wwood-bioruby 1.2.11
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- data/README.rdoc +205 -0
- data/README_DEV.rdoc +285 -0
- data/VERSION.yml +4 -0
- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +293 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/lib/bio.rb +306 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +505 -0
- data/lib/bio/appl/blast/ddbj.rb +142 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/genomenet.rb +263 -0
- data/lib/bio/appl/blast/ncbioptions.rb +220 -0
- data/lib/bio/appl/blast/remote.rb +105 -0
- data/lib/bio/appl/blast/report.rb +767 -0
- data/lib/bio/appl/blast/rexml.rb +144 -0
- data/lib/bio/appl/blast/rpsblast.rb +277 -0
- data/lib/bio/appl/blast/wublast.rb +635 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blat/report.rb +530 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta.rb +235 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/gcg/msf.rb +212 -0
- data/lib/bio/appl/gcg/seq.rb +195 -0
- data/lib/bio/appl/genscan/report.rb +552 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/hmmer/report.rb +683 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/paml/baseml.rb +95 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/codeml.rb +242 -0
- data/lib/bio/appl/paml/codeml/rates.rb +67 -0
- data/lib/bio/appl/paml/codeml/report.rb +67 -0
- data/lib/bio/appl/paml/common.rb +348 -0
- data/lib/bio/appl/paml/common_report.rb +38 -0
- data/lib/bio/appl/paml/yn00.rb +103 -0
- data/lib/bio/appl/paml/yn00/report.rb +32 -0
- data/lib/bio/appl/phylip/alignment.rb +133 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/psort/report.rb +542 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +124 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sosui/report.rb +151 -0
- data/lib/bio/appl/spidey/report.rb +593 -0
- data/lib/bio/appl/targetp/report.rb +267 -0
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +231 -0
- data/lib/bio/command.rb +593 -0
- data/lib/bio/compat/features.rb +157 -0
- data/lib/bio/compat/references.rb +128 -0
- data/lib/bio/data/aa.rb +353 -0
- data/lib/bio/data/codontable.rb +722 -0
- data/lib/bio/data/na.rb +223 -0
- data/lib/bio/db.rb +329 -0
- data/lib/bio/db/aaindex.rb +357 -0
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +67 -0
- data/lib/bio/db/biosql/sequence.rb +508 -0
- data/lib/bio/db/embl/common.rb +352 -0
- data/lib/bio/db/embl/embl.rb +500 -0
- data/lib/bio/db/embl/embl_to_biosequence.rb +85 -0
- data/lib/bio/db/embl/format_embl.rb +190 -0
- data/lib/bio/db/embl/sptr.rb +1283 -0
- data/lib/bio/db/embl/swissprot.rb +42 -0
- data/lib/bio/db/embl/trembl.rb +41 -0
- data/lib/bio/db/embl/uniprot.rb +42 -0
- data/lib/bio/db/fantom.rb +597 -0
- data/lib/bio/db/fasta.rb +410 -0
- data/lib/bio/db/fasta/defline.rb +532 -0
- data/lib/bio/db/fasta/fasta_to_biosequence.rb +63 -0
- data/lib/bio/db/fasta/format_fasta.rb +97 -0
- data/lib/bio/db/genbank/common.rb +307 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/format_genbank.rb +187 -0
- data/lib/bio/db/genbank/genbank.rb +250 -0
- data/lib/bio/db/genbank/genbank_to_biosequence.rb +86 -0
- data/lib/bio/db/genbank/genpept.rb +60 -0
- data/lib/bio/db/genbank/refseq.rb +18 -0
- data/lib/bio/db/gff.rb +1846 -0
- data/lib/bio/db/go.rb +481 -0
- data/lib/bio/db/kegg/brite.rb +41 -0
- data/lib/bio/db/kegg/compound.rb +131 -0
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +148 -0
- data/lib/bio/db/kegg/expression.rb +155 -0
- data/lib/bio/db/kegg/genes.rb +263 -0
- data/lib/bio/db/kegg/genome.rb +241 -0
- data/lib/bio/db/kegg/glycan.rb +166 -0
- data/lib/bio/db/kegg/keggtab.rb +357 -0
- data/lib/bio/db/kegg/kgml.rb +256 -0
- data/lib/bio/db/kegg/orthology.rb +136 -0
- data/lib/bio/db/kegg/reaction.rb +82 -0
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +107 -0
- data/lib/bio/db/medline.rb +326 -0
- data/lib/bio/db/nbrf.rb +191 -0
- data/lib/bio/db/newick.rb +658 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +29 -0
- data/lib/bio/db/pdb/atom.rb +77 -0
- data/lib/bio/db/pdb/chain.rb +210 -0
- data/lib/bio/db/pdb/chemicalcomponent.rb +224 -0
- data/lib/bio/db/pdb/model.rb +148 -0
- data/lib/bio/db/pdb/pdb.rb +1911 -0
- data/lib/bio/db/pdb/residue.rb +176 -0
- data/lib/bio/db/pdb/utils.rb +399 -0
- data/lib/bio/db/prosite.rb +597 -0
- data/lib/bio/db/rebase.rb +456 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/db/url.rb +42 -0
- data/lib/bio/feature.rb +139 -0
- data/lib/bio/io/biosql/biodatabase.rb +64 -0
- data/lib/bio/io/biosql/bioentry.rb +29 -0
- data/lib/bio/io/biosql/bioentry_dbxref.rb +11 -0
- data/lib/bio/io/biosql/bioentry_path.rb +12 -0
- data/lib/bio/io/biosql/bioentry_qualifier_value.rb +10 -0
- data/lib/bio/io/biosql/bioentry_reference.rb +10 -0
- data/lib/bio/io/biosql/bioentry_relationship.rb +10 -0
- data/lib/bio/io/biosql/biosequence.rb +11 -0
- data/lib/bio/io/biosql/comment.rb +7 -0
- data/lib/bio/io/biosql/config/database.yml +20 -0
- data/lib/bio/io/biosql/dbxref.rb +13 -0
- data/lib/bio/io/biosql/dbxref_qualifier_value.rb +12 -0
- data/lib/bio/io/biosql/location.rb +32 -0
- data/lib/bio/io/biosql/location_qualifier_value.rb +11 -0
- data/lib/bio/io/biosql/ontology.rb +10 -0
- data/lib/bio/io/biosql/reference.rb +9 -0
- data/lib/bio/io/biosql/seqfeature.rb +32 -0
- data/lib/bio/io/biosql/seqfeature_dbxref.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_path.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_qualifier_value.rb +20 -0
- data/lib/bio/io/biosql/seqfeature_relationship.rb +11 -0
- data/lib/bio/io/biosql/taxon.rb +12 -0
- data/lib/bio/io/biosql/taxon_name.rb +9 -0
- data/lib/bio/io/biosql/term.rb +27 -0
- data/lib/bio/io/biosql/term_dbxref.rb +11 -0
- data/lib/bio/io/biosql/term_path.rb +12 -0
- data/lib/bio/io/biosql/term_relationship.rb +13 -0
- data/lib/bio/io/biosql/term_relationship_term.rb +11 -0
- data/lib/bio/io/biosql/term_synonym.rb +10 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +638 -0
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +163 -0
- data/lib/bio/io/fetch.rb +195 -0
- data/lib/bio/io/flatfile.rb +482 -0
- data/lib/bio/io/flatfile/autodetection.rb +545 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/buffer.rb +237 -0
- data/lib/bio/io/flatfile/index.rb +1381 -0
- data/lib/bio/io/flatfile/indexer.rb +805 -0
- data/lib/bio/io/flatfile/splitter.rb +297 -0
- data/lib/bio/io/higet.rb +73 -0
- data/lib/bio/io/hinv.rb +442 -0
- data/lib/bio/io/keggapi.rb +805 -0
- data/lib/bio/io/ncbirest.rb +733 -0
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +307 -0
- data/lib/bio/io/registry.rb +292 -0
- data/lib/bio/io/soapwsdl.rb +119 -0
- data/lib/bio/io/sql.rb +186 -0
- data/lib/bio/location.rb +867 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +960 -0
- data/lib/bio/reference.rb +602 -0
- data/lib/bio/sequence.rb +456 -0
- data/lib/bio/sequence/aa.rb +152 -0
- data/lib/bio/sequence/adapter.rb +108 -0
- data/lib/bio/sequence/common.rb +310 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/dblink.rb +54 -0
- data/lib/bio/sequence/format.rb +358 -0
- data/lib/bio/sequence/format_raw.rb +23 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +491 -0
- data/lib/bio/shell.rb +44 -0
- data/lib/bio/shell/core.rb +578 -0
- data/lib/bio/shell/demo.rb +146 -0
- data/lib/bio/shell/interface.rb +218 -0
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +71 -0
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +218 -0
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +105 -0
- data/lib/bio/shell/plugin/flatfile.rb +101 -0
- data/lib/bio/shell/plugin/keggapi.rb +181 -0
- data/lib/bio/shell/plugin/midi.rb +430 -0
- data/lib/bio/shell/plugin/obda.rb +45 -0
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +247 -0
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +102 -0
- data/lib/bio/tree.rb +852 -0
- data/lib/bio/util/color_scheme.rb +191 -0
- data/lib/bio/util/color_scheme/buried.rb +59 -0
- data/lib/bio/util/color_scheme/helix.rb +59 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +64 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +31 -0
- data/lib/bio/util/color_scheme/strand.rb +59 -0
- data/lib/bio/util/color_scheme/taylor.rb +50 -0
- data/lib/bio/util/color_scheme/turn.rb +59 -0
- data/lib/bio/util/color_scheme/zappo.rb +50 -0
- data/lib/bio/util/contingency_table.rb +370 -0
- data/lib/bio/util/restriction_enzyme.rb +228 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
- data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +200 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/aaindex/DAYM780301 +30 -0
- data/test/data/aaindex/PRAM900102 +20 -0
- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
- data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
- data/test/data/blast/2.2.15.blastp.m7 +876 -0
- data/test/data/blast/b0002.faa +15 -0
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- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/blast/blastp-multi.m7 +188 -0
- data/test/data/command/echoarg2.bat +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/embl/AB090716.embl.rel89 +63 -0
- data/test/data/fasta/example1.txt +75 -0
- data/test/data/fasta/example2.txt +21 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/paml/codeml/control_file.txt +30 -0
- data/test/data/paml/codeml/output.txt +78 -0
- data/test/data/paml/codeml/rates +217 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/rpsblast/misc.rpsblast +193 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/functional/bio/appl/test_pts1.rb +115 -0
- data/test/functional/bio/io/test_ensembl.rb +229 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -0
- data/test/functional/bio/sequence/test_output_embl.rb +51 -0
- data/test/functional/bio/test_command.rb +301 -0
- data/test/runner.rb +14 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_ncbioptions.rb +112 -0
- data/test/unit/bio/appl/blast/test_report.rb +1135 -0
- data/test/unit/bio/appl/blast/test_rpsblast.rb +398 -0
- data/test/unit/bio/appl/genscan/test_report.rb +182 -0
- data/test/unit/bio/appl/hmmer/test_report.rb +342 -0
- data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
- data/test/unit/bio/appl/mafft/test_report.rb +63 -0
- data/test/unit/bio/appl/paml/codeml/test_rates.rb +45 -0
- data/test/unit/bio/appl/paml/codeml/test_report.rb +45 -0
- data/test/unit/bio/appl/paml/test_codeml.rb +174 -0
- data/test/unit/bio/appl/sosui/test_report.rb +81 -0
- data/test/unit/bio/appl/targetp/test_report.rb +146 -0
- data/test/unit/bio/appl/test_blast.rb +277 -0
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_psort.rb +57 -0
- data/test/unit/bio/appl/test_pts1.rb +77 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +126 -0
- data/test/unit/bio/data/test_aa.rb +90 -0
- data/test/unit/bio/data/test_codontable.rb +107 -0
- data/test/unit/bio/data/test_na.rb +80 -0
- data/test/unit/bio/db/embl/test_common.rb +117 -0
- data/test/unit/bio/db/embl/test_embl.rb +214 -0
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +203 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1812 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +31 -0
- data/test/unit/bio/db/kegg/test_genes.rb +45 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +152 -0
- data/test/unit/bio/db/test_aaindex.rb +197 -0
- data/test/unit/bio/db/test_fasta.rb +250 -0
- data/test/unit/bio/db/test_gff.rb +1190 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_medline.rb +127 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +364 -0
- data/test/unit/bio/db/test_prosite.rb +1437 -0
- data/test/unit/bio/db/test_rebase.rb +101 -0
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/db/test_url.rb +36 -0
- data/test/unit/bio/io/flatfile/test_autodetection.rb +375 -0
- data/test/unit/bio/io/flatfile/test_buffer.rb +251 -0
- data/test/unit/bio/io/flatfile/test_splitter.rb +369 -0
- data/test/unit/bio/io/test_ddbjxml.rb +80 -0
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +42 -0
- data/test/unit/bio/io/test_flatfile.rb +505 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +115 -0
- data/test/unit/bio/sequence/test_common.rb +373 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -0
- data/test/unit/bio/sequence/test_dblink.rb +58 -0
- data/test/unit/bio/sequence/test_na.rb +330 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +185 -0
- data/test/unit/bio/test_alignment.rb +1025 -0
- data/test/unit/bio/test_command.rb +349 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +144 -0
- data/test/unit/bio/test_location.rb +599 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +499 -0
- data/test/unit/bio/test_reference.rb +252 -0
- data/test/unit/bio/test_sequence.rb +329 -0
- data/test/unit/bio/test_shell.rb +18 -0
- data/test/unit/bio/test_tree.rb +593 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +101 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
- data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
- data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
- data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
- data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
- data/test/unit/bio/util/test_color_scheme.rb +33 -0
- data/test/unit/bio/util/test_contingency_table.rb +94 -0
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +245 -0
- metadata +543 -0
@@ -0,0 +1,301 @@
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#
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# test/unit/bio/test_command.rb - Functional test for external command execution methods in Bio::Command
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#
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# Copyright:: Copyright (C) 2008
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# Naohisa Goto <ng@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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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'test/unit'
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require 'tempfile'
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require 'bio/command'
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module Bio
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class FuncTestCommandCall < Test::Unit::TestCase
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def setup
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case RUBY_PLATFORM
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when /mswin32|bccwin32/
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bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3)).cleanpath.to_s
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cmd = File.expand_path(File.join(bioruby_root, 'test', 'data', 'command', 'echoarg2.bat'))
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@arg = [ cmd, 'test "argument 1"', '"test" argument 2', 'arg3' ]
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@expected = '"""test"" argument 2"'
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else
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cmd = "/bin/echo"
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@arg = [ cmd, "test (echo) command" ]
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@expected = "test (echo) command"
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unless FileTest.executable?(cmd) then
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raise "Unsupported environment: /bin/echo not found"
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end
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end
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end
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def test_call_command
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ret = Bio::Command.call_command(@arg) do |io|
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io.close_write
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io.read
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end
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assert_equal(@expected, ret.to_s.strip)
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end
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def test_call_command_popen
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ret = Bio::Command.call_command_popen(@arg) do |io|
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io.close_write
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io.read
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end
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assert_equal(@expected, ret.to_s.strip)
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end
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def test_call_command_fork
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begin
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ret = Bio::Command.call_command_fork(@arg) do |io|
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io.close_write
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io.read
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end
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rescue Errno::ENOENT, NotImplementedError
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# fork() not supported
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return
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end
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assert_equal(@expected, ret.to_s.strip)
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end
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def test_call_command_open3
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begin
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ret = Bio::Command.call_command_open3(@arg) do |pin, pout, perr|
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t = Thread.start { perr.read }
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begin
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pin.close
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output = pout.read
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ensure
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t.join
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end
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output
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end
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rescue NotImplementedError
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# fork() not supported
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return
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end
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assert_equal(@expected, ret.to_s.strip)
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end
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end #class FuncTestCommandCall
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class FuncTestCommandQuery < Test::Unit::TestCase
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def setup
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@data = [ "987", "123", "567", "456", "345" ]
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@sorted = @data.sort
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case RUBY_PLATFORM
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when /mswin32|bccwin32/
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@sort = "sort"
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@data = @data.join("\r\n") + "\r\n"
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else
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@sort = "/usr/bin/sort"
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unless FileTest.executable?(@sort) then
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raise "Unsupported environment: /usr/bin/sort not found"
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end
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@data = @data.join("\n") + "\n"
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end
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end
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def test_query_command
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ary = [ @sort ]
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assert_equal('', Bio::Command.query_command(ary).to_s.strip)
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str = Bio::Command.query_command(ary, @data).to_s
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assert_equal(@sorted, str.strip.split(/\s+/))
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end
|
114
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|
115
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def test_query_command_popen
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ary = [ @sort ]
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assert_equal('', Bio::Command.query_command_popen(ary).to_s.strip)
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str = Bio::Command.query_command_popen(ary, @data).to_s
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assert_equal(@sorted, str.strip.split(/\s+/))
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end
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def test_query_command_fork
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ary = [ @sort ]
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begin
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str = Bio::Command.query_command_fork(ary).to_s
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rescue Errno::ENOENT, NotImplementedError
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# fork() not supported
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return
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end
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assert_equal('', str.strip)
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str = Bio::Command.query_command_fork(ary, @data).to_s
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assert_equal(@sorted, str.strip.split(/\s+/))
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end
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def test_query_command_open3
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ary = [ @sort ]
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begin
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str, err = Bio::Command.query_command_open3(ary)
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rescue NotImplementedError
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# fork() not supported
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return
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end
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assert_equal('', str.to_s.strip)
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str, err = Bio::Command.query_command_open3(ary, @data)
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assert_equal(@sorted, str.to_s.strip.split(/\s+/))
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end
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end #class FuncTestCommandQuery
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|
149
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class FuncTestCommandChdir < Test::Unit::TestCase
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def setup
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151
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case RUBY_PLATFORM
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when /mswin32|bccwin32/
|
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@arg = [ 'dir', '/B', '/-P' ]
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else
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cmd = '/bin/ls'
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@arg = [ cmd ]
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unless FileTest.executable?(cmd) then
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raise "Unsupported environment: #{cmd} not found"
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end
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end
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@tempfile = Tempfile.new('chdir')
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@tempfile.close(false)
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@filename = File.basename(@tempfile.path)
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@dirname = File.dirname(@tempfile.path)
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end
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|
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def teardown
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@tempfile.close(true)
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end
|
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def test_call_command_chdir
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str = nil
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Bio::Command.call_command(@arg, { :chdir => @dirname }) do |io|
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io.close_write
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str = io.read
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end
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assert(str.index(@filename))
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end
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def test_call_command_popen_chdir
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str = nil
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Bio::Command.call_command_popen(@arg,
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{ :chdir => @dirname }) do |io|
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io.close_write
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str = io.read
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end
|
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assert(str.index(@filename))
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end
|
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|
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def test_call_command_fork_chdir
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str = nil
|
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begin
|
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Bio::Command.call_command_fork(@arg,
|
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{ :chdir => @dirname }) do |io|
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io.close_write
|
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str = io.read
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end
|
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rescue Errno::ENOENT, NotImplementedError
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# fork() not supported
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return
|
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end
|
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assert(str.index(@filename))
|
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end
|
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|
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def test_query_command_chdir
|
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str = Bio::Command.query_command(@arg, nil,
|
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{ :chdir => @dirname }).to_s
|
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assert(str.index(@filename))
|
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+
end
|
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|
211
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def test_query_command_popen_chdir
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str = Bio::Command.query_command_popen(@arg, nil,
|
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{ :chdir => @dirname }).to_s
|
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assert(str.index(@filename))
|
215
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end
|
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|
217
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def test_query_command_fork_chdir
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begin
|
219
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str = Bio::Command.query_command_fork(@arg, nil,
|
220
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{ :chdir => @dirname }).to_s
|
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rescue Errno::ENOENT, NotImplementedError
|
222
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+
# fork() not supported
|
223
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+
return
|
224
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+
end
|
225
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assert(str.index(@filename))
|
226
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+
end
|
227
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end #class FuncTestCommandChdir
|
228
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+
|
229
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+
class FuncTestCommandBackports < Test::Unit::TestCase
|
230
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+
def setup
|
231
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+
if RUBY_VERSION < "1.8.3"
|
232
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+
@notest = true
|
233
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+
else
|
234
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+
@notest = false
|
235
|
+
end
|
236
|
+
end
|
237
|
+
|
238
|
+
def test_remove_entry_secure
|
239
|
+
return if @notest
|
240
|
+
begin
|
241
|
+
tempfile = Tempfile.new('removed')
|
242
|
+
tempfile.close(false)
|
243
|
+
assert(File.exist?(tempfile.path))
|
244
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+
Bio::Command.remove_entry_secure(tempfile.path)
|
245
|
+
assert_equal(false, File.exist?(tempfile.path))
|
246
|
+
ensure
|
247
|
+
tempfile.close(true) if tempfile
|
248
|
+
end
|
249
|
+
end
|
250
|
+
|
251
|
+
def test_mktmpdir_with_block
|
252
|
+
return if @notest
|
253
|
+
tmpdirpath = nil
|
254
|
+
Bio::Command.mktmpdir('bioruby') do |path|
|
255
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+
tmpdirpath = path
|
256
|
+
assert(File.directory?(path))
|
257
|
+
assert_nothing_raised {
|
258
|
+
File.open(File.join(path, 'test'), 'w') do |w|
|
259
|
+
w.print "This is test."
|
260
|
+
end
|
261
|
+
}
|
262
|
+
end
|
263
|
+
assert_equal(false, File.directory?(tmpdirpath))
|
264
|
+
end
|
265
|
+
|
266
|
+
def test_mktmpdir_without_block
|
267
|
+
return if @notest
|
268
|
+
path = nil
|
269
|
+
begin
|
270
|
+
assert_nothing_raised {
|
271
|
+
path = Bio::Command.mktmpdir('bioruby')
|
272
|
+
}
|
273
|
+
assert(File.directory?(path))
|
274
|
+
assert_nothing_raised {
|
275
|
+
File.open(File.join(path, 'test'), 'w') do |w|
|
276
|
+
w.print "This is test."
|
277
|
+
end
|
278
|
+
}
|
279
|
+
ensure
|
280
|
+
Bio::Command.remove_entry_secure(path) if path
|
281
|
+
end
|
282
|
+
end
|
283
|
+
end #class FuncTestCommandBackports
|
284
|
+
|
285
|
+
class FuncTestCommandNet < Test::Unit::TestCase
|
286
|
+
def test_read_uri
|
287
|
+
assert_nothing_raised {
|
288
|
+
Bio::Command.read_uri("http://bioruby.open-bio.org/")
|
289
|
+
}
|
290
|
+
end
|
291
|
+
|
292
|
+
def test_start_http
|
293
|
+
end
|
294
|
+
|
295
|
+
def test_new_http
|
296
|
+
end
|
297
|
+
|
298
|
+
def test_post_form
|
299
|
+
end
|
300
|
+
end #class FuncTestCommandNet
|
301
|
+
end #module Bio
|
data/test/runner.rb
ADDED
@@ -0,0 +1,14 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
|
3
|
+
require 'test/unit'
|
4
|
+
require 'pathname'
|
5
|
+
|
6
|
+
bioruby_libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'], 'lib')).cleanpath.to_s
|
7
|
+
$:.unshift(bioruby_libpath) unless $:.include?(bioruby_libpath)
|
8
|
+
|
9
|
+
if RUBY_VERSION > "1.8.2"
|
10
|
+
exit Test::Unit::AutoRunner.run(true, File.dirname($0))
|
11
|
+
else
|
12
|
+
exit Test::Unit::AutoRunner.run(false, File.dirname($0))
|
13
|
+
end
|
14
|
+
|
@@ -0,0 +1,134 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/appl/bl2seq/test_report.rb - Unit test for
|
3
|
+
# Bio::Blast::Bl2seq::Report
|
4
|
+
#
|
5
|
+
# Copyright:: Copyright (C) 2006
|
6
|
+
# Mitsuteru C. Nakao <n@bioruby.org>
|
7
|
+
# License:: The Ruby License
|
8
|
+
#
|
9
|
+
# $Id: test_report.rb,v 1.3 2007/04/05 23:35:43 trevor Exp $
|
10
|
+
#
|
11
|
+
|
12
|
+
require 'pathname'
|
13
|
+
libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
|
14
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
15
|
+
|
16
|
+
require 'test/unit'
|
17
|
+
require 'bio/appl/bl2seq/report'
|
18
|
+
|
19
|
+
|
20
|
+
module Bio
|
21
|
+
class TestBl2seqReportData
|
22
|
+
bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
|
23
|
+
TestDataBl2seq = Pathname.new(File.join(bioruby_root, 'test', 'data', 'bl2seq')).cleanpath.to_s
|
24
|
+
|
25
|
+
def self.output(format = 7)
|
26
|
+
case format
|
27
|
+
when 'empty'
|
28
|
+
File.open(File.join(TestDataBl2seq, 'cd8a_p53_e-5blastp.bl2seq')).read
|
29
|
+
when 'blastp'
|
30
|
+
File.open(File.join(TestDataBl2seq, 'cd8a_cd8b_blastp.bl2seq')).read
|
31
|
+
when 'blastn'
|
32
|
+
when 'blastx'
|
33
|
+
when 'tblastn'
|
34
|
+
when 'tblastx'
|
35
|
+
end
|
36
|
+
end
|
37
|
+
end
|
38
|
+
|
39
|
+
|
40
|
+
class TestBl2seqReportConstants < Test::Unit::TestCase
|
41
|
+
def test_rs
|
42
|
+
rs = nil
|
43
|
+
assert_equal(nil, Bio::Blast::Bl2seq::Report::RS)
|
44
|
+
assert_equal(nil, Bio::Blast::Bl2seq::Report::DELIMITER)
|
45
|
+
end
|
46
|
+
end
|
47
|
+
|
48
|
+
|
49
|
+
class TestBl2seqReport < Test::Unit::TestCase
|
50
|
+
|
51
|
+
def setup
|
52
|
+
@empty = Bio::Blast::Bl2seq::Report.new(Bio::TestBl2seqReportData.output('empty'))
|
53
|
+
@blastp = Bio::Blast::Bl2seq::Report.new(Bio::TestBl2seqReportData.output('blastp'))
|
54
|
+
end
|
55
|
+
|
56
|
+
def test_new
|
57
|
+
assert(@empty)
|
58
|
+
assert(@blastp)
|
59
|
+
end
|
60
|
+
|
61
|
+
def test_undefed_methods
|
62
|
+
methods = ['format0_parse_header',
|
63
|
+
'program',
|
64
|
+
'version',
|
65
|
+
'version_number',
|
66
|
+
'version_date',
|
67
|
+
'message',
|
68
|
+
'converged?',
|
69
|
+
'reference',
|
70
|
+
'db']
|
71
|
+
|
72
|
+
methods.each do |x|
|
73
|
+
assert_nil(@empty.methods.include?(x))
|
74
|
+
end
|
75
|
+
|
76
|
+
methods.each do |x|
|
77
|
+
assert_nil(@blastp.methods.include?(x))
|
78
|
+
end
|
79
|
+
end
|
80
|
+
|
81
|
+
# TestF0dbstat < Test::Unit::TestCase
|
82
|
+
|
83
|
+
def test_db_num
|
84
|
+
assert_equal(0, @empty.db_num)
|
85
|
+
assert_equal(0, @blastp.db_num)
|
86
|
+
end
|
87
|
+
|
88
|
+
def test_db_len
|
89
|
+
assert_equal(393, @empty.db_len)
|
90
|
+
assert_equal(210, @blastp.db_len)
|
91
|
+
end
|
92
|
+
|
93
|
+
# TestIteration < Test::Unit::TestCase
|
94
|
+
def test_undefed_methods
|
95
|
+
methods = ['message',
|
96
|
+
'pattern_in_database',
|
97
|
+
'pattern',
|
98
|
+
'pattern_positions',
|
99
|
+
'hits_found_again',
|
100
|
+
'hits_newly_found',
|
101
|
+
'hits_for_pattern',
|
102
|
+
'parse_hitlist',
|
103
|
+
'converged?']
|
104
|
+
|
105
|
+
methods.each do |x|
|
106
|
+
assert_equal(false, @empty.iterations.first.methods.include?(x), "undifined? : #{x}")
|
107
|
+
end
|
108
|
+
|
109
|
+
methods.each do |x|
|
110
|
+
assert_equal(false, @blastp.iterations.first.methods.include?(x), "undefined? : #{x}")
|
111
|
+
end
|
112
|
+
end
|
113
|
+
end
|
114
|
+
|
115
|
+
|
116
|
+
class TestBl2seqReportHit < Test::Unit::TestCase
|
117
|
+
def setup
|
118
|
+
@empty = Bio::Blast::Bl2seq::Report.new(Bio::TestBl2seqReportData.output('empty'))
|
119
|
+
@blastp = Bio::Blast::Bl2seq::Report.new(Bio::TestBl2seqReportData.output('blastp'))
|
120
|
+
@empty_hit = @empty.hits.first
|
121
|
+
@blastp_hit = @blastp.hits.first
|
122
|
+
end
|
123
|
+
|
124
|
+
def test_empty_hits
|
125
|
+
assert_equal(0, @empty.hits.size)
|
126
|
+
end
|
127
|
+
|
128
|
+
def test_hits
|
129
|
+
assert_equal(Bio::Blast::Bl2seq::Report::Hit, @blastp.hits.first.class)
|
130
|
+
assert_equal(1, @blastp.hits.size)
|
131
|
+
end
|
132
|
+
end
|
133
|
+
|
134
|
+
end # module Bio
|