bio 2.0.4 → 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.
Files changed (55) hide show
  1. checksums.yaml +4 -4
  2. data/.github/workflows/ruby.yml +29 -0
  3. data/.gitignore +32 -0
  4. data/ChangeLog +433 -0
  5. data/Gemfile +3 -0
  6. data/LEGAL +2 -0
  7. data/README.rdoc +1 -1
  8. data/RELEASE_NOTES.rdoc +64 -0
  9. data/appveyor.yml +14 -13
  10. data/bioruby.gemspec +9 -10
  11. data/doc/Tutorial.md +1274 -0
  12. data/doc/Tutorial_ja.md +2595 -0
  13. data/lib/bio/appl/blast/genomenet.rb +2 -1
  14. data/lib/bio/appl/clustalw/report.rb +3 -2
  15. data/lib/bio/appl/iprscan/report.rb +2 -1
  16. data/lib/bio/appl/meme/mast.rb +2 -1
  17. data/lib/bio/appl/paml/common.rb +2 -1
  18. data/lib/bio/appl/pts1.rb +1 -1
  19. data/lib/bio/db/embl/common.rb +5 -2
  20. data/lib/bio/db/embl/uniprotkb.rb +52 -19
  21. data/lib/bio/db/fastq.rb +3 -2
  22. data/lib/bio/db/gff.rb +14 -8
  23. data/lib/bio/db/newick.rb +6 -5
  24. data/lib/bio/db/pdb/chain.rb +2 -1
  25. data/lib/bio/db/pdb/pdb.rb +2 -1
  26. data/lib/bio/db/prosite.rb +2 -0
  27. data/lib/bio/db.rb +5 -4
  28. data/lib/bio/io/flatfile/buffer.rb +2 -1
  29. data/lib/bio/io/flatfile/splitter.rb +2 -1
  30. data/lib/bio/pathway.rb +2 -1
  31. data/lib/bio/sequence/common.rb +2 -1
  32. data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +3 -2
  33. data/lib/bio/util/sirna.rb +3 -2
  34. data/lib/bio/version.rb +1 -1
  35. data/test/data/uniprot/P03589.uniprot +127 -0
  36. data/test/data/uniprot/P49144.uniprot +232 -0
  37. data/test/functional/bio/test_command.rb +2 -0
  38. data/test/network/bio/db/kegg/test_genes_hsa7422.rb +29 -17
  39. data/test/unit/bio/appl/iprscan/test_report.rb +3 -2
  40. data/test/unit/bio/db/embl/test_uniprotkb_P03589.rb +378 -0
  41. data/test/unit/bio/db/embl/test_uniprotkb_P49144.rb +359 -0
  42. data/test/unit/bio/io/flatfile/test_splitter.rb +7 -4
  43. data/test/unit/bio/sequence/test_common.rb +3 -2
  44. data/test/unit/bio/test_alignment.rb +17 -16
  45. data/test/unit/bio/test_sequence.rb +3 -2
  46. metadata +11 -15
  47. data/.travis.yml +0 -71
  48. data/gemfiles/Gemfile.travis-jruby1.8 +0 -6
  49. data/gemfiles/Gemfile.travis-jruby1.9 +0 -5
  50. data/gemfiles/Gemfile.travis-rbx +0 -10
  51. data/gemfiles/Gemfile.travis-ruby1.8 +0 -6
  52. data/gemfiles/Gemfile.travis-ruby1.9 +0 -5
  53. data/gemfiles/Gemfile.windows +0 -6
  54. data/gemfiles/modify-Gemfile.rb +0 -28
  55. data/gemfiles/prepare-gemspec.rb +0 -29
data/bioruby.gemspec CHANGED
@@ -3,7 +3,7 @@
3
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  #
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  Gem::Specification.new do |s|
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  s.name = 'bio'
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- s.version = "2.0.4"
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+ s.version = "2.0.6"
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  s.author = "BioRuby project"
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  s.email = "staff@bioruby.org"
@@ -15,7 +15,8 @@ Gem::Specification.new do |s|
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  s.platform = Gem::Platform::RUBY
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  s.files = [
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- ".travis.yml",
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+ ".github/workflows/ruby.yml",
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+ ".gitignore",
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  "BSDL",
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  "COPYING",
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  "COPYING.ja",
@@ -43,20 +44,14 @@ Gem::Specification.new do |s|
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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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- "gemfiles/Gemfile.travis-jruby1.8",
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- "gemfiles/Gemfile.travis-jruby1.9",
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- "gemfiles/Gemfile.travis-rbx",
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- "gemfiles/Gemfile.travis-ruby1.8",
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- "gemfiles/Gemfile.travis-ruby1.9",
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- "gemfiles/Gemfile.windows",
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- "gemfiles/modify-Gemfile.rb",
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- "gemfiles/prepare-gemspec.rb",
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  "lib/bio.rb",
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  "lib/bio/alignment.rb",
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  "lib/bio/appl/bl2seq/report.rb",
@@ -454,7 +449,9 @@ 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/P03589.uniprot",
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  "test/data/uniprot/P28907.uniprot",
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+ "test/data/uniprot/P49144.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",
@@ -499,7 +496,9 @@ Gem::Specification.new do |s|
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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_P03589.rb",
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  "test/unit/bio/db/embl/test_uniprotkb_P28907.rb",
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+ "test/unit/bio/db/embl/test_uniprotkb_P49144.rb",
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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",