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 +1,101 @@
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#
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# = bio/shell/plugin/flatfile.rb - plugin for flatfile database
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#
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4
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# Copyright:: Copyright (C) 2005
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5
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# Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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7
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#
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8
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# $Id: flatfile.rb,v 1.13 2007/04/05 23:45:11 trevor Exp $
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9
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+
#
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10
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+
|
11
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module Bio::Shell
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|
13
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private
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15
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def flatfile(filename)
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if block_given?
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Bio::FlatFile.auto(filename) do |flat|
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flat.each do |entry|
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yield flat.entry_raw
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end
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end
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else
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entry = ''
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Bio::FlatFile.auto(filename) do |flat|
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flat.next_entry
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entry = flat.entry_raw
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end
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return entry
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end
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end
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|
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def flatauto(filename)
|
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if block_given?
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Bio::FlatFile.auto(filename) do |flat|
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flat.each do |entry|
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yield entry
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end
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end
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else
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entry = ''
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Bio::FlatFile.auto(filename) do |flat|
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entry = flat.next_entry
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end
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return entry
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end
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end
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def flatparse(entry)
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if cls = Bio::FlatFile.autodetect(entry)
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return cls.new(entry)
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end
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end
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def flatfasta(fastafile, *flatfiles)
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puts "Saving fasta file (#{fastafile}) ... "
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File.open(fastafile, "w") do |fasta|
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flatfiles.each do |flatfile|
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puts " converting -- #{flatfile}"
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Bio::FlatFile.auto(flatfile) do |flat|
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flat.each do |entry|
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header = "#{entry.entry_id} #{entry.definition}"
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fasta.puts entry.seq.to_fasta(header, 50)
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end
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end
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end
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end
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puts "done"
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end
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|
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def flatindex(dbname, *flatfiles)
|
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begin
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dir = Bio::Shell.create_flat_dir(dbname)
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print "Creating BioFlat index (#{dir}) ... "
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bdb = format = options = nil
|
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Bio::FlatFileIndex.makeindex(bdb, dir, format, options, *flatfiles)
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puts "done"
|
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+
rescue
|
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+
warn "Error: Failed to create index (#{dir}) : #{$!}"
|
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+
end
|
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+
end
|
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+
|
82
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def flatsearch(dbname, keyword)
|
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+
dir = Bio::Shell.find_flat_dir(dbname)
|
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+
unless dir
|
85
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+
warn "Error: Failed to open database (#{dbname})"
|
86
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+
return
|
87
|
+
end
|
88
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+
entry = ''
|
89
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+
Bio::FlatFileIndex.open(dir) do |db|
|
90
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+
if results = db.include?(keyword)
|
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results.each do |entry_id|
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+
entry << db.search_primary(entry_id).to_s
|
93
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+
end
|
94
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+
else
|
95
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+
warn "Error: No hits found in #{dbname} (#{keyword})"
|
96
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+
end
|
97
|
+
end
|
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return entry
|
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end
|
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|
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end
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@@ -0,0 +1,181 @@
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#
|
2
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# = bio/shell/plugin/keggapi.rb - plugin for KEGG API
|
3
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#
|
4
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# Copyright:: Copyright (C) 2005
|
5
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# Toshiaki Katayama <k@bioruby.org>
|
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# License:: The Ruby License
|
7
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+
#
|
8
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# $Id: keggapi.rb,v 1.12 2007/04/05 23:35:41 trevor Exp $
|
9
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+
#
|
10
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+
|
11
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module Bio::Shell
|
12
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|
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module Private
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|
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module_function
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|
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def keggapi_definition2tab(list)
|
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ary = []
|
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list.each do |entry|
|
20
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ary << "#{entry.entry_id}\t#{entry.definition}"
|
21
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+
end
|
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return ary
|
23
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end
|
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end
|
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|
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private
|
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|
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def keggapi(wsdl = nil)
|
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if wsdl
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@keggapi = Bio::KEGG::API.new(wsdl)
|
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+
else
|
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@keggapi ||= Bio::KEGG::API.new
|
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end
|
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return @keggapi
|
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end
|
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|
37
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# DBGET
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def binfo(db = "all")
|
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result = keggapi.binfo(db)
|
41
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puts result
|
42
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return result
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+
end
|
44
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|
45
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def bfind(str)
|
46
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result = keggapi.bfind(str)
|
47
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return result
|
48
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+
end
|
49
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+
|
50
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+
def bget(str)
|
51
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+
result = keggapi.bget(str)
|
52
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+
if block_given?
|
53
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+
yield result
|
54
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+
else
|
55
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puts result
|
56
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return result
|
57
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+
end
|
58
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+
end
|
59
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+
|
60
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def btit(str)
|
61
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+
result = keggapi.btit(str)
|
62
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+
puts result
|
63
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+
return result
|
64
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+
end
|
65
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+
|
66
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def bconv(str)
|
67
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result = keggapi.bconv(str)
|
68
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+
puts result
|
69
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+
return result
|
70
|
+
end
|
71
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+
|
72
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+
# DATABASES
|
73
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+
|
74
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+
def keggdbs
|
75
|
+
list = keggapi.list_databases
|
76
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+
result = Bio::Shell::Private.keggapi_definition2tab(list).join("\n")
|
77
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puts result
|
78
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+
return list.map {|x| x.entry_id}
|
79
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+
end
|
80
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+
|
81
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+
def keggorgs
|
82
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+
list = keggapi.list_organisms
|
83
|
+
result = Bio::Shell::Private.keggapi_definition2tab(list).sort.join("\n")
|
84
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+
puts result
|
85
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return list.map {|x| x.entry_id}
|
86
|
+
end
|
87
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+
|
88
|
+
def keggpathways(org = "map")
|
89
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+
list = keggapi.list_pathways(org)
|
90
|
+
result = Bio::Shell::Private.keggapi_definition2tab(list).join("\n")
|
91
|
+
puts result
|
92
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+
return list.map {|x| x.entry_id}
|
93
|
+
end
|
94
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+
|
95
|
+
# use KEGG DAS insetad
|
96
|
+
def kegggenomeseq(org)
|
97
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+
result = ""
|
98
|
+
require 'net/ftp'
|
99
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+
Net::FTP.open("ftp.genome.jp", "anonymous") do |ftp|
|
100
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+
path = "/pub/kegg/genomes/#{org}"
|
101
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+
list = ftp.nlst(path)
|
102
|
+
file = list.grep(/.*genome$/).shift
|
103
|
+
if file
|
104
|
+
open("ftp://ftp.genome.jp/#{file}") do |file|
|
105
|
+
result = file.read
|
106
|
+
end
|
107
|
+
end
|
108
|
+
end
|
109
|
+
return result
|
110
|
+
end
|
111
|
+
|
112
|
+
end
|
113
|
+
|
114
|
+
=begin
|
115
|
+
|
116
|
+
== BioRuby extensions
|
117
|
+
|
118
|
+
--- get_all_best_best_neighbors_by_gene(genes_id)
|
119
|
+
--- get_all_best_neighbors_by_gene(genes_id)
|
120
|
+
--- get_all_reverse_best_neighbors_by_gene(genes_id)
|
121
|
+
--- get_all_paralogs_by_gene(genes_id)
|
122
|
+
--- get_all_genes_by_motifs(motif_id_list)
|
123
|
+
--- get_all_oc_members_by_gene(genes_id)
|
124
|
+
--- get_all_pc_members_by_gene(genes_id)
|
125
|
+
--- get_all_genes_by_organism(org)
|
126
|
+
--- get_all_linkdb_by_entry(entry_id, db)
|
127
|
+
--- save_image(url, filename = nil)
|
128
|
+
--- get_entries(ary = [])
|
129
|
+
--- get_aaseqs(ary = [])
|
130
|
+
--- get_naseqs(ary = [])
|
131
|
+
--- get_definitions(ary = [])
|
132
|
+
|
133
|
+
== Original KEGG API methods
|
134
|
+
|
135
|
+
--- get_linkdb_by_entry(entry_id, db, start, max_results)
|
136
|
+
--- get_best_best_neighbors_by_gene(genes_id, start, max_results)
|
137
|
+
--- get_best_neighbors_by_gene(genes_id, start, max_results)
|
138
|
+
--- get_reverse_best_neighbors_by_gene(genes_id, start, max_results)
|
139
|
+
--- get_paralogs_by_gene(genes_id, start, max_results)
|
140
|
+
--- get_motifs_by_gene(genes_id, db)
|
141
|
+
--- get_genes_by_motifs(motif_id_list, start, max_results)
|
142
|
+
--- get_ko_by_gene(genes_id)
|
143
|
+
--- get_ko_by_ko_class(ko_class_id)
|
144
|
+
--- get_genes_by_ko_class(ko_class_id, org, start, max_results)
|
145
|
+
--- get_genes_by_ko(ko_id, org)
|
146
|
+
--- get_oc_members_by_gene(genes_id, start, max_results)
|
147
|
+
--- get_pc_members_by_gene(genes_id, start, max_results)
|
148
|
+
--- mark_pathway_by_objects(pathway_id, object_id_list)
|
149
|
+
--- color_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
|
150
|
+
--- get_html_of_marked_pathway_by_objects(pathway_id, object_id_list)
|
151
|
+
--- get_html_of_colored_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
|
152
|
+
--- get_genes_by_pathway(pathway_id)
|
153
|
+
--- get_enzymes_by_pathway(pathway_id)
|
154
|
+
--- get_compounds_by_pathway(pathway_id)
|
155
|
+
--- get_glycans_by_pathway(pathway_id)
|
156
|
+
--- get_reactions_by_pathway(pathway_id)
|
157
|
+
--- get_kos_by_pathway(pathway_id)
|
158
|
+
--- get_pathways_by_genes(genes_id_list)
|
159
|
+
--- get_pathways_by_enzymes(enzyme_id_list)
|
160
|
+
--- get_pathways_by_compounds(compound_id_list)
|
161
|
+
--- get_pathways_by_glycans(glycan_id_list)
|
162
|
+
--- get_pathways_by_reactions(reaction_id_list)
|
163
|
+
--- get_pathways_by_kos(ko_id_list, org)
|
164
|
+
--- get_linked_pathways(pathway_id)
|
165
|
+
--- get_genes_by_enzyme(enzyme_id, org)
|
166
|
+
--- get_enzymes_by_gene(genes_id)
|
167
|
+
--- get_enzymes_by_compound(compound_id)
|
168
|
+
--- get_enzymes_by_glycan(glycan_id)
|
169
|
+
--- get_enzymes_by_reaction(reaction_id)
|
170
|
+
--- get_compounds_by_enzyme(enzyme_id)
|
171
|
+
--- get_compounds_by_reaction(reaction_id)
|
172
|
+
--- get_glycans_by_enzyme(enzyme_id)
|
173
|
+
--- get_glycans_by_reaction(reaction_id)
|
174
|
+
--- get_reactions_by_enzyme(enzyme_id)
|
175
|
+
--- get_reactions_by_compound(compound_id)
|
176
|
+
--- get_reactions_by_glycan(glycan_id)
|
177
|
+
--- get_genes_by_organism(org, start, max_results)
|
178
|
+
--- get_number_of_genes_by_organism(org)
|
179
|
+
--- convert_mol_to_kcf(mol_text)
|
180
|
+
|
181
|
+
=end
|
@@ -0,0 +1,430 @@
|
|
1
|
+
#
|
2
|
+
# = bio/shell/plugin/midi.rb - Sequence to MIDI converter
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2003, 2005
|
5
|
+
# Natsuhiro Ichinose <ichinose@genome.ist.i.kyoto-u.ac.jp>,
|
6
|
+
# Toshiaki Katayama <k@bioruby.org>
|
7
|
+
# License:: The Ruby License
|
8
|
+
#
|
9
|
+
# $Id: midi.rb,v 1.9 2007/04/05 23:35:41 trevor Exp $
|
10
|
+
#
|
11
|
+
|
12
|
+
#--
|
13
|
+
# *TODO*
|
14
|
+
# - add "Ohno" style
|
15
|
+
# - add a accessor to drum pattern
|
16
|
+
# - add a new feature to select music style (pop, trans, ryukyu, ...)
|
17
|
+
# - what is the base?
|
18
|
+
#++
|
19
|
+
|
20
|
+
class Bio::Sequence::NA
|
21
|
+
|
22
|
+
class MidiTrack
|
23
|
+
|
24
|
+
MidiProg = [
|
25
|
+
"Acoustic Grand Piano",
|
26
|
+
"Bright Acoustic Piano",
|
27
|
+
"Electric grand Piano",
|
28
|
+
"Honky Tonk Piano",
|
29
|
+
"Eiectric Piano 1",
|
30
|
+
"Electric Piano 2",
|
31
|
+
"Harpsichord",
|
32
|
+
"Clavinet",
|
33
|
+
"Celesra",
|
34
|
+
"Glockenspiel",
|
35
|
+
"Music Box",
|
36
|
+
"Vibraphone",
|
37
|
+
"Marimba",
|
38
|
+
"Xylophone",
|
39
|
+
"Tubular bells",
|
40
|
+
"Dulcimer",
|
41
|
+
"Drawbar Organ",
|
42
|
+
"Percussive Organ",
|
43
|
+
"Rock Organ",
|
44
|
+
"Church Organ",
|
45
|
+
"Reed Organ",
|
46
|
+
"Accordion",
|
47
|
+
"Harmonica",
|
48
|
+
"Tango Accordion",
|
49
|
+
"Nylon Accustic Guitar",
|
50
|
+
"Steel Acoustic Guitar",
|
51
|
+
"Jazz Electric Guitar",
|
52
|
+
"Ciean Electric Guitar",
|
53
|
+
"Muted Electric Guitar",
|
54
|
+
"Overdrive Guitar",
|
55
|
+
"Distorted Guitar",
|
56
|
+
"Guitar Harmonics",
|
57
|
+
"Acoustic Bass",
|
58
|
+
"Electric Fingered Bass",
|
59
|
+
"Electric Picked Bass",
|
60
|
+
"Fretless Bass",
|
61
|
+
"Slap Bass 1",
|
62
|
+
"Slap Bass 2",
|
63
|
+
"Syn Bass 1",
|
64
|
+
"Syn Bass 2",
|
65
|
+
"Violin",
|
66
|
+
"Viola",
|
67
|
+
"Cello",
|
68
|
+
"Contrabass",
|
69
|
+
"Tremolo Strings",
|
70
|
+
"Pizzicato Strings",
|
71
|
+
"Orchestral Harp",
|
72
|
+
"Timpani",
|
73
|
+
"String Ensemble 1",
|
74
|
+
"String Ensemble 2 (Slow)",
|
75
|
+
"Syn Strings 1",
|
76
|
+
"Syn Strings 2",
|
77
|
+
"Choir Aahs",
|
78
|
+
"Voice Oohs",
|
79
|
+
"Syn Choir",
|
80
|
+
"Orchestral Hit",
|
81
|
+
"Trumpet",
|
82
|
+
"Trombone",
|
83
|
+
"Tuba",
|
84
|
+
"Muted Trumpet",
|
85
|
+
"French Horn",
|
86
|
+
"Brass Section",
|
87
|
+
"Syn Brass 1",
|
88
|
+
"Syn Brass 2",
|
89
|
+
"Soprano Sax",
|
90
|
+
"Alto Sax",
|
91
|
+
"Tenor Sax",
|
92
|
+
"Baritone Sax",
|
93
|
+
"Oboe",
|
94
|
+
"English Horn",
|
95
|
+
"Bassoon",
|
96
|
+
"Clarinet",
|
97
|
+
"Piccolo",
|
98
|
+
"Flute",
|
99
|
+
"Recorder",
|
100
|
+
"Pan Flute",
|
101
|
+
"Bottle Blow",
|
102
|
+
"Shakuhachi",
|
103
|
+
"Whistle",
|
104
|
+
"Ocarina",
|
105
|
+
"Syn Square Wave",
|
106
|
+
"Syn Sawtooth Wave",
|
107
|
+
"Syn Calliope",
|
108
|
+
"Syn Chiff",
|
109
|
+
"Syn Charang",
|
110
|
+
"Syn Voice",
|
111
|
+
"Syn Fifths Sawtooth Wave",
|
112
|
+
"Syn Brass & Lead",
|
113
|
+
"New Age Syn Pad",
|
114
|
+
"Warm Syn Pad",
|
115
|
+
"Polysynth Syn Pad",
|
116
|
+
"Choir Syn Pad",
|
117
|
+
"Bowed Syn Pad",
|
118
|
+
"Metal Syn Pad",
|
119
|
+
"Halo Syn Pad",
|
120
|
+
"Sweep Syn Pad",
|
121
|
+
"SFX Rain",
|
122
|
+
"SFX Soundtrack",
|
123
|
+
"SFX Crystal",
|
124
|
+
"SFX Atmosphere",
|
125
|
+
"SFX Brightness",
|
126
|
+
"SFX Goblins",
|
127
|
+
"SFX Echoes",
|
128
|
+
"SFX Sci-fi",
|
129
|
+
"Sitar",
|
130
|
+
"Banjo",
|
131
|
+
"Shamisen",
|
132
|
+
"Koto",
|
133
|
+
"Kalimba",
|
134
|
+
"Bag Pipe",
|
135
|
+
"Fiddle",
|
136
|
+
"Shanai",
|
137
|
+
"Tinkle Bell",
|
138
|
+
"Agogo",
|
139
|
+
"Steel Drums",
|
140
|
+
"Woodblock",
|
141
|
+
"Taiko Drum",
|
142
|
+
"Melodic Tom",
|
143
|
+
"Syn Drum",
|
144
|
+
"Reverse Cymbal",
|
145
|
+
"Guitar Fret Noise",
|
146
|
+
"Breath Noise",
|
147
|
+
"Seashore",
|
148
|
+
"Bird Tweet",
|
149
|
+
"Telephone Ring",
|
150
|
+
"Helicopter",
|
151
|
+
"Applause",
|
152
|
+
"Gun Shot"
|
153
|
+
]
|
154
|
+
|
155
|
+
Styles = {
|
156
|
+
# "Ohno" => {
|
157
|
+
# # http://home.hiroshima-u.ac.jp/cato/bunkakoryuron.html
|
158
|
+
# },
|
159
|
+
"Ichinose" => {
|
160
|
+
:tempo => 120,
|
161
|
+
:scale => [0, 2, 4, 5, 7, 9, 11],
|
162
|
+
:tones => [
|
163
|
+
{:prog => 9, :base => 60, :range => 2},
|
164
|
+
{:prog => 13, :base => 48, :range => 2},
|
165
|
+
{:prog => 41, :base => 48, :range => 2},
|
166
|
+
{:prog => 44, :base => 36, :range => 2},
|
167
|
+
]
|
168
|
+
},
|
169
|
+
"Okinawan" => {
|
170
|
+
:tempo => 180,
|
171
|
+
:scale => [0,4,5,7,11],
|
172
|
+
:tones => [
|
173
|
+
{:prog => MidiProg.index("Harpsichord"), :base => 60, :range => 2},
|
174
|
+
{:prog => MidiProg.index("Dulcimer"), :base => 48, :range => 2},
|
175
|
+
{:prog => MidiProg.index("Fretless Base"), :base => 36, :range => 1},
|
176
|
+
]
|
177
|
+
},
|
178
|
+
"Major" => {
|
179
|
+
:scale => [0,2,4,5,7,9,11],
|
180
|
+
},
|
181
|
+
"Minor" => {
|
182
|
+
:scale => [0,2,3,5,7,9,10],
|
183
|
+
},
|
184
|
+
"Harmonic minor" => {
|
185
|
+
:scale => [0,2,3,5,7,9,11],
|
186
|
+
},
|
187
|
+
"Whole tone" => {
|
188
|
+
:scale => [0,2,4,6,8,10],
|
189
|
+
},
|
190
|
+
"Half tone" => {
|
191
|
+
:scale => [0,1,2,3,4,5,6,7,8,9,10,11],
|
192
|
+
},
|
193
|
+
"Indian" => {
|
194
|
+
:scale => [0,1,4,5,7,8,11],
|
195
|
+
},
|
196
|
+
"Arabic" => {
|
197
|
+
:scale => [0,2,3,6,7,8,11],
|
198
|
+
},
|
199
|
+
"Spanish" => {
|
200
|
+
:scale => [0,1,3,4,5,7,8,10],
|
201
|
+
},
|
202
|
+
"Japanese" => {
|
203
|
+
:scale => [0,2,5,7,9],
|
204
|
+
},
|
205
|
+
}
|
206
|
+
|
207
|
+
def initialize(channel = 0, program = nil, base = nil, range = nil, scale = nil)
|
208
|
+
@channel = channel & 0xff
|
209
|
+
@program = program || 0
|
210
|
+
@base = base || 60
|
211
|
+
@range = range || 2
|
212
|
+
@scale = scale || [0, 2, 4, 5, 7, 9, 11]
|
213
|
+
|
214
|
+
@tunes = []
|
215
|
+
@tune = 0
|
216
|
+
@code = []
|
217
|
+
@time = 0
|
218
|
+
|
219
|
+
@range.times do |i|
|
220
|
+
@scale.each do |c|
|
221
|
+
@tunes.push c + i * 12
|
222
|
+
end
|
223
|
+
end
|
224
|
+
|
225
|
+
@ttype = {
|
226
|
+
'aa' => 1, 'at' => 0, 'ac' => 3, 'ag' => -1,
|
227
|
+
'ta' => 0, 'tt' => -1, 'tc' => 1, 'tg' => -2,
|
228
|
+
'ca' => 2, 'ct' => 1, 'cc' => 2, 'cg' => 6,
|
229
|
+
'ga' => -1, 'gt' => -3, 'gc' => 0, 'gg' => -2,
|
230
|
+
}
|
231
|
+
@dtype = [
|
232
|
+
{ 'aa' => 2, 'at' => 4, 'ac' => 4, 'ag' => 2,
|
233
|
+
'ta' => 2, 'tt' => 4, 'tc' => 4, 'tg' => 2,
|
234
|
+
'ca' => 2, 'ct' => 3, 'cc' => 1, 'cg' => 2,
|
235
|
+
'ga' => 1, 'gt' => 2, 'gc' => 2, 'gg' => 3,
|
236
|
+
},
|
237
|
+
{ 'aa' => 3, 'at' => 3, 'ac' => 2, 'ag' => 3,
|
238
|
+
'ta' => 3, 'tt' => 3, 'tc' => 2, 'tg' => 2,
|
239
|
+
'ca' => 3, 'ct' => 2, 'cc' => 1, 'cg' => 1,
|
240
|
+
'ga' => 1, 'gt' => 1, 'gc' => 1, 'gg' => 1,
|
241
|
+
},
|
242
|
+
{ 'aa' => 2, 'at' => 2, 'ac' => 2, 'ag' => 2,
|
243
|
+
'ta' => 1, 'tt' => 1, 'tc' => 2, 'tg' => 2,
|
244
|
+
'ca' => 2, 'ct' => 2, 'cc' => 2, 'cg' => 3,
|
245
|
+
'ga' => 2, 'gt' => 2, 'gc' => 3, 'gg' => 1,
|
246
|
+
},
|
247
|
+
{ 'aa' => 1, 'at' => 1, 'ac' => 1, 'ag' => 1,
|
248
|
+
'ta' => 1, 'tt' => 1, 'tc' => 1, 'tg' => 1,
|
249
|
+
'ca' => 1, 'ct' => 1, 'cc' => 1, 'cg' => 3,
|
250
|
+
'ga' => 1, 'gt' => 1, 'gc' => 1, 'gg' => 1,
|
251
|
+
},
|
252
|
+
]
|
253
|
+
|
254
|
+
@code.concat [0x00, 0xc0 | (@channel & 0xff)]
|
255
|
+
@code.concat icode(@program & 0xff, 1)
|
256
|
+
end
|
257
|
+
|
258
|
+
def icode(num, n)
|
259
|
+
code = []
|
260
|
+
n.times do |i|
|
261
|
+
code.push num & 0xff
|
262
|
+
num >>= 8
|
263
|
+
end
|
264
|
+
code.reverse
|
265
|
+
end
|
266
|
+
|
267
|
+
def rcode(num)
|
268
|
+
code = []
|
269
|
+
code.push num & 0x7f
|
270
|
+
while num > 0x7f
|
271
|
+
num >>= 7
|
272
|
+
code.push num & 0x7f | 0x80
|
273
|
+
end
|
274
|
+
code.reverse
|
275
|
+
end
|
276
|
+
|
277
|
+
def c2s(code)
|
278
|
+
ans = ""
|
279
|
+
code.each do |c|
|
280
|
+
ans += c.chr
|
281
|
+
end
|
282
|
+
ans
|
283
|
+
end
|
284
|
+
|
285
|
+
def push(s)
|
286
|
+
tt = @time % 4
|
287
|
+
t = @ttype[s[0, 2]]
|
288
|
+
d = @dtype[tt][s[2, 2]]
|
289
|
+
if !t.nil? && !d.nil?
|
290
|
+
@tune += t
|
291
|
+
@tune %= @tunes.length
|
292
|
+
if tt == 0
|
293
|
+
vel = 90
|
294
|
+
elsif tt == 1 && d > 1
|
295
|
+
vel = 100
|
296
|
+
elsif tt == 2
|
297
|
+
vel = 60
|
298
|
+
else
|
299
|
+
vel = 50
|
300
|
+
end
|
301
|
+
@code.concat rcode(1)
|
302
|
+
@code.concat [0x90 | @channel, @tunes[@tune] + @base, vel]
|
303
|
+
@code.concat rcode(240 * d)
|
304
|
+
@code.concat [0x80 | @channel, @tunes[@tune] + @base, 0]
|
305
|
+
@time += d
|
306
|
+
end
|
307
|
+
end
|
308
|
+
|
309
|
+
def push_silent(d)
|
310
|
+
@code.concat rcode(1)
|
311
|
+
@code.concat [0x90 | @channel, 0, 0]
|
312
|
+
@code.concat rcode(240 * d)
|
313
|
+
@code.concat [0x80 | @channel, 0, 0]
|
314
|
+
@time += d;
|
315
|
+
end
|
316
|
+
|
317
|
+
def encode
|
318
|
+
ans ="MTrk"
|
319
|
+
ans += c2s(icode(@code.length + 4, 4))
|
320
|
+
ans += c2s(@code)
|
321
|
+
ans += c2s([0x00, 0xff, 0x2f, 0x00])
|
322
|
+
ans
|
323
|
+
end
|
324
|
+
|
325
|
+
def header(num, tempo = 120)
|
326
|
+
ans = "MThd"
|
327
|
+
ans += c2s(icode(6, 4))
|
328
|
+
ans += c2s(icode(1, 2))
|
329
|
+
ans += c2s(icode(num + 1, 2))
|
330
|
+
ans += c2s(icode(480, 2))
|
331
|
+
ans += "MTrk"
|
332
|
+
ans += c2s(icode(11, 4))
|
333
|
+
ans += c2s([0x00, 0xff, 0x51, 0x03])
|
334
|
+
ans += c2s(icode(60000000 / tempo, 3))
|
335
|
+
ans += c2s([0x00, 0xff, 0x2f, 0x00])
|
336
|
+
ans
|
337
|
+
end
|
338
|
+
|
339
|
+
end # MidiTrack
|
340
|
+
|
341
|
+
|
342
|
+
# style:
|
343
|
+
# Hash of :tempo, :scale, :tones
|
344
|
+
# scale:
|
345
|
+
# C C# D D# E F F# G G# A A# B
|
346
|
+
# 0 1 2 3 4 5 6 7 8 9 10 11
|
347
|
+
# tones:
|
348
|
+
# Hash of :prog, :base, :range -- tone, vol? or len?, octaves
|
349
|
+
# drum:
|
350
|
+
# true (with rhythm part), false (without rhythm part)
|
351
|
+
def to_midi(style = {}, drum = true)
|
352
|
+
default = MidiTrack::Styles["Ichinose"]
|
353
|
+
if style.is_a?(String)
|
354
|
+
style = MidiTrack::Styles[style] || default
|
355
|
+
end
|
356
|
+
tempo = style[:tempo] || default[:tempo]
|
357
|
+
scale = style[:scale] || default[:scale]
|
358
|
+
tones = style[:tones] || default[:tones]
|
359
|
+
|
360
|
+
track = []
|
361
|
+
|
362
|
+
tones.each_with_index do |tone, i|
|
363
|
+
ch = i
|
364
|
+
ch += 1 if i >= 9 # skip rythm track
|
365
|
+
track.push MidiTrack.new(ch, tone[:prog], tone[:base], tone[:range], scale)
|
366
|
+
end
|
367
|
+
|
368
|
+
if drum
|
369
|
+
rhythm = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]
|
370
|
+
track.push(MidiTrack.new(9, 0, 35, 2, rhythm))
|
371
|
+
end
|
372
|
+
|
373
|
+
cur = 0
|
374
|
+
window_search(4) do |s|
|
375
|
+
track[cur % track.length].push(s)
|
376
|
+
cur += 1
|
377
|
+
end
|
378
|
+
|
379
|
+
track.each do |t|
|
380
|
+
t.push_silent(12)
|
381
|
+
end
|
382
|
+
|
383
|
+
ans = track[0].header(track.length, tempo)
|
384
|
+
track.each do |t|
|
385
|
+
ans += t.encode
|
386
|
+
end
|
387
|
+
return ans
|
388
|
+
end
|
389
|
+
|
390
|
+
end
|
391
|
+
|
392
|
+
|
393
|
+
module Bio::Shell
|
394
|
+
|
395
|
+
private
|
396
|
+
|
397
|
+
def midifile(filename, seq, *args)
|
398
|
+
begin
|
399
|
+
print "Saving MIDI file (#{filename}) ... "
|
400
|
+
File.open(filename, "w") do |file|
|
401
|
+
file.puts seq.to_midi(*args)
|
402
|
+
end
|
403
|
+
puts "done"
|
404
|
+
rescue
|
405
|
+
warn "Error: Failed to save (#{filename}) : #{$!}"
|
406
|
+
end
|
407
|
+
end
|
408
|
+
|
409
|
+
end
|
410
|
+
|
411
|
+
|
412
|
+
if $0 == __FILE__
|
413
|
+
|
414
|
+
# % for i in file*
|
415
|
+
# do
|
416
|
+
# ruby -r bio bio/shell/plugin/midi.rb $i ${i}.mid
|
417
|
+
# done
|
418
|
+
|
419
|
+
include Bio::Shell
|
420
|
+
|
421
|
+
seq_file = ARGV.shift
|
422
|
+
mid_file = ARGV.shift
|
423
|
+
|
424
|
+
Bio::FlatFile.auto(seq_file) do |ff|
|
425
|
+
ff.each do |f|
|
426
|
+
midifile(mid_file, f.naseq[0..1000])
|
427
|
+
end
|
428
|
+
end
|
429
|
+
end
|
430
|
+
|