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
data/lib/bio/sequence.rb
ADDED
@@ -0,0 +1,456 @@
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#
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# = bio/sequence.rb - biological sequence class
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#
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# Copyright:: Copyright (C) 2000-2006
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# Toshiaki Katayama <k@bioruby.org>,
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# Yoshinori K. Okuji <okuji@enbug.org>,
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# Naohisa Goto <ng@bioruby.org>,
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# Ryan Raaum <ryan@raaum.org>,
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# Jan Aerts <jan.aerts@bbsrc.ac.uk>
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# License:: The Ruby License
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#
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# $Id: sequence.rb,v 0.58.2.12 2008/06/17 15:25:22 ngoto Exp $
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#
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require 'bio/sequence/compat'
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module Bio
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# = DESCRIPTION
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# Bio::Sequence objects represent annotated sequences in bioruby.
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# A Bio::Sequence object is a wrapper around the actual sequence,
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# represented as either a Bio::Sequence::NA or a Bio::Sequence::AA object.
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# For most users, this encapsulation will be completely transparent.
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# Bio::Sequence responds to all methods defined for Bio::Sequence::NA/AA
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# objects using the same arguments and returning the same values (even though
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# these methods are not documented specifically for Bio::Sequence).
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#
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# = USAGE
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# # Create a nucleic or amino acid sequence
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# dna = Bio::Sequence.auto('atgcatgcATGCATGCAAAA')
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# rna = Bio::Sequence.auto('augcaugcaugcaugcaaaa')
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# aa = Bio::Sequence.auto('ACDEFGHIKLMNPQRSTVWYU')
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#
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# # Print it out
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# puts dna.to_s
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# puts aa.to_s
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#
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# # Get a subsequence, bioinformatics style (first nucleotide is '1')
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# puts dna.subseq(2,6)
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#
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# # Get a subsequence, informatics style (first nucleotide is '0')
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# puts dna[2,6]
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#
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# # Print in FASTA format
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# puts dna.output(:fasta)
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#
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# # Print all codons
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# dna.window_search(3,3) do |codon|
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# puts codon
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# end
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#
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# # Splice or otherwise mangle your sequence
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# puts dna.splicing("complement(join(1..5,16..20))")
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# puts rna.splicing("complement(join(1..5,16..20))")
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#
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# # Convert a sequence containing ambiguity codes into a
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# # regular expression you can use for subsequent searching
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# puts aa.to_re
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#
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# # These should speak for themselves
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# puts dna.complement
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# puts dna.composition
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# puts dna.molecular_weight
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# puts dna.translate
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# puts dna.gc_percent
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class Sequence
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autoload :Common, 'bio/sequence/common'
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autoload :NA, 'bio/sequence/na'
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autoload :AA, 'bio/sequence/aa'
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autoload :Generic, 'bio/sequence/generic'
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autoload :Format, 'bio/sequence/format'
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autoload :Adapter, 'bio/sequence/adapter'
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include Format
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# Create a new Bio::Sequence object
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#
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# s = Bio::Sequence.new('atgc')
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# puts s #=> 'atgc'
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#
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# Note that this method does not intialize the contained sequence
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# as any kind of bioruby object, only as a simple string
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#
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# puts s.seq.class #=> String
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#
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# See Bio::Sequence#na, Bio::Sequence#aa, and Bio::Sequence#auto
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# for methods to transform the basic String of a just created
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# Bio::Sequence object to a proper bioruby object
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# ---
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# *Arguments*:
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# * (required) _str_: String or Bio::Sequence::NA/AA object
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# *Returns*:: Bio::Sequence object
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def initialize(str)
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@seq = str
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end
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# Pass any unknown method calls to the wrapped sequence object. see
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# http://www.rubycentral.com/book/ref_c_object.html#Object.method_missing
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def method_missing(sym, *args, &block) #:nodoc:
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begin
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seq.__send__(sym, *args, &block)
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rescue NoMethodError => evar
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lineno = __LINE__ - 2
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file = __FILE__
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bt_here = [ "#{file}:#{lineno}:in \`__send__\'",
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"#{file}:#{lineno}:in \`method_missing\'"
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]
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if bt_here == evar.backtrace[0, 2] then
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bt = evar.backtrace[2..-1]
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evar = evar.class.new("undefined method \`#{sym.to_s}\' for #{self.inspect}")
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evar.set_backtrace(bt)
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end
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#p lineno
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#p file
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#p bt_here
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#p evar.backtrace
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raise(evar)
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end
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end
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# The sequence identifier (String). For example, for a sequence
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# of Genbank origin, this is the locus name.
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# For a sequence of EMBL origin, this is the primary accession number.
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attr_accessor :entry_id
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# A String with a description of the sequence (String)
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attr_accessor :definition
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# Features (An Array of Bio::Feature objects)
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attr_accessor :features
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# References (An Array of Bio::Reference objects)
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attr_accessor :references
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# Comments (String or an Array of String)
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attr_accessor :comments
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# Keywords (An Array of String)
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attr_accessor :keywords
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# Links to other database entries.
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# (An Array of Bio::Sequence::DBLink objects)
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attr_accessor :dblinks
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# Bio::Sequence::NA/AA
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attr_accessor :moltype
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# The sequence object, usually Bio::Sequence::NA/AA,
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# but could be a simple String
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attr_accessor :seq
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#---
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# Attributes below have been added during BioHackathon2008
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#+++
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# Version number of the sequence (String or Integer).
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# Unlike <tt>entry_version</tt>, <tt>sequence_version</tt> will be changed
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# when the submitter of the sequence updates the entry.
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# Normally, the same entry taken from different databases (EMBL, GenBank,
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# and DDBJ) may have the same sequence_version.
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attr_accessor :sequence_version
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# Topology (String). "circular", "linear", or nil.
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attr_accessor :topology
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# Strandedness (String). "single" (single-stranded),
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# "double" (double-stranded), "mixed" (mixed-stranded), or nil.
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attr_accessor :strandedness
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# molecular type (String). "DNA" or "RNA" for nucleotide sequence.
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attr_accessor :molecule_type
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# Data Class defined by EMBL (String)
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# See http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3_1
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attr_accessor :data_class
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# Taxonomic Division defined by EMBL/GenBank/DDBJ (String)
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# See http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3_2
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attr_accessor :division
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# Primary accession number (String)
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attr_accessor :primary_accession
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# Secondary accession numbers (Array of String)
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attr_accessor :secondary_accessions
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# Created date of the sequence entry (Date, DateTime, Time, or String)
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attr_accessor :date_created
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# Last modified date of the sequence entry (Date, DateTime, Time, or String)
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attr_accessor :date_modified
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# Release information when created (String)
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attr_accessor :release_created
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# Release information when last-modified (String)
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attr_accessor :release_modified
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# Version of the entry (String or Integer).
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# Unlike <tt>sequence_version</tt>, <tt>entry_version</tt> is a database
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# maintainer's internal version number.
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# The version number will be changed when the database maintainer
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# modifies the entry.
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# The same enrty in EMBL, GenBank, and DDBJ may have different
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# entry_version.
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attr_accessor :entry_version
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# Organism species (String). For example, "Escherichia coli".
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attr_accessor :species
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+
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# Organism classification, taxonomic classification of the source organism.
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# (Array of String)
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attr_accessor :classification
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alias taxonomy classification
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# (not well supported) Organelle information (String).
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attr_accessor :organelle
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+
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# Namespace of the sequence IDs described in entry_id, primary_accession,
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# and secondary_accessions methods (String).
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# For example, 'EMBL', 'GenBank', 'DDBJ', 'RefSeq'.
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223
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attr_accessor :id_namespace
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224
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+
|
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# Sequence identifiers which are not described in entry_id,
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# primary_accession,and secondary_accessions methods
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# (Array of Bio::Sequence::DBLink objects).
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# For example, NCBI GI number can be stored.
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# Note that only identifiers of the entry itself should be stored.
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230
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# For database cross references, <tt>dblinks</tt> should be used.
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231
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attr_accessor :other_seqids
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232
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+
|
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# Guess the type of sequence, Amino Acid or Nucleic Acid, and create a
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234
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# new sequence object (Bio::Sequence::AA or Bio::Sequence::NA) on the basis
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235
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# of this guess. This method will change the current Bio::Sequence object.
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236
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#
|
237
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# s = Bio::Sequence.new('atgc')
|
238
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# puts s.seq.class #=> String
|
239
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# s.auto
|
240
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# puts s.seq.class #=> Bio::Sequence::NA
|
241
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# ---
|
242
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# *Returns*:: Bio::Sequence::NA/AA object
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243
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def auto
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244
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@moltype = guess
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245
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if @moltype == NA
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246
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@seq = NA.new(seq)
|
247
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else
|
248
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@seq = AA.new(seq)
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249
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+
end
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250
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end
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251
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+
|
252
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# Given a sequence String, guess its type, Amino Acid or Nucleic Acid, and
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253
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# return a new Bio::Sequence object wrapping a sequence of the guessed type
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254
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# (either Bio::Sequence::AA or Bio::Sequence::NA)
|
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#
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256
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# s = Bio::Sequence.auto('atgc')
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257
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# puts s.seq.class #=> Bio::Sequence::NA
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258
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# ---
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259
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# *Arguments*:
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260
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# * (required) _str_: String *or* Bio::Sequence::NA/AA object
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261
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# *Returns*:: Bio::Sequence object
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262
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def self.auto(str)
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263
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seq = self.new(str)
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264
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seq.auto
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return seq
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266
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end
|
267
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+
|
268
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# Guess the class of the current sequence. Returns the class
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# (Bio::Sequence::AA or Bio::Sequence::NA) guessed. In general, used by
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270
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# developers only, but if you know what you are doing, feel free.
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#
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# s = Bio::Sequence.new('atgc')
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273
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# puts s.guess #=> Bio::Sequence::NA
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274
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#
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275
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# There are three parameters: `threshold`, `length`, and `index`.
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276
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#
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# The `threshold` value (defaults to 0.9) is the frequency of
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278
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# nucleic acid bases [AGCTUagctu] required in the sequence for this method
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279
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# to produce a Bio::Sequence::NA "guess". In the default case, if less
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280
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# than 90% of the bases (after excluding [Nn]) are in the set [AGCTUagctu],
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# then the guess is Bio::Sequence::AA.
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#
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283
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# s = Bio::Sequence.new('atgcatgcqq')
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284
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# puts s.guess #=> Bio::Sequence::AA
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285
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# puts s.guess(0.8) #=> Bio::Sequence::AA
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286
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# puts s.guess(0.7) #=> Bio::Sequence::NA
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#
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288
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# The `length` value is how much of the total sequence to use in the
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289
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# guess (default 10000). If your sequence is very long, you may
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290
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# want to use a smaller amount to reduce the computational burden.
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291
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#
|
292
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# s = Bio::Sequence.new(A VERY LONG SEQUENCE)
|
293
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# puts s.guess(0.9, 1000) # limit the guess to the first 1000 positions
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294
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+
#
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295
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# The `index` value is where to start the guess. Perhaps you know there
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296
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+
# are a lot of gaps at the start...
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297
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#
|
298
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# s = Bio::Sequence.new('-----atgcc')
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299
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# puts s.guess #=> Bio::Sequence::AA
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300
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# puts s.guess(0.9,10000,5) #=> Bio::Sequence::NA
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301
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# ---
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302
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# *Arguments*:
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303
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+
# * (optional) _threshold_: Float in range 0,1 (default 0.9)
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304
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# * (optional) _length_: Fixnum (default 10000)
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305
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# * (optional) _index_: Fixnum (default 1)
|
306
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+
# *Returns*:: Bio::Sequence::NA/AA
|
307
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def guess(threshold = 0.9, length = 10000, index = 0)
|
308
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+
str = seq.to_s[index,length].to_s.extend Bio::Sequence::Common
|
309
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cmp = str.composition
|
310
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+
|
311
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+
bases = cmp['A'] + cmp['T'] + cmp['G'] + cmp['C'] + cmp['U'] +
|
312
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+
cmp['a'] + cmp['t'] + cmp['g'] + cmp['c'] + cmp['u']
|
313
|
+
|
314
|
+
total = str.length - cmp['N'] - cmp['n']
|
315
|
+
|
316
|
+
if bases.to_f / total > threshold
|
317
|
+
return NA
|
318
|
+
else
|
319
|
+
return AA
|
320
|
+
end
|
321
|
+
end
|
322
|
+
|
323
|
+
# Guess the class of a given sequence. Returns the class
|
324
|
+
# (Bio::Sequence::AA or Bio::Sequence::NA) guessed. In general, used by
|
325
|
+
# developers only, but if you know what you are doing, feel free.
|
326
|
+
#
|
327
|
+
# puts .guess('atgc') #=> Bio::Sequence::NA
|
328
|
+
#
|
329
|
+
# There are three optional parameters: `threshold`, `length`, and `index`.
|
330
|
+
#
|
331
|
+
# The `threshold` value (defaults to 0.9) is the frequency of
|
332
|
+
# nucleic acid bases [AGCTUagctu] required in the sequence for this method
|
333
|
+
# to produce a Bio::Sequence::NA "guess". In the default case, if less
|
334
|
+
# than 90% of the bases (after excluding [Nn]) are in the set [AGCTUagctu],
|
335
|
+
# then the guess is Bio::Sequence::AA.
|
336
|
+
#
|
337
|
+
# puts Bio::Sequence.guess('atgcatgcqq') #=> Bio::Sequence::AA
|
338
|
+
# puts Bio::Sequence.guess('atgcatgcqq', 0.8) #=> Bio::Sequence::AA
|
339
|
+
# puts Bio::Sequence.guess('atgcatgcqq', 0.7) #=> Bio::Sequence::NA
|
340
|
+
#
|
341
|
+
# The `length` value is how much of the total sequence to use in the
|
342
|
+
# guess (default 10000). If your sequence is very long, you may
|
343
|
+
# want to use a smaller amount to reduce the computational burden.
|
344
|
+
#
|
345
|
+
# # limit the guess to the first 1000 positions
|
346
|
+
# puts Bio::Sequence.guess('A VERY LONG SEQUENCE', 0.9, 1000)
|
347
|
+
#
|
348
|
+
# The `index` value is where to start the guess. Perhaps you know there
|
349
|
+
# are a lot of gaps at the start...
|
350
|
+
#
|
351
|
+
# puts Bio::Sequence.guess('-----atgcc') #=> Bio::Sequence::AA
|
352
|
+
# puts Bio::Sequence.guess('-----atgcc',0.9,10000,5) #=> Bio::Sequence::NA
|
353
|
+
# ---
|
354
|
+
# *Arguments*:
|
355
|
+
# * (required) _str_: String *or* Bio::Sequence::NA/AA object
|
356
|
+
# * (optional) _threshold_: Float in range 0,1 (default 0.9)
|
357
|
+
# * (optional) _length_: Fixnum (default 10000)
|
358
|
+
# * (optional) _index_: Fixnum (default 1)
|
359
|
+
# *Returns*:: Bio::Sequence::NA/AA
|
360
|
+
def self.guess(str, *args)
|
361
|
+
self.new(str).guess(*args)
|
362
|
+
end
|
363
|
+
|
364
|
+
# Transform the sequence wrapped in the current Bio::Sequence object
|
365
|
+
# into a Bio::Sequence::NA object. This method will change the current
|
366
|
+
# object. This method does not validate your choice, so be careful!
|
367
|
+
#
|
368
|
+
# s = Bio::Sequence.new('RRLE')
|
369
|
+
# puts s.seq.class #=> String
|
370
|
+
# s.na
|
371
|
+
# puts s.seq.class #=> Bio::Sequence::NA !!!
|
372
|
+
#
|
373
|
+
# However, if you know your sequence type, this method may be
|
374
|
+
# constructively used after initialization,
|
375
|
+
#
|
376
|
+
# s = Bio::Sequence.new('atgc')
|
377
|
+
# s.na
|
378
|
+
# ---
|
379
|
+
# *Returns*:: Bio::Sequence::NA
|
380
|
+
def na
|
381
|
+
@seq = NA.new(seq)
|
382
|
+
@moltype = NA
|
383
|
+
end
|
384
|
+
|
385
|
+
# Transform the sequence wrapped in the current Bio::Sequence object
|
386
|
+
# into a Bio::Sequence::NA object. This method will change the current
|
387
|
+
# object. This method does not validate your choice, so be careful!
|
388
|
+
#
|
389
|
+
# s = Bio::Sequence.new('atgc')
|
390
|
+
# puts s.seq.class #=> String
|
391
|
+
# s.aa
|
392
|
+
# puts s.seq.class #=> Bio::Sequence::AA !!!
|
393
|
+
#
|
394
|
+
# However, if you know your sequence type, this method may be
|
395
|
+
# constructively used after initialization,
|
396
|
+
#
|
397
|
+
# s = Bio::Sequence.new('RRLE')
|
398
|
+
# s.aa
|
399
|
+
# ---
|
400
|
+
# *Returns*:: Bio::Sequence::AA
|
401
|
+
def aa
|
402
|
+
@seq = AA.new(seq)
|
403
|
+
@moltype = AA
|
404
|
+
end
|
405
|
+
|
406
|
+
# Create a new Bio::Sequence object from a formatted string
|
407
|
+
# (GenBank, EMBL, fasta format, etc.)
|
408
|
+
#
|
409
|
+
# s = Bio::Sequence.input(str)
|
410
|
+
# ---
|
411
|
+
# *Arguments*:
|
412
|
+
# * (required) _str_: string
|
413
|
+
# * (optional) _format_: format specification (class or nil)
|
414
|
+
# *Returns*:: Bio::Sequence object
|
415
|
+
def self.input(str, format = nil)
|
416
|
+
if format then
|
417
|
+
klass = format
|
418
|
+
else
|
419
|
+
klass = Bio::FlatFile::AutoDetect.default.autodetect(str)
|
420
|
+
end
|
421
|
+
obj = klass.new(str)
|
422
|
+
obj.to_biosequence
|
423
|
+
end
|
424
|
+
|
425
|
+
# alias of Bio::Sequence.input
|
426
|
+
def self.read(str, format = nil)
|
427
|
+
input(str, format)
|
428
|
+
end
|
429
|
+
|
430
|
+
# accession numbers of the sequence
|
431
|
+
#
|
432
|
+
# *Returns*:: Array of String
|
433
|
+
def accessions
|
434
|
+
[ primary_accession, secondary_accessions ].flatten.compact
|
435
|
+
end
|
436
|
+
|
437
|
+
# Normally, users should not call this method directly.
|
438
|
+
# Use Bio::*#to_biosequence (e.g. Bio::GenBank#to_biosequence).
|
439
|
+
#
|
440
|
+
# Creates a new Bio::Sequence object from database data with an
|
441
|
+
# adapter module.
|
442
|
+
def self.adapter(source_data, adapter_module)
|
443
|
+
biosequence = self.new(nil)
|
444
|
+
biosequence.instance_eval {
|
445
|
+
remove_instance_variable(:@seq)
|
446
|
+
@source_data = source_data
|
447
|
+
}
|
448
|
+
biosequence.extend(adapter_module)
|
449
|
+
biosequence
|
450
|
+
end
|
451
|
+
|
452
|
+
end # Sequence
|
453
|
+
|
454
|
+
|
455
|
+
end # Bio
|
456
|
+
|