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 +1,157 @@
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#
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# = bio/compat/features.rb - Obsoleted Features class
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#
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# Copyright:: Copyright (c) 2002, 2005 Toshiaki Katayama <k@bioruby.org>
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# 2006 Jan Aerts <jan.aerts@bbsrc.ac.uk>
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# 2008 Naohisa Goto <ng@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: features.rb,v 1.1.2.2 2008/03/10 13:42:26 ngoto Exp $
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#
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# == Description
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#
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# The Bio::Features class was obsoleted after BioRuby 1.2.1.
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# To keep compatibility, some wrapper methods are provided in this file.
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# As the compatibility methods (and Bio::Features) will soon be removed,
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# Please change your code not to use Bio::Features.
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#
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# Note that Bio::Feature is different from the Bio::Features.
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# Bio::Feature still exists to store DDBJ/GenBank/EMBL feature information.
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require 'bio/location'
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module Bio
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# = DESCRIPTION
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#
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# This class is OBSOLETED, and will soon be removed.
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# Instead of this class, an array is to be used.
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#
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#
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# Container for a list of Feature objects.
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#
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# = USAGE
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# # First, create some Bio::Feature objects
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# feature1 = Bio::Feature.new('intron','3627..4059')
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# feature2 = Bio::Feature.new('exon','4060..4236')
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# feature3 = Bio::Feature.new('intron','4237..4426')
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# feature4 = Bio::Feature.new('CDS','join(2538..3626,4060..4236)',
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# [ Bio::Feature::Qualifier.new('gene', 'CYP2D6'),
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# Bio::Feature::Qualifier.new('translation','MGXXTVMHLL...')
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# ])
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#
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# # And create a container for them
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# feature_container = Bio::Features.new([ feature1, feature2, feature3, feature4 ])
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#
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# # Iterate over all features and print
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# feature_container.each do |feature|
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# puts feature.feature + "\t" + feature.position
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# feature.each do |qualifier|
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# puts "- " + qualifier.qualifier + ": " + qualifier.value
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# end
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# end
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#
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# # Iterate only over CDS features and extract translated amino acid sequences
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# features.each("CDS") do |feature|
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# hash = feature.to_hash
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# name = hash["gene"] || hash["product"] || hash["note"]
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# aaseq = hash["translation"]
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# pos = feature.position
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# if name and seq
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# puts ">#{gene} #{feature.position}"
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# puts aaseq
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# end
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# end
|
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class Features
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# module to keep backward compatibility with obsoleted Bio::Features
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module BackwardCompatibility #:nodoc:
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# Backward compatibility with Bio::Features#features.
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# Now, features are stored in an array, and
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72
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# you should change your code not to use this method.
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def features
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warn 'Bio::Features is obsoleted. Now, features are stored in an array.'
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self
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end
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# Backward compatibility with Bio::Features#append.
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# Now, references are stored in an array, and
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# you should change your code not to use this method.
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def append(feature)
|
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warn 'Bio::Features is obsoleted. Now, features are stored in an array.'
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self.push(feature) if feature.is_a? Feature
|
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self
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end
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end #module BackwardCompatibility
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# This method should not be used.
|
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# Only for backward compatibility of existing code.
|
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#
|
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# Since Bio::Features is obsoleted,
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# Bio::Features.new not returns Bio::Features object,
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# but modifies given _ary_ and returns the _ary_.
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#
|
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# *Arguments*:
|
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# * (optional) __: Array of Bio::Feature objects
|
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# *Returns*:: the given array
|
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def self.new(ary = [])
|
99
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warn 'Bio::Features is obsoleted. Some methods are added to given array to keep backward compatibility.'
|
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ary.extend(BackwardCompatibility)
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ary
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end
|
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|
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# Normally, users can not call this method.
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#
|
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# Create a new Bio::Features object.
|
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#
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# *Arguments*:
|
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# * (optional) _list of features_: list of Bio::Feature objects
|
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# *Returns*:: Bio::Features object
|
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def initialize(ary = [])
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@features = ary
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end
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# Returns an Array of Feature objects.
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attr_accessor :features
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# Appends a Feature object to Features.
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#
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# *Arguments*:
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# * (required) _feature_: Bio::Feature object
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# *Returns*:: Bio::Features object
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def append(a)
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@features.push(a) if a.is_a? Feature
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return self
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end
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# Iterates on each feature object.
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#
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# *Arguments*:
|
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# * (optional) _key_: if specified, only iterates over features with this key
|
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def each(arg = nil)
|
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@features.each do |x|
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next if arg and x.feature != arg
|
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yield x
|
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end
|
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end
|
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|
139
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# Short cut for the Features#features[n]
|
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def [](*arg)
|
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@features[*arg]
|
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end
|
143
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|
144
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# Short cut for the Features#features.first
|
145
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def first
|
146
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@features.first
|
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end
|
148
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+
|
149
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# Short cut for the Features#features.last
|
150
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def last
|
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@features.last
|
152
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end
|
153
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|
154
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end # Features
|
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|
156
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end # Bio
|
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@@ -0,0 +1,128 @@
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#
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2
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# = bio/compat/references.rb - Obsoleted References class
|
3
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#
|
4
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# Copyright:: Copyright (C) 2008
|
5
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# Toshiaki Katayama <k@bioruby.org>,
|
6
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# Ryan Raaum <ryan@raaum.org>,
|
7
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# Jan Aerts <jandot@bioruby.org>,
|
8
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# Naohisa Goto <ng@bioruby.org>
|
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# License:: The Ruby License
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10
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#
|
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# $Id: references.rb,v 1.1.2.1 2008/03/04 10:07:49 ngoto Exp $
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12
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#
|
13
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# == Description
|
14
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#
|
15
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# The Bio::References class was obsoleted after BioRuby 1.2.1.
|
16
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# To keep compatibility, some wrapper methods are provided in this file.
|
17
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# As the compatibility methods (and Bio::References) will soon be removed,
|
18
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# Please change your code not to use Bio::References.
|
19
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#
|
20
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# Note that Bio::Reference is different from Bio::References.
|
21
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+
# Bio::Reference still exists for storing a reference information
|
22
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# in sequence entries.
|
23
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+
|
24
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module Bio
|
25
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|
26
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# = DESCRIPTION
|
27
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#
|
28
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# This class is OBSOLETED, and will soon be removed.
|
29
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# Instead of this class, an array is to be used.
|
30
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#
|
31
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+
#
|
32
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# A container class for Bio::Reference objects.
|
33
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#
|
34
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# = USAGE
|
35
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#
|
36
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# This class should NOT be used.
|
37
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#
|
38
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# refs = Bio::References.new
|
39
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+
# refs.append(Bio::Reference.new(hash))
|
40
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+
# refs.each do |reference|
|
41
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# ...
|
42
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+
# end
|
43
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#
|
44
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class References
|
45
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+
|
46
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# module to keep backward compatibility with obsoleted Bio::References
|
47
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module BackwardCompatibility #:nodoc:
|
48
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+
|
49
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+
# Backward compatibility with Bio::References#references.
|
50
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+
# Now, references are stored in an array, and
|
51
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# you should change your code not to use this method.
|
52
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+
def references
|
53
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+
warn 'Bio::References is obsoleted. Now, references are stored in an array.'
|
54
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+
self
|
55
|
+
end
|
56
|
+
|
57
|
+
# Backward compatibility with Bio::References#append.
|
58
|
+
# Now, references are stored in an array, and
|
59
|
+
# you should change your code not to use this method.
|
60
|
+
def append(reference)
|
61
|
+
warn 'Bio::References is obsoleted. Now, references are stored in an array.'
|
62
|
+
self.push(reference) if reference.is_a? Reference
|
63
|
+
self
|
64
|
+
end
|
65
|
+
end #module BackwardCompatibility
|
66
|
+
|
67
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# This method should not be used.
|
68
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+
# Only for backward compatibility of existing code.
|
69
|
+
#
|
70
|
+
# Since Bio::References is obsoleted,
|
71
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+
# Bio::References.new not returns Bio::References object,
|
72
|
+
# but modifies given _ary_ and returns the _ary_.
|
73
|
+
#
|
74
|
+
# *Arguments*:
|
75
|
+
# * (optional) __: Array of Bio::Reference objects
|
76
|
+
# *Returns*:: the given array
|
77
|
+
def self.new(ary = [])
|
78
|
+
warn 'Bio::References is obsoleted. Some methods are added to given array to keep backward compatibility.'
|
79
|
+
ary.extend(BackwardCompatibility)
|
80
|
+
ary
|
81
|
+
end
|
82
|
+
|
83
|
+
# Array of Bio::Reference objects
|
84
|
+
attr_accessor :references
|
85
|
+
|
86
|
+
# Normally, users can not call this method.
|
87
|
+
#
|
88
|
+
# Create a new Bio::References object
|
89
|
+
#
|
90
|
+
# refs = Bio::References.new
|
91
|
+
# ---
|
92
|
+
# *Arguments*:
|
93
|
+
# * (optional) __: Array of Bio::Reference objects
|
94
|
+
# *Returns*:: Bio::References object
|
95
|
+
def initialize(ary = [])
|
96
|
+
@references = ary
|
97
|
+
end
|
98
|
+
|
99
|
+
|
100
|
+
# Add a Bio::Reference object to the container.
|
101
|
+
#
|
102
|
+
# refs.append(reference)
|
103
|
+
# ---
|
104
|
+
# *Arguments*:
|
105
|
+
# * (required) _reference_: Bio::Reference object
|
106
|
+
# *Returns*:: current Bio::References object
|
107
|
+
def append(reference)
|
108
|
+
@references.push(reference) if reference.is_a? Reference
|
109
|
+
return self
|
110
|
+
end
|
111
|
+
|
112
|
+
# Iterate through Bio::Reference objects.
|
113
|
+
#
|
114
|
+
# refs.each do |reference|
|
115
|
+
# ...
|
116
|
+
# end
|
117
|
+
# ---
|
118
|
+
# *Block*:: yields each Bio::Reference object
|
119
|
+
def each
|
120
|
+
@references.each do |reference|
|
121
|
+
yield reference
|
122
|
+
end
|
123
|
+
end
|
124
|
+
|
125
|
+
end #class References
|
126
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+
end #module Bio
|
127
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+
|
128
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|
data/lib/bio/data/aa.rb
ADDED
@@ -0,0 +1,353 @@
|
|
1
|
+
#
|
2
|
+
# = bio/data/aa.rb - Amino Acids
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2001, 2005
|
5
|
+
# Toshiaki Katayama <k@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: aa.rb,v 0.22 2007/04/06 04:44:51 k Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
module Bio
|
12
|
+
|
13
|
+
class AminoAcid
|
14
|
+
|
15
|
+
module Data
|
16
|
+
|
17
|
+
# IUPAC code
|
18
|
+
# * http://www.iupac.org/
|
19
|
+
# * http://www.chem.qmw.ac.uk/iubmb/newsletter/1999/item3.html
|
20
|
+
# * http://www.ebi.ac.uk/RESID/faq.html
|
21
|
+
|
22
|
+
NAMES = {
|
23
|
+
|
24
|
+
'A' => 'Ala',
|
25
|
+
'C' => 'Cys',
|
26
|
+
'D' => 'Asp',
|
27
|
+
'E' => 'Glu',
|
28
|
+
'F' => 'Phe',
|
29
|
+
'G' => 'Gly',
|
30
|
+
'H' => 'His',
|
31
|
+
'I' => 'Ile',
|
32
|
+
'K' => 'Lys',
|
33
|
+
'L' => 'Leu',
|
34
|
+
'M' => 'Met',
|
35
|
+
'N' => 'Asn',
|
36
|
+
'P' => 'Pro',
|
37
|
+
'Q' => 'Gln',
|
38
|
+
'R' => 'Arg',
|
39
|
+
'S' => 'Ser',
|
40
|
+
'T' => 'Thr',
|
41
|
+
'V' => 'Val',
|
42
|
+
'W' => 'Trp',
|
43
|
+
'Y' => 'Tyr',
|
44
|
+
'B' => 'Asx', # D/N
|
45
|
+
'Z' => 'Glx', # E/Q
|
46
|
+
'J' => 'Xle', # I/L
|
47
|
+
'U' => 'Sec', # 'uga' (stop)
|
48
|
+
'O' => 'Pyl', # 'uag' (stop)
|
49
|
+
'X' => 'Xaa', # (unknown)
|
50
|
+
|
51
|
+
'Ala' => 'alanine',
|
52
|
+
'Cys' => 'cysteine',
|
53
|
+
'Asp' => 'aspartic acid',
|
54
|
+
'Glu' => 'glutamic acid',
|
55
|
+
'Phe' => 'phenylalanine',
|
56
|
+
'Gly' => 'glycine',
|
57
|
+
'His' => 'histidine',
|
58
|
+
'Ile' => 'isoleucine',
|
59
|
+
'Lys' => 'lysine',
|
60
|
+
'Leu' => 'leucine',
|
61
|
+
'Met' => 'methionine',
|
62
|
+
'Asn' => 'asparagine',
|
63
|
+
'Pro' => 'proline',
|
64
|
+
'Gln' => 'glutamine',
|
65
|
+
'Arg' => 'arginine',
|
66
|
+
'Ser' => 'serine',
|
67
|
+
'Thr' => 'threonine',
|
68
|
+
'Val' => 'valine',
|
69
|
+
'Trp' => 'tryptophan',
|
70
|
+
'Tyr' => 'tyrosine',
|
71
|
+
'Asx' => 'asparagine/aspartic acid [DN]',
|
72
|
+
'Glx' => 'glutamine/glutamic acid [EQ]',
|
73
|
+
'Xle' => 'isoleucine/leucine [IL]',
|
74
|
+
'Sec' => 'selenocysteine',
|
75
|
+
'Pyl' => 'pyrrolysine',
|
76
|
+
'Xaa' => 'unknown [A-Z]',
|
77
|
+
|
78
|
+
}
|
79
|
+
|
80
|
+
# AAindex FASG760101 - Molecular weight (Fasman, 1976)
|
81
|
+
# Fasman, G.D., ed.
|
82
|
+
# Handbook of Biochemistry and Molecular Biology", 3rd ed.,
|
83
|
+
# Proteins - Volume 1, CRC Press, Cleveland (1976)
|
84
|
+
|
85
|
+
WEIGHT = {
|
86
|
+
|
87
|
+
'A' => 89.09,
|
88
|
+
'C' => 121.15, # 121.16 according to the Wikipedia
|
89
|
+
'D' => 133.10,
|
90
|
+
'E' => 147.13,
|
91
|
+
'F' => 165.19,
|
92
|
+
'G' => 75.07,
|
93
|
+
'H' => 155.16,
|
94
|
+
'I' => 131.17,
|
95
|
+
'K' => 146.19,
|
96
|
+
'L' => 131.17,
|
97
|
+
'M' => 149.21,
|
98
|
+
'N' => 132.12,
|
99
|
+
'P' => 115.13,
|
100
|
+
'Q' => 146.15,
|
101
|
+
'R' => 174.20,
|
102
|
+
'S' => 105.09,
|
103
|
+
'T' => 119.12,
|
104
|
+
'U' => 168.06,
|
105
|
+
'V' => 117.15,
|
106
|
+
'W' => 204.23,
|
107
|
+
'Y' => 181.19,
|
108
|
+
}
|
109
|
+
|
110
|
+
|
111
|
+
ACIDIC_AMINO_ACIDS = %w(D E)
|
112
|
+
BASIC_AMINO_ACIDS = %w(H K R)
|
113
|
+
|
114
|
+
def weight(x = nil)
|
115
|
+
if x
|
116
|
+
if x.length > 1
|
117
|
+
total = 0.0
|
118
|
+
x.each_byte do |byte|
|
119
|
+
aa = byte.chr.upcase
|
120
|
+
if WEIGHT[aa]
|
121
|
+
total += WEIGHT[aa]
|
122
|
+
else
|
123
|
+
raise "Error: invalid amino acid '#{aa}'"
|
124
|
+
end
|
125
|
+
end
|
126
|
+
total -= NucleicAcid.weight[:water] * (x.length - 1)
|
127
|
+
else
|
128
|
+
WEIGHT[x]
|
129
|
+
end
|
130
|
+
else
|
131
|
+
WEIGHT
|
132
|
+
end
|
133
|
+
end
|
134
|
+
|
135
|
+
def [](x)
|
136
|
+
NAMES[x]
|
137
|
+
end
|
138
|
+
|
139
|
+
# backward compatibility
|
140
|
+
def names
|
141
|
+
NAMES
|
142
|
+
end
|
143
|
+
alias aa names
|
144
|
+
|
145
|
+
def name(x)
|
146
|
+
str = NAMES[x]
|
147
|
+
if str and str.length == 3
|
148
|
+
NAMES[str]
|
149
|
+
else
|
150
|
+
str
|
151
|
+
end
|
152
|
+
end
|
153
|
+
|
154
|
+
def to_1(x)
|
155
|
+
case x.to_s.length
|
156
|
+
when 1
|
157
|
+
x
|
158
|
+
when 3
|
159
|
+
three2one(x)
|
160
|
+
else
|
161
|
+
name2one(x)
|
162
|
+
end
|
163
|
+
end
|
164
|
+
alias one to_1
|
165
|
+
|
166
|
+
def to_3(x)
|
167
|
+
case x.to_s.length
|
168
|
+
when 1
|
169
|
+
one2three(x)
|
170
|
+
when 3
|
171
|
+
x
|
172
|
+
else
|
173
|
+
name2three(x)
|
174
|
+
end
|
175
|
+
end
|
176
|
+
alias three to_3
|
177
|
+
|
178
|
+
def one2three(x)
|
179
|
+
if x and x.length != 1
|
180
|
+
raise ArgumentError
|
181
|
+
else
|
182
|
+
NAMES[x]
|
183
|
+
end
|
184
|
+
end
|
185
|
+
|
186
|
+
def three2one(x)
|
187
|
+
if x and x.length != 3
|
188
|
+
raise ArgumentError
|
189
|
+
else
|
190
|
+
reverse[x]
|
191
|
+
end
|
192
|
+
end
|
193
|
+
|
194
|
+
def one2name(x)
|
195
|
+
if x and x.length != 1
|
196
|
+
raise ArgumentError
|
197
|
+
else
|
198
|
+
three2name(NAMES[x])
|
199
|
+
end
|
200
|
+
end
|
201
|
+
|
202
|
+
def name2one(x)
|
203
|
+
str = reverse[x.to_s.downcase]
|
204
|
+
if str and str.length == 3
|
205
|
+
three2one(str)
|
206
|
+
else
|
207
|
+
str
|
208
|
+
end
|
209
|
+
end
|
210
|
+
|
211
|
+
def three2name(x)
|
212
|
+
if x and x.length != 3
|
213
|
+
raise ArgumentError
|
214
|
+
else
|
215
|
+
NAMES[x]
|
216
|
+
end
|
217
|
+
end
|
218
|
+
|
219
|
+
def name2three(x)
|
220
|
+
reverse[x.downcase]
|
221
|
+
end
|
222
|
+
|
223
|
+
def to_re(seq)
|
224
|
+
replace = {
|
225
|
+
'B' => '[DNB]',
|
226
|
+
'Z' => '[EQZ]',
|
227
|
+
'J' => '[ILJ]',
|
228
|
+
'X' => '[ACDEFGHIKLMNPQRSTVWYUOX]',
|
229
|
+
}
|
230
|
+
replace.default = '.'
|
231
|
+
|
232
|
+
str = seq.to_s.upcase
|
233
|
+
str.gsub!(/[^ACDEFGHIKLMNPQRSTVWYUO]/) { |aa|
|
234
|
+
replace[aa]
|
235
|
+
}
|
236
|
+
Regexp.new(str)
|
237
|
+
end
|
238
|
+
|
239
|
+
|
240
|
+
private
|
241
|
+
|
242
|
+
|
243
|
+
def reverse
|
244
|
+
hash = Hash.new
|
245
|
+
NAMES.each do |k, v|
|
246
|
+
hash[v] = k
|
247
|
+
end
|
248
|
+
hash
|
249
|
+
end
|
250
|
+
|
251
|
+
end
|
252
|
+
|
253
|
+
|
254
|
+
# as instance methods
|
255
|
+
include Data
|
256
|
+
|
257
|
+
# as class methods
|
258
|
+
extend Data
|
259
|
+
|
260
|
+
|
261
|
+
private
|
262
|
+
|
263
|
+
|
264
|
+
# override when used as an instance method to improve performance
|
265
|
+
alias orig_reverse reverse
|
266
|
+
def reverse
|
267
|
+
unless @reverse
|
268
|
+
@reverse = orig_reverse
|
269
|
+
end
|
270
|
+
@reverse
|
271
|
+
end
|
272
|
+
|
273
|
+
end
|
274
|
+
|
275
|
+
end # module Bio
|
276
|
+
|
277
|
+
|
278
|
+
if __FILE__ == $0
|
279
|
+
|
280
|
+
puts "### aa = Bio::AminoAcid.new"
|
281
|
+
aa = Bio::AminoAcid.new
|
282
|
+
|
283
|
+
puts "# Bio::AminoAcid['A']"
|
284
|
+
p Bio::AminoAcid['A']
|
285
|
+
puts "# aa['A']"
|
286
|
+
p aa['A']
|
287
|
+
|
288
|
+
puts "# Bio::AminoAcid.name('A'), Bio::AminoAcid.name('Ala')"
|
289
|
+
p Bio::AminoAcid.name('A'), Bio::AminoAcid.name('Ala')
|
290
|
+
puts "# aa.name('A'), aa.name('Ala')"
|
291
|
+
p aa.name('A'), aa.name('Ala')
|
292
|
+
|
293
|
+
puts "# Bio::AminoAcid.to_1('alanine'), Bio::AminoAcid.one('alanine')"
|
294
|
+
p Bio::AminoAcid.to_1('alanine'), Bio::AminoAcid.one('alanine')
|
295
|
+
puts "# aa.to_1('alanine'), aa.one('alanine')"
|
296
|
+
p aa.to_1('alanine'), aa.one('alanine')
|
297
|
+
puts "# Bio::AminoAcid.to_1('Ala'), Bio::AminoAcid.one('Ala')"
|
298
|
+
p Bio::AminoAcid.to_1('Ala'), Bio::AminoAcid.one('Ala')
|
299
|
+
puts "# aa.to_1('Ala'), aa.one('Ala')"
|
300
|
+
p aa.to_1('Ala'), aa.one('Ala')
|
301
|
+
puts "# Bio::AminoAcid.to_1('A'), Bio::AminoAcid.one('A')"
|
302
|
+
p Bio::AminoAcid.to_1('A'), Bio::AminoAcid.one('A')
|
303
|
+
puts "# aa.to_1('A'), aa.one('A')"
|
304
|
+
p aa.to_1('A'), aa.one('A')
|
305
|
+
|
306
|
+
puts "# Bio::AminoAcid.to_3('alanine'), Bio::AminoAcid.three('alanine')"
|
307
|
+
p Bio::AminoAcid.to_3('alanine'), Bio::AminoAcid.three('alanine')
|
308
|
+
puts "# aa.to_3('alanine'), aa.three('alanine')"
|
309
|
+
p aa.to_3('alanine'), aa.three('alanine')
|
310
|
+
puts "# Bio::AminoAcid.to_3('Ala'), Bio::AminoAcid.three('Ala')"
|
311
|
+
p Bio::AminoAcid.to_3('Ala'), Bio::AminoAcid.three('Ala')
|
312
|
+
puts "# aa.to_3('Ala'), aa.three('Ala')"
|
313
|
+
p aa.to_3('Ala'), aa.three('Ala')
|
314
|
+
puts "# Bio::AminoAcid.to_3('A'), Bio::AminoAcid.three('A')"
|
315
|
+
p Bio::AminoAcid.to_3('A'), Bio::AminoAcid.three('A')
|
316
|
+
puts "# aa.to_3('A'), aa.three('A')"
|
317
|
+
p aa.to_3('A'), aa.three('A')
|
318
|
+
|
319
|
+
puts "# Bio::AminoAcid.one2three('A')"
|
320
|
+
p Bio::AminoAcid.one2three('A')
|
321
|
+
puts "# aa.one2three('A')"
|
322
|
+
p aa.one2three('A')
|
323
|
+
|
324
|
+
puts "# Bio::AminoAcid.three2one('Ala')"
|
325
|
+
p Bio::AminoAcid.three2one('Ala')
|
326
|
+
puts "# aa.three2one('Ala')"
|
327
|
+
p aa.three2one('Ala')
|
328
|
+
|
329
|
+
puts "# Bio::AminoAcid.one2name('A')"
|
330
|
+
p Bio::AminoAcid.one2name('A')
|
331
|
+
puts "# aa.one2name('A')"
|
332
|
+
p aa.one2name('A')
|
333
|
+
|
334
|
+
puts "# Bio::AminoAcid.name2one('alanine')"
|
335
|
+
p Bio::AminoAcid.name2one('alanine')
|
336
|
+
puts "# aa.name2one('alanine')"
|
337
|
+
p aa.name2one('alanine')
|
338
|
+
|
339
|
+
puts "# Bio::AminoAcid.three2name('Ala')"
|
340
|
+
p Bio::AminoAcid.three2name('Ala')
|
341
|
+
puts "# aa.three2name('Ala')"
|
342
|
+
p aa.three2name('Ala')
|
343
|
+
|
344
|
+
puts "# Bio::AminoAcid.name2three('alanine')"
|
345
|
+
p Bio::AminoAcid.name2three('alanine')
|
346
|
+
puts "# aa.name2three('alanine')"
|
347
|
+
p aa.name2three('alanine')
|
348
|
+
|
349
|
+
puts "# Bio::AminoAcid.to_re('BZACDEFGHIKLMNPQRSTVWYU')"
|
350
|
+
p Bio::AminoAcid.to_re('BZACDEFGHIKLMNPQRSTVWYU')
|
351
|
+
|
352
|
+
end
|
353
|
+
|