wwood-bioruby 1.2.11
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- data/README.rdoc +205 -0
- data/README_DEV.rdoc +285 -0
- data/VERSION.yml +4 -0
- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +293 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/lib/bio.rb +306 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +505 -0
- data/lib/bio/appl/blast/ddbj.rb +142 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/genomenet.rb +263 -0
- data/lib/bio/appl/blast/ncbioptions.rb +220 -0
- data/lib/bio/appl/blast/remote.rb +105 -0
- data/lib/bio/appl/blast/report.rb +767 -0
- data/lib/bio/appl/blast/rexml.rb +144 -0
- data/lib/bio/appl/blast/rpsblast.rb +277 -0
- data/lib/bio/appl/blast/wublast.rb +635 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blat/report.rb +530 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta.rb +235 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/gcg/msf.rb +212 -0
- data/lib/bio/appl/gcg/seq.rb +195 -0
- data/lib/bio/appl/genscan/report.rb +552 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/hmmer/report.rb +683 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/paml/baseml.rb +95 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/codeml.rb +242 -0
- data/lib/bio/appl/paml/codeml/rates.rb +67 -0
- data/lib/bio/appl/paml/codeml/report.rb +67 -0
- data/lib/bio/appl/paml/common.rb +348 -0
- data/lib/bio/appl/paml/common_report.rb +38 -0
- data/lib/bio/appl/paml/yn00.rb +103 -0
- data/lib/bio/appl/paml/yn00/report.rb +32 -0
- data/lib/bio/appl/phylip/alignment.rb +133 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/psort/report.rb +542 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +124 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sosui/report.rb +151 -0
- data/lib/bio/appl/spidey/report.rb +593 -0
- data/lib/bio/appl/targetp/report.rb +267 -0
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +231 -0
- data/lib/bio/command.rb +593 -0
- data/lib/bio/compat/features.rb +157 -0
- data/lib/bio/compat/references.rb +128 -0
- data/lib/bio/data/aa.rb +353 -0
- data/lib/bio/data/codontable.rb +722 -0
- data/lib/bio/data/na.rb +223 -0
- data/lib/bio/db.rb +329 -0
- data/lib/bio/db/aaindex.rb +357 -0
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +67 -0
- data/lib/bio/db/biosql/sequence.rb +508 -0
- data/lib/bio/db/embl/common.rb +352 -0
- data/lib/bio/db/embl/embl.rb +500 -0
- data/lib/bio/db/embl/embl_to_biosequence.rb +85 -0
- data/lib/bio/db/embl/format_embl.rb +190 -0
- data/lib/bio/db/embl/sptr.rb +1283 -0
- data/lib/bio/db/embl/swissprot.rb +42 -0
- data/lib/bio/db/embl/trembl.rb +41 -0
- data/lib/bio/db/embl/uniprot.rb +42 -0
- data/lib/bio/db/fantom.rb +597 -0
- data/lib/bio/db/fasta.rb +410 -0
- data/lib/bio/db/fasta/defline.rb +532 -0
- data/lib/bio/db/fasta/fasta_to_biosequence.rb +63 -0
- data/lib/bio/db/fasta/format_fasta.rb +97 -0
- data/lib/bio/db/genbank/common.rb +307 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/format_genbank.rb +187 -0
- data/lib/bio/db/genbank/genbank.rb +250 -0
- data/lib/bio/db/genbank/genbank_to_biosequence.rb +86 -0
- data/lib/bio/db/genbank/genpept.rb +60 -0
- data/lib/bio/db/genbank/refseq.rb +18 -0
- data/lib/bio/db/gff.rb +1846 -0
- data/lib/bio/db/go.rb +481 -0
- data/lib/bio/db/kegg/brite.rb +41 -0
- data/lib/bio/db/kegg/compound.rb +131 -0
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +148 -0
- data/lib/bio/db/kegg/expression.rb +155 -0
- data/lib/bio/db/kegg/genes.rb +263 -0
- data/lib/bio/db/kegg/genome.rb +241 -0
- data/lib/bio/db/kegg/glycan.rb +166 -0
- data/lib/bio/db/kegg/keggtab.rb +357 -0
- data/lib/bio/db/kegg/kgml.rb +256 -0
- data/lib/bio/db/kegg/orthology.rb +136 -0
- data/lib/bio/db/kegg/reaction.rb +82 -0
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +107 -0
- data/lib/bio/db/medline.rb +326 -0
- data/lib/bio/db/nbrf.rb +191 -0
- data/lib/bio/db/newick.rb +658 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +29 -0
- data/lib/bio/db/pdb/atom.rb +77 -0
- data/lib/bio/db/pdb/chain.rb +210 -0
- data/lib/bio/db/pdb/chemicalcomponent.rb +224 -0
- data/lib/bio/db/pdb/model.rb +148 -0
- data/lib/bio/db/pdb/pdb.rb +1911 -0
- data/lib/bio/db/pdb/residue.rb +176 -0
- data/lib/bio/db/pdb/utils.rb +399 -0
- data/lib/bio/db/prosite.rb +597 -0
- data/lib/bio/db/rebase.rb +456 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/db/url.rb +42 -0
- data/lib/bio/feature.rb +139 -0
- data/lib/bio/io/biosql/biodatabase.rb +64 -0
- data/lib/bio/io/biosql/bioentry.rb +29 -0
- data/lib/bio/io/biosql/bioentry_dbxref.rb +11 -0
- data/lib/bio/io/biosql/bioentry_path.rb +12 -0
- data/lib/bio/io/biosql/bioentry_qualifier_value.rb +10 -0
- data/lib/bio/io/biosql/bioentry_reference.rb +10 -0
- data/lib/bio/io/biosql/bioentry_relationship.rb +10 -0
- data/lib/bio/io/biosql/biosequence.rb +11 -0
- data/lib/bio/io/biosql/comment.rb +7 -0
- data/lib/bio/io/biosql/config/database.yml +20 -0
- data/lib/bio/io/biosql/dbxref.rb +13 -0
- data/lib/bio/io/biosql/dbxref_qualifier_value.rb +12 -0
- data/lib/bio/io/biosql/location.rb +32 -0
- data/lib/bio/io/biosql/location_qualifier_value.rb +11 -0
- data/lib/bio/io/biosql/ontology.rb +10 -0
- data/lib/bio/io/biosql/reference.rb +9 -0
- data/lib/bio/io/biosql/seqfeature.rb +32 -0
- data/lib/bio/io/biosql/seqfeature_dbxref.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_path.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_qualifier_value.rb +20 -0
- data/lib/bio/io/biosql/seqfeature_relationship.rb +11 -0
- data/lib/bio/io/biosql/taxon.rb +12 -0
- data/lib/bio/io/biosql/taxon_name.rb +9 -0
- data/lib/bio/io/biosql/term.rb +27 -0
- data/lib/bio/io/biosql/term_dbxref.rb +11 -0
- data/lib/bio/io/biosql/term_path.rb +12 -0
- data/lib/bio/io/biosql/term_relationship.rb +13 -0
- data/lib/bio/io/biosql/term_relationship_term.rb +11 -0
- data/lib/bio/io/biosql/term_synonym.rb +10 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +638 -0
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +163 -0
- data/lib/bio/io/fetch.rb +195 -0
- data/lib/bio/io/flatfile.rb +482 -0
- data/lib/bio/io/flatfile/autodetection.rb +545 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/buffer.rb +237 -0
- data/lib/bio/io/flatfile/index.rb +1381 -0
- data/lib/bio/io/flatfile/indexer.rb +805 -0
- data/lib/bio/io/flatfile/splitter.rb +297 -0
- data/lib/bio/io/higet.rb +73 -0
- data/lib/bio/io/hinv.rb +442 -0
- data/lib/bio/io/keggapi.rb +805 -0
- data/lib/bio/io/ncbirest.rb +733 -0
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +307 -0
- data/lib/bio/io/registry.rb +292 -0
- data/lib/bio/io/soapwsdl.rb +119 -0
- data/lib/bio/io/sql.rb +186 -0
- data/lib/bio/location.rb +867 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +960 -0
- data/lib/bio/reference.rb +602 -0
- data/lib/bio/sequence.rb +456 -0
- data/lib/bio/sequence/aa.rb +152 -0
- data/lib/bio/sequence/adapter.rb +108 -0
- data/lib/bio/sequence/common.rb +310 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/dblink.rb +54 -0
- data/lib/bio/sequence/format.rb +358 -0
- data/lib/bio/sequence/format_raw.rb +23 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +491 -0
- data/lib/bio/shell.rb +44 -0
- data/lib/bio/shell/core.rb +578 -0
- data/lib/bio/shell/demo.rb +146 -0
- data/lib/bio/shell/interface.rb +218 -0
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +71 -0
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +218 -0
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +105 -0
- data/lib/bio/shell/plugin/flatfile.rb +101 -0
- data/lib/bio/shell/plugin/keggapi.rb +181 -0
- data/lib/bio/shell/plugin/midi.rb +430 -0
- data/lib/bio/shell/plugin/obda.rb +45 -0
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +247 -0
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +102 -0
- data/lib/bio/tree.rb +852 -0
- data/lib/bio/util/color_scheme.rb +191 -0
- data/lib/bio/util/color_scheme/buried.rb +59 -0
- data/lib/bio/util/color_scheme/helix.rb +59 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +64 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +31 -0
- data/lib/bio/util/color_scheme/strand.rb +59 -0
- data/lib/bio/util/color_scheme/taylor.rb +50 -0
- data/lib/bio/util/color_scheme/turn.rb +59 -0
- data/lib/bio/util/color_scheme/zappo.rb +50 -0
- data/lib/bio/util/contingency_table.rb +370 -0
- data/lib/bio/util/restriction_enzyme.rb +228 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
- data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +200 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/aaindex/DAYM780301 +30 -0
- data/test/data/aaindex/PRAM900102 +20 -0
- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
- data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
- data/test/data/blast/2.2.15.blastp.m7 +876 -0
- data/test/data/blast/b0002.faa +15 -0
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- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/blast/blastp-multi.m7 +188 -0
- data/test/data/command/echoarg2.bat +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/embl/AB090716.embl.rel89 +63 -0
- data/test/data/fasta/example1.txt +75 -0
- data/test/data/fasta/example2.txt +21 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/paml/codeml/control_file.txt +30 -0
- data/test/data/paml/codeml/output.txt +78 -0
- data/test/data/paml/codeml/rates +217 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/rpsblast/misc.rpsblast +193 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/functional/bio/appl/test_pts1.rb +115 -0
- data/test/functional/bio/io/test_ensembl.rb +229 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -0
- data/test/functional/bio/sequence/test_output_embl.rb +51 -0
- data/test/functional/bio/test_command.rb +301 -0
- data/test/runner.rb +14 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_ncbioptions.rb +112 -0
- data/test/unit/bio/appl/blast/test_report.rb +1135 -0
- data/test/unit/bio/appl/blast/test_rpsblast.rb +398 -0
- data/test/unit/bio/appl/genscan/test_report.rb +182 -0
- data/test/unit/bio/appl/hmmer/test_report.rb +342 -0
- data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
- data/test/unit/bio/appl/mafft/test_report.rb +63 -0
- data/test/unit/bio/appl/paml/codeml/test_rates.rb +45 -0
- data/test/unit/bio/appl/paml/codeml/test_report.rb +45 -0
- data/test/unit/bio/appl/paml/test_codeml.rb +174 -0
- data/test/unit/bio/appl/sosui/test_report.rb +81 -0
- data/test/unit/bio/appl/targetp/test_report.rb +146 -0
- data/test/unit/bio/appl/test_blast.rb +277 -0
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_psort.rb +57 -0
- data/test/unit/bio/appl/test_pts1.rb +77 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +126 -0
- data/test/unit/bio/data/test_aa.rb +90 -0
- data/test/unit/bio/data/test_codontable.rb +107 -0
- data/test/unit/bio/data/test_na.rb +80 -0
- data/test/unit/bio/db/embl/test_common.rb +117 -0
- data/test/unit/bio/db/embl/test_embl.rb +214 -0
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +203 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1812 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +31 -0
- data/test/unit/bio/db/kegg/test_genes.rb +45 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +152 -0
- data/test/unit/bio/db/test_aaindex.rb +197 -0
- data/test/unit/bio/db/test_fasta.rb +250 -0
- data/test/unit/bio/db/test_gff.rb +1190 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_medline.rb +127 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +364 -0
- data/test/unit/bio/db/test_prosite.rb +1437 -0
- data/test/unit/bio/db/test_rebase.rb +101 -0
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/db/test_url.rb +36 -0
- data/test/unit/bio/io/flatfile/test_autodetection.rb +375 -0
- data/test/unit/bio/io/flatfile/test_buffer.rb +251 -0
- data/test/unit/bio/io/flatfile/test_splitter.rb +369 -0
- data/test/unit/bio/io/test_ddbjxml.rb +80 -0
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +42 -0
- data/test/unit/bio/io/test_flatfile.rb +505 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +115 -0
- data/test/unit/bio/sequence/test_common.rb +373 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -0
- data/test/unit/bio/sequence/test_dblink.rb +58 -0
- data/test/unit/bio/sequence/test_na.rb +330 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +185 -0
- data/test/unit/bio/test_alignment.rb +1025 -0
- data/test/unit/bio/test_command.rb +349 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +144 -0
- data/test/unit/bio/test_location.rb +599 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +499 -0
- data/test/unit/bio/test_reference.rb +252 -0
- data/test/unit/bio/test_sequence.rb +329 -0
- data/test/unit/bio/test_shell.rb +18 -0
- data/test/unit/bio/test_tree.rb +593 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +101 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
- data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
- data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
- data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
- data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
- data/test/unit/bio/util/test_color_scheme.rb +33 -0
- data/test/unit/bio/util/test_contingency_table.rb +94 -0
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +245 -0
- metadata +543 -0
data/lib/bio/io/dbget.rb
ADDED
@@ -0,0 +1,194 @@
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#
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# = bio/io/dbget.rb - GenomeNet/DBGET client module
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#
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# Copyright:: Copyright (C) 2000, 2001
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# Mitsuteru C. Nakao <n@bioruby.org>,
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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: dbget.rb,v 1.13 2007/04/05 23:35:41 trevor Exp $
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#
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# == DBGET
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#
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# Accessing the GenomeNet/DBGET data retrieval system
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# http://www.genome.jp/dbget/ within the intranet.
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#
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require 'socket'
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module Bio
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class DBGET
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# default DBGET server address
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# SERV = "dbgetserv.genome.jp"
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SERV = "dbget.genome.jp"
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# default DBGET port number
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PORT = "3266"
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# Main class method to access DBGET server. Optionally, this method
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# can be called with the alternative DBGET server address and the
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# TCP/IP port number.
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#
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33
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# 'com' should be one of the following DBGET commands:
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#
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35
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# * alink, bfind, bget, binfo, blink, bman, bref, btab, btit
|
36
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#
|
37
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# These methods are shortcut for the dbget commands. Actually,
|
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# Bio::DBGET.((|com|))(arg) internally calls Bio::DBGET.dbget(com, arg).
|
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# Most of these methods accept the argument "-h" for help.
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#
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# 'arg' should be one of the following formats :
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#
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# * [options] db
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# * specify the database name only for binfo, bman etc.
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# * [options] db:entry
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# * specify the database name and the entry name to retrieve.
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# * [options] db entry1 entry2 ...
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# * specify the database name and the list of entries to retrieve.
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#
|
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# Note that options in the above example can be omitted. If 'arg' is
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# empty, the help message with a list of options for 'com' will be
|
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# shown by default. Supported database names will be found at the
|
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# GenomeNet DBGET web page http://www.genome.jp/dbget/.
|
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#
|
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def DBGET.dbget(com, arg, serv = nil, port = nil)
|
56
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|
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unless serv or port # if both of serv and port are nil
|
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if ENV["DBGET"] =~ /:/ # and ENV["DBGET"] exists
|
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serv, port = ENV["DBGET"].split(':')
|
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+
end
|
61
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end
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serv = serv ? serv : SERV
|
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port = port ? port : PORT
|
64
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|
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if arg.empty?
|
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arg = "-h" # DBGET help message
|
67
|
+
end
|
68
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+
|
69
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query = "#{com} #{arg}\n" # DBGET query string
|
70
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+
|
71
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sock = TCPSocket.open("#{serv}", "#{port}")
|
72
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+
|
73
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sock.write(query) # submit query
|
74
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sock.flush # buffer flush
|
75
|
+
|
76
|
+
sock.gets # skip "+Helo DBgetServ ..."
|
77
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+
sock.gets # skip "#If you see this message, ..."
|
78
|
+
sock.gets # skip "*Request-IDent"
|
79
|
+
|
80
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+
result = sock.read # DBGET result
|
81
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+
|
82
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sock.close
|
83
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+
|
84
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return result
|
85
|
+
end
|
86
|
+
|
87
|
+
# Show the version information of the DBGET server.
|
88
|
+
def DBGET.version
|
89
|
+
dbget("bget", "-V")
|
90
|
+
end
|
91
|
+
|
92
|
+
|
93
|
+
#--
|
94
|
+
# bacc("db entry") - not supported : get accession(s)
|
95
|
+
# bent("db entry") - not supported : get entry name
|
96
|
+
# lmarge("db entry") - not supported
|
97
|
+
#++
|
98
|
+
|
99
|
+
# alink("db entry") method returns relations
|
100
|
+
def DBGET.alink(arg)
|
101
|
+
dbget("alink", arg)
|
102
|
+
end
|
103
|
+
|
104
|
+
# bfind("db keyword") method searches entries by keyword
|
105
|
+
def DBGET.bfind(arg)
|
106
|
+
dbget("bfind", arg)
|
107
|
+
end
|
108
|
+
|
109
|
+
# bget("db entry") method retrieves entries specified by the entry names
|
110
|
+
def DBGET.bget(arg)
|
111
|
+
dbget("bget", arg)
|
112
|
+
end
|
113
|
+
|
114
|
+
# seq("db entry") method retrieves the first sequence of the entry
|
115
|
+
#
|
116
|
+
# Shortcut to retrieve the sequence of the entry in FASTA format.
|
117
|
+
# This method is equivalent to Bio::DBGET.bget("-f -n 1 #{arg}") and
|
118
|
+
# 'arg' should be the "db:entry" or "db entry1 entry2 ..." format.
|
119
|
+
def DBGET.seq(arg)
|
120
|
+
dbget("bget", "-f -n 1 #{arg}")
|
121
|
+
end
|
122
|
+
|
123
|
+
# seq2("db entry") method retrieves the second sequence of the entry if any
|
124
|
+
#
|
125
|
+
# Shortcut to retrieve the second sequence of the entry in FASTA format.
|
126
|
+
# This method is equivalent to Bio::DBGET.bget("-f -n 2 #{arg}").
|
127
|
+
# Only useful when treating the KEGG GENES database entries which have
|
128
|
+
# both AASEQ and NTSEQ fields. This method is obsolete and it is
|
129
|
+
# recommended to use 'naseq' and 'aaseq' instead.
|
130
|
+
def DBGET.seq2(arg)
|
131
|
+
dbget("bget", "-f -n 2 #{arg}")
|
132
|
+
end
|
133
|
+
|
134
|
+
# naseq("db entry") method retrieves the nucleic acid sequence of the
|
135
|
+
# entry if any.
|
136
|
+
def DBGET.naseq(arg)
|
137
|
+
dbget("bget", "-f -n n #{arg}")
|
138
|
+
end
|
139
|
+
|
140
|
+
# aaseq("db entry") method retrieves the amino acid sequence of the
|
141
|
+
# entry if any.
|
142
|
+
def DBGET.aaseq(arg)
|
143
|
+
dbget("bget", "-f -n a #{arg}")
|
144
|
+
end
|
145
|
+
|
146
|
+
# binfo("db") method retrieves the database information
|
147
|
+
def DBGET.binfo(arg)
|
148
|
+
dbget("binfo", arg)
|
149
|
+
end
|
150
|
+
|
151
|
+
# blink("db entry") method retrieves the link information
|
152
|
+
def DBGET.blink(arg)
|
153
|
+
dbget("blink", arg)
|
154
|
+
end
|
155
|
+
|
156
|
+
# bman ("db entry") method shows the manual page
|
157
|
+
def DBGET.bman(arg)
|
158
|
+
dbget("bman", arg)
|
159
|
+
end
|
160
|
+
|
161
|
+
# bref("db entry") method retrieves the references and authors
|
162
|
+
def DBGET.bref(arg)
|
163
|
+
dbget("bref", arg)
|
164
|
+
end
|
165
|
+
|
166
|
+
# btab ("db entry") method retrives (and generates) the database alias table
|
167
|
+
def DBGET.btab(arg)
|
168
|
+
dbget("btab", arg)
|
169
|
+
end
|
170
|
+
|
171
|
+
# btit("db entry ..") method retrieves the entry definition
|
172
|
+
def DBGET.btit(arg)
|
173
|
+
dbget("btit", arg)
|
174
|
+
end
|
175
|
+
|
176
|
+
end
|
177
|
+
|
178
|
+
end # module Bio
|
179
|
+
|
180
|
+
|
181
|
+
if __FILE__ == $0
|
182
|
+
puts "### DBGET version"
|
183
|
+
p Bio::DBGET.version
|
184
|
+
puts "### DBGET.dbget('bfind', 'sce tyrosin kinase')"
|
185
|
+
puts Bio::DBGET.dbget('bfind', 'sce tyrosin kinase')
|
186
|
+
puts "### DBGET.bfind('sce tyrosin kinase')"
|
187
|
+
puts Bio::DBGET.bfind('sce tyrosin kinase')
|
188
|
+
puts "### DBGET.bget('sce:YDL028C')"
|
189
|
+
puts Bio::DBGET.bget('sce:YDL028C')
|
190
|
+
puts "### DBGET.binfo('dbget')"
|
191
|
+
puts Bio::DBGET.binfo('dbget')
|
192
|
+
end
|
193
|
+
|
194
|
+
|
@@ -0,0 +1,638 @@
|
|
1
|
+
#
|
2
|
+
# = bio/io/ddbjxml.rb - DDBJ SOAP server access class
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2003, 2004
|
5
|
+
# Toshiaki Katayama <k@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: ddbjxml.rb,v 1.14 2007/04/05 23:35:41 trevor Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
require 'bio/io/soapwsdl'
|
12
|
+
require 'bio/db/genbank/ddbj'
|
13
|
+
|
14
|
+
|
15
|
+
module Bio
|
16
|
+
class DDBJ
|
17
|
+
|
18
|
+
|
19
|
+
# = Bio::DDBJ::XML
|
20
|
+
#
|
21
|
+
# Accessing the DDBJ web services.
|
22
|
+
#
|
23
|
+
# * http://xml.nig.ac.jp/
|
24
|
+
# * http://xml.nig.ac.jp/wsdl/index.jsp
|
25
|
+
#
|
26
|
+
class XML < Bio::SOAPWSDL
|
27
|
+
|
28
|
+
BASE_URI = "http://xml.nig.ac.jp/wsdl/"
|
29
|
+
|
30
|
+
# set default to GetEntry
|
31
|
+
SERVER_URI = BASE_URI + "GetEntry.wsdl"
|
32
|
+
|
33
|
+
def initialize(wsdl = nil)
|
34
|
+
super(wsdl || self.class::SERVER_URI)
|
35
|
+
end
|
36
|
+
|
37
|
+
# === Description
|
38
|
+
#
|
39
|
+
# DDBJ XML BLAST Database Search
|
40
|
+
#
|
41
|
+
# * http://xml.nig.ac.jp/doc/Blast.txt
|
42
|
+
#
|
43
|
+
# === Examples
|
44
|
+
#
|
45
|
+
# serv = Bio::DDBJ::XML::Blast.new
|
46
|
+
# program = 'blastp'
|
47
|
+
# database = 'SWISS'
|
48
|
+
# query = "MSSRIARALALVVTLLHLTRLALSTCPAACHCPLEAPKCAPGVGLVRDGCGCCKVCAKQL"
|
49
|
+
#
|
50
|
+
# report = serv.searchSimple(program, database, query)
|
51
|
+
# Bio::Blast::Default::Report.new(report).each_hit do |hit|
|
52
|
+
# hit.hsps.find_all {|x| x.evalue < 0.1 }.each do |hsp|
|
53
|
+
# p [hsps.evalue, hsps.identity, hsps.definition]
|
54
|
+
# end
|
55
|
+
# end
|
56
|
+
#
|
57
|
+
# program = 'tblastn'
|
58
|
+
# database = 'ddbjvrl'
|
59
|
+
# param = '-m 8 -e 0.001'
|
60
|
+
# puts serv.searchParam(program, database, query, param)
|
61
|
+
#
|
62
|
+
# === WSDL Methods
|
63
|
+
#
|
64
|
+
# * searchSimple(program, database, query)
|
65
|
+
#
|
66
|
+
# Returns a blast report in the default format.
|
67
|
+
#
|
68
|
+
# * searchParam(program, database, query, param)
|
69
|
+
#
|
70
|
+
# Blasts with param and returns a blast report.
|
71
|
+
#
|
72
|
+
# === References
|
73
|
+
#
|
74
|
+
# * http://xml.nig.ac.jp/doc/Blast.txt
|
75
|
+
#
|
76
|
+
class Blast < XML
|
77
|
+
SERVER_URI = BASE_URI + "Blast.wsdl"
|
78
|
+
end
|
79
|
+
|
80
|
+
|
81
|
+
# === ClustalW
|
82
|
+
#
|
83
|
+
# Multiple seaquece alignment using ClustalW.
|
84
|
+
#
|
85
|
+
# * http://xml.nig.ac.jp/doc/ClustalW.txt
|
86
|
+
#
|
87
|
+
# === Examples
|
88
|
+
#
|
89
|
+
# serv = Bio::DDBJ::XML::ClustalW.new
|
90
|
+
#
|
91
|
+
# query = <<END
|
92
|
+
# > RABSTOUT rabbit Guinness receptor
|
93
|
+
# LKMHLMGHLKMGLKMGLKGMHLMHLKHMHLMTYTYTTYRRWPLWMWLPDFGHAS
|
94
|
+
# ADSCVCAHGFAVCACFAHFDVCFGAVCFHAVCFAHVCFAAAVCFAVCAC
|
95
|
+
# > MUSNOSE mouse nose drying factor
|
96
|
+
# mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt
|
97
|
+
# fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv
|
98
|
+
# > HSHEAVEN human Guinness receptor repeat
|
99
|
+
# mhkmmhkgmkhmhgmhmhg lhmkmhlkmgkhmgkmk ytytytryrwtqtqwtwyt
|
100
|
+
# fdgfdsgafdagfdgfsag dfavdfdvgavfsvfgv dfsvdgvagvfdv
|
101
|
+
# mhkmmhkgmkhmhgmhmhg lhmkmhlkmgkhmgkmk ytytytryrwtqtqwtwyt
|
102
|
+
# fdgfdsgafdagfdgfsag dfavdfdvgavfsvfgv dfsvdgvagvfdv
|
103
|
+
# END
|
104
|
+
#
|
105
|
+
# puts serv.analyzeSimple(query)
|
106
|
+
# puts serv.analyzeParam(query, '-align -matrix=blosum')
|
107
|
+
#
|
108
|
+
# === WSDL Methods
|
109
|
+
#
|
110
|
+
# * analyzeSimple(query)
|
111
|
+
# * analyzeParam(query, param)
|
112
|
+
#
|
113
|
+
# === References
|
114
|
+
#
|
115
|
+
# * http://xml.nig.ac.jp/doc/ClustalW.txt
|
116
|
+
#
|
117
|
+
class ClustalW < XML
|
118
|
+
SERVER_URI = BASE_URI + "ClustalW.wsdl"
|
119
|
+
end
|
120
|
+
|
121
|
+
|
122
|
+
# == DDBJ
|
123
|
+
#
|
124
|
+
# Retrieves a sequence entry from the DDBJ DNA Data Bank Japan.
|
125
|
+
#
|
126
|
+
# * http://xml.nig.ac.jp/doc/DDBJ.txt
|
127
|
+
#
|
128
|
+
# === Examples
|
129
|
+
#
|
130
|
+
# serv = Bio::DDBJ::XML::DDBJ.new
|
131
|
+
# puts serv.getFFEntry('AB000050')
|
132
|
+
# puts serv.getXMLEntry('AB000050')
|
133
|
+
# puts serv.getFeatureInfo('AB000050', 'cds')
|
134
|
+
# puts serv.getAllFeatures('AB000050')
|
135
|
+
# puts serv.getRelatedFeatures('AL121903', '59000', '64000')
|
136
|
+
# puts serv.getRelatedFeaturesSeq('AL121903', '59000', '64000')
|
137
|
+
#
|
138
|
+
# === WSDL Methods
|
139
|
+
#
|
140
|
+
# * getFFEntry(accession)
|
141
|
+
# * getXMLEntry(accession)
|
142
|
+
# * getFeatureInfo(accession, feature)
|
143
|
+
# * getAllFeatures(accession)
|
144
|
+
# * getRelatedFeatures(accession, start, stop)
|
145
|
+
# * getRelatedFeaturesSeq(accession, start, stop)
|
146
|
+
#
|
147
|
+
# === References
|
148
|
+
#
|
149
|
+
# * http://xml.nig.ac.jp/doc/DDBJ.txt
|
150
|
+
#
|
151
|
+
class DDBJ < XML
|
152
|
+
SERVER_URI = BASE_URI + "DDBJ.wsdl"
|
153
|
+
end
|
154
|
+
|
155
|
+
|
156
|
+
# == Fasta
|
157
|
+
#
|
158
|
+
# Searching database using the Fasta package.
|
159
|
+
#
|
160
|
+
# * http://xml.nig.ac.jp/doc/Fasta.txt
|
161
|
+
#
|
162
|
+
# === Examples
|
163
|
+
#
|
164
|
+
# serv = Bio::DDBJ::XML::Fasta.new
|
165
|
+
# query = ">Test\nMSDGAVQPDG GQPAVRNERA TGSGNGSGGG GGGGSGGVGI"
|
166
|
+
#
|
167
|
+
# puts serv.searchSimple('fasta34', 'PDB', query)
|
168
|
+
# query = ">Test\nAGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC"
|
169
|
+
# puts serv.searchParam('fastx34_t', 'PDB', query, '-n')
|
170
|
+
#
|
171
|
+
# === WSDL Methods
|
172
|
+
#
|
173
|
+
# * searchSimple(program, database, query)
|
174
|
+
# * searchParam(program, database, query, param)
|
175
|
+
#
|
176
|
+
# === References
|
177
|
+
#
|
178
|
+
# * http://xml.nig.ac.jp/doc/Fasta.txt
|
179
|
+
#
|
180
|
+
class Fasta < XML
|
181
|
+
SERVER_URI = BASE_URI + "Fasta.wsdl"
|
182
|
+
end
|
183
|
+
|
184
|
+
|
185
|
+
# == GetEntry
|
186
|
+
#
|
187
|
+
# Retrieves database entries.
|
188
|
+
#
|
189
|
+
# * http://xml.nig.ac.jp/doc/GetEntry.txt
|
190
|
+
#
|
191
|
+
# === Examples
|
192
|
+
#
|
193
|
+
# serv = Bio::DDBJ::XML::GetEntry.new
|
194
|
+
# puts serv.getDDBJEntry('AB000050')
|
195
|
+
# puts serv. getPDBEntry('1AAR')
|
196
|
+
#
|
197
|
+
# === WSDL Methods
|
198
|
+
#
|
199
|
+
# * getEntry(database, var, param1, param2)
|
200
|
+
# * getEntry(database, var)
|
201
|
+
# * getDDBJEntry(accession)
|
202
|
+
# * getDDBJCONEntry(accession)
|
203
|
+
# * getDDBJVerEntry(accession)
|
204
|
+
# * getLocus_DDBJEntry(locus)
|
205
|
+
# * getGene_DDBJEntry(gene)
|
206
|
+
# * getProd_DDBJEntry(products)
|
207
|
+
# * getPID_DDBJEntry(pid)
|
208
|
+
# * getClone_DDBJEntry(clone)
|
209
|
+
# * getXML_DDBJEntry(accession)
|
210
|
+
# * getEMBLEntry(accession)
|
211
|
+
# * getSWISSEntry(accession)
|
212
|
+
# * getPIREntry(accession)
|
213
|
+
# * getPRFEntry(accession)
|
214
|
+
# * getPDBEntry(accession)
|
215
|
+
# * getQVEntry(accession)
|
216
|
+
# * getDADEntry(accession)
|
217
|
+
# * getPID_DADEntry(pid)
|
218
|
+
# * getFASTA_DDBJEntry(accession)
|
219
|
+
# * getFASTA_DDBJCONEntry(accession)
|
220
|
+
# * getFASTA_DDBJVerEntry(accession)
|
221
|
+
# * getFASTA_DDBJSeqEntry(accession, start, end)
|
222
|
+
# * getFASTA_DADEntry(accession)
|
223
|
+
# * getFASTA_PIREntry(accession)
|
224
|
+
# * getFASTA_SWISSEntry(accession)
|
225
|
+
# * getFASTA_PDBEntry(accession)
|
226
|
+
# * getFASTA_PRFEntry(accession)
|
227
|
+
# * getFASTA_CDSEntry(accession)
|
228
|
+
#
|
229
|
+
# === References
|
230
|
+
#
|
231
|
+
# * http://xml.nig.ac.jp/doc/GetEntry.txt
|
232
|
+
#
|
233
|
+
class GetEntry < XML
|
234
|
+
SERVER_URI = BASE_URI + "GetEntry.wsdl"
|
235
|
+
end
|
236
|
+
|
237
|
+
|
238
|
+
# === Gib
|
239
|
+
#
|
240
|
+
# Genome Information broker
|
241
|
+
#
|
242
|
+
# * http://xml.nig.ac.jp/doc/Gib.txt
|
243
|
+
#
|
244
|
+
# === Examples
|
245
|
+
#
|
246
|
+
# serv = Bio::DDBJ::XML::Gib.new
|
247
|
+
# puts serv.getOrganismList
|
248
|
+
# puts serv.getChIDList
|
249
|
+
# puts serv.getOrganismNameFromChid('Sent_CT18:')
|
250
|
+
# puts serv.getChIDFromOrganismName('Aquifex aeolicus VF5')
|
251
|
+
# puts serv.getAccession('Ecol_K12_MG1655:')
|
252
|
+
# puts serv.getPieceNumber('Mgen_G37:')
|
253
|
+
# puts serv.getDivision('Mgen_G37:')
|
254
|
+
# puts serv.getType('Mgen_G37:')
|
255
|
+
# puts serv.getCDS('Aaeo_VF5:ece1')
|
256
|
+
# puts serv.getFlatFile('Nost_PCC7120:pCC7120zeta')
|
257
|
+
# puts serv.getFastaFile('Nost_PCC7120:pCC7120zeta', 'cdsaa')
|
258
|
+
#
|
259
|
+
# === WSDL Methods
|
260
|
+
#
|
261
|
+
# * getOrganismList
|
262
|
+
# * getChIDList
|
263
|
+
# * getOrganismNameFromChid(chid)
|
264
|
+
# * getChIDFromOrganismName(orgName)
|
265
|
+
# * getAccession(chid)
|
266
|
+
# * getPieceNumber(chid)
|
267
|
+
# * getDivision(chid)
|
268
|
+
# * getType(chid)
|
269
|
+
# * getFlatFile(chid)
|
270
|
+
# * getFastaFile(chid, type)
|
271
|
+
# * getCDS(chid)
|
272
|
+
#
|
273
|
+
# === References
|
274
|
+
#
|
275
|
+
# * http://xml.nig.ac.jp/doc/Gib.txt
|
276
|
+
#
|
277
|
+
class Gib < XML
|
278
|
+
SERVER_URI = BASE_URI + "Gib.wsdl"
|
279
|
+
end
|
280
|
+
|
281
|
+
|
282
|
+
# === Gtop
|
283
|
+
#
|
284
|
+
# GTOP: Gene to protein.
|
285
|
+
#
|
286
|
+
# * http://xml.nig.ac.jp/doc/Gtop.txt
|
287
|
+
#
|
288
|
+
# === Examples
|
289
|
+
#
|
290
|
+
# serv = Bio::DDBJ::XML::Gtop.new
|
291
|
+
# puts serv.getOrganismList
|
292
|
+
# puts serv.getMasterInfo('thrA', 'ecol0')
|
293
|
+
#
|
294
|
+
# === WSDL Methods
|
295
|
+
#
|
296
|
+
# * getOrganismList
|
297
|
+
# * getMasterInfo(orfID, organism)
|
298
|
+
#
|
299
|
+
# === References
|
300
|
+
#
|
301
|
+
# * http://xml.nig.ac.jp/doc/Gtop.txt
|
302
|
+
#
|
303
|
+
class Gtop < XML
|
304
|
+
SERVER_URI = BASE_URI + "Gtop.wsdl"
|
305
|
+
end
|
306
|
+
|
307
|
+
|
308
|
+
# === PML
|
309
|
+
#
|
310
|
+
# Variation database
|
311
|
+
#
|
312
|
+
# * http://xml.nig.ac.jp/doc/PML.txt
|
313
|
+
#
|
314
|
+
# === Examples
|
315
|
+
#
|
316
|
+
# serv = Bio::DDBJ::XML::PML.new
|
317
|
+
# puts serv.getVariation('1')
|
318
|
+
#
|
319
|
+
# === WSDL Methods
|
320
|
+
#
|
321
|
+
# * searchVariation(field, query, order)
|
322
|
+
# * searchVariationSimple(field, query)
|
323
|
+
# * searchFrequency(field, query, order)
|
324
|
+
# * searchFrequencySimple(field, query)
|
325
|
+
# * getVariation(variation_id)
|
326
|
+
# * getFrequency(variation_id, population_id)
|
327
|
+
#
|
328
|
+
# === References
|
329
|
+
#
|
330
|
+
# * http://xml.nig.ac.jp/doc/PML.txt
|
331
|
+
#
|
332
|
+
class PML < XML
|
333
|
+
SERVER_URI = BASE_URI + "PML.wsdl"
|
334
|
+
end
|
335
|
+
|
336
|
+
# === RequestManager
|
337
|
+
#
|
338
|
+
# Sequence Retrieving System
|
339
|
+
#
|
340
|
+
# * http://xml.nig.ac.jp/doc/RequestManager.txt
|
341
|
+
#
|
342
|
+
# === Examples
|
343
|
+
#
|
344
|
+
# serv = Bio::DDBJ::XML::RequestManager.new
|
345
|
+
# puts serv.getAsyncResult('20070420102828140')
|
346
|
+
#
|
347
|
+
# === WSDL Methods
|
348
|
+
#
|
349
|
+
# * getAsyncResult( requestId )
|
350
|
+
# * getAsyncResultMime( requestId )
|
351
|
+
#
|
352
|
+
# === Examples
|
353
|
+
#
|
354
|
+
# * http://xml.nig.ac.jp/doc/RequestManager.txt
|
355
|
+
#
|
356
|
+
class RequestManager < XML
|
357
|
+
SERVER_URI = BASE_URI + "RequestManager.wsdl"
|
358
|
+
|
359
|
+
# RequestManager using DDBJ REST interface
|
360
|
+
class REST
|
361
|
+
require 'bio/command'
|
362
|
+
|
363
|
+
Uri = 'http://xml.nig.ac.jp/rest/Invoke'
|
364
|
+
Service = 'RequestManager'
|
365
|
+
|
366
|
+
def getAsyncResult(requestId)
|
367
|
+
params = {
|
368
|
+
'service' => Service,
|
369
|
+
'method' => 'getAsyncResult',
|
370
|
+
'requestId' => requestId.to_s
|
371
|
+
}
|
372
|
+
r = Bio::Command.post_form(Uri, params)
|
373
|
+
r.body
|
374
|
+
end
|
375
|
+
end #class REST
|
376
|
+
|
377
|
+
unless defined? new_orig then
|
378
|
+
class << RequestManager
|
379
|
+
alias new_orig new
|
380
|
+
private :new_orig
|
381
|
+
end
|
382
|
+
end
|
383
|
+
|
384
|
+
# creates a new driver
|
385
|
+
def self.new(wsdl = nil)
|
386
|
+
begin
|
387
|
+
new_orig(wsdl)
|
388
|
+
rescue RuntimeError
|
389
|
+
REST.new
|
390
|
+
end
|
391
|
+
end
|
392
|
+
end #class RequestManager
|
393
|
+
|
394
|
+
# === SRS
|
395
|
+
#
|
396
|
+
# Sequence Retrieving System
|
397
|
+
#
|
398
|
+
# * http://xml.nig.ac.jp/doc/SRS.txt
|
399
|
+
#
|
400
|
+
# === Examples
|
401
|
+
#
|
402
|
+
# serv = Bio::DDBJ::XML::SRS.new
|
403
|
+
# puts serv.searchSimple('[pathway-des:sugar]')
|
404
|
+
# puts serv.searchParam('[swissprot-des:cohesin]', '-f seq -sf fasta')
|
405
|
+
#
|
406
|
+
# === WSDL Methods
|
407
|
+
#
|
408
|
+
# * searchSimple(query)
|
409
|
+
# * searchParam(query, param)
|
410
|
+
#
|
411
|
+
# === Examples
|
412
|
+
#
|
413
|
+
# * http://xml.nig.ac.jp/doc/SRS.txt
|
414
|
+
#
|
415
|
+
class SRS < XML
|
416
|
+
SERVER_URI = BASE_URI + "SRS.wsdl"
|
417
|
+
end
|
418
|
+
|
419
|
+
|
420
|
+
# === TxSearch
|
421
|
+
#
|
422
|
+
# Searching taxonomy information.
|
423
|
+
#
|
424
|
+
# * http://xml.nig.ac.jp/doc/TxSearch.txt
|
425
|
+
#
|
426
|
+
# === Examples
|
427
|
+
#
|
428
|
+
# serv = Bio::DDBJ::XML::TxSearch.new
|
429
|
+
# puts serv.searchSimple('*coli')
|
430
|
+
# puts serv.searchSimple('*tardigrada*')
|
431
|
+
# puts serv.getTxId('Escherichia coli')
|
432
|
+
# puts serv.getTxName('562')
|
433
|
+
#
|
434
|
+
# query = ["Campylobacter coli", "Escherichia coli"].join("\n")
|
435
|
+
# rank = ["family", "genus"].join("\n")
|
436
|
+
# puts serv.searchLineage(query, rank, 'Bacteria')
|
437
|
+
#
|
438
|
+
# === WSDL Methdos
|
439
|
+
#
|
440
|
+
# * searchSimple(tx_Name)
|
441
|
+
# * searchParam(tx_Name, tx_Clas, tx_Rank, tx_Rmax, tx_Dcls)
|
442
|
+
# * getTxId(tx_Name)
|
443
|
+
# * getTxName(tx_Id)
|
444
|
+
# * searchLineage(query, ranks, superkingdom)
|
445
|
+
#
|
446
|
+
# === References
|
447
|
+
#
|
448
|
+
# * http://xml.nig.ac.jp/doc/TxSearch.txt
|
449
|
+
#
|
450
|
+
class TxSearch < XML
|
451
|
+
SERVER_URI = BASE_URI + "TxSearch.wsdl"
|
452
|
+
end
|
453
|
+
|
454
|
+
end # XML
|
455
|
+
|
456
|
+
end # DDBJ
|
457
|
+
end # Bio
|
458
|
+
|
459
|
+
|
460
|
+
|
461
|
+
if __FILE__ == $0
|
462
|
+
|
463
|
+
begin
|
464
|
+
require 'pp'
|
465
|
+
alias p pp
|
466
|
+
rescue LoadError
|
467
|
+
end
|
468
|
+
|
469
|
+
puts ">>> Bio::DDBJ::XML::Blast"
|
470
|
+
serv = Bio::DDBJ::XML::Blast.new
|
471
|
+
# serv.log = STDERR
|
472
|
+
|
473
|
+
query = "MSSRIARALALVVTLLHLTRLALSTCPAACHCPLEAPKCAPGVGLVRDGCGCCKVCAKQL"
|
474
|
+
|
475
|
+
puts "### searchSimple('blastp', 'SWISS', query)"
|
476
|
+
puts serv.searchSimple('blastp', 'SWISS', query)
|
477
|
+
|
478
|
+
puts "### searchParam('tblastn', 'ddbjvrl', query, '-m 8')"
|
479
|
+
puts serv.searchParam('tblastn', 'ddbjvrl', query, '-m 8')
|
480
|
+
|
481
|
+
|
482
|
+
puts ">>> Bio::DDBJ::XML::ClustalW"
|
483
|
+
serv = Bio::DDBJ::XML::ClustalW.new
|
484
|
+
|
485
|
+
query = <<END
|
486
|
+
> RABSTOUT rabbit Guinness receptor
|
487
|
+
LKMHLMGHLKMGLKMGLKGMHLMHLKHMHLMTYTYTTYRRWPLWMWLPDFGHAS
|
488
|
+
ADSCVCAHGFAVCACFAHFDVCFGAVCFHAVCFAHVCFAAAVCFAVCAC
|
489
|
+
> MUSNOSE mouse nose drying factor
|
490
|
+
mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt
|
491
|
+
fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv
|
492
|
+
> HSHEAVEN human Guinness receptor repeat
|
493
|
+
mhkmmhkgmkhmhgmhmhg lhmkmhlkmgkhmgkmk ytytytryrwtqtqwtwyt
|
494
|
+
fdgfdsgafdagfdgfsag dfavdfdvgavfsvfgv dfsvdgvagvfdv
|
495
|
+
mhkmmhkgmkhmhgmhmhg lhmkmhlkmgkhmgkmk ytytytryrwtqtqwtwyt
|
496
|
+
fdgfdsgafdagfdgfsag dfavdfdvgavfsvfgv dfsvdgvagvfdv
|
497
|
+
END
|
498
|
+
|
499
|
+
puts "### analyzeSimple(query)"
|
500
|
+
puts serv.analyzeSimple(query)
|
501
|
+
|
502
|
+
puts "### analyzeParam(query, '-align -matrix=blosum')"
|
503
|
+
puts serv.analyzeParam(query, '-align -matrix=blosum')
|
504
|
+
|
505
|
+
|
506
|
+
puts ">>> Bio::DDBJ::XML::DDBJ"
|
507
|
+
serv = Bio::DDBJ::XML::DDBJ.new
|
508
|
+
|
509
|
+
puts "### getFFEntry('AB000050')"
|
510
|
+
puts serv.getFFEntry('AB000050')
|
511
|
+
|
512
|
+
puts "### getXMLEntry('AB000050')"
|
513
|
+
puts serv.getXMLEntry('AB000050')
|
514
|
+
|
515
|
+
puts "### getFeatureInfo('AB000050', 'cds')"
|
516
|
+
puts serv.getFeatureInfo('AB000050', 'cds')
|
517
|
+
|
518
|
+
puts "### getAllFeatures('AB000050')"
|
519
|
+
puts serv.getAllFeatures('AB000050')
|
520
|
+
|
521
|
+
puts "### getRelatedFeatures('AL121903', '59000', '64000')"
|
522
|
+
puts serv.getRelatedFeatures('AL121903', '59000', '64000')
|
523
|
+
|
524
|
+
puts "### getRelatedFeaturesSeq('AL121903', '59000', '64000')"
|
525
|
+
puts serv.getRelatedFeaturesSeq('AL121903', '59000', '64000')
|
526
|
+
|
527
|
+
|
528
|
+
puts ">>> Bio::DDBJ::XML::Fasta"
|
529
|
+
serv = Bio::DDBJ::XML::Fasta.new
|
530
|
+
|
531
|
+
query = ">Test\nMSDGAVQPDG GQPAVRNERA TGSGNGSGGG GGGGSGGVGI"
|
532
|
+
|
533
|
+
puts "### searchSimple('fasta34', 'PDB', query)"
|
534
|
+
puts serv.searchSimple('fasta34', 'PDB', query)
|
535
|
+
|
536
|
+
query = ">Test\nAGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC"
|
537
|
+
|
538
|
+
puts "### searchParam('fastx34_t', 'PDB', query, '-n')"
|
539
|
+
puts serv.searchParam('fastx34_t', 'PDB', query, '-n')
|
540
|
+
|
541
|
+
|
542
|
+
puts ">>> Bio::DDBJ::XML::GetEntry"
|
543
|
+
serv = Bio::DDBJ::XML::GetEntry.new
|
544
|
+
|
545
|
+
puts "### getDDBJEntry('AB000050')"
|
546
|
+
puts serv.getDDBJEntry('AB000050')
|
547
|
+
|
548
|
+
puts "### getPDBEntry('1AAR')"
|
549
|
+
puts serv. getPDBEntry('1AAR')
|
550
|
+
|
551
|
+
|
552
|
+
puts ">>> Bio::DDBJ::XML::Gib"
|
553
|
+
serv = Bio::DDBJ::XML::Gib.new
|
554
|
+
|
555
|
+
puts "### getOrganismList"
|
556
|
+
puts serv.getOrganismList
|
557
|
+
|
558
|
+
puts "### getChIDList"
|
559
|
+
puts serv.getChIDList
|
560
|
+
|
561
|
+
puts "### getOrganismNameFromChid('Sent_CT18:')"
|
562
|
+
puts serv.getOrganismNameFromChid('Sent_CT18:')
|
563
|
+
|
564
|
+
puts "### getChIDFromOrganismName('Aquifex aeolicus VF5')"
|
565
|
+
puts serv.getChIDFromOrganismName('Aquifex aeolicus VF5')
|
566
|
+
|
567
|
+
puts "### getAccession('Ecol_K12_MG1655:')"
|
568
|
+
puts serv.getAccession('Ecol_K12_MG1655:')
|
569
|
+
|
570
|
+
puts "### getPieceNumber('Mgen_G37:')"
|
571
|
+
puts serv.getPieceNumber('Mgen_G37:')
|
572
|
+
|
573
|
+
puts "### getDivision('Mgen_G37:')"
|
574
|
+
puts serv.getDivision('Mgen_G37:')
|
575
|
+
|
576
|
+
puts "### getType('Mgen_G37:')"
|
577
|
+
puts serv.getType('Mgen_G37:')
|
578
|
+
|
579
|
+
puts "### getCDS('Aaeo_VF5:ece1')"
|
580
|
+
puts serv.getCDS('Aaeo_VF5:ece1')
|
581
|
+
|
582
|
+
puts "### getFlatFile('Nost_PCC7120:pCC7120zeta')"
|
583
|
+
puts serv.getFlatFile('Nost_PCC7120:pCC7120zeta')
|
584
|
+
|
585
|
+
puts "### getFastaFile('Nost_PCC7120:pCC7120zeta')"
|
586
|
+
puts serv.getFastaFile('Nost_PCC7120:pCC7120zeta', 'cdsaa')
|
587
|
+
|
588
|
+
|
589
|
+
puts ">>> Bio::DDBJ::XML::Gtop"
|
590
|
+
serv = Bio::DDBJ::XML::Gtop.new
|
591
|
+
|
592
|
+
puts "### getOrganismList"
|
593
|
+
puts serv.getOrganismList
|
594
|
+
|
595
|
+
puts "### getMasterInfo"
|
596
|
+
puts serv.getMasterInfo('thrA', 'ecol0')
|
597
|
+
|
598
|
+
|
599
|
+
# puts ">>> Bio::DDBJ::XML::PML"
|
600
|
+
# serv = Bio::DDBJ::XML::PML.new
|
601
|
+
#
|
602
|
+
# puts "### getVariation('1')"
|
603
|
+
# puts serv.getVariation('1')
|
604
|
+
|
605
|
+
|
606
|
+
puts ">>> Bio::DDBJ::XML::SRS"
|
607
|
+
serv = Bio::DDBJ::XML::SRS.new
|
608
|
+
|
609
|
+
puts "### searchSimple('[pathway-des:sugar]')"
|
610
|
+
puts serv.searchSimple('[pathway-des:sugar]')
|
611
|
+
|
612
|
+
puts "### searchParam('[swissprot-des:cohesin]', '-f seq -sf fasta')"
|
613
|
+
puts serv.searchParam('[swissprot-des:cohesin]', '-f seq -sf fasta')
|
614
|
+
|
615
|
+
|
616
|
+
puts ">>> Bio::DDBJ::XML::TxSearch"
|
617
|
+
serv = Bio::DDBJ::XML::TxSearch.new
|
618
|
+
|
619
|
+
puts "### searchSimple('*coli')"
|
620
|
+
puts serv.searchSimple('*coli')
|
621
|
+
|
622
|
+
puts "### searchSimple('*tardigrada*')"
|
623
|
+
puts serv.searchSimple('*tardigrada*')
|
624
|
+
|
625
|
+
puts "### getTxId('Escherichia coli')"
|
626
|
+
puts serv.getTxId('Escherichia coli')
|
627
|
+
|
628
|
+
puts "### getTxName('562')"
|
629
|
+
puts serv.getTxName('562')
|
630
|
+
|
631
|
+
query = "Campylobacter coli\nEscherichia coli"
|
632
|
+
rank = "family\ngenus"
|
633
|
+
|
634
|
+
puts "### searchLineage(query, rank, 'Bacteria')"
|
635
|
+
puts serv.searchLineage(query, rank, 'Bacteria')
|
636
|
+
|
637
|
+
end
|
638
|
+
|