bio 1.5.1 → 2.0.2
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- checksums.yaml +5 -5
- data/.travis.yml +35 -36
- data/ChangeLog +911 -2554
- data/{gemfiles/Gemfile.travis-ruby2.2 → Gemfile} +0 -3
- data/KNOWN_ISSUES.rdoc +10 -13
- data/LEGAL +0 -10
- data/README.rdoc +40 -96
- data/README_DEV.rdoc +5 -5
- data/RELEASE_NOTES.rdoc +118 -234
- data/Rakefile +13 -43
- data/appveyor.yml +29 -0
- data/bioruby.gemspec +18 -81
- data/bioruby.gemspec.erb +8 -28
- data/doc/ChangeLog-1.5.0 +2919 -0
- data/doc/RELEASE_NOTES-1.5.0.rdoc +285 -0
- data/doc/Tutorial.rd +6 -108
- data/doc/Tutorial.rd.html +19 -98
- data/gemfiles/Gemfile.travis-jruby1.8 +3 -5
- data/gemfiles/Gemfile.travis-jruby1.9 +0 -3
- data/gemfiles/Gemfile.travis-rbx +0 -3
- data/gemfiles/Gemfile.travis-ruby1.8 +3 -5
- data/gemfiles/Gemfile.travis-ruby1.9 +0 -3
- data/gemfiles/Gemfile.windows +6 -0
- data/gemfiles/prepare-gemspec.rb +4 -0
- data/lib/bio.rb +0 -10
- data/lib/bio/appl/blast/genomenet.rb +4 -4
- data/lib/bio/appl/blast/report.rb +40 -8
- data/lib/bio/appl/fasta/format10.rb +2 -1
- data/lib/bio/command.rb +10 -0
- data/lib/bio/data/codontable.rb +99 -3
- data/lib/bio/db/aaindex.rb +74 -5
- data/lib/bio/db/gff.rb +3 -1
- data/lib/bio/db/kegg/common.rb +14 -0
- data/lib/bio/db/kegg/genes.rb +26 -0
- data/lib/bio/db/kegg/pathway.rb +5 -11
- data/lib/bio/db/soft.rb +2 -2
- data/lib/bio/io/flatfile/autodetection.rb +5 -0
- data/lib/bio/io/togows.rb +5 -5
- data/lib/bio/map.rb +4 -4
- data/lib/bio/sequence/format.rb +1 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +1 -1
- data/lib/bio/util/sirna.rb +2 -0
- data/lib/bio/version.rb +6 -8
- data/sample/color_scheme_aa.rb +82 -0
- data/sample/color_scheme_na.rb +5 -6
- data/sample/fastq2html.cwl +23 -0
- data/sample/fastq2html.rb +94 -0
- data/sample/fastq2html.testdata.yaml +5 -0
- data/sample/na2aa.cwl +23 -0
- data/sample/na2aa.rb +11 -25
- data/sample/na2aa.testdata.yaml +7 -0
- data/sample/rev_comp.cwl +23 -0
- data/sample/rev_comp.rb +20 -0
- data/sample/rev_comp.testdata.yaml +7 -0
- data/sample/test_restriction_enzyme_long.rb +1 -1
- data/test/network/bio/db/kegg/test_genes_hsa7422.rb +91 -0
- data/test/unit/bio/appl/blast/test_report.rb +4 -4
- data/test/unit/bio/data/test_codontable.rb +3 -0
- data/test/unit/bio/db/test_gff.rb +5 -0
- data/test/unit/bio/test_alignment.rb +2 -2
- metadata +20 -77
- data/bin/bioruby +0 -47
- data/bin/br_biofetch.rb +0 -71
- data/bin/br_bioflat.rb +0 -293
- data/bin/br_biogetseq.rb +0 -45
- data/bin/br_pmfetch.rb +0 -422
- data/lib/bio/appl/blast/xmlparser.rb +0 -236
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +0 -78
- data/lib/bio/db/biosql/sequence.rb +0 -444
- data/lib/bio/db/phyloxml/phyloxml.xsd +0 -582
- data/lib/bio/db/phyloxml/phyloxml_elements.rb +0 -1197
- data/lib/bio/db/phyloxml/phyloxml_parser.rb +0 -1001
- data/lib/bio/db/phyloxml/phyloxml_writer.rb +0 -227
- data/lib/bio/io/biosql/ar-biosql.rb +0 -257
- data/lib/bio/io/biosql/biosql.rb +0 -39
- data/lib/bio/io/biosql/config/database.yml +0 -21
- data/lib/bio/io/sql.rb +0 -79
- data/lib/bio/shell.rb +0 -44
- data/lib/bio/shell/core.rb +0 -578
- data/lib/bio/shell/demo.rb +0 -146
- data/lib/bio/shell/interface.rb +0 -217
- data/lib/bio/shell/irb.rb +0 -94
- data/lib/bio/shell/object.rb +0 -71
- data/lib/bio/shell/plugin/blast.rb +0 -42
- data/lib/bio/shell/plugin/codon.rb +0 -218
- data/lib/bio/shell/plugin/das.rb +0 -58
- data/lib/bio/shell/plugin/emboss.rb +0 -23
- data/lib/bio/shell/plugin/entry.rb +0 -137
- data/lib/bio/shell/plugin/flatfile.rb +0 -101
- data/lib/bio/shell/plugin/midi.rb +0 -430
- data/lib/bio/shell/plugin/ncbirest.rb +0 -68
- data/lib/bio/shell/plugin/obda.rb +0 -45
- data/lib/bio/shell/plugin/psort.rb +0 -56
- data/lib/bio/shell/plugin/seq.rb +0 -248
- data/lib/bio/shell/plugin/togows.rb +0 -40
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +0 -29
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +0 -4
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +0 -27
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +0 -11
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +0 -4
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +0 -7
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +0 -368
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +0 -47
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +0 -144
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +0 -47
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +0 -8
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +0 -10
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +0 -26
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +0 -25
- data/lib/bio/shell/setup.rb +0 -108
- data/lib/bio/shell/web.rb +0 -102
- data/sample/test_phyloxml_big.rb +0 -205
- data/setup.rb +0 -1600
- data/test/data/phyloxml/apaf.xml +0 -666
- data/test/data/phyloxml/bcl_2.xml +0 -2097
- data/test/data/phyloxml/made_up.xml +0 -144
- data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +0 -65
- data/test/data/phyloxml/phyloxml_examples.xml +0 -415
- data/test/unit/bio/db/biosql/tc_biosql.rb +0 -114
- data/test/unit/bio/db/biosql/ts_suite_biosql.rb +0 -8
- data/test/unit/bio/db/test_phyloxml.rb +0 -821
- data/test/unit/bio/db/test_phyloxml_writer.rb +0 -334
- data/test/unit/bio/shell/plugin/test_seq.rb +0 -187
- data/test/unit/bio/test_shell.rb +0 -20
data/test/unit/bio/test_shell.rb
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#
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# test/unit/bio/test_shell.rb - Unit test for Bio::Shell
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#
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# Copyright:: Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
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# License:: The Ruby License
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#
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# $Id:$
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#
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# loading helper routine for testing bioruby
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require 'pathname'
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load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
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'bioruby_test_helper.rb')).cleanpath.to_s
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# libraries needed for the tests
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require 'test/unit'
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require 'bio/shell'
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module Bio
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end
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