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 +1,722 @@
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#
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# = bio/data/codontable.rb - Codon Table
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#
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# Copyright:: Copyright (C) 2001, 2004
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# Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: codontable.rb,v 0.18 2007/04/05 23:35:40 trevor Exp $
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#
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# == Data source
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#
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# Data in this class is converted from the NCBI's genetic codes page.
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#
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# * ((<URL:http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t>))
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#
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# === Examples
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#
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# Obtain a codon table No.1 -- Standard (Eukaryote)
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#
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# table = Bio::CodonTable[1]
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#
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# Obtain a copy of the codon table No.1 to modify. In this example,
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# reassign a seleno cystein ('U') to the 'tga' codon.
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#
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# table = Bio::CodonTable.copy(1)
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# table['tga'] = 'U'
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#
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# Create a new codon table by your own from the Hash which contains
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# pairs of codon and amino acid. You can also define the table name
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# in the second argument.
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#
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# hash = { 'ttt' => 'F', 'ttc' => 'ttc', ... }
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# table = Bio::CodonTable.new(hash, "my codon table")
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#
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# Obtain a translated amino acid by codon.
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#
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# table = Bio::CodonTable[1]
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# table['ttt'] # => F
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#
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# Reverse translation of a amino acid into a list of relevant codons.
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#
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# table = Bio::CodonTable[1]
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# table.revtrans("A") # => ["gcg", "gct", "gca", "gcc"]
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#
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module Bio
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class CodonTable
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# Select a codon table by number. This method will return one of the
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# hard coded codon tables in this class as a Bio::CodonTable object.
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def self.[](i)
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hash = TABLES[i]
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raise "ERROR: Unknown codon table No.#{i}" unless hash
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definition = DEFINITIONS[i]
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start = STARTS[i]
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stop = STOPS[i]
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self.new(hash, definition, start, stop)
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end
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# Similar to Bio::CodonTable[num] but returns a copied codon table.
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# You can modify the codon table without influencing hard coded tables.
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def self.copy(i)
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ct = self[i]
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return Marshal.load(Marshal.dump(ct))
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end
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# Create your own codon table by giving a Hash table of codons and relevant
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# amino acids. You can also able to define the table's name as a second
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# argument.
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#
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# Two Arrays 'start' and 'stop' can be specified which contains a list of
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# start and stop codons used by 'start_codon?' and 'stop_codon?' methods.
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def initialize(hash, definition = nil, start = [], stop = [])
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@table = hash
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@definition = definition
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@start = start
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@stop = stop.empty? ? generate_stop : stop
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end
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# Accessor methods for a Hash of the currently selected codon table.
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attr_accessor :table
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# Accessor methods for the name of the currently selected table.
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attr_accessor :definition
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# Accessor methods for an Array which contains a list of start or stop
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# codons respectively.
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attr_accessor :start, :stop
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# Translate a codon into a relevant amino acid. This method is used for
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# translating a DNA sequence into amino acid sequence.
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def [](codon)
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@table[codon]
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end
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# Modify the codon table. Use with caution as it may break hard coded
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# tables. If you want to modify existing table, you should use copy
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# method instead of [] method to generate CodonTable object to be modified.
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#
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# # This is OK.
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# table = Bio::CodonTable.copy(1)
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# table['tga'] = 'U'
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#
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# # Not recommended as it overrides the hard coded table
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# table = Bio::CodonTable[1]
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# table['tga'] = 'U'
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#
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def []=(codon, aa)
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@table[codon] = aa
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end
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# Iterates on codon table hash.
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#
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# table = Bio::CodonTable[1]
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# table.each do |codon, aa|
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# puts "#{codon} -- #{aa}"
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# end
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#
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def each(&block)
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@table.each(&block)
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end
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# Reverse translation of a amino acid into a list of relevant codons.
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#
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# table = Bio::CodonTable[1]
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# table.revtrans("A") # => ["gcg", "gct", "gca", "gcc"]
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#
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def revtrans(aa)
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unless @reverse
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@reverse = {}
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@table.each do |k, v|
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@reverse[v] ||= []
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@reverse[v] << k
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end
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end
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@reverse[aa.upcase]
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end
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# Returns true if the codon is a start codon in the currently selected
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# codon table, otherwise false.
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def start_codon?(codon)
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@start.include?(codon.downcase)
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end
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# Returns true if the codon is a stop codon in the currently selected
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# codon table, otherwise false.
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def stop_codon?(codon)
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@stop.include?(codon.downcase)
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end
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def generate_stop
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list = []
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@table.each do |codon, aa|
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if aa == '*'
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list << codon
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end
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end
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return list
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end
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private :generate_stop
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DEFINITIONS = {
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1 => "Standard (Eukaryote)",
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2 => "Vertebrate Mitochondrial",
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3 => "Yeast Mitochondorial",
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4 => "Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma",
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5 => "Invertebrate Mitochondrial",
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6 => "Ciliate Macronuclear and Dasycladacean",
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9 => "Echinoderm Mitochondrial",
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10 => "Euplotid Nuclear",
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11 => "Bacteria",
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12 => "Alternative Yeast Nuclear",
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13 => "Ascidian Mitochondrial",
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14 => "Flatworm Mitochondrial",
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15 => "Blepharisma Macronuclear",
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16 => "Chlorophycean Mitochondrial",
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21 => "Trematode Mitochondrial",
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22 => "Scenedesmus obliquus mitochondrial",
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23 => "Thraustochytrium Mitochondrial",
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}
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STARTS = {
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1 => %w(ttg ctg atg gtg), # gtg added (cf. NCBI #SG1 document)
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2 => %w(att atc ata atg gtg),
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3 => %w(ata atg),
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4 => %w(tta ttg ctg att atc ata atg gtg),
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5 => %w(ttg att atc ata atg gtg),
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6 => %w(atg),
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9 => %w(atg gtg),
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10 => %w(atg),
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11 => %w(ttg ctg att atc ata atg gtg),
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12 => %w(ctg atg),
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13 => %w(atg),
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14 => %w(atg),
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15 => %w(atg),
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16 => %w(atg),
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21 => %w(atg gtg),
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22 => %w(atg),
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23 => %w(att atg gtg),
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}
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STOPS = {
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1 => %w(taa tag tga),
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2 => %w(taa tag aga agg),
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3 => %w(taa tag),
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4 => %w(taa tag),
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5 => %w(taa tag),
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6 => %w(tga),
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9 => %w(taa tag),
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10 => %w(taa tag),
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11 => %w(taa tag tga),
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12 => %w(taa tag tga),
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13 => %w(taa tag),
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14 => %w(tag),
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15 => %w(taa tga),
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16 => %w(taa tga),
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21 => %w(taa tag),
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22 => %w(tca taa tga),
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23 => %w(tta taa tag tga),
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}
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TABLES = {
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# codon table 1
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1 => {
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'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
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'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
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'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => '*',
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'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
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'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
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'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
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'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
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'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
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'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
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'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
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'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
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'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
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'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
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'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
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'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
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'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
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},
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# codon table 2
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2 => {
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'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
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'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
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'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'W',
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'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
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'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
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'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
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'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
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'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
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'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
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'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
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'ata' => 'M', 'aca' => 'T', 'aaa' => 'K', 'aga' => '*',
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'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => '*',
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'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
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'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
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'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
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'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
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},
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# codon table 3
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3 => {
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'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
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'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
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'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'W',
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'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
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'ctt' => 'T', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
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'ctc' => 'T', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
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'cta' => 'T', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
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'ctg' => 'T', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
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'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
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'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
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'ata' => 'M', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
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'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
|
293
|
+
|
294
|
+
'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
|
295
|
+
'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
|
296
|
+
'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
|
297
|
+
'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
|
298
|
+
},
|
299
|
+
|
300
|
+
# codon table 4
|
301
|
+
4 => {
|
302
|
+
'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
|
303
|
+
'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
|
304
|
+
'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'W',
|
305
|
+
'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
|
306
|
+
|
307
|
+
'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
|
308
|
+
'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
|
309
|
+
'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
|
310
|
+
'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
|
311
|
+
|
312
|
+
'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
|
313
|
+
'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
|
314
|
+
'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
|
315
|
+
'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
|
316
|
+
|
317
|
+
'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
|
318
|
+
'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
|
319
|
+
'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
|
320
|
+
'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
|
321
|
+
},
|
322
|
+
|
323
|
+
# codon table 5
|
324
|
+
5 => {
|
325
|
+
'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
|
326
|
+
'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
|
327
|
+
'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'W',
|
328
|
+
'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
|
329
|
+
|
330
|
+
'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
|
331
|
+
'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
|
332
|
+
'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
|
333
|
+
'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
|
334
|
+
|
335
|
+
'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
|
336
|
+
'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
|
337
|
+
'ata' => 'M', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'S',
|
338
|
+
'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'S',
|
339
|
+
|
340
|
+
'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
|
341
|
+
'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
|
342
|
+
'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
|
343
|
+
'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
|
344
|
+
},
|
345
|
+
|
346
|
+
# codon table 6
|
347
|
+
6 => {
|
348
|
+
'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
|
349
|
+
'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
|
350
|
+
'tta' => 'L', 'tca' => 'S', 'taa' => 'Q', 'tga' => '*',
|
351
|
+
'ttg' => 'L', 'tcg' => 'S', 'tag' => 'Q', 'tgg' => 'W',
|
352
|
+
|
353
|
+
'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
|
354
|
+
'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
|
355
|
+
'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
|
356
|
+
'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
|
357
|
+
|
358
|
+
'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
|
359
|
+
'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
|
360
|
+
'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
|
361
|
+
'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
|
362
|
+
|
363
|
+
'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
|
364
|
+
'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
|
365
|
+
'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
|
366
|
+
'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
|
367
|
+
},
|
368
|
+
|
369
|
+
# codon table 9
|
370
|
+
9 => {
|
371
|
+
'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
|
372
|
+
'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
|
373
|
+
'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'W',
|
374
|
+
'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
|
375
|
+
|
376
|
+
'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
|
377
|
+
'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
|
378
|
+
'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
|
379
|
+
'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
|
380
|
+
|
381
|
+
'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
|
382
|
+
'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
|
383
|
+
'ata' => 'I', 'aca' => 'T', 'aaa' => 'N', 'aga' => 'S',
|
384
|
+
'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'S',
|
385
|
+
|
386
|
+
'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
|
387
|
+
'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
|
388
|
+
'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
|
389
|
+
'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
|
390
|
+
},
|
391
|
+
|
392
|
+
# codon table 10
|
393
|
+
10 => {
|
394
|
+
|
395
|
+
'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
|
396
|
+
'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
|
397
|
+
'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'C',
|
398
|
+
'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
|
399
|
+
|
400
|
+
'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
|
401
|
+
'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
|
402
|
+
'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
|
403
|
+
'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
|
404
|
+
|
405
|
+
'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
|
406
|
+
'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
|
407
|
+
'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
|
408
|
+
'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
|
409
|
+
|
410
|
+
'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
|
411
|
+
'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
|
412
|
+
'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
|
413
|
+
'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
|
414
|
+
},
|
415
|
+
|
416
|
+
# codon table 11
|
417
|
+
11 => {
|
418
|
+
'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
|
419
|
+
'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
|
420
|
+
'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => '*',
|
421
|
+
'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
|
422
|
+
|
423
|
+
'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
|
424
|
+
'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
|
425
|
+
'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
|
426
|
+
'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
|
427
|
+
|
428
|
+
'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
|
429
|
+
'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
|
430
|
+
'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
|
431
|
+
'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
|
432
|
+
|
433
|
+
'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
|
434
|
+
'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
|
435
|
+
'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
|
436
|
+
'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
|
437
|
+
},
|
438
|
+
|
439
|
+
# codon table 12
|
440
|
+
12 => {
|
441
|
+
'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
|
442
|
+
'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
|
443
|
+
'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => '*',
|
444
|
+
'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
|
445
|
+
|
446
|
+
'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
|
447
|
+
'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
|
448
|
+
'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
|
449
|
+
'ctg' => 'S', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
|
450
|
+
|
451
|
+
'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
|
452
|
+
'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
|
453
|
+
'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
|
454
|
+
'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
|
455
|
+
|
456
|
+
'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
|
457
|
+
'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
|
458
|
+
'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
|
459
|
+
'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
|
460
|
+
},
|
461
|
+
|
462
|
+
# codon table 13
|
463
|
+
13 => {
|
464
|
+
'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
|
465
|
+
'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
|
466
|
+
'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'W',
|
467
|
+
'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
|
468
|
+
|
469
|
+
'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
|
470
|
+
'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
|
471
|
+
'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
|
472
|
+
'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
|
473
|
+
|
474
|
+
'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
|
475
|
+
'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
|
476
|
+
'ata' => 'M', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'G',
|
477
|
+
'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'G',
|
478
|
+
|
479
|
+
'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
|
480
|
+
'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
|
481
|
+
'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
|
482
|
+
'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
|
483
|
+
},
|
484
|
+
|
485
|
+
# codon table 14
|
486
|
+
14 => {
|
487
|
+
'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
|
488
|
+
'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
|
489
|
+
'tta' => 'L', 'tca' => 'S', 'taa' => 'Y', 'tga' => 'W',
|
490
|
+
'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
|
491
|
+
|
492
|
+
'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
|
493
|
+
'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
|
494
|
+
'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
|
495
|
+
'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
|
496
|
+
|
497
|
+
'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
|
498
|
+
'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
|
499
|
+
'ata' => 'I', 'aca' => 'T', 'aaa' => 'N', 'aga' => 'S',
|
500
|
+
'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'S',
|
501
|
+
|
502
|
+
'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
|
503
|
+
'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
|
504
|
+
'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
|
505
|
+
'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
|
506
|
+
},
|
507
|
+
|
508
|
+
# codon table 15
|
509
|
+
15 => {
|
510
|
+
'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
|
511
|
+
'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
|
512
|
+
'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => '*',
|
513
|
+
'ttg' => 'L', 'tcg' => 'S', 'tag' => 'Q', 'tgg' => 'W',
|
514
|
+
|
515
|
+
'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
|
516
|
+
'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
|
517
|
+
'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
|
518
|
+
'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
|
519
|
+
|
520
|
+
'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
|
521
|
+
'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
|
522
|
+
'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
|
523
|
+
'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
|
524
|
+
|
525
|
+
'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
|
526
|
+
'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
|
527
|
+
'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
|
528
|
+
'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
|
529
|
+
},
|
530
|
+
|
531
|
+
# codon table 16
|
532
|
+
16 => {
|
533
|
+
'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
|
534
|
+
'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
|
535
|
+
'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => '*',
|
536
|
+
'ttg' => 'L', 'tcg' => 'S', 'tag' => 'L', 'tgg' => 'W',
|
537
|
+
|
538
|
+
'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
|
539
|
+
'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
|
540
|
+
'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
|
541
|
+
'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
|
542
|
+
|
543
|
+
'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
|
544
|
+
'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
|
545
|
+
'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
|
546
|
+
'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
|
547
|
+
|
548
|
+
'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
|
549
|
+
'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
|
550
|
+
'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
|
551
|
+
'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
|
552
|
+
},
|
553
|
+
|
554
|
+
# codon table 21
|
555
|
+
21 => {
|
556
|
+
'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
|
557
|
+
'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
|
558
|
+
'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'W',
|
559
|
+
'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
|
560
|
+
|
561
|
+
'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
|
562
|
+
'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
|
563
|
+
'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
|
564
|
+
'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
|
565
|
+
|
566
|
+
'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
|
567
|
+
'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
|
568
|
+
'ata' => 'M', 'aca' => 'T', 'aaa' => 'N', 'aga' => 'S',
|
569
|
+
'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'S',
|
570
|
+
|
571
|
+
'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
|
572
|
+
'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
|
573
|
+
'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
|
574
|
+
'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
|
575
|
+
},
|
576
|
+
|
577
|
+
# codon table 22
|
578
|
+
22 => {
|
579
|
+
'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
|
580
|
+
'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
|
581
|
+
'tta' => 'L', 'tca' => '*', 'taa' => '*', 'tga' => '*',
|
582
|
+
'ttg' => 'L', 'tcg' => 'S', 'tag' => 'L', 'tgg' => 'W',
|
583
|
+
|
584
|
+
'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
|
585
|
+
'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
|
586
|
+
'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
|
587
|
+
'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
|
588
|
+
|
589
|
+
'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
|
590
|
+
'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
|
591
|
+
'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
|
592
|
+
'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
|
593
|
+
|
594
|
+
'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
|
595
|
+
'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
|
596
|
+
'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
|
597
|
+
'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
|
598
|
+
},
|
599
|
+
|
600
|
+
# codon table 23
|
601
|
+
23 => {
|
602
|
+
'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
|
603
|
+
'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
|
604
|
+
'tta' => '*', 'tca' => 'S', 'taa' => '*', 'tga' => '*',
|
605
|
+
'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
|
606
|
+
|
607
|
+
'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
|
608
|
+
'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
|
609
|
+
'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
|
610
|
+
'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
|
611
|
+
|
612
|
+
'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
|
613
|
+
'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
|
614
|
+
'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
|
615
|
+
'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
|
616
|
+
|
617
|
+
'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
|
618
|
+
'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
|
619
|
+
'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
|
620
|
+
'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
|
621
|
+
},
|
622
|
+
|
623
|
+
}
|
624
|
+
|
625
|
+
end # CodonTable
|
626
|
+
|
627
|
+
end # module Bio
|
628
|
+
|
629
|
+
|
630
|
+
if __FILE__ == $0
|
631
|
+
|
632
|
+
begin
|
633
|
+
require 'pp'
|
634
|
+
alias p pp
|
635
|
+
rescue LoadError
|
636
|
+
end
|
637
|
+
|
638
|
+
puts "### Bio::CodonTable[1]"
|
639
|
+
p ct1 = Bio::CodonTable[1]
|
640
|
+
|
641
|
+
puts ">>> Bio::CodonTable#table"
|
642
|
+
p ct1.table
|
643
|
+
|
644
|
+
puts ">>> Bio::CodonTable#each"
|
645
|
+
ct1.each do |codon, aa|
|
646
|
+
puts "#{codon} -- #{aa}"
|
647
|
+
end
|
648
|
+
|
649
|
+
puts ">>> Bio::CodonTable#definition"
|
650
|
+
p ct1.definition
|
651
|
+
|
652
|
+
puts ">>> Bio::CodonTable#['atg']"
|
653
|
+
p ct1['atg']
|
654
|
+
|
655
|
+
puts ">>> Bio::CodonTable#revtrans('A')"
|
656
|
+
p ct1.revtrans('A')
|
657
|
+
|
658
|
+
puts ">>> Bio::CodonTable#start_codon?('atg')"
|
659
|
+
p ct1.start_codon?('atg')
|
660
|
+
|
661
|
+
puts ">>> Bio::CodonTable#start_codon?('aaa')"
|
662
|
+
p ct1.start_codon?('aaa')
|
663
|
+
|
664
|
+
puts ">>> Bio::CodonTable#stop_codon?('tag')"
|
665
|
+
p ct1.stop_codon?('tag')
|
666
|
+
|
667
|
+
puts ">>> Bio::CodonTable#stop_codon?('aaa')"
|
668
|
+
p ct1.stop_codon?('aaa')
|
669
|
+
|
670
|
+
puts ">>> ct1_copy = Bio::CodonTable.copy(1)"
|
671
|
+
p ct1_copy = Bio::CodonTable.copy(1)
|
672
|
+
puts ">>> ct1_copy['tga'] = 'U'"
|
673
|
+
p ct1_copy['tga'] = 'U'
|
674
|
+
puts " orig : #{ct1['tga']}"
|
675
|
+
puts " copy : #{ct1_copy['tga']}"
|
676
|
+
|
677
|
+
|
678
|
+
puts "### ct = Bio::CodonTable.new(hash, definition)"
|
679
|
+
hash = {
|
680
|
+
'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
|
681
|
+
'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
|
682
|
+
'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'U',
|
683
|
+
'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
|
684
|
+
|
685
|
+
'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
|
686
|
+
'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
|
687
|
+
'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
|
688
|
+
'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
|
689
|
+
|
690
|
+
'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
|
691
|
+
'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
|
692
|
+
'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
|
693
|
+
'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
|
694
|
+
|
695
|
+
'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
|
696
|
+
'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
|
697
|
+
'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
|
698
|
+
'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
|
699
|
+
}
|
700
|
+
my_ct = Bio::CodonTable.new(hash, "my codon table")
|
701
|
+
|
702
|
+
puts ">>> ct.definition"
|
703
|
+
puts my_ct.definition
|
704
|
+
|
705
|
+
puts ">>> ct.definition=(str)"
|
706
|
+
my_ct.definition = "selenoproteins (Eukaryote)"
|
707
|
+
puts my_ct.definition
|
708
|
+
|
709
|
+
puts ">>> ct['tga']"
|
710
|
+
puts my_ct['tga']
|
711
|
+
|
712
|
+
puts ">>> ct.revtrans('U')"
|
713
|
+
puts my_ct.revtrans('U')
|
714
|
+
|
715
|
+
puts ">>> ct.stop_codon?('tga')"
|
716
|
+
puts my_ct.stop_codon?('tga')
|
717
|
+
|
718
|
+
puts ">>> ct.stop_codon?('tag')"
|
719
|
+
puts my_ct.stop_codon?('tag')
|
720
|
+
|
721
|
+
end
|
722
|
+
|