soon be removed in the future.
|
|
74
79
|
|
75
80
|
== Incompatible changes
|
76
81
|
|
82
|
+
=== Bio::BIORUBY_VERSION
|
83
|
+
|
84
|
+
Definition of the constant Bio::BIORUBY_VERSION is moved from lib/bio.rb to
|
85
|
+
lib/bio/version.rb. Normally, the autoload mechanism of Ruby correctly loads
|
86
|
+
the version.rb, but special scripts directly using bio.rb may be needed to
|
87
|
+
be changed.
|
88
|
+
|
89
|
+
Bio::BIORUBY_VERSION is changed to be frozen.
|
90
|
+
|
91
|
+
New constants Bio::BIORUBY_EXTRA_VERSION and Bio::BIORUBY_VERSION_ID are
|
92
|
+
added. See their RDoc for details.
|
93
|
+
|
77
94
|
=== Bio::Sequence
|
78
95
|
|
79
96
|
Bio::Sequence#date is removed. Alternatively, date_created or date_modified
|