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 +1,32 @@
|
|
1
|
+
|
2
|
+
module Bio
|
3
|
+
class SQL
|
4
|
+
class Seqfeature <DummyBase
|
5
|
+
set_sequence_name "seqfeature_pk_seq"
|
6
|
+
belongs_to :bioentry
|
7
|
+
#, :class_name => "Bioentry"
|
8
|
+
belongs_to :type_term, :class_name => "Term", :foreign_key => "type_term_id"
|
9
|
+
belongs_to :source_term, :class_name => "Term", :foreign_key =>"source_term_id"
|
10
|
+
has_many :seqfeature_dbxrefs, :class_name => "SeqfeatureDbxref", :foreign_key => "seqfeature_id"
|
11
|
+
has_many :seqfeature_qualifier_values, :order=>'rank', :foreign_key => "seqfeature_id"
|
12
|
+
#, :class_name => "SeqfeatureQualifierValue"
|
13
|
+
has_many :locations, :class_name => "Location", :order=>'rank'
|
14
|
+
has_many :object_seqfeature_paths, :class_name => "SeqfeaturePath", :foreign_key => "object_seqfeature_id"
|
15
|
+
has_many :subject_seqfeature_paths, :class_name => "SeqfeaturePath", :foreign_key => "subject_seqfeature_id"
|
16
|
+
has_many :object_seqfeature_relationships, :class_name => "SeqfeatureRelationship", :foreign_key => "object_seqfeature_id"
|
17
|
+
has_many :subject_seqfeature_relationships, :class_name => "SeqfeatureRelationship", :foreign_key => "subject_seqfeature_id"
|
18
|
+
|
19
|
+
#get the subsequence described by the locations objects
|
20
|
+
def sequence
|
21
|
+
return self.locations.inject(Bio::Sequence::NA.new("")){|seq, location| seq<<location.sequence}
|
22
|
+
end
|
23
|
+
|
24
|
+
#translate the subsequences represented by the feature and its locations
|
25
|
+
#not considering the qualifiers
|
26
|
+
#Return a Bio::Sequence::AA object
|
27
|
+
def translate(*args)
|
28
|
+
self.sequence.translate(*args)
|
29
|
+
end
|
30
|
+
end
|
31
|
+
end #SQL
|
32
|
+
end #Bio
|
@@ -0,0 +1,11 @@
|
|
1
|
+
|
2
|
+
module Bio
|
3
|
+
class SQL
|
4
|
+
class SeqfeatureDbxref < DummyBase
|
5
|
+
set_primary_keys :seqfeature_id, :dbxref_id
|
6
|
+
#delete set_sequence_name nil
|
7
|
+
belongs_to :seqfeature, :class_name => "Seqfeature", :foreign_key => "seqfeature_id"
|
8
|
+
belongs_to :dbxref, :class_name => "Dbxref", :foreign_key => "dbxref_id"
|
9
|
+
end
|
10
|
+
end #SQL
|
11
|
+
end #Bio
|
@@ -0,0 +1,11 @@
|
|
1
|
+
module Bio
|
2
|
+
class SQL
|
3
|
+
class SeqfeaturePath < DummyBase
|
4
|
+
set_primary_keys :object_seqfeature_id, :subject_seqfeature_id, :term_id
|
5
|
+
set_sequence_name nil
|
6
|
+
belongs_to :object_seqfeature, :class_name => "Seqfeature", :foreign_key => "object_seqfeature_id"
|
7
|
+
belongs_to :subject_seqfeature, :class_name => "Seqfeature", :foreign_key => "subject_seqfeature_id"
|
8
|
+
belongs_to :term, :class_name => "Term"
|
9
|
+
end
|
10
|
+
end #SQL
|
11
|
+
end #Bio
|
@@ -0,0 +1,20 @@
|
|
1
|
+
|
2
|
+
module Bio
|
3
|
+
class SQL
|
4
|
+
class SeqfeatureQualifierValue < DummyBase
|
5
|
+
set_primary_keys :seqfeature_id, :term_id, :rank
|
6
|
+
set_sequence_name nil
|
7
|
+
belongs_to :seqfeature
|
8
|
+
belongs_to :term, :class_name => "Term"
|
9
|
+
|
10
|
+
def self.find_cluster(query)
|
11
|
+
term_note= Term.find_by_name('note')
|
12
|
+
find(:all, :conditions =>["value like ? and term_id = ?", "cl:#{query}", term_note])
|
13
|
+
end
|
14
|
+
def self.find_cluster_info(query)
|
15
|
+
term_note= Term.find_by_name('note')
|
16
|
+
find(:all, :conditions =>["value like ? and term_id = ?", "cli:#{query}", term_note])
|
17
|
+
end
|
18
|
+
end
|
19
|
+
end #SQL
|
20
|
+
end #Bio
|
@@ -0,0 +1,11 @@
|
|
1
|
+
|
2
|
+
module Bio
|
3
|
+
class SQL
|
4
|
+
class SeqfeatureRelationship <DummyBase
|
5
|
+
set_sequence_name "seqfeatue_relationship_pk_seq"
|
6
|
+
belongs_to :term, :class_name => "Term"
|
7
|
+
belongs_to :object_seqfeature, :class_name => "Seqfeature"
|
8
|
+
belongs_to :subject_seqfeature, :class_name => "Seqfeature"
|
9
|
+
end
|
10
|
+
end #SQL
|
11
|
+
end #Bio
|
@@ -0,0 +1,12 @@
|
|
1
|
+
|
2
|
+
module Bio
|
3
|
+
class SQL
|
4
|
+
class Taxon < DummyBase
|
5
|
+
set_sequence_name "taxon_pk_seq"
|
6
|
+
has_many :taxon_names, :class_name => "TaxonName"
|
7
|
+
has_one :taxon_scientific_name, :class_name => "TaxonName", :conditions=>"name_class = 'scientific name'"
|
8
|
+
has_one :taxon_genbank_common_name, :class_name => "TaxonName", :conditions=>"name_class = 'genbank common name'"
|
9
|
+
has_one :bioentry, :class_name => "Bioentry"
|
10
|
+
end
|
11
|
+
end #SQL
|
12
|
+
end #Bio
|
@@ -0,0 +1,27 @@
|
|
1
|
+
|
2
|
+
module Bio
|
3
|
+
class SQL
|
4
|
+
class Term < DummyBase
|
5
|
+
belongs_to :ontology, :class_name => "Ontology"
|
6
|
+
has_many :seqfeature_qualifier_values, :class_name => "SeqfeatureQualifierValue"
|
7
|
+
has_many :dbxref_qualifier_values, :class_name => "DbxrefQualifierValue"
|
8
|
+
has_many :bioentry_qualifer_values, :class_name => "BioentryQualifierValue"
|
9
|
+
has_many :bioentries, :through=>:bioentry_qualifier_values
|
10
|
+
has_many :locations, :class_name => "Location"
|
11
|
+
has_many :seqfeature_relationships, :class_name => "SeqfeatureRelationship"
|
12
|
+
has_many :term_dbxrefs, :class_name => "TermDbxref"
|
13
|
+
has_many :term_relationship_terms, :class_name => "TermRelationshipTerm"
|
14
|
+
has_many :term_synonyms, :class_name => "TermSynonym"
|
15
|
+
has_many :location_qualifier_values, :class_name => "LocationQualifierValue"
|
16
|
+
has_many :seqfeature_types, :class_name => "Seqfeature", :foreign_key => "type_term_id"
|
17
|
+
has_many :seqfeature_sources, :class_name => "Seqfeature", :foreign_key => "source_term_id"
|
18
|
+
has_many :term_path_subjects, :class_name => "TermPath", :foreign_key => "subject_term_id"
|
19
|
+
has_many :term_path_predicates, :class_name => "TermPath", :foreign_key => "predicate_term_id"
|
20
|
+
has_many :term_path_objects, :class_name => "TermPath", :foreign_key => "object_term_id"
|
21
|
+
has_many :term_relationship_subjects, :class_name => "TermRelationship", :foreign_key =>"subject_term_id"
|
22
|
+
has_many :term_relationship_predicates, :class_name => "TermRelationship", :foreign_key =>"predicate_term_id"
|
23
|
+
has_many :term_relationship_objects, :class_name => "TermRelationship", :foreign_key =>"object_term_id"
|
24
|
+
has_many :seqfeature_paths, :class_name => "SeqfeaturePath"
|
25
|
+
end
|
26
|
+
end #SQL
|
27
|
+
end #Bio
|
@@ -0,0 +1,12 @@
|
|
1
|
+
|
2
|
+
module Bio
|
3
|
+
class SQL
|
4
|
+
class TermPath < DummyBase
|
5
|
+
set_sequence_name "term_path_pk_seq"
|
6
|
+
belongs_to :ontology, :class_name => "Ontology"
|
7
|
+
belongs_to :subject_term, :class_name => "Term"
|
8
|
+
belongs_to :object_term, :class_name => "Term"
|
9
|
+
belongs_to :predicate_term, :class_name => "Term"
|
10
|
+
end
|
11
|
+
end #SQL
|
12
|
+
end #Bio
|
@@ -0,0 +1,13 @@
|
|
1
|
+
|
2
|
+
module Bio
|
3
|
+
class SQL
|
4
|
+
class TermRelationship < DummyBase
|
5
|
+
set_sequence_name "term_relationship_pk_seq"
|
6
|
+
belongs_to :ontology, :class_name => "Ontology"
|
7
|
+
belongs_to :subject_term, :class_name => "Term"
|
8
|
+
belongs_to :predicate_term, :class_name => "Term"
|
9
|
+
belongs_to :object_term, :class_name => "Term"
|
10
|
+
has_one :term_relationship_term, :class_name => "TermRelationshipTerm"
|
11
|
+
end
|
12
|
+
end #SQL
|
13
|
+
end #Bio
|
@@ -0,0 +1,11 @@
|
|
1
|
+
|
2
|
+
module Bio
|
3
|
+
class SQL
|
4
|
+
class TermRelationshipTerm < DummyBase
|
5
|
+
#delete set_sequence_name nil
|
6
|
+
set_primary_key :term_relationship_id
|
7
|
+
belongs_to :term_relationship, :class_name => "TermRelationship"
|
8
|
+
belongs_to :term, :class_name => "Term"
|
9
|
+
end
|
10
|
+
end #SQL
|
11
|
+
end #Bio
|
data/lib/bio/io/das.rb
ADDED
@@ -0,0 +1,461 @@
|
|
1
|
+
#
|
2
|
+
# = bio/io/das.rb - BioDAS access module
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2003, 2004, 2007
|
5
|
+
# Shuichi Kawashima <shuichi@hgc.jp>,
|
6
|
+
# Toshiaki Katayama <k@bioruby.org>
|
7
|
+
# License:: The Ruby License
|
8
|
+
#
|
9
|
+
# $Id:$
|
10
|
+
#
|
11
|
+
#--
|
12
|
+
# == TODO
|
13
|
+
#
|
14
|
+
# link, stylesheet
|
15
|
+
#
|
16
|
+
#++
|
17
|
+
#
|
18
|
+
|
19
|
+
begin
|
20
|
+
require 'rexml/document'
|
21
|
+
rescue LoadError
|
22
|
+
end
|
23
|
+
require 'bio/command'
|
24
|
+
require 'bio/sequence'
|
25
|
+
|
26
|
+
|
27
|
+
module Bio
|
28
|
+
|
29
|
+
class DAS
|
30
|
+
|
31
|
+
# Specify DAS server to connect
|
32
|
+
def initialize(url = 'http://www.wormbase.org:80/db/')
|
33
|
+
@server = url.chomp('/')
|
34
|
+
end
|
35
|
+
|
36
|
+
def dna(dsn, entry_point, start, stop)
|
37
|
+
seg = Bio::DAS::SEGMENT.region(entry_point, start, stop)
|
38
|
+
self.get_dna(dsn, seg).first.sequence
|
39
|
+
end
|
40
|
+
|
41
|
+
def features(dsn, entry_point, start, stop)
|
42
|
+
seg = Bio::DAS::SEGMENT.region(entry_point, start, stop)
|
43
|
+
self.get_features(dsn, seg)
|
44
|
+
end
|
45
|
+
|
46
|
+
|
47
|
+
# Returns an Array of Bio::DAS::DSN
|
48
|
+
def get_dsn
|
49
|
+
ary = []
|
50
|
+
result = Bio::Command.post_form("#{@server}/das/dsn")
|
51
|
+
doc = REXML::Document.new(result.body)
|
52
|
+
doc.elements.each('/descendant::DSN') do |e|
|
53
|
+
dsn = DSN.new
|
54
|
+
e.elements.each do |e|
|
55
|
+
case e.name
|
56
|
+
when 'SOURCE'
|
57
|
+
dsn.source = e.text
|
58
|
+
dsn.source_id = e.attributes['id']
|
59
|
+
dsn.source_version = e.attributes['version']
|
60
|
+
when 'MAPMASTER'
|
61
|
+
dsn.mapmaster = e.text
|
62
|
+
when 'DESCRIPTION'
|
63
|
+
dsn.description = e.text
|
64
|
+
dsn.description_href = e.attributes['href']
|
65
|
+
end
|
66
|
+
end
|
67
|
+
ary << dsn
|
68
|
+
end
|
69
|
+
ary
|
70
|
+
end
|
71
|
+
|
72
|
+
# Returns Bio::DAS::ENTRY_POINT.
|
73
|
+
# The 'dsn' can be a String or a Bio::DAS::DSN object.
|
74
|
+
def get_entry_points(dsn)
|
75
|
+
entry_point = ENTRY_POINT.new
|
76
|
+
if dsn.instance_of?(Bio::DAS::DSN)
|
77
|
+
src = dsn.source
|
78
|
+
else
|
79
|
+
src = dsn
|
80
|
+
end
|
81
|
+
result = Bio::Command.post_form("#{@server}/das/#{src}/entry_points")
|
82
|
+
doc = REXML::Document.new(result.body)
|
83
|
+
doc.elements.each('/descendant::ENTRY_POINTS') do |e|
|
84
|
+
entry_point.href = e.attributes['href']
|
85
|
+
entry_point.version = e.attributes['version']
|
86
|
+
e.elements.each do |e|
|
87
|
+
segment = SEGMENT.new
|
88
|
+
segment.entry_id = e.attributes['id']
|
89
|
+
segment.start = e.attributes['start']
|
90
|
+
segment.stop = e.attributes['stop'] || e.attributes['size']
|
91
|
+
segment.orientation = e.attributes['orientation']
|
92
|
+
segment.subparts = e.attributes['subparts']
|
93
|
+
segment.description = e.text
|
94
|
+
entry_point.segments << segment
|
95
|
+
end
|
96
|
+
end
|
97
|
+
entry_point
|
98
|
+
end
|
99
|
+
|
100
|
+
# Returns an Array of Bio::DAS::DNA.
|
101
|
+
# The 'dsn' can be a String or a Bio::DAS::DSN object.
|
102
|
+
# The 'segments' can be a Bio::DAS::SEGMENT object or an Array of
|
103
|
+
# Bio::DAS::SEGMENT
|
104
|
+
def get_dna(dsn, segments)
|
105
|
+
ary = []
|
106
|
+
|
107
|
+
dsn = dsn.source if dsn.instance_of?(DSN)
|
108
|
+
segments = [segments] if segments.instance_of?(SEGMENT)
|
109
|
+
|
110
|
+
opts = []
|
111
|
+
segments.each do |s|
|
112
|
+
opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
|
113
|
+
end
|
114
|
+
|
115
|
+
result = Bio::Command.post_form("#{@server}/das/#{dsn}/dna", opts)
|
116
|
+
doc = REXML::Document.new(result.body)
|
117
|
+
doc.elements.each('/descendant::SEQUENCE') do |e|
|
118
|
+
sequence = DNA.new
|
119
|
+
sequence.entry_id = e.attributes['id']
|
120
|
+
sequence.start = e.attributes['start']
|
121
|
+
sequence.stop = e.attributes['stop']
|
122
|
+
sequence.version = e.attributes['version']
|
123
|
+
e.elements.each do |e|
|
124
|
+
sequence.sequence = Bio::Sequence::NA.new(e.text)
|
125
|
+
sequence.length = e.attributes['length'].to_i
|
126
|
+
end
|
127
|
+
ary << sequence
|
128
|
+
end
|
129
|
+
ary
|
130
|
+
end
|
131
|
+
|
132
|
+
# Returns an Array of Bio::DAS::SEQUENCE.
|
133
|
+
# The 'dsn' can be a String or a Bio::DAS::DSN object.
|
134
|
+
# The 'segments' can be a Bio::DAS::SEGMENT object or an Array of
|
135
|
+
# Bio::DAS::SEGMENT
|
136
|
+
def get_sequence(dsn, segments)
|
137
|
+
ary = []
|
138
|
+
|
139
|
+
dsn = dsn.source if dsn.instance_of?(DSN)
|
140
|
+
segments = [segments] if segments.instance_of?(SEGMENT)
|
141
|
+
|
142
|
+
opts = []
|
143
|
+
segments.each do |s|
|
144
|
+
opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
|
145
|
+
end
|
146
|
+
|
147
|
+
result = Bio::Command.post_form("#{@server}/das/#{dsn}/sequence", opts)
|
148
|
+
doc = REXML::Document.new(result.body)
|
149
|
+
doc.elements.each('/descendant::SEQUENCE') do |e|
|
150
|
+
sequence = SEQUENCE.new
|
151
|
+
sequence.entry_id = e.attributes['id']
|
152
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+
sequence.start = e.attributes['start']
|
153
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+
sequence.stop = e.attributes['stop']
|
154
|
+
sequence.moltype = e.attributes['moltype']
|
155
|
+
sequence.version = e.attributes['version']
|
156
|
+
case sequence.moltype
|
157
|
+
when /dna|rna/i # 'DNA', 'ssRNA', 'dsRNA'
|
158
|
+
sequence.sequence = Bio::Sequence::NA.new(e.text)
|
159
|
+
when /protein/i # 'Protein
|
160
|
+
sequence.sequence = Bio::Sequence::AA.new(e.text)
|
161
|
+
else
|
162
|
+
sequence.sequence = e.text
|
163
|
+
end
|
164
|
+
ary << sequence
|
165
|
+
end
|
166
|
+
ary
|
167
|
+
end
|
168
|
+
|
169
|
+
# Returns a Bio::DAS::TYPES object.
|
170
|
+
# The 'dsn' can be a String or a Bio::DAS::DSN object.
|
171
|
+
# The 'segments' is optional and can be a Bio::DAS::SEGMENT object or
|
172
|
+
# an Array of Bio::DAS::SEGMENT
|
173
|
+
def get_types(dsn, segments = []) # argument 'type' is deprecated
|
174
|
+
types = TYPES.new
|
175
|
+
|
176
|
+
dsn = dsn.source if dsn.instance_of?(DSN)
|
177
|
+
segments = [segments] if segments.instance_of?(SEGMENT)
|
178
|
+
|
179
|
+
opts = []
|
180
|
+
segments.each do |s|
|
181
|
+
opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
|
182
|
+
end
|
183
|
+
|
184
|
+
result = Bio::Command.post_form("#{@server}/das/#{dsn}/types", opts)
|
185
|
+
doc = REXML::Document.new(result.body)
|
186
|
+
doc.elements.each('/descendant::GFF') do |e|
|
187
|
+
types.version = e.attributes['version']
|
188
|
+
types.href = e.attributes['href']
|
189
|
+
e.elements.each do |e|
|
190
|
+
segment = SEGMENT.new
|
191
|
+
segment.entry_id = e.attributes['id']
|
192
|
+
segment.start = e.attributes['start']
|
193
|
+
segment.stop = e.attributes['stop']
|
194
|
+
segment.version = e.attributes['version']
|
195
|
+
segment.label = e.attributes['label']
|
196
|
+
e.elements.each do |e|
|
197
|
+
t = TYPE.new
|
198
|
+
t.entry_id = e.attributes['id']
|
199
|
+
t.method = e.attributes['method']
|
200
|
+
t.category = e.attributes['category']
|
201
|
+
t.count = e.text.to_i
|
202
|
+
segment.types << t
|
203
|
+
end
|
204
|
+
types.segments << segment
|
205
|
+
end
|
206
|
+
end
|
207
|
+
types
|
208
|
+
end
|
209
|
+
|
210
|
+
# Returns a Bio::DAS::GFF object.
|
211
|
+
# The 'dsn' can be a String or a Bio::DAS::DSN object.
|
212
|
+
# The 'segments' is optional and can be a Bio::DAS::SEGMENT object or
|
213
|
+
# an Array of Bio::DAS::SEGMENT
|
214
|
+
def get_features(dsn, segments = [], categorize = false, feature_ids = [], group_ids = [])
|
215
|
+
# arguments 'type' and 'category' are deprecated
|
216
|
+
gff = GFF.new
|
217
|
+
|
218
|
+
dsn = dsn.source if dsn.instance_of?(DSN)
|
219
|
+
segments = [segments] if segments.instance_of?(SEGMENT)
|
220
|
+
|
221
|
+
opts = []
|
222
|
+
segments.each do |s|
|
223
|
+
opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
|
224
|
+
end
|
225
|
+
if categorize
|
226
|
+
opts << "categorize=yes" # default is 'no'
|
227
|
+
end
|
228
|
+
feature_ids.each do |fid|
|
229
|
+
opts << "feature_id=#{fid}"
|
230
|
+
end
|
231
|
+
group_ids.each do |gid|
|
232
|
+
opts << "group_id=#{gid}"
|
233
|
+
end
|
234
|
+
|
235
|
+
result = Bio::Command.post_form("#{@server}/das/#{dsn}/features", opts)
|
236
|
+
doc = REXML::Document.new(result.body)
|
237
|
+
doc.elements.each('/descendant::GFF') do |e|
|
238
|
+
gff.version = e.attributes['version']
|
239
|
+
gff.href = e.attributes['href']
|
240
|
+
e.elements.each('SEGMENT') do |e|
|
241
|
+
segment = SEGMENT.new
|
242
|
+
segment.entry_id = e.attributes['id']
|
243
|
+
segment.start = e.attributes['start']
|
244
|
+
segment.stop = e.attributes['stop']
|
245
|
+
segment.version = e.attributes['version']
|
246
|
+
segment.label = e.attributes['label']
|
247
|
+
e.elements.each do |e|
|
248
|
+
feature = FEATURE.new
|
249
|
+
feature.entry_id = e.attributes['id']
|
250
|
+
feature.label = e.attributes['label']
|
251
|
+
e.elements.each do |e|
|
252
|
+
case e.name
|
253
|
+
when 'TYPE'
|
254
|
+
type = TYPE.new
|
255
|
+
type.entry_id = e.attributes['id']
|
256
|
+
type.category = e.attributes['category']
|
257
|
+
type.reference = e.attributes['referrence']
|
258
|
+
type.label = e.text
|
259
|
+
feature.types << type
|
260
|
+
when 'METHOD'
|
261
|
+
feature.method_id = e.attributes['id']
|
262
|
+
feature.method = e.text
|
263
|
+
when 'START'
|
264
|
+
feature.start = e.text
|
265
|
+
when 'STOP', 'END'
|
266
|
+
feature.stop = e.text
|
267
|
+
when 'SCORE'
|
268
|
+
feature.score = e.text
|
269
|
+
when 'ORIENTATION'
|
270
|
+
feature.orientation = e.text
|
271
|
+
when 'PHASE'
|
272
|
+
feature.phase = e.text
|
273
|
+
when 'NOTE'
|
274
|
+
feature.notes << e.text
|
275
|
+
when 'LINK'
|
276
|
+
link = LINK.new
|
277
|
+
link.href = e.attributes['href']
|
278
|
+
link.text = e.text
|
279
|
+
feature.links << link
|
280
|
+
when 'TARGET'
|
281
|
+
target = TARGET.new
|
282
|
+
target.entry_id = e.attributes['id']
|
283
|
+
target.start = e.attributes['start']
|
284
|
+
target.stop = e.attributes['stop']
|
285
|
+
target.name = e.text
|
286
|
+
feature.targets << target
|
287
|
+
when 'GROUP'
|
288
|
+
group = GROUP.new
|
289
|
+
group.entry_id = e.attributes['id']
|
290
|
+
group.label = e.attributes['label']
|
291
|
+
group.type = e.attributes['type']
|
292
|
+
e.elements.each do |e|
|
293
|
+
case e.name
|
294
|
+
when 'NOTE' # in GROUP
|
295
|
+
group.notes << e.text
|
296
|
+
when 'LINK' # in GROUP
|
297
|
+
link = LINK.new
|
298
|
+
link.href = e.attributes['href']
|
299
|
+
link.text = e.text
|
300
|
+
group.links << link
|
301
|
+
when 'TARGET' # in GROUP
|
302
|
+
target = TARGET.new
|
303
|
+
target.entry_id = e.attributes['id']
|
304
|
+
target.start = e.attributes['start']
|
305
|
+
target.stop = e.attributes['stop']
|
306
|
+
target.name = e.text
|
307
|
+
group.targets << target
|
308
|
+
end
|
309
|
+
end
|
310
|
+
feature.groups << group
|
311
|
+
end
|
312
|
+
end
|
313
|
+
segment.features << feature
|
314
|
+
end
|
315
|
+
gff.segments << segment
|
316
|
+
end
|
317
|
+
end
|
318
|
+
gff
|
319
|
+
end
|
320
|
+
|
321
|
+
|
322
|
+
class DSN
|
323
|
+
attr_accessor :source, :source_id, :source_version,
|
324
|
+
:mapmaster, :description, :description_href
|
325
|
+
end
|
326
|
+
|
327
|
+
class ENTRY_POINT
|
328
|
+
def initialize
|
329
|
+
@segments = Array.new
|
330
|
+
end
|
331
|
+
attr_reader :segments
|
332
|
+
attr_accessor :href, :version
|
333
|
+
|
334
|
+
def each
|
335
|
+
@segments.each do |x|
|
336
|
+
yield x
|
337
|
+
end
|
338
|
+
end
|
339
|
+
end
|
340
|
+
|
341
|
+
class SEGMENT
|
342
|
+
def self.region(entry_id, start, stop)
|
343
|
+
segment = self.new
|
344
|
+
segment.entry_id = entry_id
|
345
|
+
segment.start = start
|
346
|
+
segment.stop = stop
|
347
|
+
return segment
|
348
|
+
end
|
349
|
+
|
350
|
+
def initialize
|
351
|
+
@features = Array.new # for FEATURE
|
352
|
+
@types = Array.new # for TYPE
|
353
|
+
end
|
354
|
+
attr_accessor :entry_id, :start, :stop, :orientation, :description,
|
355
|
+
:subparts, # optional
|
356
|
+
:features, :version, :label, # for FEATURE
|
357
|
+
:types # for TYPE
|
358
|
+
end
|
359
|
+
|
360
|
+
class DNA
|
361
|
+
attr_accessor :entry_id, :start, :stop, :version, :sequence, :length
|
362
|
+
end
|
363
|
+
|
364
|
+
class SEQUENCE
|
365
|
+
attr_accessor :entry_id, :start, :stop, :moltype, :version, :sequence
|
366
|
+
end
|
367
|
+
|
368
|
+
class TYPES < ENTRY_POINT; end
|
369
|
+
|
370
|
+
class TYPE
|
371
|
+
attr_accessor :entry_id, :method, :category, :count,
|
372
|
+
:reference, :label # for FEATURE
|
373
|
+
end
|
374
|
+
|
375
|
+
class GFF
|
376
|
+
def initialize
|
377
|
+
@segments = Array.new
|
378
|
+
end
|
379
|
+
attr_reader :segments
|
380
|
+
attr_accessor :version, :href
|
381
|
+
end
|
382
|
+
|
383
|
+
class FEATURE
|
384
|
+
def initialize
|
385
|
+
@notes = Array.new
|
386
|
+
@links = Array.new
|
387
|
+
@types = Array.new
|
388
|
+
@targets = Array.new
|
389
|
+
@groups = Array.new
|
390
|
+
end
|
391
|
+
attr_accessor :entry_id, :label,
|
392
|
+
:method_id, :method, :start, :stop, :score, :orientation, :phase
|
393
|
+
attr_reader :notes, :links, :types, :targets, :groups
|
394
|
+
end
|
395
|
+
|
396
|
+
class LINK
|
397
|
+
attr_accessor :href, :text
|
398
|
+
end
|
399
|
+
|
400
|
+
class TARGET
|
401
|
+
attr_accessor :entry_id, :start, :stop, :name
|
402
|
+
end
|
403
|
+
|
404
|
+
class GROUP
|
405
|
+
def initialize
|
406
|
+
@notes = Array.new
|
407
|
+
@links = Array.new
|
408
|
+
@targets = Array.new
|
409
|
+
end
|
410
|
+
attr_accessor :entry_id, :label, :type
|
411
|
+
attr_reader :notes, :links, :targets
|
412
|
+
end
|
413
|
+
|
414
|
+
end
|
415
|
+
|
416
|
+
end # module Bio
|
417
|
+
|
418
|
+
|
419
|
+
if __FILE__ == $0
|
420
|
+
|
421
|
+
# begin
|
422
|
+
# require 'pp'
|
423
|
+
# alias p pp
|
424
|
+
# rescue LoadError
|
425
|
+
# end
|
426
|
+
|
427
|
+
puts "### WormBase"
|
428
|
+
wormbase = Bio::DAS.new('http://www.wormbase.org/db/')
|
429
|
+
|
430
|
+
puts ">>> test get_dsn"
|
431
|
+
p wormbase.get_dsn
|
432
|
+
|
433
|
+
puts ">>> create segment obj Bio::DAS::SEGMENT.region('I', 1, 1000)"
|
434
|
+
seg = Bio::DAS::SEGMENT.region('I', 1, 1000)
|
435
|
+
p seg
|
436
|
+
|
437
|
+
puts ">>> test get_dna"
|
438
|
+
p wormbase.get_dna('elegans', seg)
|
439
|
+
|
440
|
+
puts "### test get_features"
|
441
|
+
p wormbase.get_features('elegans', seg)
|
442
|
+
|
443
|
+
puts "### KEGG DAS"
|
444
|
+
kegg_das = Bio::DAS.new("http://das.hgc.jp/cgi-bin/")
|
445
|
+
|
446
|
+
dsn_list = kegg_das.get_dsn
|
447
|
+
org_list = dsn_list.collect {|x| x.source}
|
448
|
+
|
449
|
+
puts ">>> dsn : entry_points"
|
450
|
+
org_list.each do |org|
|
451
|
+
print "#{org} : "
|
452
|
+
list = kegg_das.get_entry_points(org)
|
453
|
+
list.segments.each do |seg|
|
454
|
+
print " #{seg.entry_id}"
|
455
|
+
end
|
456
|
+
puts
|
457
|
+
end
|
458
|
+
|
459
|
+
end
|
460
|
+
|
461
|
+
|