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
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# = bio/io/keggapi.rb - KEGG API access class
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#
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# Copyright:: Copyright (C) 2003, 2004 Toshiaki Katayama <k@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/io/soapwsdl'
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require 'uri'
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require 'net/http'
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require 'bio/command'
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module Bio
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class KEGG
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# == Description
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#
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# KEGG API is a web service to use KEGG system via SOAP/WSDL.
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#
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# == References
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#
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# For more informations on KEGG API, see the following site and read the
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# reference manual.
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#
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# * http://www.genome.jp/kegg/soap/
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# * http://www.genome.jp/kegg/soap/doc/keggapi_manual.html
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#
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# == List of methods
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#
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# As of KEGG API v5.0
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#
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# * list_databases
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# * list_organisms
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# * list_pathways(org)
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# * binfo(string)
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# * bget(string)
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# * bfind(string)
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# * btit(string)
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# * get_linkdb_by_entry(entry_id, db, start, max_results)
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# * get_best_best_neighbors_by_gene(genes_id, start, max_results)
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# * get_best_neighbors_by_gene(genes_id, start, max_results)
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# * get_reverse_best_neighbors_by_gene(genes_id, start, max_results)
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# * get_paralogs_by_gene(genes_id, start, max_results)
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# * get_similarity_between_genes(genes_id1, genes_id2)
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# * get_motifs_by_gene(genes_id, db)
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# * get_genes_by_motifs(motif_id_list, start, max_results)
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# * get_ko_by_gene(genes_id)
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# * get_ko_members(ko_id)
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# * get_oc_members_by_gene(genes_id, start, max_results)
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# * get_pc_members_by_gene(genes_id, start, max_results)
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# * mark_pathway_by_objects(pathway_id, object_id_list)
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# * color_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
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# * get_genes_by_pathway(pathway_id)
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# * get_enzymes_by_pathway(pathway_id)
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# * get_compounds_by_pathway(pathway_id)
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# * get_reactions_by_pathway(pathway_id)
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# * get_pathways_by_genes(genes_id_list)
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# * get_pathways_by_enzymes(enzyme_id_list)
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# * get_pathways_by_compounds(compound_id_list)
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# * get_pathways_by_reactions(reaction_id_list)
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# * get_linked_pathways(pathway_id)
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# * get_genes_by_enzyme(enzyme_id, org)
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# * get_enzymes_by_gene(genes_id)
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# * get_enzymes_by_compound(compound_id)
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# * get_enzymes_by_reaction(reaction_id)
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# * get_compounds_by_enzyme(enzyme_id)
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# * get_compounds_by_reaction(reaction_id)
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# * get_reactions_by_enzyme(enzyme_id)
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# * get_reactions_by_compound(compound_id)
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# * get_genes_by_organism(org, start, max_results)
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# * get_number_of_genes_by_organism(org)
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#
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# == KEGG API methods implemented only in BioRuby
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#
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# In BioRuby, returned values are added filter method to pick up
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# values in a complex data type as an array.
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#
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# #!/usr/bin/env ruby
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#
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# require 'bio'
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#
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# serv = Bio::KEGG::API.new
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# results = serv.get_best_neighbors_by_gene("eco:b0002", "bsu")
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#
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# # case 0 : without filter
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# results.each do |hit|
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# print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
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# end
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#
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# # case 1 : select gene names and SW score only
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# fields = [:genes_id1, :genes_id2, :sw_score]
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# results.each do |hit|
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# puts hit.filter(fields).join("\t")
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# end
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#
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# # case 2 : also uses aligned position in each amino acid sequence etc.
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# fields1 = [:genes_id1, :start_position1, :end_position1, :best_flag_1to2]
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# fields2 = [:genes_id2, :start_position2, :end_position2, :best_flag_2to1]
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# results.each do |hit|
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# print "> score: ", hit.sw_score, ", identity: ", hit.identity, "\n"
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# print "1:\t", hit.filter(fields1).join("\t"), "\n"
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# print "2:\t", hit.filter(fields2).join("\t"), "\n"
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# end
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#
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# Using filter method will make it easy to change fields to select and
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# keep the script clean.
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#
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# * Bio::KEGG::API#get_all_neighbors_by_gene(genes_id, org)
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# * Bio::KEGG::API#get_all_best_best_neighbors_by_gene(genes_id)
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# * Bio::KEGG::API#get_all_best_neighbors_by_gene(genes_id)
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# * Bio::KEGG::API#get_all_reverse_best_neighbors_by_gene(genes_id)
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# * Bio::KEGG::API#get_all_paralogs_by_gene(genes_id)
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# * Bio::KEGG::API#get_all_genes_by_motifs(motif_id_list)
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# * Bio::KEGG::API#get_all_oc_members_by_gene(genes_id)
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# * Bio::KEGG::API#get_all_pc_members_by_gene(genes_id)
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# * Bio::KEGG::API#get_all_genes_by_organism(org)
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#
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# These methods are wrapper for the methods without _all_ in its name
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# and internally iterate to retrive all the results using start/max_results
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# value pairs described above. For example,
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#
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# #!/usr/bin/env ruby
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#
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# require 'soap/wsdlDriver'
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#
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# wsdl = "http://soap.genome.jp/KEGG.wsdl"
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# serv = SOAP::WSDLDriverFactory.new(wsdl).create_driver
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# serv.generate_explicit_type = true
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#
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# start = 1
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# max_results = 100
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#
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# loop do
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# results = serv.get_best_neighbors_by_gene('eco:b0002', start, max_results)
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# break unless results # when no more results returned
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# results.each do |hit|
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# print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
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# end
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# start += max_results
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# end
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#
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# can be witten as
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#
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# #!/usr/bin/env ruby
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#
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# require 'bio'
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#
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# serv = Bio::KEGG::API.new
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#
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# results = serv.get_all_best_neighbors_by_gene('eco:b0002')
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# results.each do |hit|
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# print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
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# end
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#
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#
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# * Bio::KEGG::API#save_image(url, filename = nil)
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#
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# Some methods of the KEGG API will return a URL of the generated image.
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# This method save an image specified by the URL. The filename can be
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# specified by its second argument, otherwise basename of the URL will
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# be used.
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#
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# #!/usr/bin/env ruby
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#
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# require 'bio'
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#
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# serv = Bio::KEGG::API.new("http://soap.genome.jp/v3.0/KEGG.wsdl")
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#
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# list = ["eco:b1002", "eco:b2388"]
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# url = serv.mark_pathway_by_objects("path:eco00010", list)
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#
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# # Save with the original filename (eco00010.gif in this case)
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# serv.save_image(url)
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#
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# # or save as "save_image.gif"
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# serv.save_image(url, "save_image.gif")
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#
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# * Bio::KEGG::API#get_entries(entry_id_list)
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# * Bio::KEGG::API#get_aaseqs(entry_id_list)
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# * Bio::KEGG::API#get_naseqs(entry_id_list)
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# * Bio::KEGG::API#get_definitions(entry_id_list)
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#
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# These methods are for the shortcut and backward compatibility
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# (these methods existed in the older version of the KEGG API).
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#
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class API < Bio::SOAPWSDL
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SERVER_URI = "http://soap.genome.jp/KEGG.wsdl"
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# Connect to the KEGG API's SOAP server. A WSDL file will be automatically
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# downloaded and parsed to generate the SOAP client driver. The default URL
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# for the WSDL is http://soap.genome.jp/KEGG.wsdl but it can be changed by
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# the argument or by wsdl= method.
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def initialize(wsdl = nil)
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@wsdl = wsdl || SERVER_URI
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@log = nil
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@start = 1
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@max_results = 100
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create_driver
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end
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# Returns current value for the 'start' count for the methods having
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# start/max_results argument pairs or changes the default value for
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# the 'start' count.
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attr_accessor :start
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# Returns current value for the 'max_results' number for the methods having
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# start/max_results argument pairs or changes the default value for the
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# 'max_results' count. If your request timeouts, try smaller value for
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# the max_results.
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attr_accessor :max_results
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def method_missing(*arg)
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begin
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results = @driver.send(*arg)
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rescue Timeout::Error
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retry
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end
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results = add_filter(results)
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return results
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end
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# def get_all_neighbors_by_gene(genes_id, org)
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# get_all(:get_neighbors_by_gene, genes_id, org)
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# end
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def get_all_best_best_neighbors_by_gene(genes_id)
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get_all(:get_best_best_neighbors_by_gene, genes_id)
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end
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def get_all_best_neighbors_by_gene(genes_id)
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get_all(:get_best_neighbors_by_gene, genes_id)
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end
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def get_all_reverse_best_neighbors_by_gene(genes_id)
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get_all(:get_reverse_best_neighbors_by_gene, genes_id)
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end
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def get_all_paralogs_by_gene(genes_id)
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get_all(:get_paralogs_by_gene, genes_id)
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end
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def get_all_genes_by_motifs(motif_id_list)
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get_all(:get_genes_by_motifs, motif_id_list)
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end
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def get_all_oc_members_by_gene(genes_id)
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get_all(:get_oc_members_by_gene, genes_id)
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end
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def get_all_pc_members_by_gene(genes_id)
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get_all(:get_pc_members_by_gene, genes_id)
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end
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def get_all_genes_by_organism(org)
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get_all(:get_genes_by_organism, org)
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end
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def get_all_linkdb_by_entry(entry_id, db)
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get_all(:get_linkdb_by_entry, entry_id, db)
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end
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def save_image(url, filename = nil)
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schema, user, host, port, reg, path, = URI.split(url)
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filename ||= File.basename(path)
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http = Bio::Command.new_http(host, port)
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response = http.get(path)
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File.open(filename, "w+") do |f|
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f.print response.body
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end
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return filename
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end
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def get_entries(ary = [])
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result = ''
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step = [@max_results, 50].min
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0.step(ary.length, step) do |i|
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str = ary[i, step].join(" ")
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if entry = @driver.send(:bget, str)
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result << entry.to_s
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end
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end
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return result
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end
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def get_aaseqs(ary = [])
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result = ''
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step = [@max_results, 50].min
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0.step(ary.length, step) do |i|
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str = "-f -n a " + ary[i, step].join(" ")
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if entry = @driver.send(:bget, str)
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result << entry.to_s
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end
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end
|
301
|
+
return result
|
302
|
+
end
|
303
|
+
|
304
|
+
def get_naseqs(ary = [])
|
305
|
+
result = ''
|
306
|
+
step = [@max_results, 50].min
|
307
|
+
0.step(ary.length, step) do |i|
|
308
|
+
str = "-f -n n " + ary[i, step].join(" ")
|
309
|
+
if entry = @driver.send(:bget, str)
|
310
|
+
result << entry.to_s
|
311
|
+
end
|
312
|
+
end
|
313
|
+
return result
|
314
|
+
end
|
315
|
+
|
316
|
+
def get_definitions(ary = [])
|
317
|
+
result = ''
|
318
|
+
step = [@max_results, 50].min
|
319
|
+
0.step(ary.length, step) do |i|
|
320
|
+
str = ary[i, step].join(" ")
|
321
|
+
if entry = @driver.send(:btit, str)
|
322
|
+
result << entry.to_s
|
323
|
+
end
|
324
|
+
end
|
325
|
+
return result
|
326
|
+
end
|
327
|
+
|
328
|
+
|
329
|
+
private
|
330
|
+
|
331
|
+
def add_filter(results)
|
332
|
+
if results.is_a?(Array)
|
333
|
+
results.each do |result|
|
334
|
+
next if result.is_a?(Fixnum)
|
335
|
+
def result.filter(fields)
|
336
|
+
fields.collect { |field| self.send(field) }
|
337
|
+
end
|
338
|
+
end
|
339
|
+
end
|
340
|
+
return results
|
341
|
+
end
|
342
|
+
|
343
|
+
def get_all(method, *args)
|
344
|
+
args << @start
|
345
|
+
args << @max_results
|
346
|
+
|
347
|
+
ary = []
|
348
|
+
loop do
|
349
|
+
results = @driver.send(method, *args)
|
350
|
+
break unless results
|
351
|
+
break if results.empty?
|
352
|
+
results = add_filter(results)
|
353
|
+
ary << results
|
354
|
+
args[-2] += @max_results # next start count
|
355
|
+
end
|
356
|
+
return ary.flatten
|
357
|
+
end
|
358
|
+
|
359
|
+
end # API
|
360
|
+
|
361
|
+
end # KEGG
|
362
|
+
end # Bio
|
363
|
+
|
364
|
+
|
365
|
+
if __FILE__ == $0
|
366
|
+
|
367
|
+
begin
|
368
|
+
require 'pp'
|
369
|
+
alias p pp
|
370
|
+
rescue LoadError
|
371
|
+
end
|
372
|
+
|
373
|
+
puts ">>> KEGG API"
|
374
|
+
serv = Bio::KEGG::API.new
|
375
|
+
# serv.log = STDERR
|
376
|
+
|
377
|
+
puts "# * parameters"
|
378
|
+
puts " wsdl : #{serv.wsdl}"
|
379
|
+
puts " log : #{serv.log}"
|
380
|
+
puts " start : #{serv.start}"
|
381
|
+
puts " max_results : #{serv.max_results}"
|
382
|
+
|
383
|
+
puts "=== META"
|
384
|
+
|
385
|
+
puts "### list_databases"
|
386
|
+
list = serv.list_databases
|
387
|
+
list.each do |db|
|
388
|
+
print db.entry_id, "\t", db.definition, "\n"
|
389
|
+
end
|
390
|
+
|
391
|
+
puts "### list_organisms"
|
392
|
+
list = serv.list_organisms
|
393
|
+
list.each do |org|
|
394
|
+
print org.entry_id, "\t", org.definition, "\n"
|
395
|
+
end
|
396
|
+
|
397
|
+
puts "### list_pathways('map') : reference pathway"
|
398
|
+
list = serv.list_pathways("map")
|
399
|
+
list.each do |path|
|
400
|
+
print path.entry_id, "\t", path.definition, "\n"
|
401
|
+
end
|
402
|
+
|
403
|
+
puts "### list_pathways('eco') : E. coli pathway"
|
404
|
+
list = serv.list_pathways("eco")
|
405
|
+
list.each do |path|
|
406
|
+
print path.entry_id, "\t", path.definition, "\n"
|
407
|
+
end
|
408
|
+
|
409
|
+
puts "=== DBGET"
|
410
|
+
|
411
|
+
puts "### binfo('all')"
|
412
|
+
puts serv.binfo("all")
|
413
|
+
|
414
|
+
puts "### binfo('genbank')"
|
415
|
+
puts serv.binfo("genbank")
|
416
|
+
|
417
|
+
puts "### bfind('genbank kinase cell cycle human')"
|
418
|
+
puts serv.bfind("genbank kinase cell cycle human")
|
419
|
+
|
420
|
+
puts "### bget('gb:AJ617376')"
|
421
|
+
puts serv.bget("gb:AJ617376")
|
422
|
+
|
423
|
+
puts "### bget('eco:b0002 eco:b0003')"
|
424
|
+
puts serv.bget("eco:b0002 eco:b0003")
|
425
|
+
|
426
|
+
puts "### btit('eco:b0002 eco:b0003')"
|
427
|
+
puts serv.btit("eco:b0002 eco:b0003")
|
428
|
+
|
429
|
+
puts "# * get_entries(['eco:b0002', 'eco:b0003'])"
|
430
|
+
puts serv.get_entries(["eco:b0002", "eco:b0003"])
|
431
|
+
|
432
|
+
puts "# * get_aaseqs(['eco:b0002', 'eco:b0003'])"
|
433
|
+
puts serv.get_aaseqs(["eco:b0002", "eco:b0003"])
|
434
|
+
|
435
|
+
puts "# * get_naseqs(['eco:b0002', 'eco:b0003'])"
|
436
|
+
puts serv.get_naseqs(["eco:b0002", "eco:b0003"])
|
437
|
+
|
438
|
+
puts "# * get_definitions(['eco:b0002', 'eco:b0003'])"
|
439
|
+
puts serv.get_definitions(["eco:b0002", "eco:b0003"])
|
440
|
+
|
441
|
+
puts "# * get_definitions(('eco:b0001'..'eco:b0200').to_a)"
|
442
|
+
puts serv.get_definitions(("eco:b0001".."eco:b0200").to_a)
|
443
|
+
|
444
|
+
puts "=== LinkDB"
|
445
|
+
|
446
|
+
puts "### get_linkdb_by_entry('eco:b0002', 'pathway', 1, 5)"
|
447
|
+
list = serv.get_linkdb_by_entry("eco:b0002", "pathway", 1, 5)
|
448
|
+
list.each do |link|
|
449
|
+
puts [ link.entry_id1, link.entry_id2, link.type, link.path ].join("\t")
|
450
|
+
end
|
451
|
+
|
452
|
+
puts "# * get_all_linkdb_by_entry('eco:b0002', 'pathway')"
|
453
|
+
list = serv.get_all_linkdb_by_entry("eco:b0002", "pathway")
|
454
|
+
list.each do |link|
|
455
|
+
puts [ link.entry_id1, link.entry_id2, link.type, link.path ].join("\t")
|
456
|
+
end
|
457
|
+
|
458
|
+
puts "=== SSDB"
|
459
|
+
|
460
|
+
puts "### get_neighbors_by_gene('eco:b0002', 'all', 1, 5)"
|
461
|
+
list = serv.get_neighbors_by_gene("eco:b0002", "all", 1, 5)
|
462
|
+
list.each do |hit|
|
463
|
+
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
464
|
+
end
|
465
|
+
|
466
|
+
puts "# * get_all_neighbors_by_gene('eco:b0002', 'bsu')"
|
467
|
+
list = serv.get_all_neighbors_by_gene("eco:b0002", "bsu")
|
468
|
+
list.each do |hit|
|
469
|
+
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
470
|
+
end
|
471
|
+
|
472
|
+
puts "### get_best_best_neighbors_by_gene('eco:b0002', 1, 5)"
|
473
|
+
list = serv.get_best_best_neighbors_by_gene("eco:b0002", 1, 5)
|
474
|
+
list.each do |hit|
|
475
|
+
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
476
|
+
end
|
477
|
+
|
478
|
+
puts "# * get_all_best_best_neighbors_by_gene('eco:b0002')"
|
479
|
+
list = serv.get_all_best_best_neighbors_by_gene("eco:b0002")
|
480
|
+
list.each do |hit|
|
481
|
+
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
482
|
+
end
|
483
|
+
|
484
|
+
puts "### get_best_neighbors_by_gene('eco:b0002', 1, 5)"
|
485
|
+
list = serv.get_best_neighbors_by_gene("eco:b0002", 1, 5)
|
486
|
+
list.each do |hit|
|
487
|
+
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
488
|
+
end
|
489
|
+
|
490
|
+
puts "# * get_all_best_neighbors_by_gene('eco:b0002')"
|
491
|
+
list = serv.get_all_best_neighbors_by_gene("eco:b0002")
|
492
|
+
list.each do |hit|
|
493
|
+
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
494
|
+
end
|
495
|
+
|
496
|
+
puts "### get_reverse_best_neighbors_by_gene('eco:b0002', 1, 5)"
|
497
|
+
list = serv.get_reverse_best_neighbors_by_gene("eco:b0002", 1, 5)
|
498
|
+
list.each do |hit|
|
499
|
+
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
500
|
+
end
|
501
|
+
|
502
|
+
puts "# * get_all_reverse_best_neighbors_by_gene('eco:b0002')"
|
503
|
+
list = serv.get_all_reverse_best_neighbors_by_gene("eco:b0002")
|
504
|
+
list.each do |hit|
|
505
|
+
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
506
|
+
end
|
507
|
+
|
508
|
+
puts "### get_paralogs_by_gene('eco:b0002', 1, 5)"
|
509
|
+
list = serv.get_paralogs_by_gene("eco:b0002", 1, 5)
|
510
|
+
list.each do |hit|
|
511
|
+
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
512
|
+
end
|
513
|
+
|
514
|
+
puts "# * get_all_paralogs_by_gene('eco:b0002')"
|
515
|
+
list = serv.get_all_paralogs_by_gene("eco:b0002")
|
516
|
+
list.each do |hit|
|
517
|
+
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
518
|
+
end
|
519
|
+
|
520
|
+
puts "### get_similarity_between_genes('eco:b0002', 'bsu:BG10350')"
|
521
|
+
relation = serv.get_similarity_between_genes("eco:b0002", "bsu:BG10350")
|
522
|
+
puts " genes_id1 : #{relation.genes_id1}" # string
|
523
|
+
puts " genes_id2 : #{relation.genes_id2}" # string
|
524
|
+
puts " sw_score : #{relation.sw_score}" # int
|
525
|
+
puts " bit_score : #{relation.bit_score}" # float
|
526
|
+
puts " identity : #{relation.identity}" # float
|
527
|
+
puts " overlap : #{relation.overlap}" # int
|
528
|
+
puts " start_position1 : #{relation.start_position1}" # int
|
529
|
+
puts " end_position1 : #{relation.end_position1}" # int
|
530
|
+
puts " start_position2 : #{relation.start_position2}" # int
|
531
|
+
puts " end_position2 : #{relation.end_position2}" # int
|
532
|
+
puts " best_flag_1to2 : #{relation.best_flag_1to2}" # boolean
|
533
|
+
puts " best_flag_2to1 : #{relation.best_flag_2to1}" # boolean
|
534
|
+
puts " definition1 : #{relation.definition1}" # string
|
535
|
+
puts " definition2 : #{relation.definition2}" # string
|
536
|
+
puts " length1 : #{relation.length1}" # int
|
537
|
+
puts " length2 : #{relation.length2}" # int
|
538
|
+
|
539
|
+
puts "=== MOTIF"
|
540
|
+
|
541
|
+
puts "### get_motifs_by_gene('eco:b0002', 'pfam')"
|
542
|
+
list = serv.get_motifs_by_gene("eco:b0002", "pfam")
|
543
|
+
list.each do |motif|
|
544
|
+
puts motif.motif_id
|
545
|
+
end if list
|
546
|
+
|
547
|
+
puts "### get_motifs_by_gene('eco:b0002', 'tfam')"
|
548
|
+
list = serv.get_motifs_by_gene("eco:b0002", "tfam")
|
549
|
+
list.each do |motif|
|
550
|
+
puts motif.motif_id
|
551
|
+
end if list
|
552
|
+
|
553
|
+
puts "### get_motifs_by_gene('eco:b0002', 'pspt')"
|
554
|
+
list = serv.get_motifs_by_gene("eco:b0002", "pspt")
|
555
|
+
list.each do |motif|
|
556
|
+
puts motif.motif_id
|
557
|
+
end if list
|
558
|
+
|
559
|
+
puts "### get_motifs_by_gene('eco:b0002', 'pspf')"
|
560
|
+
list = serv.get_motifs_by_gene("eco:b0002", "pspf")
|
561
|
+
list.each do |motif|
|
562
|
+
puts motif.motif_id
|
563
|
+
end if list
|
564
|
+
|
565
|
+
puts "### get_motifs_by_gene('eco:b0002', 'all')"
|
566
|
+
list = serv.get_motifs_by_gene("eco:b0002", "all")
|
567
|
+
list.each do |motif|
|
568
|
+
puts "# * motif result"
|
569
|
+
puts " motif_id : #{motif.motif_id}"
|
570
|
+
puts " definition : #{motif.definition}"
|
571
|
+
puts " genes_id : #{motif.genes_id}"
|
572
|
+
puts " start_position : #{motif.start_position}"
|
573
|
+
puts " end_position : #{motif.end_position}"
|
574
|
+
puts " score : #{motif.score}"
|
575
|
+
puts " evalue : #{motif.evalue}"
|
576
|
+
end
|
577
|
+
|
578
|
+
puts "### get_genes_by_motifs(['pf:ACT', 'ps:ASPARTOKINASE'], 1, 5)"
|
579
|
+
list = serv.get_genes_by_motifs(["pf:ACT", "ps:ASPARTOKINASE"], 1, 5)
|
580
|
+
list.each do |gene|
|
581
|
+
puts [ gene.entry_id, gene.definition ].join("\t")
|
582
|
+
end
|
583
|
+
|
584
|
+
puts "# * get_all_genes_by_motifs(['pf:ACT', 'ps:ASPARTOKINASE'])"
|
585
|
+
list = serv.get_all_genes_by_motifs(["pf:ACT", "ps:ASPARTOKINASE"])
|
586
|
+
list.each do |gene|
|
587
|
+
puts [ gene.entry_id, gene.definition ].join("\t")
|
588
|
+
end
|
589
|
+
|
590
|
+
puts "=== KO, OC, PC"
|
591
|
+
|
592
|
+
puts "### get_ko_by_gene('eco:b0002')"
|
593
|
+
list = serv.get_ko_by_gene("eco:b0002")
|
594
|
+
list.each do |ko|
|
595
|
+
puts ko
|
596
|
+
end
|
597
|
+
|
598
|
+
puts "### get_ko_members('ko:K00003')"
|
599
|
+
list = serv.get_ko_members("ko:K00003")
|
600
|
+
list.each do |gene|
|
601
|
+
puts gene
|
602
|
+
end
|
603
|
+
|
604
|
+
puts "### get_oc_members_by_gene('eco:b0002', 1, 5)"
|
605
|
+
list = serv.get_oc_members_by_gene("eco:b0002", 1, 5)
|
606
|
+
list.each do |gene|
|
607
|
+
puts gene
|
608
|
+
end
|
609
|
+
|
610
|
+
puts "# * get_all_oc_members_by_gene('eco:b0002')"
|
611
|
+
list = serv.get_all_oc_members_by_gene("eco:b0002")
|
612
|
+
list.each do |gene|
|
613
|
+
puts gene
|
614
|
+
end
|
615
|
+
|
616
|
+
puts "### get_pc_members_by_gene('eco:b0002', 1, 5)"
|
617
|
+
list = serv.get_pc_members_by_gene("eco:b0002", 1, 5)
|
618
|
+
list.each do |gene|
|
619
|
+
puts gene
|
620
|
+
end
|
621
|
+
|
622
|
+
puts "# * get_all_pc_members_by_gene('eco:b0002')"
|
623
|
+
list = serv.get_all_pc_members_by_gene("eco:b0002")
|
624
|
+
list.each do |gene|
|
625
|
+
puts gene
|
626
|
+
end
|
627
|
+
|
628
|
+
puts "=== PATHWAY"
|
629
|
+
|
630
|
+
puts "==== coloring pathway"
|
631
|
+
|
632
|
+
puts "### mark_pathway_by_objects('path:eco00260', obj_list)"
|
633
|
+
puts " obj_list = ['eco:b0002', 'cpd:C00263']"
|
634
|
+
obj_list = ["eco:b0002", "cpd:C00263"]
|
635
|
+
url = serv.mark_pathway_by_objects("path:eco00260", obj_list)
|
636
|
+
puts url
|
637
|
+
|
638
|
+
puts "### color_pathway_by_objects('path:eco00053', obj_list, fg_list, bg_list)"
|
639
|
+
puts " obj_list = ['eco:b0207', 'eco:b1300']"
|
640
|
+
puts " fg_list = ['blue', '#00ff00']"
|
641
|
+
puts " bg_list = ['#ff0000', 'yellow']"
|
642
|
+
obj_list = ["eco:b0207", "eco:b1300"]
|
643
|
+
fg_list = ["blue", "#00ff00"]
|
644
|
+
bg_list = ["#ff0000", "yellow"]
|
645
|
+
url = serv.color_pathway_by_objects("path:eco00053", obj_list, fg_list, bg_list)
|
646
|
+
puts url
|
647
|
+
|
648
|
+
#puts "# * save_image(#{url})"
|
649
|
+
#filename = serv.save_image(url, "test.gif")
|
650
|
+
#filename = serv.save_image(url)
|
651
|
+
#puts filename
|
652
|
+
|
653
|
+
puts "==== objects on pathway"
|
654
|
+
|
655
|
+
puts "### get_genes_by_pathway('path:map00010')"
|
656
|
+
list = serv.get_genes_by_pathway("path:map00010")
|
657
|
+
list.each do |gene|
|
658
|
+
puts gene
|
659
|
+
end
|
660
|
+
|
661
|
+
puts "### get_genes_by_pathway('path:eco00010')"
|
662
|
+
list = serv.get_genes_by_pathway("path:eco00010")
|
663
|
+
list.each do |gene|
|
664
|
+
puts gene
|
665
|
+
end
|
666
|
+
|
667
|
+
puts "### get_enzymes_by_pathway('path:map00010')"
|
668
|
+
list = serv.get_enzymes_by_pathway("path:map00010")
|
669
|
+
list.each do |enzyme|
|
670
|
+
puts enzyme
|
671
|
+
end
|
672
|
+
|
673
|
+
puts "### get_enzymes_by_pathway('path:eco00010')"
|
674
|
+
list = serv.get_enzymes_by_pathway("path:eco00010")
|
675
|
+
list.each do |enzyme|
|
676
|
+
puts enzyme
|
677
|
+
end
|
678
|
+
|
679
|
+
puts "### get_compounds_by_pathway('path:map00010')"
|
680
|
+
list = serv.get_compounds_by_pathway("path:map00010")
|
681
|
+
list.each do |compound|
|
682
|
+
puts compound
|
683
|
+
end
|
684
|
+
|
685
|
+
puts "### get_compounds_by_pathway('path:eco00010')"
|
686
|
+
list = serv.get_compounds_by_pathway("path:eco00010")
|
687
|
+
list.each do |compound|
|
688
|
+
puts compound
|
689
|
+
end
|
690
|
+
|
691
|
+
puts "### get_reactions_by_pathway('path:map00010')"
|
692
|
+
list = serv.get_reactions_by_pathway("path:map00010")
|
693
|
+
list.each do |reaction|
|
694
|
+
puts reaction
|
695
|
+
end
|
696
|
+
|
697
|
+
puts "### get_reactions_by_pathway('path:eco00010')"
|
698
|
+
list = serv.get_reactions_by_pathway("path:eco00010")
|
699
|
+
list.each do |reaction|
|
700
|
+
puts reaction
|
701
|
+
end
|
702
|
+
|
703
|
+
puts "==== pathway by objects"
|
704
|
+
|
705
|
+
puts "### get_pathways_by_genes(['eco:b0756', 'eco:b1002'])"
|
706
|
+
list = serv.get_pathways_by_genes(["eco:b0756", "eco:b1002"])
|
707
|
+
list.each do |path|
|
708
|
+
puts path
|
709
|
+
end
|
710
|
+
|
711
|
+
puts "### get_pathways_by_enzymes(['ec:5.1.3.3', 'ec:3.1.3.10'])"
|
712
|
+
list = serv.get_pathways_by_enzymes(["ec:5.1.3.3", "ec:3.1.3.10"])
|
713
|
+
list.each do |path|
|
714
|
+
puts path
|
715
|
+
end
|
716
|
+
|
717
|
+
puts "### get_pathways_by_compounds(['cpd:C00221', 'cpd:C00267'])"
|
718
|
+
list = serv.get_pathways_by_compounds(["cpd:C00221", "cpd:C00267"])
|
719
|
+
list.each do |path|
|
720
|
+
puts path
|
721
|
+
end
|
722
|
+
|
723
|
+
puts "### get_pathways_by_reactions(['rn:R00014', 'rn:R00710'])"
|
724
|
+
list = serv.get_pathways_by_reactions(["rn:R00014", "rn:R00710"])
|
725
|
+
list.each do |path|
|
726
|
+
puts path
|
727
|
+
end
|
728
|
+
|
729
|
+
puts "==== relation between objects"
|
730
|
+
|
731
|
+
puts "### get_linked_pathways('path:eco00620')"
|
732
|
+
list = serv.get_linked_pathways('path:eco00620')
|
733
|
+
list.each do |path|
|
734
|
+
puts path
|
735
|
+
end
|
736
|
+
|
737
|
+
puts "### get_genes_by_enzyme('ec:1.1.1.1', 'eco')"
|
738
|
+
list = serv.get_genes_by_enzyme("ec:1.1.1.1", "eco")
|
739
|
+
list.each do |gene|
|
740
|
+
puts gene
|
741
|
+
end
|
742
|
+
|
743
|
+
puts "### get_enzymes_by_gene('eco:b0002')"
|
744
|
+
list = serv.get_enzymes_by_gene("eco:b0002")
|
745
|
+
list.each do |enzyme|
|
746
|
+
puts enzyme
|
747
|
+
end
|
748
|
+
|
749
|
+
puts "### get_enzymes_by_compound('cpd:C00345')"
|
750
|
+
list = serv.get_enzymes_by_compound("cpd:C00345")
|
751
|
+
list.each do |enzyme|
|
752
|
+
puts enzyme
|
753
|
+
end
|
754
|
+
|
755
|
+
puts "### get_enzymes_by_reaction('rn:R00100')"
|
756
|
+
list = serv.get_enzymes_by_reaction("rn:R00100")
|
757
|
+
list.each do |enzyme|
|
758
|
+
puts enzyme
|
759
|
+
end
|
760
|
+
|
761
|
+
puts "### get_compounds_by_enzyme('ec:2.7.1.12')"
|
762
|
+
list = serv.get_compounds_by_enzyme("ec:2.7.1.12")
|
763
|
+
list.each do |compound|
|
764
|
+
puts compound
|
765
|
+
end
|
766
|
+
|
767
|
+
puts "### get_compounds_by_reaction('rn:R00100')"
|
768
|
+
list = serv.get_compounds_by_reaction("rn:R00100")
|
769
|
+
list.each do |compound|
|
770
|
+
puts compound
|
771
|
+
end
|
772
|
+
|
773
|
+
puts "### get_reactions_by_enzyme('ec:2.7.1.12')"
|
774
|
+
list = serv.get_reactions_by_enzyme("ec:2.7.1.12")
|
775
|
+
list.each do |reaction|
|
776
|
+
puts reaction
|
777
|
+
end
|
778
|
+
|
779
|
+
puts "### get_reactions_by_compound('cpd:C00199')"
|
780
|
+
list = serv.get_reactions_by_compound("cpd:C00199")
|
781
|
+
list.each do |reaction|
|
782
|
+
puts reaction
|
783
|
+
end
|
784
|
+
|
785
|
+
puts "=== GENES"
|
786
|
+
|
787
|
+
puts "### get_genes_by_organism('mge', 1, 5)"
|
788
|
+
list = serv.get_genes_by_organism("mge", 1, 5)
|
789
|
+
list.each do |gene|
|
790
|
+
puts gene
|
791
|
+
end
|
792
|
+
|
793
|
+
puts "# * get_all_genes_by_organism('mge')"
|
794
|
+
list = serv.get_all_genes_by_organism("mge")
|
795
|
+
list.each do |gene|
|
796
|
+
puts gene
|
797
|
+
end
|
798
|
+
|
799
|
+
puts "=== GENOME"
|
800
|
+
|
801
|
+
puts "### get_number_of_genes_by_organism(org)"
|
802
|
+
puts serv.get_number_of_genes_by_organism("mge")
|
803
|
+
|
804
|
+
end
|
805
|
+
|