bio 1.6.0.pre.20181210 → 2.0.3

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Files changed (48) hide show
  1. checksums.yaml +4 -4
  2. data/.travis.yml +32 -34
  3. data/ChangeLog +1462 -8
  4. data/Gemfile +0 -2
  5. data/KNOWN_ISSUES.rdoc +4 -10
  6. data/LEGAL +0 -10
  7. data/README.rdoc +31 -80
  8. data/README_DEV.rdoc +5 -5
  9. data/RELEASE_NOTES.rdoc +171 -18
  10. data/Rakefile +0 -34
  11. data/appveyor.yml +15 -7
  12. data/bioruby.gemspec +13 -4
  13. data/bioruby.gemspec.erb +0 -1
  14. data/gemfiles/Gemfile.travis-rbx +0 -2
  15. data/gemfiles/Gemfile.travis-ruby1.8 +0 -2
  16. data/gemfiles/Gemfile.travis-ruby1.9 +0 -2
  17. data/gemfiles/Gemfile.windows +6 -0
  18. data/lib/bio/appl/blast/report.rb +40 -8
  19. data/lib/bio/appl/iprscan/report.rb +3 -3
  20. data/lib/bio/appl/sosui/report.rb +1 -1
  21. data/lib/bio/db/embl/uniprotkb.rb +1 -1
  22. data/lib/bio/db/gff.rb +3 -1
  23. data/lib/bio/db/go.rb +2 -2
  24. data/lib/bio/db/kegg/common.rb +14 -0
  25. data/lib/bio/db/kegg/genes.rb +26 -0
  26. data/lib/bio/db/kegg/pathway.rb +5 -11
  27. data/lib/bio/sequence/common.rb +112 -0
  28. data/lib/bio/sequence/format.rb +1 -0
  29. data/lib/bio/tree.rb +1 -1
  30. data/lib/bio/version.rb +3 -3
  31. data/sample/color_scheme_aa.rb +82 -0
  32. data/sample/color_scheme_na.rb +5 -6
  33. data/sample/fastq2html.cwl +23 -0
  34. data/sample/fastq2html.rb +94 -0
  35. data/sample/fastq2html.testdata.yaml +5 -0
  36. data/sample/na2aa.cwl +23 -0
  37. data/sample/na2aa.rb +11 -25
  38. data/sample/na2aa.testdata.yaml +7 -0
  39. data/sample/rev_comp.cwl +23 -0
  40. data/sample/rev_comp.rb +20 -0
  41. data/sample/rev_comp.testdata.yaml +7 -0
  42. data/test/network/bio/db/kegg/test_genes_hsa7422.rb +91 -0
  43. data/test/unit/bio/appl/blast/test_report.rb +4 -4
  44. data/test/unit/bio/db/test_gff.rb +5 -0
  45. data/test/unit/bio/sequence/test_ruby3.rb +462 -0
  46. metadata +17 -8
  47. data/lib/bio/appl/blast/xmlparser.rb +0 -236
  48. data/setup.rb +0 -1600
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
1
1
  ---
2
2
  SHA256:
3
- metadata.gz: e7709c923030d4637615ea2e30de470129ab4947321320ec59c725f5959ce360
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- data.tar.gz: b8d7f1e108ffc6be38e05c31bc97013bbc4a3d9590e702bf2ca486aa8483e6c7
3
+ metadata.gz: 990d6888c3a4e53089aaf8332c4bc87bb9cc40efe25e1aa13b7337be69145227
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+ data.tar.gz: 361fad495b8f8ee3528a6729b8a52a3522a6d594353679a6a84993e97e1e8f6a
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  SHA512:
6
- metadata.gz: 3b00ee9cdbbe10c6a51485e31286a18c4438a42918f71421901ad31979435d2e24a68524a4b6ab88c3e47b2fd96af872227c8f501f9f18e9e2de931f352de64d
7
- data.tar.gz: 813a702da62076cfbe32ef7e26d944d57eebf12bb5592bb7dad4739456170d525e90e6123d20fa6f1414c523f202cef3b4a49f3e80d37f8c289196b23e1cf312
6
+ metadata.gz: 52c72d6055da72526d208e85b42ad75b150b4538b62c2552323e5f344721b9fe0ed3b18adf5e9d570f9d34fba019379fc6528a329a1340962f5a9c6c279e458c
7
+ data.tar.gz: f8894738bbb973722b77f65559f56b2ec661619e9f2dfe060456d63523fb921d4697d619171a8998686d234ac6bb5f3a300cbd140c8a78f8083b36029b536825
data/.travis.yml CHANGED
@@ -1,61 +1,58 @@
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- sudo: false
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  language: ruby
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  rvm:
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- - 2.1.10
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- - 2.0.0
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- - 1.9.3
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+ - 2.6
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+ - 2.5
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+ - 2.4
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+ - 2.3.8
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+ - 2.2.10
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  env:
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  - TESTOPTS=-v
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  gemfile:
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- - gemfiles/Gemfile.travis-ruby1.9
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+ - Gemfile
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  before_install:
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  - mkdir /tmp/bioruby
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  - ruby gemfiles/modify-Gemfile.rb
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  - ruby gemfiles/prepare-gemspec.rb
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  matrix:
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  include:
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- - rvm: 1.8.7
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- gemfile: gemfiles/Gemfile.travis-ruby1.8
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+ - rvm: 2.0.0
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+ gemfile: gemfiles/Gemfile.travis-ruby1.9
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+ env: TESTOPTS=-v
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+ - rvm: 2.1.10
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+ gemfile: gemfiles/Gemfile.travis-ruby1.9
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+ env: TESTOPTS=-v
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+ - rvm: truffleruby
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+ gemfile: gemfiles/Gemfile.travis-jruby1.9
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  env: TESTOPTS=-v
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  - rvm: rbx-3.29
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  gemfile: gemfiles/Gemfile.travis-rbx
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  env: TESTOPTS=-v
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- - rvm: jruby-18mode
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- gemfile: gemfiles/Gemfile.travis-jruby1.8
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- env: TMPDIR=/tmp/bioruby TESTOPTS=-v
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- - rvm: jruby-19mode
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+ - rvm: jruby
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  gemfile: gemfiles/Gemfile.travis-jruby1.9
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  env: TMPDIR=/tmp/bioruby TESTOPTS=-v
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- - rvm: 2.3.1
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- gemfile: Gemfile
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- - rvm: 2.2.5
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- gemfile: Gemfile
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- - rvm: 2.2.5
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- gemfile: Gemfile
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- env: BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test TESTOPTS=-v
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- - rvm: 2.2.5
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+ - rvm: 2.5
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  gemfile: Gemfile
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  env: BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
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- - rvm: jruby-19mode
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- gemfile: gemfiles/Gemfile.travis-jruby1.9
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- env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test TESTOPTS=-v
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- - rvm: jruby-19mode
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+ - rvm: jruby
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  gemfile: gemfiles/Gemfile.travis-jruby1.9
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  env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
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  allow_failures:
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+ - rvm: 1.8.7
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+ gemfile: gemfiles/Gemfile.travis-ruby1.8
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+ env: TESTOPTS=-v
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+ - rvm: 1.9.3
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+ gemfile: gemfiles/Gemfile.travis-ruby1.9
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+ env: TESTOPTS=-v
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+ - rvm: truffleruby
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+ gemfile: gemfiles/Gemfile.travis-jruby1.9
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+ env: TESTOPTS=-v
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  - rvm: rbx-3.29
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  gemfile: gemfiles/Gemfile.travis-rbx
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  env: TESTOPTS=-v
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- - rvm: jruby-18mode
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- gemfile: gemfiles/Gemfile.travis-jruby1.8
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- env: TMPDIR=/tmp/bioruby TESTOPTS=-v
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- - rvm: jruby-19mode
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+ - rvm: jruby
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  gemfile: gemfiles/Gemfile.travis-jruby1.9
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  env: TMPDIR=/tmp/bioruby TESTOPTS=-v
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- - rvm: jruby-19mode
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- gemfile: gemfiles/Gemfile.travis-jruby1.9
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- env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test TESTOPTS=-v
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- - rvm: jruby-19mode
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+ - rvm: jruby
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  gemfile: gemfiles/Gemfile.travis-jruby1.9
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  env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
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@@ -66,8 +63,9 @@ matrix:
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  # - sudo apt-get update
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  # - sudo apt-get install libxml2-dev libexpat1-dev
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- # whitelist branches
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+ # block build for the branches
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  branches:
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- only:
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- - master
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+ except:
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+ - biohackathon2008
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+ - bioruby-1.4.3
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