bio 2.0.5 → 2.0.6
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/.github/workflows/ruby.yml +7 -16
- data/ChangeLog +146 -0
- data/README.rdoc +1 -1
- data/RELEASE_NOTES.rdoc +28 -0
- data/bioruby.gemspec +3 -1
- data/doc/Tutorial.md +1274 -0
- data/doc/Tutorial_ja.md +2595 -0
- data/lib/bio/appl/clustalw/report.rb +3 -2
- data/lib/bio/appl/iprscan/report.rb +2 -1
- data/lib/bio/appl/meme/mast.rb +2 -1
- data/lib/bio/appl/paml/common.rb +2 -1
- data/lib/bio/db/embl/common.rb +5 -2
- data/lib/bio/db/fastq.rb +3 -2
- data/lib/bio/db/gff.rb +14 -8
- data/lib/bio/db/newick.rb +6 -5
- data/lib/bio/db/pdb/chain.rb +2 -1
- data/lib/bio/db/pdb/pdb.rb +2 -1
- data/lib/bio/db/prosite.rb +2 -0
- data/lib/bio/db.rb +5 -4
- data/lib/bio/io/flatfile/buffer.rb +2 -1
- data/lib/bio/io/flatfile/splitter.rb +2 -1
- data/lib/bio/pathway.rb +2 -1
- data/lib/bio/sequence/common.rb +2 -1
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +3 -2
- data/lib/bio/util/sirna.rb +3 -2
- data/lib/bio/version.rb +1 -1
- data/test/network/bio/db/kegg/test_genes_hsa7422.rb +8 -10
- data/test/unit/bio/appl/iprscan/test_report.rb +3 -2
- data/test/unit/bio/io/flatfile/test_splitter.rb +7 -4
- data/test/unit/bio/sequence/test_common.rb +3 -2
- data/test/unit/bio/test_alignment.rb +17 -16
- data/test/unit/bio/test_sequence.rb +3 -2
- metadata +5 -6
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@@ -1,3 +1,4 @@
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# frozen_string_literal: true
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#
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# test/unit/bio/test_sequence.rb - Unit test for Bio::Sequencce
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#
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@@ -233,7 +234,7 @@ module Bio
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end
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def test_randomize_dna_with_block
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appended =
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appended = String.new
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@na.randomize {|x| appended << x}
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assert_equal(@na.composition, Sequence::NA.new(appended).composition)
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end
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@@ -247,7 +248,7 @@ module Bio
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end
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def test_NA_randomize_with_counts_and_block
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appended =
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appended = String.new
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counts = {'a'=>10,'c'=>20,'g'=>30,'u'=>40}
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counts.default = 0
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Sequence::NA.randomize(counts) {|x| appended << x}
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metadata
CHANGED
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--- !ruby/object:Gem::Specification
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name: bio
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version: !ruby/object:Gem::Version
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version: 2.0.
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version: 2.0.6
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platform: ruby
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authors:
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- BioRuby project
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autorequire:
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bindir: bin
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cert_chain: []
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date:
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date: 2025-03-07 00:00:00.000000000 Z
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dependencies: []
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description: BioRuby is a library for bioinformatics (biology + information science).
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email: staff@bioruby.org
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@@ -55,10 +54,12 @@ files:
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- doc/RELEASE_NOTES-1.4.2.rdoc
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- doc/RELEASE_NOTES-1.4.3.rdoc
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- doc/RELEASE_NOTES-1.5.0.rdoc
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- doc/Tutorial.md
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- doc/Tutorial.rd
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- doc/Tutorial.rd.html
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- doc/Tutorial.rd.ja
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- doc/Tutorial.rd.ja.html
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- doc/Tutorial_ja.md
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- doc/bioruby.css
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- etc/bioinformatics/seqdatabase.ini
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- lib/bio.rb
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@@ -593,7 +594,6 @@ homepage: http://bioruby.org/
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licenses:
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- Ruby
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metadata: {}
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post_install_message:
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rdoc_options:
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- "--main"
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- README.rdoc
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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rubygems_version: 3.
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signing_key:
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rubygems_version: 3.6.2
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specification_version: 4
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summary: Bioinformatics library
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test_files: []
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