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/.travis.yml DELETED
@@ -1,71 +0,0 @@
1
- language: ruby
2
- rvm:
3
- - 2.6
4
- - 2.5
5
- - 2.4
6
- - 2.3.8
7
- - 2.2.10
8
- env:
9
- - TESTOPTS=-v
10
- gemfile:
11
- - Gemfile
12
- before_install:
13
- - mkdir /tmp/bioruby
14
- - ruby gemfiles/modify-Gemfile.rb
15
- - ruby gemfiles/prepare-gemspec.rb
16
- matrix:
17
- include:
18
- - rvm: 2.0.0
19
- gemfile: gemfiles/Gemfile.travis-ruby1.9
20
- env: TESTOPTS=-v
21
- - rvm: 2.1.10
22
- gemfile: gemfiles/Gemfile.travis-ruby1.9
23
- env: TESTOPTS=-v
24
- - rvm: truffleruby
25
- gemfile: gemfiles/Gemfile.travis-jruby1.9
26
- env: TESTOPTS=-v
27
- - rvm: rbx-3.29
28
- gemfile: gemfiles/Gemfile.travis-rbx
29
- env: TESTOPTS=-v
30
- - rvm: jruby
31
- gemfile: gemfiles/Gemfile.travis-jruby1.9
32
- env: TMPDIR=/tmp/bioruby TESTOPTS=-v
33
- - rvm: 2.5
34
- gemfile: Gemfile
35
- env: BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
36
- - rvm: jruby
37
- gemfile: gemfiles/Gemfile.travis-jruby1.9
38
- env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
39
- allow_failures:
40
- - rvm: 1.8.7
41
- gemfile: gemfiles/Gemfile.travis-ruby1.8
42
- env: TESTOPTS=-v
43
- - rvm: 1.9.3
44
- gemfile: gemfiles/Gemfile.travis-ruby1.9
45
- env: TESTOPTS=-v
46
- - rvm: truffleruby
47
- gemfile: gemfiles/Gemfile.travis-jruby1.9
48
- env: TESTOPTS=-v
49
- - rvm: rbx-3.29
50
- gemfile: gemfiles/Gemfile.travis-rbx
51
- env: TESTOPTS=-v
52
- - rvm: jruby
53
- gemfile: gemfiles/Gemfile.travis-jruby1.9
54
- env: TMPDIR=/tmp/bioruby TESTOPTS=-v
55
- - rvm: jruby
56
- gemfile: gemfiles/Gemfile.travis-jruby1.9
57
- env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
58
-
59
- # uncomment this line if your project needs to run something other than `rake`:
60
- # script: bundle exec rspec spec
61
-
62
- #before_install:
63
- # - sudo apt-get update
64
- # - sudo apt-get install libxml2-dev libexpat1-dev
65
-
66
- # block build for the branches
67
- branches:
68
- except:
69
- - biohackathon2008
70
- - bioruby-1.4.3
71
-
data/gemfiles/Gemfile.travis-jruby1.8 DELETED
@@ -1,6 +0,0 @@
1
- source "https://rubygems.org"
2
-
3
- gem "rake", "~>10.4"
4
- # rdoc 4.3.0 requires Ruby >= 1.9.3
5
- gem "rdoc", "~>4.2.0"
6
-
data/gemfiles/Gemfile.travis-jruby1.9 DELETED
@@ -1,5 +0,0 @@
1
- source "https://rubygems.org"
2
-
3
- gem "rake"
4
- gem "rdoc"
5
-
data/gemfiles/Gemfile.travis-rbx DELETED
@@ -1,10 +0,0 @@
1
- source "https://rubygems.org"
2
-
3
- gem "rake"
4
- gem "rdoc"
5
-
6
- platforms :rbx do
7
- gem 'racc'
8
- gem 'rubysl', '~> 2.0'
9
- gem 'psych'
10
- end
data/gemfiles/Gemfile.travis-ruby1.8 DELETED
@@ -1,6 +0,0 @@
1
- source "https://rubygems.org"
2
-
3
- gem "rake", "~>10.4"
4
- # rdoc 4.3.0 requires Ruby >= 1.9.3
5
- gem "rdoc", "~>4.2.0"
6
-
data/gemfiles/Gemfile.travis-ruby1.9 DELETED
@@ -1,5 +0,0 @@
1
- source "https://rubygems.org"
2
-
3
- gem "rake"
4
- gem "rdoc"
5
-
data/gemfiles/Gemfile.windows DELETED
@@ -1,6 +0,0 @@
1
- source "https://rubygems.org"
2
-
3
- gem "rake"
4
- gem "rdoc"
5
- gem "test-unit"
6
-
data/gemfiles/modify-Gemfile.rb DELETED
@@ -1,28 +0,0 @@
1
- #
2
-
3
- require 'pathname'
4
-
5
- envname_default_task = 'BIORUBY_RAKE_DEFAULT_TASK'
6
-
7
- gem_dir = Pathname.new(File.join(File.dirname(__FILE__), '..')).realpath
8
-
9
- case t = ENV[envname_default_task]
10
- when 'gem-test'
11
- # do nothing
12
- else
13
- $stderr.print "#{$0}: skipped: ENV[#{envname_default_task}]=#{t.inspect}\n"
14
- exit(0)
15
- end
16
-
17
- target = ENV['BUNDLE_GEMFILE']
18
- unless target then
19
- $stderr.puts("Error: env BUNDLE_GEMFILE is not set.")
20
- end
21
-
22
- File.open(target, 'a') do |w|
23
- $stderr.puts "Add a line to #{target}"
24
- $stderr.puts "gem 'bio', :path => '#{gem_dir}'"
25
- w.puts ""
26
- w.puts "gem 'bio', :path => '#{gem_dir}'"
27
- end
28
-
data/gemfiles/prepare-gemspec.rb DELETED
@@ -1,29 +0,0 @@
1
- #
2
-
3
- require 'pathname'
4
- require 'fileutils'
5
-
6
- envname_default_task = 'BIORUBY_RAKE_DEFAULT_TASK'
7
-
8
- gem_dir = Pathname.new(File.join(File.dirname(__FILE__), '..')).realpath
9
-
10
- case t = ENV[envname_default_task]
11
- when 'gem-test'
12
- # do nothing
13
- else
14
- $stderr.print "#{$0}: skipped: ENV[#{envname_default_task}]=#{t.inspect}\n"
15
- exit(0)
16
- end
17
-
18
- # update bundler to avoid Bundler's bug fixed in the latest version
19
- $stderr.puts "gem update bundler"
20
- system("gem update bundler")
21
-
22
- $stderr.puts "cd #{gem_dir}"
23
- Dir.chdir(gem_dir)
24
-
25
- args = [ 'bioruby.gemspec', '.gemspec' ]
26
-
27
- $stderr.puts(['cp', *args].join(" "))
28
- FileUtils.cp(*args)
29
-