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 +1,63 @@
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#
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# = bio/db/fasta/fasta_to_biosequence.rb - Bio::FastaFormat to Bio::Sequence adapter module
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#
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# Copyright:: Copyright (C) 2008
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# Naohisa Goto <ng@bioruby.org>,
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# License:: The Ruby License
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#
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# $Id:$
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#
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require 'bio/sequence'
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require 'bio/sequence/adapter'
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# Internal use only. Normal users should not use this module.
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#
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# Bio::FastaFormat to Bio::Sequence adapter module.
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# It is internally used in Bio::FastaFormat#to_biosequence.
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#
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module Bio::Sequence::Adapter::FastaFormat
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extend Bio::Sequence::Adapter
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private
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def_biosequence_adapter :seq
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# primary accession
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def_biosequence_adapter :primary_accession do |orig|
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orig.identifiers.accessions.first or orig.identifiers.entry_id
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end
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# secondary accessions
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def_biosequence_adapter :secondary_accessions do |orig|
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orig.identifiers.accessions[1..-1]
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end
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# entry_id
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def_biosequence_adapter :entry_id do |orig|
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orig.identifiers.locus or orig.identifiers.accessions.first or
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orig.identifiers.entry_id
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end
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# NCBI GI is stored on other_seqids
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def_biosequence_adapter :other_seqids do |orig|
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other = []
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if orig.identifiers.gi then
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other.push Bio::Sequence::DBLink.new('GI', orig.identifiers.gi)
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end
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other.empty? ? nil : other
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end
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# definition
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def_biosequence_adapter :definition do |orig|
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if orig.identifiers.accessions.empty? and
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!(orig.identifiers.gi) then
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orig.definition
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else
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orig.identifiers.description
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end
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end
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end #module Bio::Sequence::Adapter::FastaFormat
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#
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# = bio/db/fasta/format_fasta.rb - Fasta format generater
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#
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# Copyright:: Copyright (C) 2006-2008
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# Toshiaki Katayama <k@bioruby.org>,
|
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# Naohisa Goto <ng@bioruby.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: format_fasta.rb,v 1.1.2.1 2008/03/04 11:26:59 ngoto Exp $
|
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#
|
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|
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require 'bio/sequence/format'
|
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|
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module Bio::Sequence::Format::Formatter
|
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|
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# INTERNAL USE ONLY, YOU SHOULD NOT USE THIS CLASS.
|
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# Simple Fasta format output class for Bio::Sequence.
|
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class Fasta < Bio::Sequence::Format::FormatterBase
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|
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# INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD.
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#
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# Creates a new Fasta format generater object from the sequence.
|
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#
|
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# ---
|
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# *Arguments*:
|
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# * _sequence_: Bio::Sequence object
|
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# * (optional) :header => _header_: String (default nil)
|
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# * (optional) :width => _width_: Fixnum (default 70)
|
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def initialize; end if false # dummy for RDoc
|
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|
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# INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD.
|
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#
|
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# Output the FASTA format string of the sequence.
|
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#
|
36
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# Currently, this method is used in Bio::Sequence#output like so,
|
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#
|
38
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# s = Bio::Sequence.new('atgc')
|
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# puts s.output(:fasta) #=> "> \natgc\n"
|
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# ---
|
41
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# *Returns*:: String object
|
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def output
|
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header = @options[:header]
|
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width = @options.has_key?(:width) ? @options[:width] : 70
|
45
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+
seq = @sequence.seq
|
46
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entry_id = @sequence.entry_id ||
|
47
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"#{@sequence.primary_accession}.#{@sequence.sequence_version}"
|
48
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definition = @sequence.definition
|
49
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header ||= "#{entry_id} #{definition}"
|
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+
|
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">#{header}\n" +
|
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if width
|
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seq.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
|
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else
|
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seq.to_s + "\n"
|
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end
|
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end
|
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end #class Fasta
|
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|
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# INTERNAL USE ONLY, YOU SHOULD NOT USE THIS CLASS.
|
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# NCBI-Style Fasta format output class for Bio::Sequence.
|
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# (like "ncbi" format in EMBOSS)
|
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#
|
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# Note that this class is under construction.
|
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class Fasta_ncbi < Bio::Sequence::Format::FormatterBase
|
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|
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# INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD.
|
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#
|
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# Output the FASTA format string of the sequence.
|
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#
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# Currently, this method is used in Bio::Sequence#output like so,
|
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#
|
73
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# s = Bio::Sequence.new('atgc')
|
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# puts s.output(:ncbi) #=> "> \natgc\n"
|
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# ---
|
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# *Returns*:: String object
|
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def output
|
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width = 70
|
79
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seq = @sequence.seq
|
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+
#gi = @sequence.gi_number
|
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+
dbname = 'lcl'
|
82
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+
if @sequence.primary_accession.to_s.empty? then
|
83
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idstr = @sequence.entry_id
|
84
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else
|
85
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+
idstr = "#{@sequence.primary_accession}.#{@sequence.sequence_version}"
|
86
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+
end
|
87
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|
88
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definition = @sequence.definition
|
89
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header = "#{dbname}|#{idstr} #{definition}"
|
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+
|
91
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+
">#{header}\n" + seq.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
|
92
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end
|
93
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end #class Ncbi
|
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+
|
95
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+
end #module Bio::Sequence::Format::Formatter
|
96
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+
|
97
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+
|
@@ -0,0 +1,307 @@
|
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1
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#
|
2
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# = bio/db/genbank/common.rb - Common methods for GenBank style database classes
|
3
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+
#
|
4
|
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# Copyright:: Copyright (C) 2004 Toshiaki Katayama <k@bioruby.org>
|
5
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# License:: The Ruby License
|
6
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#
|
7
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# $Id: common.rb,v 1.11.2.5 2008/06/17 15:53:21 ngoto Exp $
|
8
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#
|
9
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+
|
10
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require 'bio/db'
|
11
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|
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module Bio
|
13
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class NCBIDB
|
14
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+
|
15
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# == Description
|
16
|
+
#
|
17
|
+
# This module defines a common framework among GenBank, GenPept, RefSeq, and
|
18
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+
# DDBJ. For more details, see the documentations in each genbank/*.rb files.
|
19
|
+
#
|
20
|
+
# == References
|
21
|
+
#
|
22
|
+
# * ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt
|
23
|
+
# * http://www.ncbi.nlm.nih.gov/collab/FT/index.html
|
24
|
+
#
|
25
|
+
module Common
|
26
|
+
|
27
|
+
DELIMITER = RS = "\n//\n"
|
28
|
+
TAGSIZE = 12
|
29
|
+
|
30
|
+
def initialize(entry)
|
31
|
+
super(entry, TAGSIZE)
|
32
|
+
end
|
33
|
+
|
34
|
+
# LOCUS -- Locus class must be defined in child classes.
|
35
|
+
def locus
|
36
|
+
# must be overrided in each subclass
|
37
|
+
end
|
38
|
+
|
39
|
+
# DEFINITION -- Returns contents of the DEFINITION record as a String.
|
40
|
+
def definition
|
41
|
+
field_fetch('DEFINITION')
|
42
|
+
end
|
43
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+
|
44
|
+
|
45
|
+
# ACCESSION -- Returns contents of the ACCESSION record as an Array.
|
46
|
+
def accessions
|
47
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+
field_fetch('ACCESSION').strip.split(/\s+/)
|
48
|
+
end
|
49
|
+
|
50
|
+
|
51
|
+
# VERSION -- Returns contents of the VERSION record as an Array of Strings.
|
52
|
+
def versions
|
53
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+
@data['VERSION'] ||= fetch('VERSION').split(/\s+/)
|
54
|
+
end
|
55
|
+
|
56
|
+
# Returns the first part of the VERSION record as "ACCESSION.VERSION" String.
|
57
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+
def acc_version
|
58
|
+
versions.first.to_s
|
59
|
+
end
|
60
|
+
|
61
|
+
# Returns the ACCESSION part of the acc_version.
|
62
|
+
def accession
|
63
|
+
acc_version.split(/\./).first.to_s
|
64
|
+
end
|
65
|
+
|
66
|
+
# Returns the VERSION part of the acc_version as a Fixnum
|
67
|
+
def version
|
68
|
+
acc_version.split(/\./).last.to_i
|
69
|
+
end
|
70
|
+
|
71
|
+
# Returns the second part of the VERSION record as a "GI:#######" String.
|
72
|
+
def gi
|
73
|
+
versions.last
|
74
|
+
end
|
75
|
+
|
76
|
+
|
77
|
+
# NID -- Returns contents of the NID record as a String.
|
78
|
+
def nid
|
79
|
+
field_fetch('NID')
|
80
|
+
end
|
81
|
+
|
82
|
+
|
83
|
+
# KEYWORDS -- Returns contents of the KEYWORDS record as an Array of Strings.
|
84
|
+
def keywords
|
85
|
+
@data['KEYWORDS'] ||= fetch('KEYWORDS').chomp('.').split(/; /)
|
86
|
+
end
|
87
|
+
|
88
|
+
|
89
|
+
# SEGMENT -- Returns contents of the SEGMENT record as a "m/n" form String.
|
90
|
+
def segment
|
91
|
+
@data['SEGMENT'] ||= fetch('SEGMENT').scan(/\d+/).join("/")
|
92
|
+
end
|
93
|
+
|
94
|
+
|
95
|
+
# SOURCE -- Returns contents of the SOURCE record as a Hash.
|
96
|
+
def source
|
97
|
+
unless @data['SOURCE']
|
98
|
+
name, org = get('SOURCE').split('ORGANISM')
|
99
|
+
org ||= ""
|
100
|
+
if org[/\S+;/]
|
101
|
+
organism = $`
|
102
|
+
taxonomy = $& + $'
|
103
|
+
elsif org[/\S+\./] # rs:NC_001741
|
104
|
+
organism = $`
|
105
|
+
taxonomy = $& + $'
|
106
|
+
else
|
107
|
+
organism = org
|
108
|
+
taxonomy = ''
|
109
|
+
end
|
110
|
+
@data['SOURCE'] = {
|
111
|
+
'common_name' => truncate(tag_cut(name)),
|
112
|
+
'organism' => truncate(organism),
|
113
|
+
'taxonomy' => truncate(taxonomy),
|
114
|
+
}
|
115
|
+
@data['SOURCE'].default = ''
|
116
|
+
end
|
117
|
+
@data['SOURCE']
|
118
|
+
end
|
119
|
+
|
120
|
+
def common_name
|
121
|
+
source['common_name']
|
122
|
+
end
|
123
|
+
alias vernacular_name common_name
|
124
|
+
|
125
|
+
def organism
|
126
|
+
source['organism']
|
127
|
+
end
|
128
|
+
|
129
|
+
def taxonomy
|
130
|
+
source['taxonomy']
|
131
|
+
end
|
132
|
+
|
133
|
+
|
134
|
+
# REFERENCE -- Returns contents of the REFERENCE records as an Array of
|
135
|
+
# Bio::Reference objects.
|
136
|
+
def references
|
137
|
+
unless @data['REFERENCE']
|
138
|
+
ary = []
|
139
|
+
toptag2array(get('REFERENCE')).each do |ref|
|
140
|
+
hash = Hash.new
|
141
|
+
subtag2array(ref).each do |field|
|
142
|
+
case tag_get(field)
|
143
|
+
when /REFERENCE/
|
144
|
+
if /(\d+)(\s*\((.+)\))?/m =~ tag_cut(field) then
|
145
|
+
hash['embl_gb_record_number'] = $1.to_i
|
146
|
+
if $3 and $3 != 'sites' then
|
147
|
+
seqpos = $3
|
148
|
+
seqpos.sub!(/\A\s*bases\s+/, '')
|
149
|
+
seqpos.gsub!(/(\d+)\s+to\s+(\d+)/, "\\1-\\2")
|
150
|
+
seqpos.gsub!(/\s*\;\s*/, ', ')
|
151
|
+
hash['sequence_position'] = seqpos
|
152
|
+
end
|
153
|
+
end
|
154
|
+
when /AUTHORS/
|
155
|
+
authors = truncate(tag_cut(field))
|
156
|
+
authors = authors.split(/, /)
|
157
|
+
authors[-1] = authors[-1].split(/\s+and\s+/) if authors[-1]
|
158
|
+
authors = authors.flatten.map { |a| a.sub(/,/, ', ') }
|
159
|
+
hash['authors'] = authors
|
160
|
+
when /TITLE/
|
161
|
+
hash['title'] = truncate(tag_cut(field)) + '.'
|
162
|
+
when /JOURNAL/
|
163
|
+
journal = truncate(tag_cut(field))
|
164
|
+
if journal =~ /(.*) (\d+) \((\d+)\), (\d+-\d+) \((\d+)\)$/
|
165
|
+
hash['journal'] = $1
|
166
|
+
hash['volume'] = $2
|
167
|
+
hash['issue'] = $3
|
168
|
+
hash['pages'] = $4
|
169
|
+
hash['year'] = $5
|
170
|
+
else
|
171
|
+
hash['journal'] = journal
|
172
|
+
end
|
173
|
+
when /MEDLINE/
|
174
|
+
hash['medline'] = truncate(tag_cut(field))
|
175
|
+
when /PUBMED/
|
176
|
+
hash['pubmed'] = truncate(tag_cut(field))
|
177
|
+
when /REMARK/
|
178
|
+
hash['comments'] ||= []
|
179
|
+
hash['comments'].push truncate(tag_cut(field))
|
180
|
+
end
|
181
|
+
end
|
182
|
+
ary.push(Reference.new(hash))
|
183
|
+
end
|
184
|
+
@data['REFERENCE'] = ary.extend(Bio::References::BackwardCompatibility)
|
185
|
+
end
|
186
|
+
if block_given?
|
187
|
+
@data['REFERENCE'].each do |r|
|
188
|
+
yield r
|
189
|
+
end
|
190
|
+
else
|
191
|
+
@data['REFERENCE']
|
192
|
+
end
|
193
|
+
end
|
194
|
+
|
195
|
+
|
196
|
+
# COMMENT -- Returns contents of the COMMENT record as a String.
|
197
|
+
def comment
|
198
|
+
str = get('COMMENT').to_s.sub(/\ACOMMENT /, '')
|
199
|
+
str.gsub!(/^ {12}/, '')
|
200
|
+
str.chomp!
|
201
|
+
str
|
202
|
+
end
|
203
|
+
|
204
|
+
|
205
|
+
# FEATURES -- Returns contents of the FEATURES record as an array of
|
206
|
+
# Bio::Feature objects.
|
207
|
+
def features
|
208
|
+
unless @data['FEATURES']
|
209
|
+
ary = []
|
210
|
+
in_quote = false
|
211
|
+
get('FEATURES').each_line do |line|
|
212
|
+
next if line =~ /^FEATURES/
|
213
|
+
|
214
|
+
# feature type (source, CDS, ...)
|
215
|
+
head = line[0,20].to_s.strip
|
216
|
+
|
217
|
+
# feature value (position or /qualifier=)
|
218
|
+
body = line[20,60].to_s.chomp
|
219
|
+
|
220
|
+
# sub-array [ feature type, position, /q="data", ... ]
|
221
|
+
if line =~ /^ {5}\S/
|
222
|
+
ary.push([ head, body ])
|
223
|
+
|
224
|
+
# feature qualifier start (/q="data..., /q="data...", /q=data, /q)
|
225
|
+
elsif body =~ /^ \// and not in_quote # gb:IRO125195
|
226
|
+
ary.last.push(body)
|
227
|
+
|
228
|
+
# flag for open quote (/q="data...)
|
229
|
+
if body =~ /="/ and body !~ /"$/
|
230
|
+
in_quote = true
|
231
|
+
end
|
232
|
+
|
233
|
+
# feature qualifier continued (...data..., ...data...")
|
234
|
+
else
|
235
|
+
ary.last.last << body
|
236
|
+
|
237
|
+
# flag for closing quote (/q="data... lines ...")
|
238
|
+
if body =~ /"$/
|
239
|
+
in_quote = false
|
240
|
+
end
|
241
|
+
end
|
242
|
+
end
|
243
|
+
|
244
|
+
ary.collect! do |subary|
|
245
|
+
parse_qualifiers(subary)
|
246
|
+
end
|
247
|
+
|
248
|
+
@data['FEATURES'] = ary.extend(Bio::Features::BackwardCompatibility)
|
249
|
+
end
|
250
|
+
if block_given?
|
251
|
+
@data['FEATURES'].each do |f|
|
252
|
+
yield f
|
253
|
+
end
|
254
|
+
else
|
255
|
+
@data['FEATURES']
|
256
|
+
end
|
257
|
+
end
|
258
|
+
|
259
|
+
|
260
|
+
# ORIGIN -- Returns contents of the ORIGIN record as a String.
|
261
|
+
def origin
|
262
|
+
unless @data['ORIGIN']
|
263
|
+
ori, seqstr = get('ORIGIN').split("\n", 2)
|
264
|
+
seqstr ||= ""
|
265
|
+
@data['ORIGIN'] = truncate(tag_cut(ori))
|
266
|
+
@data['SEQUENCE'] = seqstr.tr("0-9 \t\n\r\/", '')
|
267
|
+
end
|
268
|
+
@data['ORIGIN']
|
269
|
+
end
|
270
|
+
|
271
|
+
|
272
|
+
### private methods
|
273
|
+
|
274
|
+
private
|
275
|
+
|
276
|
+
def parse_qualifiers(ary)
|
277
|
+
feature = Feature.new
|
278
|
+
|
279
|
+
feature.feature = ary.shift
|
280
|
+
feature.position = ary.shift.gsub(/\s/, '')
|
281
|
+
|
282
|
+
ary.each do |f|
|
283
|
+
if f =~ %r{/([^=]+)=?"?([^"]*)"?}
|
284
|
+
qualifier, value = $1, $2
|
285
|
+
|
286
|
+
case qualifier
|
287
|
+
when 'translation'
|
288
|
+
value = Sequence::AA.new(value)
|
289
|
+
when 'codon_start'
|
290
|
+
value = value.to_i
|
291
|
+
else
|
292
|
+
value = true if value.empty?
|
293
|
+
end
|
294
|
+
|
295
|
+
feature.append(Feature::Qualifier.new(qualifier, value))
|
296
|
+
end
|
297
|
+
end
|
298
|
+
|
299
|
+
return feature
|
300
|
+
end
|
301
|
+
|
302
|
+
end # Common
|
303
|
+
|
304
|
+
end # GenBank
|
305
|
+
end # Bio
|
306
|
+
|
307
|
+
|