bio 2.0.1 → 2.0.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/ChangeLog +313 -0
- data/KNOWN_ISSUES.rdoc +1 -1
- data/LEGAL +9 -0
- data/README.rdoc +3 -3
- data/RELEASE_NOTES.rdoc +59 -0
- data/bioruby.gemspec +4 -2
- data/bioruby.gemspec.erb +0 -1
- data/lib/bio/appl/iprscan/report.rb +3 -3
- data/lib/bio/appl/sosui/report.rb +1 -1
- data/lib/bio/db/embl/uniprotkb.rb +137 -12
- data/lib/bio/db/go.rb +2 -2
- data/lib/bio/sequence/common.rb +112 -0
- data/lib/bio/sequence/format.rb +1 -0
- data/lib/bio/tree.rb +1 -1
- data/lib/bio/version.rb +1 -1
- data/test/data/uniprot/P28907.uniprot +551 -0
- data/test/unit/bio/db/embl/test_uniprotkb_P28907.rb +325 -0
- data/test/unit/bio/sequence/test_ruby3.rb +462 -0
- metadata +6 -4
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data/ChangeLog
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commit 1bc877e557e165b42eea992d89f19a63996cb586
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Tue Sep 13 21:19:01 2022 +0900
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regenerate bioruby.gemspec with rake regemspec
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bioruby.gemspec | 4 +++-
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1 file changed, 3 insertions(+), 1 deletion(-)
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commit 190e4751b84cc45cbce636c4414482a8169b08df
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Tue Sep 13 21:18:06 2022 +0900
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prepare for BioRuby 2.0.4 release
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lib/bio/version.rb | 2 +-
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1 file changed, 1 insertion(+), 1 deletion(-)
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commit a666639e0393e96b2de0bbcb447c13f8a14ad06d
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Tue Sep 13 21:17:11 2022 +0900
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update release notes for upcoming BioRuby 2.0.4
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RELEASE_NOTES.rdoc | 14 ++++++++++++++
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1 file changed, 14 insertions(+)
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commit c0d197343dd7fd8999d04083c9e8f24fa37a2f93
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Tue Sep 13 21:13:40 2022 +0900
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License of UniProt data is CC BY 4.0
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LEGAL | 9 +++++++++
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1 file changed, 9 insertions(+)
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commit e670102e6d4deb04c1fcae62459cc02861132d25
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Tue Sep 13 21:01:50 2022 +0900
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Bug fix: Bio::UniProtKB#protein_name and #synonyms may raise error
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* Bug fix: Bio::UniProtKB#protein_name and #synonyms may raise error
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after calling Bio::UniProtKB#de method.
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lib/bio/db/embl/uniprotkb.rb | 25 ++++++++++++++++++-------
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test/unit/bio/db/embl/test_uniprotkb_P28907.rb | 11 +++++++++++
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2 files changed, 29 insertions(+), 7 deletions(-)
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commit 9c04e08e8d1316ffd7fc15ab311cea5dd6937d36
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Tue Sep 13 20:44:46 2022 +0900
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Supports format change of FT lines since UniProt release 2019_11
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* Bio::UniProtKB#ft: Supports text format change of FT lines since
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UniProt release 2019_11. (Details of the format changes:
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https://www.uniprot.org/release-notes/2019-12-18-release#text%5Fft )
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This closes https://github.com/bioruby/bioruby/issues/147 .
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* Tests are added with a new test data
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lib/bio/db/embl/uniprotkb.rb | 122 +++++-
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test/data/uniprot/P28907.uniprot | 551 +++++++++++++++++++++++++
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test/unit/bio/db/embl/test_uniprotkb_P28907.rb | 314 ++++++++++++++
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3 files changed, 983 insertions(+), 4 deletions(-)
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create mode 100644 test/data/uniprot/P28907.uniprot
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create mode 100644 test/unit/bio/db/embl/test_uniprotkb_P28907.rb
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commit b18ee463d4328b5ef619733b46f568b18459be7a
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Fri Nov 5 23:49:18 2021 +0900
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BioRuby 2.0.3 is released
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ChangeLog | 136 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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1 file changed, 136 insertions(+)
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commit c16e230d15cf30478a3739563b4e4745dc57ef82
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Fri Nov 5 23:44:45 2021 +0900
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regenerate bioruby.gemspec with rake regemspec
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bioruby.gemspec | 3 ++-
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1 file changed, 2 insertions(+), 1 deletion(-)
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commit 1a8c44dc5b8d24342550273a594e5f75e41f41df
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Fri Nov 5 23:41:29 2021 +0900
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prepare for BioRuby 2.0.3 release
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lib/bio/version.rb | 2 +-
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1 file changed, 1 insertion(+), 1 deletion(-)
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commit 863242cdb9a748ba9efb3be3b39f92c17ed3ea84
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Fri Nov 5 23:36:27 2021 +0900
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update release notes for upcoming BioRuby 2.0.3
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RELEASE_NOTES.rdoc | 26 ++++++++++++++++++++++++++
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1 file changed, 26 insertions(+)
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commit b97794d632c73dc45639cec000fb11238740eb30
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Fri Nov 5 23:26:20 2021 +0900
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Ruby 3.0 compatibility fix: Bio::Sequence::*#partition, #rpartiton
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* Behaviors of Bio::Sequence::*#partition and #rpartition in Ruby 3.0
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are changed to mimic those in Ruby 2.x.
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lib/bio/sequence/common.rb | 17 +++++++
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test/unit/bio/sequence/test_ruby3.rb | 94 ++++++++++++++++++++++++++++++++++++
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2 files changed, 111 insertions(+)
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commit 7ff79cd449ee03e0063120fb9abec50d9b08e979
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Fri Nov 5 22:24:16 2021 +0900
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remove resolved Ruby 3.0 issue
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KNOWN_ISSUES.rdoc | 8 --------
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1 file changed, 8 deletions(-)
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commit 24bb3c3cf417837ad63a27913db7237aef1414c6
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Fri Nov 5 21:24:26 2021 +0900
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Bio::Sequence::NA,AA,Generic: workaround for Ruby 3.0.0 incompatible change
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* Since Ruby 3.0.0, over 30 methods in subclass of String class are
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changed to return/yield String instance instead of the subclass
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instance. (https://github.com/ruby/ruby/blob/v3_0_0/NEWS.md )
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* In this commit, workaround is made for the following methods:
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* *
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* capitalize
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* center
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* chomp
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* chop
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* delete
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* delete_prefix
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* delete_suffix
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* downcase
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* each_char
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* each_grapheme_cluster
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* each_line
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* gsub
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* gsub!
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* ljust
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* lstrip
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* revserse
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* rjust
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* rstrip
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* slice!
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* slice / []
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* split
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* squeeze
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* strip
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* sub
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* sub!
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* succ / next
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* swapcase
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* tr
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* tr_s
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* upcase
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* Note: sub! and gsub! are not described in the NEWS.md
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but are also affected by this Ruby 3.0.0 incompatible changes.
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* The following methods are not patched i.e. they return/yield
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String instances.
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* dump
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* partition
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* rpartition
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* scrub
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* Note: In Ruby 2.7 or earlier, Bio::Sequence::NA#partition
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and #rpartition methods return an array that may contain
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mixture of Bio::Sequence::NA instances and String instances.
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* test/unit/bio/sequence/test_ruby3.rb: unit tests for the
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above methods.
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* Close https://github.com/bioruby/bioruby/issues/137
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lib/bio/sequence/common.rb | 95 +++++++++
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test/unit/bio/sequence/test_ruby3.rb | 368 +++++++++++++++++++++++++++++++++++
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2 files changed, 463 insertions(+)
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create mode 100644 test/unit/bio/sequence/test_ruby3.rb
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commit 0efc0a54685d43645daa9c53d7140bfb81577777
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Author: kojix2 <2xijok@gmail.com>
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Date: Tue Aug 31 19:39:25 2021 +0900
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Fix typos: Retrun -> Return
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lib/bio/appl/iprscan/report.rb | 6 +++---
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lib/bio/appl/sosui/report.rb | 2 +-
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lib/bio/db/embl/uniprotkb.rb | 2 +-
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lib/bio/db/go.rb | 4 ++--
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lib/bio/tree.rb | 2 +-
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commit a291b5a72da12a5cc8b006d1dd63d002fda5dff3
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Thu Dec 31 23:52:54 2020 +0900
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BioRuby 2.0.2 is released
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ChangeLog | 98 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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1 file changed, 98 insertions(+)
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commit fd420b713ca364e677ef3551919ec907791df86d
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Thu Dec 31 23:51:08 2020 +0900
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RELEASE_NOTES.rdoc: change some description
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RELEASE_NOTES.rdoc | 2 +-
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1 file changed, 1 insertion(+), 1 deletion(-)
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commit 0ed9b37f38fa1b00dcc1d422914e4cbdbbc5f6ab
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Thu Dec 31 23:46:46 2020 +0900
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regenerate bioruby.gemspec with rake regemspec
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bioruby.gemspec | 2 +-
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1 file changed, 1 insertion(+), 1 deletion(-)
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commit fa84b8fac653c26b9f8db429321ef49202554a69
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Thu Dec 31 23:45:38 2020 +0900
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prepare for BioRuby 2.0.2 release
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lib/bio/version.rb | 2 +-
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commit 32c5efccbad4e0d3440726383f863520ee242cc5
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Thu Dec 31 23:39:18 2020 +0900
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update release notes for upcoming BioRuby 2.0.2
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RELEASE_NOTES.rdoc | 19 +++++++++++++++++++
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1 file changed, 19 insertions(+)
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commit c2f6e62ab64bc532f442bccc0d76ced5380664ec
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Thu Dec 31 23:38:43 2020 +0900
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add a known issue about Ruby 3.0
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KNOWN_ISSUES.rdoc | 10 +++++++++-
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1 file changed, 9 insertions(+), 1 deletion(-)
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commit a733c0816da7c97ca0c23016b473b004fb755f54
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Thu Dec 31 23:04:55 2020 +0900
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remove deprecation warning of Gem::Specification#has_rdoc=
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Gem::Specification#has_rdoc= have been deprecated since RubyGems 1.3.3
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in 2009. (https://blog.rubygems.org/2009/05/04/1.3.3-released.html )
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This fixes https://github.com/bioruby/bioruby/issues/138 .
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Thanks to @jaysonvirissimo for reporting the issue.
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bioruby.gemspec | 1 -
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bioruby.gemspec.erb | 1 -
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2 files changed, 2 deletions(-)
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commit bed6746ce62059795996eeb6e5ac65655bab12b5
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+
Author: Naohisa Goto <ng@bioruby.org>
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Date: Thu Dec 31 22:51:56 2020 +0900
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+
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require ruby's date library to avoid NameError for Date
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+
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In Bio::Sequence#output(:embl), NameError (uninitialized constant
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+
Bio::Sequence::Format::INSDFeatureHelper::Date) is observed.
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The error message is misleading because Date is provided by Ruby's
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standard date library.
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+
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This fixes https://github.com/bioruby/bioruby/issues/135 .
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Thanks to Dr. Mark Wilkinson for reporting the issue.
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lib/bio/sequence/format.rb | 1 +
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1 file changed, 1 insertion(+)
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commit 5f3aa79fdaf6dd5551d51663ca2e9b6f5e56d855
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Fri Nov 6 17:45:12 2020 +0900
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+
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fix mistaken URLs
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+
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README.rdoc | 6 +++---
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1 file changed, 3 insertions(+), 3 deletions(-)
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commit d5e1670ee4863cc60d3aa08432a7ee3b1e445439
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Author: Naohisa Goto <ng@bioruby.org>
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Date: Fri Sep 6 15:48:45 2019 +0900
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BioRuby 2.0.1 is released
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ChangeLog | 185 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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1 file changed, 185 insertions(+)
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1
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commit 21bf51a1ec8c18c9cdf8528ffc3c59c503cef042
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2
315
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Author: Naohisa Goto <ng@bioruby.org>
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3
316
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Date: Fri Sep 6 15:45:47 2019 +0900
|
data/KNOWN_ISSUES.rdoc
CHANGED
data/LEGAL
CHANGED
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@@ -114,6 +114,15 @@ test/data/uniprot/p53_human.uniprot:
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removed.
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test/data/uniprot/P28907.uniprot:
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119
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Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
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Distributed under the Creative Commons Attribution (CC BY 4.0) License
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121
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+
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https://www.uniprot.org/help/license
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https://creativecommons.org/licenses/by/4.0/
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GPL:
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Copyright (C) 1989, 1991 Free Software Foundation, Inc.
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data/README.rdoc
CHANGED
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@@ -206,9 +206,9 @@ Plugins (Biogems) listed below had been included in BioRuby in former days,
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and were split to separate packages to reduce complexity and external
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dependencies.
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-
* {bio-shell}[https://rubygems.org/gems/
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* {bio-executables}[https://rubygems.org/gems/
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* {bio-blast-xmlparser}[https://rubygems.org/gems/
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* {bio-shell}[https://rubygems.org/gems/bio-shell]
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* {bio-executables}[https://rubygems.org/gems/bio-executables]
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* {bio-blast-xmlparser}[https://rubygems.org/gems/bio-blast-xmlparser]
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* {bioruby-phyloxml}[https://rubygems.org/gems/bioruby-phyloxml]
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* NOTE: Please uninstall bio-phyloxml, that have been created as a
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preliminary trial of splitting a module in 2012 and have not been
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data/RELEASE_NOTES.rdoc
CHANGED
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@@ -1,3 +1,62 @@
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1
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+
= BioRuby 2.0.4 RELEASE NOTES
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2
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3
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Some fixes have been made in BioRuby 2.0.4 after the release of 2.0.3.
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== Fixes
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* Bio::UniProtKB#ft: Supports text format change of FT lines since
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UniProt release 2019_11.
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(https://github.com/bioruby/bioruby/issues/147 )
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* Bio::UniProtKB#protein_name and #synonyms methods may raise error
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after calling Bio::UniProtKB#de method.
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= BioRuby 2.0.3 RELEASE NOTES
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Some bug fixes have been made in BioRuby 2.0.3 after the release of 2.0.2.
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== Bug fixes
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20
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+
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* Fix Ruby 3.0.0 Bio::Sequence::* issue.
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(https://github.com/bioruby/bioruby/issues/137 )
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* Fix typo (https://github.com/bioruby/bioruby/pull/145 )
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== Incompatible changes
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=== Bio::Sequence::* incompatible changes since Ruby 3.0.0
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Since Ruby 3.0.0, the following methods in Bio::Sequence::NA,
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Bio::Sequence::AA, and Bio::Sequence::Generic return or yield
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String instance, instead of the Bio::Sequence::* instance.
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* dump
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* scrub
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For details about Ruby 3.0.0 incompatible changes, see
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{News for Ruby 3.0.0}[https://github.com/ruby/ruby/blob/v3_0_0/NEWS.md].
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= BioRuby 2.0.2 RELEASE NOTES
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Some bugs fixes have been made in BioRuby 2.0.2 after the release of 2.0.1.
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== Bug fixes
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* Fix NameError in Bio::Sequence#output(:embl)
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(https://github.com/bioruby/bioruby/issues/135 )
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* Suppress warning: Gem::Specification#has_rdoc= is deprecated
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(https://github.com/bioruby/bioruby/issues/138 )
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* Fix misspelling URL in README.rdoc
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== Known issues
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A known issue about Ruby 3.0 is added to KNOWN_ISSUES.rdoc.
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The issue will be fixed in the near future.
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Some bug fixes and improvements have been made to the BioRuby 2.0.1 after
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data/bioruby.gemspec
CHANGED
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@@ -3,7 +3,7 @@
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3
3
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#
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4
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Gem::Specification.new do |s|
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5
5
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s.name = 'bio'
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s.version = "2.0.
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s.version = "2.0.4"
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s.author = "BioRuby project"
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@@ -454,6 +454,7 @@ Gem::Specification.new do |s|
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"test/data/sim4/simple2-A4.sim4",
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"test/data/soft/GDS100_partial.soft",
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"test/data/soft/GSE3457_family_partial.soft",
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"test/data/uniprot/P28907.uniprot",
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"test/data/uniprot/p53_human.uniprot",
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"test/functional/bio/sequence/test_output_embl.rb",
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"test/functional/bio/test_command.rb",
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@@ -498,6 +499,7 @@ Gem::Specification.new do |s|
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499
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"test/unit/bio/db/embl/test_embl_to_bioseq.rb",
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"test/unit/bio/db/embl/test_uniprot.rb",
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"test/unit/bio/db/embl/test_uniprotkb.rb",
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"test/unit/bio/db/embl/test_uniprotkb_P28907.rb",
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503
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"test/unit/bio/db/embl/test_uniprotkb_new_part.rb",
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"test/unit/bio/db/fasta/test_defline.rb",
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"test/unit/bio/db/fasta/test_defline_misc.rb",
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"test/unit/bio/sequence/test_dblink.rb",
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"test/unit/bio/sequence/test_na.rb",
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550
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"test/unit/bio/sequence/test_quality_score.rb",
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+
"test/unit/bio/sequence/test_ruby3.rb",
|
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552
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"test/unit/bio/sequence/test_sequence_masker.rb",
|
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550
553
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"test/unit/bio/test_alignment.rb",
|
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551
554
|
"test/unit/bio/test_command.rb",
|
|
@@ -580,7 +583,6 @@ Gem::Specification.new do |s|
|
|
|
580
583
|
"test/unit/bio/util/test_sirna.rb"
|
|
581
584
|
]
|
|
582
585
|
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|
583
|
-
s.has_rdoc = true
|
|
584
586
|
s.extra_rdoc_files = [
|
|
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587
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"KNOWN_ISSUES.rdoc",
|
|
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588
|
"README.rdoc",
|
data/bioruby.gemspec.erb
CHANGED
|
@@ -83,7 +83,7 @@ module Bio
|
|
|
83
83
|
yield Bio::Iprscan::Report.parse_raw_entry(entry) if entry != ''
|
|
84
84
|
end
|
|
85
85
|
|
|
86
|
-
# Parser method for a raw formated entry.
|
|
86
|
+
# Parser method for a raw formated entry. Returns a Bio::Iprscan::Report
|
|
87
87
|
# object.
|
|
88
88
|
def self.parse_raw_entry(str)
|
|
89
89
|
report = self.new
|
|
@@ -113,7 +113,7 @@ module Bio
|
|
|
113
113
|
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|
114
114
|
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115
115
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116
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# Parser method for a xml formated entry.
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|
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|
+
# Parser method for a xml formated entry. Returns a Bio::Iprscan::Report
|
|
117
117
|
# object.
|
|
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118
|
# def self.parse_xml(str)
|
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119
|
# end
|
|
@@ -196,7 +196,7 @@ module Bio
|
|
|
196
196
|
end
|
|
197
197
|
end
|
|
198
198
|
|
|
199
|
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# Parser method for a pseudo-txt formated entry.
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|
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+
# Parser method for a pseudo-txt formated entry. Returns a Bio::Iprscan::Report
|
|
200
200
|
# object.
|
|
201
201
|
#
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|
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202
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# == Usage
|