bio 1.4.3.0001 → 1.5.0

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Files changed (158) hide show
  1. checksums.yaml +7 -0
  2. data/.travis.yml +39 -33
  3. data/BSDL +22 -0
  4. data/COPYING +2 -2
  5. data/COPYING.ja +36 -36
  6. data/ChangeLog +2404 -1025
  7. data/KNOWN_ISSUES.rdoc +15 -55
  8. data/README.rdoc +17 -23
  9. data/RELEASE_NOTES.rdoc +246 -183
  10. data/Rakefile +3 -2
  11. data/bin/br_biofetch.rb +29 -5
  12. data/bioruby.gemspec +15 -32
  13. data/bioruby.gemspec.erb +10 -20
  14. data/doc/ChangeLog-1.4.3 +1478 -0
  15. data/doc/RELEASE_NOTES-1.4.3.rdoc +204 -0
  16. data/doc/Tutorial.rd +0 -6
  17. data/doc/Tutorial.rd.html +7 -12
  18. data/doc/Tutorial.rd.ja +960 -1064
  19. data/doc/Tutorial.rd.ja.html +977 -1067
  20. data/gemfiles/Gemfile.travis-jruby1.8 +2 -1
  21. data/gemfiles/Gemfile.travis-jruby1.9 +2 -4
  22. data/gemfiles/Gemfile.travis-rbx +13 -0
  23. data/gemfiles/Gemfile.travis-ruby1.8 +2 -1
  24. data/gemfiles/Gemfile.travis-ruby1.9 +2 -4
  25. data/gemfiles/Gemfile.travis-ruby2.2 +9 -0
  26. data/lib/bio.rb +10 -43
  27. data/lib/bio/alignment.rb +8 -14
  28. data/lib/bio/appl/blast.rb +1 -2
  29. data/lib/bio/appl/blast/format0.rb +18 -7
  30. data/lib/bio/appl/blast/remote.rb +0 -9
  31. data/lib/bio/appl/blast/report.rb +1 -1
  32. data/lib/bio/appl/clustalw/report.rb +3 -1
  33. data/lib/bio/appl/genscan/report.rb +1 -2
  34. data/lib/bio/appl/iprscan/report.rb +1 -2
  35. data/lib/bio/appl/meme/mast.rb +4 -4
  36. data/lib/bio/appl/meme/mast/report.rb +1 -1
  37. data/lib/bio/appl/paml/codeml.rb +2 -2
  38. data/lib/bio/appl/paml/codeml/report.rb +1 -0
  39. data/lib/bio/appl/paml/common.rb +1 -1
  40. data/lib/bio/appl/sosui/report.rb +1 -2
  41. data/lib/bio/command.rb +62 -2
  42. data/lib/bio/data/aa.rb +13 -31
  43. data/lib/bio/data/codontable.rb +1 -2
  44. data/lib/bio/db/biosql/biosql_to_biosequence.rb +1 -0
  45. data/lib/bio/db/biosql/sequence.rb +1 -1
  46. data/lib/bio/db/embl/common.rb +1 -1
  47. data/lib/bio/db/embl/embl.rb +5 -4
  48. data/lib/bio/db/embl/format_embl.rb +3 -3
  49. data/lib/bio/db/embl/sptr.rb +9 -1444
  50. data/lib/bio/db/embl/swissprot.rb +12 -29
  51. data/lib/bio/db/embl/trembl.rb +13 -30
  52. data/lib/bio/db/embl/uniprot.rb +12 -29
  53. data/lib/bio/db/embl/uniprotkb.rb +1455 -0
  54. data/lib/bio/db/fasta.rb +17 -0
  55. data/lib/bio/db/fasta/defline.rb +1 -3
  56. data/lib/bio/db/fastq.rb +1 -1
  57. data/lib/bio/db/genbank/ddbj.rb +9 -5
  58. data/lib/bio/db/genbank/refseq.rb +11 -3
  59. data/lib/bio/db/gff.rb +3 -4
  60. data/lib/bio/db/go.rb +5 -6
  61. data/lib/bio/db/kegg/module.rb +4 -5
  62. data/lib/bio/db/kegg/pathway.rb +4 -5
  63. data/lib/bio/db/kegg/reaction.rb +1 -1
  64. data/lib/bio/db/nexus.rb +3 -2
  65. data/lib/bio/db/pdb/pdb.rb +2 -2
  66. data/lib/bio/db/phyloxml/phyloxml_elements.rb +82 -59
  67. data/lib/bio/db/phyloxml/phyloxml_parser.rb +2 -2
  68. data/lib/bio/db/phyloxml/phyloxml_writer.rb +1 -2
  69. data/lib/bio/db/sanger_chromatogram/chromatogram.rb +1 -2
  70. data/lib/bio/db/transfac.rb +1 -1
  71. data/lib/bio/io/das.rb +40 -41
  72. data/lib/bio/io/fastacmd.rb +0 -16
  73. data/lib/bio/io/fetch.rb +111 -55
  74. data/lib/bio/io/flatfile/buffer.rb +4 -5
  75. data/lib/bio/io/hinv.rb +2 -3
  76. data/lib/bio/io/ncbirest.rb +43 -6
  77. data/lib/bio/io/pubmed.rb +76 -81
  78. data/lib/bio/io/togows.rb +33 -10
  79. data/lib/bio/map.rb +1 -1
  80. data/lib/bio/pathway.rb +1 -1
  81. data/lib/bio/sequence/compat.rb +1 -1
  82. data/lib/bio/sequence/na.rb +63 -12
  83. data/lib/bio/shell.rb +0 -2
  84. data/lib/bio/shell/core.rb +5 -6
  85. data/lib/bio/shell/interface.rb +3 -4
  86. data/lib/bio/shell/irb.rb +1 -2
  87. data/lib/bio/shell/plugin/entry.rb +2 -3
  88. data/lib/bio/shell/plugin/seq.rb +7 -6
  89. data/lib/bio/shell/setup.rb +1 -2
  90. data/lib/bio/tree.rb +2 -2
  91. data/lib/bio/util/contingency_table.rb +0 -2
  92. data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +2 -2
  93. data/lib/bio/util/sirna.rb +76 -16
  94. data/lib/bio/version.rb +8 -9
  95. data/sample/benchmark_clustalw_report.rb +47 -0
  96. data/sample/biofetch.rb +248 -151
  97. data/setup.rb +6 -7
  98. data/test/data/clustalw/example1-seqnos.aln +58 -0
  99. data/test/network/bio/appl/blast/test_remote.rb +1 -15
  100. data/test/network/bio/appl/test_blast.rb +0 -12
  101. data/test/network/bio/io/test_pubmed.rb +49 -0
  102. data/test/network/bio/io/test_togows.rb +0 -1
  103. data/test/network/bio/test_command.rb +65 -2
  104. data/test/unit/bio/appl/bl2seq/test_report.rb +0 -1
  105. data/test/unit/bio/appl/blast/test_report.rb +110 -48
  106. data/test/unit/bio/appl/clustalw/test_report.rb +67 -51
  107. data/test/unit/bio/appl/sim4/test_report.rb +46 -17
  108. data/test/unit/bio/appl/test_blast.rb +2 -2
  109. data/test/unit/bio/db/embl/test_embl.rb +0 -1
  110. data/test/unit/bio/db/embl/test_embl_rel89.rb +0 -1
  111. data/test/unit/bio/db/embl/{test_sptr.rb → test_uniprotkb.rb} +111 -115
  112. data/test/unit/bio/db/embl/{test_uniprot_new_part.rb → test_uniprotkb_new_part.rb} +11 -11
  113. data/test/unit/bio/db/genbank/test_genbank.rb +10 -4
  114. data/test/unit/bio/db/pdb/test_pdb.rb +14 -8
  115. data/test/unit/bio/db/test_fasta.rb +41 -1
  116. data/test/unit/bio/db/test_fastq.rb +14 -4
  117. data/test/unit/bio/db/test_gff.rb +2 -2
  118. data/test/unit/bio/db/test_phyloxml.rb +30 -30
  119. data/test/unit/bio/db/test_phyloxml_writer.rb +2 -2
  120. data/test/unit/bio/io/flatfile/test_autodetection.rb +1 -2
  121. data/test/unit/bio/io/flatfile/test_buffer.rb +7 -1
  122. data/test/unit/bio/io/flatfile/test_splitter.rb +1 -1
  123. data/test/unit/bio/io/test_togows.rb +3 -2
  124. data/test/unit/bio/sequence/test_dblink.rb +1 -1
  125. data/test/unit/bio/sequence/test_na.rb +3 -1
  126. data/test/unit/bio/test_alignment.rb +1 -2
  127. data/test/unit/bio/test_command.rb +5 -4
  128. data/test/unit/bio/test_db.rb +4 -2
  129. data/test/unit/bio/test_pathway.rb +25 -10
  130. data/test/unit/bio/util/test_sirna.rb +22 -22
  131. metadata +656 -1430
  132. data/doc/KEGG_API.rd +0 -1843
  133. data/doc/KEGG_API.rd.ja +0 -1834
  134. data/extconf.rb +0 -2
  135. data/lib/bio/appl/blast/ddbj.rb +0 -131
  136. data/lib/bio/db/kegg/taxonomy.rb +0 -280
  137. data/lib/bio/io/dbget.rb +0 -194
  138. data/lib/bio/io/ddbjrest.rb +0 -344
  139. data/lib/bio/io/ddbjxml.rb +0 -458
  140. data/lib/bio/io/ebisoap.rb +0 -158
  141. data/lib/bio/io/ensembl.rb +0 -229
  142. data/lib/bio/io/higet.rb +0 -73
  143. data/lib/bio/io/keggapi.rb +0 -363
  144. data/lib/bio/io/ncbisoap.rb +0 -156
  145. data/lib/bio/io/soapwsdl.rb +0 -119
  146. data/lib/bio/shell/plugin/keggapi.rb +0 -181
  147. data/lib/bio/shell/plugin/soap.rb +0 -87
  148. data/sample/dbget +0 -37
  149. data/sample/demo_ddbjxml.rb +0 -212
  150. data/sample/demo_kegg_taxonomy.rb +0 -92
  151. data/sample/demo_keggapi.rb +0 -502
  152. data/sample/psortplot_html.rb +0 -214
  153. data/test/network/bio/io/test_ddbjrest.rb +0 -47
  154. data/test/network/bio/io/test_ensembl.rb +0 -230
  155. data/test/network/bio/io/test_soapwsdl.rb +0 -53
  156. data/test/unit/bio/io/test_ddbjxml.rb +0 -81
  157. data/test/unit/bio/io/test_ensembl.rb +0 -111
  158. data/test/unit/bio/io/test_soapwsdl.rb +0 -33
@@ -1,92 +0,0 @@
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- #
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- # = sample/demo_kegg_taxonomy.rb - demonstration of Bio::KEGG::Taxonomy
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- #
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- # Copyright:: Copyright (C) 2007 Toshiaki Katayama <k@bioruby.org>
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- # License:: The Ruby License
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- #
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- #
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- # == Description
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- #
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- # IMPORTANT NOTE: currently, this sample does not work!
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- #
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- # Demonstration of Bio::KEGG::Taxonomy.
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- #
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- # == Usage
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- #
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- # Specify a file containing KEGG Taxonomy data.
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- #
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- # $ ruby demo_kegg_taxonomy.rb file
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- #
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- # Optionally, when a file containing organisms list (1 line per 1 organism)
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- # is specified after the file, only the specified organisms are shown.
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- #
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- # $ ruby demo_kegg_taxonomy.rb kegg_taxonomy_file org_list_file
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- #
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- # == Example of running this script
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- #
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- # Download test data.
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- #
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- # $ wget ftp://ftp.genome.jp/pub/kegg/genes/taxonomy
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- #
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- # The downloaded filename is "taxonomy".
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- #
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- # Run this script.
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- #
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- # $ ruby -Ilib sample/demo_kegg_taxonomy.rb taxonomy
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- #
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- # == Development information
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- #
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- # The code was moved from lib/bio/db/kegg/taxonomy.rb.
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- #
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-
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- require 'bio'
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-
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- #if __FILE__ == $0
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-
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- # Usage:
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- # % wget ftp://ftp.genome.jp/pub/kegg/genes/taxonomy
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- # % ruby taxonomy.rb taxonomy | less -S
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-
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- taxonomy = ARGV.shift
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- org_list = ARGV.shift || nil
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-
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- if org_list
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- orgs = File.readlines(org_list).map{|x| x.strip}
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- else
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- orgs = nil
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- end
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-
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- tree = Bio::KEGG::Taxonomy.new(taxonomy, orgs)
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-
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- puts ">>> tree - original"
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- puts tree
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-
64
- puts ">>> tree - after compact"
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- tree.compact
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- puts tree
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-
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- puts ">>> tree - after reduce"
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- tree.reduce
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- puts tree
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-
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- puts ">>> path - sorted"
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- tree.path.sort.each do |path|
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- puts path.join("/")
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- end
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-
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- puts ">>> group : orgs"
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- tree.dfs(tree.root) do |parent, children|
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- if orgs = tree.organisms(parent)
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- puts "#{parent.ljust(30)} (#{orgs.size})\t#{orgs.join(', ')}"
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- end
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- end
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-
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- puts ">>> group : subgroups"
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- tree.dfs_with_level(tree.root) do |parent, children, level|
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- subgroups = children.keys.sort
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- indent = " " * level
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- label = "#{indent} #{level} #{parent}"
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- puts "#{label.ljust(35)}\t#{subgroups.join(', ')}"
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- end
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-
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- #end
@@ -1,502 +0,0 @@
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- #
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- # = sample/demo_keggapi.rb - demonstration of Bio::KEGG::API web service client
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- #
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- # Copyright:: Copyright (C) 2003, 2004 Toshiaki Katayama <k@bioruby.org>
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- # License:: The Ruby License
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- #
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- #
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- # == Description
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- #
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- # Demonstration of Bio::KEGG::API, the KEGG API web service client via
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- # SOAP/WSDL.
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- #
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- # == Requirements
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- #
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- # Internet connection is needed.
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- #
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- # == Usage
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- #
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- # Simply run this script.
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- #
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- # $ ruby demo_keggapi.rb
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- #
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- # == Notes
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- #
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- # * It may take long time to run this script.
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- # * It can not be run with Ruby 1.9 because SOAP4R (SOAP support for Ruby)
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- # currently does not support Ruby 1.9.
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- #
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- # == Development information
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- #
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- # The code was moved from lib/bio/io/keggapi.rb, and modified as below:
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- #
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- # * Commented out deprecated methods: get_neighbors_by_gene,
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- # get_similarity_between_genes, get_ko_members, get_oc_members_by_gene,
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- # get_pc_members_by_gene.
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- # * Commented out some methods internally using the deprecated methods:
37
- # get_all_neighbors_by_gene, get_all_oc_members_by_gene,
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- # get_all_pc_members_by_gene.
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- #
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-
41
- require 'bio'
42
-
43
- #if __FILE__ == $0
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-
45
- begin
46
- require 'pp'
47
- alias p pp
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- rescue LoadError
49
- end
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-
51
- puts ">>> KEGG API"
52
- serv = Bio::KEGG::API.new
53
- # serv.log = STDERR
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-
55
- puts "# * parameters"
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- puts " wsdl : #{serv.wsdl}"
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- puts " log : #{serv.log}"
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- puts " start : #{serv.start}"
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- puts " max_results : #{serv.max_results}"
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-
61
- puts "=== META"
62
-
63
- puts "### list_databases"
64
- list = serv.list_databases
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- list.each do |db|
66
- print db.entry_id, "\t", db.definition, "\n"
67
- end
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-
69
- puts "### list_organisms"
70
- list = serv.list_organisms
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- list.each do |org|
72
- print org.entry_id, "\t", org.definition, "\n"
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- end
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-
75
- puts "### list_pathways('map') : reference pathway"
76
- list = serv.list_pathways("map")
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- list.each do |path|
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- print path.entry_id, "\t", path.definition, "\n"
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- end
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-
81
- puts "### list_pathways('eco') : E. coli pathway"
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- list = serv.list_pathways("eco")
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- list.each do |path|
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- print path.entry_id, "\t", path.definition, "\n"
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- end
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-
87
- puts "=== DBGET"
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-
89
- puts "### binfo('all')"
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- puts serv.binfo("all")
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-
92
- puts "### binfo('genbank')"
93
- puts serv.binfo("genbank")
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-
95
- puts "### bfind('genbank kinase cell cycle human')"
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- puts serv.bfind("genbank kinase cell cycle human")
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-
98
- puts "### bget('gb:AJ617376')"
99
- puts serv.bget("gb:AJ617376")
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-
101
- puts "### bget('eco:b0002 eco:b0003')"
102
- puts serv.bget("eco:b0002 eco:b0003")
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-
104
- puts "### btit('eco:b0002 eco:b0003')"
105
- puts serv.btit("eco:b0002 eco:b0003")
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-
107
- puts "# * get_entries(['eco:b0002', 'eco:b0003'])"
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- puts serv.get_entries(["eco:b0002", "eco:b0003"])
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-
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- puts "# * get_aaseqs(['eco:b0002', 'eco:b0003'])"
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- puts serv.get_aaseqs(["eco:b0002", "eco:b0003"])
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-
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- puts "# * get_naseqs(['eco:b0002', 'eco:b0003'])"
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- puts serv.get_naseqs(["eco:b0002", "eco:b0003"])
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-
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- puts "# * get_definitions(['eco:b0002', 'eco:b0003'])"
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- puts serv.get_definitions(["eco:b0002", "eco:b0003"])
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-
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- puts "# * get_definitions(('eco:b0001'..'eco:b0200').to_a)"
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- puts serv.get_definitions(("eco:b0001".."eco:b0200").to_a)
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-
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- puts "=== LinkDB"
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-
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- puts "### get_linkdb_by_entry('eco:b0002', 'pathway', 1, 5)"
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- list = serv.get_linkdb_by_entry("eco:b0002", "pathway", 1, 5)
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- list.each do |link|
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- puts [ link.entry_id1, link.entry_id2, link.type, link.path ].join("\t")
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- end
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-
130
- puts "# * get_all_linkdb_by_entry('eco:b0002', 'pathway')"
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- list = serv.get_all_linkdb_by_entry("eco:b0002", "pathway")
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- list.each do |link|
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- puts [ link.entry_id1, link.entry_id2, link.type, link.path ].join("\t")
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- end
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-
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- puts "=== SSDB"
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-
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- # The method "get_neighbors_by_gene" is deprecated in 2005-02-20.
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- #
140
- #puts "### get_neighbors_by_gene('eco:b0002', 'all', 1, 5)"
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- #list = serv.get_neighbors_by_gene("eco:b0002", "all", 1, 5)
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- #list.each do |hit|
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- # puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
144
- #end
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-
146
- # The method "get_all_neighbors_by_gene" can not be used because
147
- # it internally uses the deprecated "get_neighbors_by_gene" method.
148
- #
149
- #puts "# * get_all_neighbors_by_gene('eco:b0002', 'bsu')"
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- #list = serv.get_all_neighbors_by_gene("eco:b0002", "bsu")
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- #list.each do |hit|
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- # puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
153
- #end
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-
155
- puts "### get_best_best_neighbors_by_gene('eco:b0002', 1, 5)"
156
- list = serv.get_best_best_neighbors_by_gene("eco:b0002", 1, 5)
157
- list.each do |hit|
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- puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
159
- end
160
-
161
- puts "# * get_all_best_best_neighbors_by_gene('eco:b0002')"
162
- list = serv.get_all_best_best_neighbors_by_gene("eco:b0002")
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- list.each do |hit|
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- puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
165
- end
166
-
167
- puts "### get_best_neighbors_by_gene('eco:b0002', 1, 5)"
168
- list = serv.get_best_neighbors_by_gene("eco:b0002", 1, 5)
169
- list.each do |hit|
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- puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
171
- end
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-
173
- puts "# * get_all_best_neighbors_by_gene('eco:b0002')"
174
- list = serv.get_all_best_neighbors_by_gene("eco:b0002")
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- list.each do |hit|
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- puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
177
- end
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-
179
- puts "### get_reverse_best_neighbors_by_gene('eco:b0002', 1, 5)"
180
- list = serv.get_reverse_best_neighbors_by_gene("eco:b0002", 1, 5)
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- list.each do |hit|
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- puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
183
- end
184
-
185
- puts "# * get_all_reverse_best_neighbors_by_gene('eco:b0002')"
186
- list = serv.get_all_reverse_best_neighbors_by_gene("eco:b0002")
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- list.each do |hit|
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- puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
189
- end
190
-
191
- puts "### get_paralogs_by_gene('eco:b0002', 1, 5)"
192
- list = serv.get_paralogs_by_gene("eco:b0002", 1, 5)
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- list.each do |hit|
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- puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
195
- end
196
-
197
- puts "# * get_all_paralogs_by_gene('eco:b0002')"
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- list = serv.get_all_paralogs_by_gene("eco:b0002")
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- list.each do |hit|
200
- puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
201
- end
202
-
203
- # The method "get_similarity_between_genes" is deprecated in 2005-02-20.
204
- #
205
- #puts "### get_similarity_between_genes('eco:b0002', 'bsu:BG10350')"
206
- #relation = serv.get_similarity_between_genes("eco:b0002", "bsu:BG10350")
207
- #puts " genes_id1 : #{relation.genes_id1}" # string
208
- #puts " genes_id2 : #{relation.genes_id2}" # string
209
- #puts " sw_score : #{relation.sw_score}" # int
210
- #puts " bit_score : #{relation.bit_score}" # float
211
- #puts " identity : #{relation.identity}" # float
212
- #puts " overlap : #{relation.overlap}" # int
213
- #puts " start_position1 : #{relation.start_position1}" # int
214
- #puts " end_position1 : #{relation.end_position1}" # int
215
- #puts " start_position2 : #{relation.start_position2}" # int
216
- #puts " end_position2 : #{relation.end_position2}" # int
217
- #puts " best_flag_1to2 : #{relation.best_flag_1to2}" # boolean
218
- #puts " best_flag_2to1 : #{relation.best_flag_2to1}" # boolean
219
- #puts " definition1 : #{relation.definition1}" # string
220
- #puts " definition2 : #{relation.definition2}" # string
221
- #puts " length1 : #{relation.length1}" # int
222
- #puts " length2 : #{relation.length2}" # int
223
-
224
- puts "=== MOTIF"
225
-
226
- puts "### get_motifs_by_gene('eco:b0002', 'pfam')"
227
- list = serv.get_motifs_by_gene("eco:b0002", "pfam")
228
- list.each do |motif|
229
- puts motif.motif_id
230
- end if list
231
-
232
- puts "### get_motifs_by_gene('eco:b0002', 'tfam')"
233
- list = serv.get_motifs_by_gene("eco:b0002", "tfam")
234
- list.each do |motif|
235
- puts motif.motif_id
236
- end if list
237
-
238
- puts "### get_motifs_by_gene('eco:b0002', 'pspt')"
239
- list = serv.get_motifs_by_gene("eco:b0002", "pspt")
240
- list.each do |motif|
241
- puts motif.motif_id
242
- end if list
243
-
244
- puts "### get_motifs_by_gene('eco:b0002', 'pspf')"
245
- list = serv.get_motifs_by_gene("eco:b0002", "pspf")
246
- list.each do |motif|
247
- puts motif.motif_id
248
- end if list
249
-
250
- puts "### get_motifs_by_gene('eco:b0002', 'all')"
251
- list = serv.get_motifs_by_gene("eco:b0002", "all")
252
- list.each do |motif|
253
- puts "# * motif result"
254
- puts " motif_id : #{motif.motif_id}"
255
- puts " definition : #{motif.definition}"
256
- puts " genes_id : #{motif.genes_id}"
257
- puts " start_position : #{motif.start_position}"
258
- puts " end_position : #{motif.end_position}"
259
- puts " score : #{motif.score}"
260
- puts " evalue : #{motif.evalue}"
261
- end
262
-
263
- puts "### get_genes_by_motifs(['pf:ACT', 'ps:ASPARTOKINASE'], 1, 5)"
264
- list = serv.get_genes_by_motifs(["pf:ACT", "ps:ASPARTOKINASE"], 1, 5)
265
- list.each do |gene|
266
- puts [ gene.entry_id, gene.definition ].join("\t")
267
- end
268
-
269
- puts "# * get_all_genes_by_motifs(['pf:ACT', 'ps:ASPARTOKINASE'])"
270
- list = serv.get_all_genes_by_motifs(["pf:ACT", "ps:ASPARTOKINASE"])
271
- list.each do |gene|
272
- puts [ gene.entry_id, gene.definition ].join("\t")
273
- end
274
-
275
- puts "=== KO, OC, PC"
276
-
277
- puts "### get_ko_by_gene('eco:b0002')"
278
- list = serv.get_ko_by_gene("eco:b0002")
279
- list.each do |ko|
280
- puts ko
281
- end
282
-
283
- # The method "get_ko_members" is removed in 2005-06-01.
284
- #
285
- #puts "### get_ko_members('ko:K00003')"
286
- #list = serv.get_ko_members("ko:K00003")
287
- #list.each do |gene|
288
- # puts gene
289
- #end
290
-
291
- # The method "get_oc_members_by_gene" is removed in 2006-10-04.
292
- #
293
- #puts "### get_oc_members_by_gene('eco:b0002', 1, 5)"
294
- #list = serv.get_oc_members_by_gene("eco:b0002", 1, 5)
295
- #list.each do |gene|
296
- # puts gene
297
- #end
298
-
299
- # The method "get_all_oc_members_by_gene" can not be used because
300
- # it internally uses the deprecated "get_oc_members_by_gene" method.
301
- #
302
- #puts "# * get_all_oc_members_by_gene('eco:b0002')"
303
- #list = serv.get_all_oc_members_by_gene("eco:b0002")
304
- #list.each do |gene|
305
- # puts gene
306
- #end
307
-
308
- # The method "get_pc_members_by_gene" is removed in 2006-10-04.
309
- #
310
- #puts "### get_pc_members_by_gene('eco:b0002', 1, 5)"
311
- #list = serv.get_pc_members_by_gene("eco:b0002", 1, 5)
312
- #list.each do |gene|
313
- # puts gene
314
- #end
315
-
316
- # The method "get_all_pc_members_by_gene" can not be used because
317
- # it internally uses the deprecated "get_pc_members_by_gene" method.
318
- #
319
- #puts "# * get_all_pc_members_by_gene('eco:b0002')"
320
- #list = serv.get_all_pc_members_by_gene("eco:b0002")
321
- #list.each do |gene|
322
- # puts gene
323
- #end
324
-
325
- puts "=== PATHWAY"
326
-
327
- puts "==== coloring pathway"
328
-
329
- puts "### mark_pathway_by_objects('path:eco00260', obj_list)"
330
- puts " obj_list = ['eco:b0002', 'cpd:C00263']"
331
- obj_list = ["eco:b0002", "cpd:C00263"]
332
- url = serv.mark_pathway_by_objects("path:eco00260", obj_list)
333
- puts url
334
-
335
- puts "### color_pathway_by_objects('path:eco00053', obj_list, fg_list, bg_list)"
336
- puts " obj_list = ['eco:b0207', 'eco:b1300']"
337
- puts " fg_list = ['blue', '#00ff00']"
338
- puts " bg_list = ['#ff0000', 'yellow']"
339
- obj_list = ["eco:b0207", "eco:b1300"]
340
- fg_list = ["blue", "#00ff00"]
341
- bg_list = ["#ff0000", "yellow"]
342
- url = serv.color_pathway_by_objects("path:eco00053", obj_list, fg_list, bg_list)
343
- puts url
344
-
345
- #puts "# * save_image(#{url})"
346
- #filename = serv.save_image(url, "test.gif")
347
- #filename = serv.save_image(url)
348
- #puts filename
349
-
350
- puts "==== objects on pathway"
351
-
352
- puts "### get_genes_by_pathway('path:map00010')"
353
- list = serv.get_genes_by_pathway("path:map00010")
354
- list.each do |gene|
355
- puts gene
356
- end
357
-
358
- puts "### get_genes_by_pathway('path:eco00010')"
359
- list = serv.get_genes_by_pathway("path:eco00010")
360
- list.each do |gene|
361
- puts gene
362
- end
363
-
364
- puts "### get_enzymes_by_pathway('path:map00010')"
365
- list = serv.get_enzymes_by_pathway("path:map00010")
366
- list.each do |enzyme|
367
- puts enzyme
368
- end
369
-
370
- puts "### get_enzymes_by_pathway('path:eco00010')"
371
- list = serv.get_enzymes_by_pathway("path:eco00010")
372
- list.each do |enzyme|
373
- puts enzyme
374
- end
375
-
376
- puts "### get_compounds_by_pathway('path:map00010')"
377
- list = serv.get_compounds_by_pathway("path:map00010")
378
- list.each do |compound|
379
- puts compound
380
- end
381
-
382
- puts "### get_compounds_by_pathway('path:eco00010')"
383
- list = serv.get_compounds_by_pathway("path:eco00010")
384
- list.each do |compound|
385
- puts compound
386
- end
387
-
388
- puts "### get_reactions_by_pathway('path:map00010')"
389
- list = serv.get_reactions_by_pathway("path:map00010")
390
- list.each do |reaction|
391
- puts reaction
392
- end
393
-
394
- puts "### get_reactions_by_pathway('path:eco00010')"
395
- list = serv.get_reactions_by_pathway("path:eco00010")
396
- list.each do |reaction|
397
- puts reaction
398
- end
399
-
400
- puts "==== pathway by objects"
401
-
402
- puts "### get_pathways_by_genes(['eco:b0756', 'eco:b1002'])"
403
- list = serv.get_pathways_by_genes(["eco:b0756", "eco:b1002"])
404
- list.each do |path|
405
- puts path
406
- end
407
-
408
- puts "### get_pathways_by_enzymes(['ec:5.1.3.3', 'ec:3.1.3.10'])"
409
- list = serv.get_pathways_by_enzymes(["ec:5.1.3.3", "ec:3.1.3.10"])
410
- list.each do |path|
411
- puts path
412
- end
413
-
414
- puts "### get_pathways_by_compounds(['cpd:C00221', 'cpd:C00267'])"
415
- list = serv.get_pathways_by_compounds(["cpd:C00221", "cpd:C00267"])
416
- list.each do |path|
417
- puts path
418
- end
419
-
420
- puts "### get_pathways_by_reactions(['rn:R00014', 'rn:R00710'])"
421
- list = serv.get_pathways_by_reactions(["rn:R00014", "rn:R00710"])
422
- list.each do |path|
423
- puts path
424
- end
425
-
426
- puts "==== relation between objects"
427
-
428
- puts "### get_linked_pathways('path:eco00620')"
429
- list = serv.get_linked_pathways('path:eco00620')
430
- list.each do |path|
431
- puts path
432
- end
433
-
434
- puts "### get_genes_by_enzyme('ec:1.1.1.1', 'eco')"
435
- list = serv.get_genes_by_enzyme("ec:1.1.1.1", "eco")
436
- list.each do |gene|
437
- puts gene
438
- end
439
-
440
- puts "### get_enzymes_by_gene('eco:b0002')"
441
- list = serv.get_enzymes_by_gene("eco:b0002")
442
- list.each do |enzyme|
443
- puts enzyme
444
- end
445
-
446
- puts "### get_enzymes_by_compound('cpd:C00345')"
447
- list = serv.get_enzymes_by_compound("cpd:C00345")
448
- list.each do |enzyme|
449
- puts enzyme
450
- end
451
-
452
- puts "### get_enzymes_by_reaction('rn:R00100')"
453
- list = serv.get_enzymes_by_reaction("rn:R00100")
454
- list.each do |enzyme|
455
- puts enzyme
456
- end
457
-
458
- puts "### get_compounds_by_enzyme('ec:2.7.1.12')"
459
- list = serv.get_compounds_by_enzyme("ec:2.7.1.12")
460
- list.each do |compound|
461
- puts compound
462
- end
463
-
464
- puts "### get_compounds_by_reaction('rn:R00100')"
465
- list = serv.get_compounds_by_reaction("rn:R00100")
466
- list.each do |compound|
467
- puts compound
468
- end
469
-
470
- puts "### get_reactions_by_enzyme('ec:2.7.1.12')"
471
- list = serv.get_reactions_by_enzyme("ec:2.7.1.12")
472
- list.each do |reaction|
473
- puts reaction
474
- end
475
-
476
- puts "### get_reactions_by_compound('cpd:C00199')"
477
- list = serv.get_reactions_by_compound("cpd:C00199")
478
- list.each do |reaction|
479
- puts reaction
480
- end
481
-
482
- puts "=== GENES"
483
-
484
- puts "### get_genes_by_organism('mge', 1, 5)"
485
- list = serv.get_genes_by_organism("mge", 1, 5)
486
- list.each do |gene|
487
- puts gene
488
- end
489
-
490
- puts "# * get_all_genes_by_organism('mge')"
491
- list = serv.get_all_genes_by_organism("mge")
492
- list.each do |gene|
493
- puts gene
494
- end
495
-
496
- puts "=== GENOME"
497
-
498
- puts "### get_number_of_genes_by_organism(org)"
499
- puts serv.get_number_of_genes_by_organism("mge")
500
-
501
- #end
502
-