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 +1,77 @@
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#
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# = test/unit/bio/appl/test_pts1.rb - Unit test for Bio::PTS1
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#
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# Copyright:: Copyright (C) 2006
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# 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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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, '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 'bio/appl/pts1'
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module Bio
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class TestPTS1Constant < Test::Unit::TestCase
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def test_FUNCTION
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keys = ['METAZOA-specific','FUNGI-specific','GENERAL'].sort
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assert_equal(keys, Bio::PTS1::FUNCTION.keys.sort)
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end
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end
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class TestPTS1New < Test::Unit::TestCase
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def test_metazoa
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pts1 = Bio::PTS1.new_with_metazoa_function
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assert_equal('METAZOA-specific', pts1.function)
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end
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def test_fungi
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pts1 = Bio::PTS1.new_with_fungi_function
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assert_equal('FUNGI-specific', pts1.function)
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end
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def test_general
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pts1 = Bio::PTS1.new_with_general_function
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assert_equal('GENERAL', pts1.function)
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end
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end
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class TestPTS1 < Test::Unit::TestCase
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def setup
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@serv = Bio::PTS1.new
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end
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def test_function_set
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@serv.function("GENERAL")
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assert_equal("GENERAL", @serv.function)
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end
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def test_function_show
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assert_equal("METAZOA-specific", @serv.function)
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end
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def test_function_set_number_1
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@serv.function(1)
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assert_equal("METAZOA-specific", @serv.function)
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end
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def test_function_set_number_2
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@serv.function(2)
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assert_equal("FUNGI-specific", @serv.function)
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end
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def test_function_set_number_3
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@serv.function(3)
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assert_equal("GENERAL", @serv.function)
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end
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end
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end
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#
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# test/unit/bio/appl/tmhmm/test_report.rb - Unit test for Bio::TMHMM::Report
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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: test_report.rb,v 1.4 2007/04/05 23:35:43 trevor Exp $
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#
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, '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 'bio/appl/tmhmm/report'
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module Bio
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bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
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test_data = Pathname.new(File.join(bioruby_root, 'test', 'data', 'TMHMM')).cleanpath.to_s
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TMHMMReport = File.open(File.join(test_data, 'sample.report')).read
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class TestTMHMMReport_reports < Test::Unit::TestCase
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def test_reports
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assert(Bio::TMHMM.reports(""))
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end
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end
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class TestTMHMMReport < Test::Unit::TestCase
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def setup
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@obj = Bio::TMHMM::Report.new(TMHMMReport)
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end
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|
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def test_entry_id
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assert_equal('O42385', @obj.entry_id)
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end
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def test_query_len
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assert_equal(423, @obj.query_len)
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end
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def test_predicted_tmhs
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assert_equal(7, @obj.predicted_tmhs)
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end
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|
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def test_tmhs
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assert_equal(Array, @obj.tmhs.class)
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assert_equal(15, @obj.tmhs.size)
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end
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def test_exp_aas_in_tmhs
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assert_equal(157.40784, @obj.exp_aas_in_tmhs)
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end
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def test_exp_first_60aa
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assert_equal(13.85627, @obj.exp_first_60aa)
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end
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def test_total_prob_of_N_in
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assert_equal(0.00993, @obj.total_prob_of_N_in)
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end
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|
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def test_helix
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assert_equal(7, @obj.helix.size)
|
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assert_equal(Bio::TMHMM::TMH, @obj.helix[0].class)
|
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end
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|
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def test_to_s
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str = ["# O42385\tLength:\t423",
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"# O42385\tNumber of predicted TMHs:\t7",
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"# O42385\tExp number of AAs in THMs:\t157.40784",
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"# O42385\tExp number, first 60 AAs:\t13.85627",
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"# O42385\tTotal prob of N-in:\t0.00993",
|
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"O42385\tTMHMM2.0\toutside\t1\t46",
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"O42385\tTMHMM2.0\tTMhelix\t47\t69",
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"O42385\tTMHMM2.0\tinside\t70\t81",
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"O42385\tTMHMM2.0\tTMhelix\t82\t104",
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"O42385\tTMHMM2.0\toutside\t105\t118",
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"O42385\tTMHMM2.0\tTMhelix\t119\t141",
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"O42385\tTMHMM2.0\tinside\t142\t161",
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"O42385\tTMHMM2.0\tTMhelix\t162\t184",
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"O42385\tTMHMM2.0\toutside\t185\t205",
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"O42385\tTMHMM2.0\tTMhelix\t206\t228",
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"O42385\tTMHMM2.0\tinside\t229\t348",
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"O42385\tTMHMM2.0\tTMhelix\t349\t371",
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"O42385\tTMHMM2.0\toutside\t372\t380",
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"O42385\tTMHMM2.0\tTMhelix\t381\t403",
|
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"O42385\tTMHMM2.0\tinside\t404\t423"].join("\n")
|
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assert_equal(str, @obj.to_s)
|
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end
|
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|
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end # TestTMHMMReport
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|
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class TestTMHMMTMH < Test::Unit::TestCase
|
98
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|
99
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def setup
|
100
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@obj = Bio::TMHMM::Report.new(TMHMMReport).tmhs.first
|
101
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end
|
102
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|
103
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def test_entry_id
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assert_equal('O42385', @obj.entry_id)
|
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end
|
106
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|
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def test_version
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assert_equal('TMHMM2.0', @obj.version)
|
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end
|
110
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|
111
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def test_status
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assert_equal('outside', @obj.status)
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end
|
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|
115
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def test_range
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assert_equal(1..46, @obj.range)
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end
|
118
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|
119
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def test_pos
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assert_equal(1..46, @obj.pos)
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end
|
122
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|
123
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end # class TestTMHMMTMH
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|
125
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end
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#
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2
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# test/unit/bio/data/test_aa.rb - Unit test for Bio::AminoAcid
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3
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#
|
4
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# Copyright:: Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
|
5
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# License:: The Ruby License
|
6
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#
|
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# $Id: test_aa.rb,v 1.7 2007/04/06 04:46:36 k Exp $
|
8
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#
|
9
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+
|
10
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require 'pathname'
|
11
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
|
12
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$:.unshift(libpath) unless $:.include?(libpath)
|
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|
14
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require 'test/unit'
|
15
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require 'bio/data/aa'
|
16
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|
17
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module Bio
|
18
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class TestAAConstants < Test::Unit::TestCase
|
19
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def test_bio_aminoacid
|
20
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+
assert_equal('Ala', Bio::AminoAcid['A'])
|
21
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+
end
|
22
|
+
end
|
23
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+
|
24
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+
|
25
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class TestAA < Test::Unit::TestCase
|
26
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+
def setup
|
27
|
+
@obj = Bio::AminoAcid.new
|
28
|
+
end
|
29
|
+
|
30
|
+
def test_13
|
31
|
+
assert_equal("Ala", @obj['A'])
|
32
|
+
end
|
33
|
+
|
34
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def test_1n
|
35
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assert_equal('alanine', @obj.name('A'))
|
36
|
+
end
|
37
|
+
|
38
|
+
def test_to_1_name
|
39
|
+
assert_equal('A', @obj.to_1('alanine'))
|
40
|
+
end
|
41
|
+
|
42
|
+
def test_to_1_3
|
43
|
+
assert_equal('A', @obj.to_1('Ala'))
|
44
|
+
end
|
45
|
+
|
46
|
+
def test_to_1_1
|
47
|
+
assert_equal('A', @obj.to_1('A'))
|
48
|
+
end
|
49
|
+
|
50
|
+
def test_to_3_name
|
51
|
+
assert_equal('Ala', @obj.to_3('alanine'))
|
52
|
+
end
|
53
|
+
|
54
|
+
def test_to_3_3
|
55
|
+
assert_equal('Ala', @obj.to_3('Ala'))
|
56
|
+
end
|
57
|
+
|
58
|
+
def test_to_3_1
|
59
|
+
assert_equal('Ala', @obj.to_3('A'))
|
60
|
+
end
|
61
|
+
|
62
|
+
def test_one2three
|
63
|
+
assert_equal('Ala', @obj.one2three('A'))
|
64
|
+
end
|
65
|
+
|
66
|
+
def test_three2one
|
67
|
+
assert_equal('A', @obj.three2one('Ala'))
|
68
|
+
end
|
69
|
+
|
70
|
+
def test_one2name
|
71
|
+
assert_equal('alanine', @obj.one2name('A'))
|
72
|
+
end
|
73
|
+
|
74
|
+
def test_name2one
|
75
|
+
assert_equal('A', @obj.name2one('alanine'))
|
76
|
+
end
|
77
|
+
|
78
|
+
def test_three2name
|
79
|
+
assert_equal('alanine', @obj.three2name('Ala'))
|
80
|
+
end
|
81
|
+
|
82
|
+
def test_name2three
|
83
|
+
assert_equal('Ala', @obj.name2three('alanine'))
|
84
|
+
end
|
85
|
+
|
86
|
+
def test_to_re
|
87
|
+
assert_equal(/[DNB][EQZ]ACDEFGHIKLMNPQRSTVWYU/, @obj.to_re('BZACDEFGHIKLMNPQRSTVWYU'))
|
88
|
+
end
|
89
|
+
end
|
90
|
+
end
|
@@ -0,0 +1,107 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/data/test_codontable.rb - Unit test for Bio::CodonTable
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
|
5
|
+
# License:: The Ruby License
|
6
|
+
#
|
7
|
+
# $Id: test_codontable.rb,v 1.6 2007/04/05 23:35:43 trevor Exp $
|
8
|
+
#
|
9
|
+
|
10
|
+
require 'pathname'
|
11
|
+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
|
12
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
13
|
+
|
14
|
+
|
15
|
+
require 'test/unit'
|
16
|
+
require 'bio/data/codontable'
|
17
|
+
|
18
|
+
module Bio
|
19
|
+
class TestCodonTableConstants < Test::Unit::TestCase
|
20
|
+
def test_Definitions
|
21
|
+
assert(Bio::CodonTable::DEFINITIONS)
|
22
|
+
assert(Bio::CodonTable::DEFINITIONS[1], "Standard (Eukaryote)")
|
23
|
+
end
|
24
|
+
|
25
|
+
def test_Starts
|
26
|
+
assert(Bio::CodonTable::STARTS)
|
27
|
+
assert_equal(['ttg', 'ctg', 'atg', 'gtg'], Bio::CodonTable::STARTS[1])
|
28
|
+
end
|
29
|
+
|
30
|
+
def test_stops
|
31
|
+
assert(Bio::CodonTable::STOPS)
|
32
|
+
assert_equal(['taa', 'tag', 'tga'], Bio::CodonTable::STOPS[1])
|
33
|
+
end
|
34
|
+
|
35
|
+
def test_Tables
|
36
|
+
assert(Bio::CodonTable::TABLES)
|
37
|
+
end
|
38
|
+
end
|
39
|
+
|
40
|
+
|
41
|
+
class TestCodonTable < Test::Unit::TestCase
|
42
|
+
|
43
|
+
def setup
|
44
|
+
@ct = Bio::CodonTable[1]
|
45
|
+
end
|
46
|
+
|
47
|
+
def test_self_accessor
|
48
|
+
assert(Bio::CodonTable[1])
|
49
|
+
end
|
50
|
+
|
51
|
+
def test_self_copy
|
52
|
+
assert(Bio::CodonTable.copy(1))
|
53
|
+
end
|
54
|
+
|
55
|
+
def test_table
|
56
|
+
assert(@ct.table)
|
57
|
+
end
|
58
|
+
|
59
|
+
def test_definition
|
60
|
+
assert_equal("Standard (Eukaryote)", @ct.definition)
|
61
|
+
end
|
62
|
+
|
63
|
+
def test_start
|
64
|
+
assert_equal(['ttg', 'ctg', 'atg', 'gtg'], @ct.start)
|
65
|
+
end
|
66
|
+
|
67
|
+
def test_stop
|
68
|
+
assert_equal(['taa', 'tag', 'tga'], @ct.stop)
|
69
|
+
end
|
70
|
+
|
71
|
+
def test_accessor #[]
|
72
|
+
assert_equal('M', @ct['atg'])
|
73
|
+
end
|
74
|
+
|
75
|
+
def test_set_accessor #[]=
|
76
|
+
alternative = 'Y'
|
77
|
+
@ct['atg'] = alternative
|
78
|
+
assert_equal(alternative, @ct['atg'])
|
79
|
+
@ct['atg'] = 'M'
|
80
|
+
assert_equal('M', @ct['atg'])
|
81
|
+
end
|
82
|
+
|
83
|
+
def test_each
|
84
|
+
assert(@ct.each {|x| })
|
85
|
+
end
|
86
|
+
|
87
|
+
def test_revtrans
|
88
|
+
assert_equal(['atg'], @ct.revtrans('M'))
|
89
|
+
end
|
90
|
+
|
91
|
+
def test_start_codon?
|
92
|
+
assert_equal(true, @ct.start_codon?('atg'))
|
93
|
+
assert_equal(false, @ct.start_codon?('taa'))
|
94
|
+
end
|
95
|
+
|
96
|
+
def test_stop_codon?
|
97
|
+
assert_equal(false, @ct.stop_codon?('atg'))
|
98
|
+
assert_equal(true, @ct.stop_codon?('taa'))
|
99
|
+
end
|
100
|
+
|
101
|
+
|
102
|
+
def test_Tables
|
103
|
+
assert_equal(@ct.table, Bio::CodonTable::TABLES[1])
|
104
|
+
end
|
105
|
+
|
106
|
+
end
|
107
|
+
end # module Bio
|
@@ -0,0 +1,80 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/data/test_na.rb - Unit test for Bio::NucleicAcid
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2005,2006 Mitsuteru Nakao <n@bioruby.org>
|
5
|
+
# License:: The Ruby License
|
6
|
+
#
|
7
|
+
# $Id: test_na.rb,v 1.9 2007/04/05 23:35:43 trevor Exp $
|
8
|
+
#
|
9
|
+
|
10
|
+
require 'pathname'
|
11
|
+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
|
12
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
13
|
+
|
14
|
+
require 'test/unit'
|
15
|
+
require 'bio/data/na'
|
16
|
+
|
17
|
+
module Bio
|
18
|
+
|
19
|
+
class TestNAConstants < Test::Unit::TestCase
|
20
|
+
def test_NAMES
|
21
|
+
assert_equal('a', Bio::NucleicAcid::NAMES['a'])
|
22
|
+
end
|
23
|
+
|
24
|
+
def test_NAMES_1_to_name
|
25
|
+
assert_equal('Adenine', Bio::NucleicAcid::NAMES['A'])
|
26
|
+
end
|
27
|
+
|
28
|
+
def test_WEIGHT
|
29
|
+
mw = 135.15
|
30
|
+
assert_equal(mw, Bio::NucleicAcid::WEIGHT['a'])
|
31
|
+
assert_equal(mw, Bio::NucleicAcid::WEIGHT[:adenine])
|
32
|
+
end
|
33
|
+
end
|
34
|
+
|
35
|
+
|
36
|
+
class TestNA < Test::Unit::TestCase
|
37
|
+
|
38
|
+
def setup
|
39
|
+
@obj = Bio::NucleicAcid.new
|
40
|
+
end
|
41
|
+
|
42
|
+
def test_to_re
|
43
|
+
re = /[tcy][agr][atw][gcw][tgk][acm][tgcyskb][atgrwkd][agcmrsv][atgcyrwskmbdhvn]atgc/
|
44
|
+
str = 'yrwskmbdvnatgc'
|
45
|
+
str0 = str.clone
|
46
|
+
assert_equal(re, @obj.to_re(str))
|
47
|
+
assert_equal(str0, str)
|
48
|
+
assert_equal(re, Bio::NucleicAcid.to_re(str))
|
49
|
+
end
|
50
|
+
|
51
|
+
|
52
|
+
def test_weight
|
53
|
+
mw = 135.15
|
54
|
+
assert_equal(mw, @obj.weight('a'))
|
55
|
+
assert_equal(mw, Bio::NucleicAcid.weight('a'))
|
56
|
+
end
|
57
|
+
|
58
|
+
def test_weight_rna
|
59
|
+
mw = 135.15
|
60
|
+
assert_equal(mw, @obj.weight('A', true))
|
61
|
+
assert_equal(mw, Bio::NucleicAcid.weight('A', true))
|
62
|
+
end
|
63
|
+
|
64
|
+
|
65
|
+
def test_accessor
|
66
|
+
assert_equal('Adenine', @obj['A'])
|
67
|
+
end
|
68
|
+
|
69
|
+
def test_names
|
70
|
+
assert_equal(Bio::NucleicAcid::NAMES, @obj.names)
|
71
|
+
end
|
72
|
+
def test_na
|
73
|
+
assert_equal(Bio::NucleicAcid::NAMES, @obj.na)
|
74
|
+
end
|
75
|
+
|
76
|
+
def test_name
|
77
|
+
assert_equal('Adenine', @obj.name('A'))
|
78
|
+
end
|
79
|
+
end
|
80
|
+
end
|