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 +1,71 @@
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#
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# = bio/shell/object.rb - Object extension for the BioRuby shell
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#
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# Copyright:: Copyright (C) 2006
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# Nobuya Tanaka <t@chemruby.org>,
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# Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: object.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
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#
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require 'pp'
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require 'cgi'
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require 'yaml'
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### Object extention
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class Object
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# Couldn't work for Fixnum (Marshal)
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attr_accessor :memo
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def output(format = :yaml)
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case format
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when :yaml
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self.to_yaml
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when :html
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format_html
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when :inspect
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format_pp
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when :png
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# *TODO*
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when :svg
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# *TODO*
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when :graph
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# *TODO* (Gruff, RSRuby etc.)
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else
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#self.inspect.to_s.fold(80)
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self.to_s
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end
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end
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private
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def format_html
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"<pre>#{CGI.escapeHTML(format_pp)}</pre>"
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end
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def format_pp
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str = ""
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PP.pp(self, str)
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return str
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end
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end
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class Hash
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private
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def format_html
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html = ""
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html += "<table>"
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@data.each do |k, v|
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html += "<tr><td>#{k}</td><td>#{v}</td></tr>"
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end
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html += "</table>"
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return html
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end
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end
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#
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# = bio/shell/plugin/blast.rb - plugin for BLAST services
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#
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# Copyright:: Copyright (C) 2006
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# Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: blast.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
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#
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module Bio::Shell
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private
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# GenomeNet
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def keggblast(query)
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server = Bio::Blast.remote("blastp", "genes", "", "genomenet_tab")
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if query[/^>/]
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data = Bio::FastaFormat.new(query)
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desc = data.definition
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tmp = getseq(data.seq)
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else
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desc = "query"
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tmp = getseq(query)
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end
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if tmp.respond_to?(:translate)
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aaseq = tmp.translate
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else
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aaseq = tmp
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end
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fasta = aaseq.to_fasta(desc, 60)
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result = server.query(fasta)
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puts server.output
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return result
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end
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end
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#
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# = bio/shell/plugin/codon.rb - plugin for the codon table
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#
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# Copyright:: Copyright (C) 2005
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# Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
|
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# $Id: codon.rb,v 1.16 2007/04/05 23:35:41 trevor Exp $
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#
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module Bio::Shell
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class ColoredCodonTable
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@@properties = {
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:basic => %w( H K R ),
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:polar => %w( S T Y Q N S ),
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:acidic => %w( D E ),
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:nonpolar => %w( F L I M V P A C W G ),
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:stop => %w( * ),
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}
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def initialize(number, cuhash = nil)
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@aacode = Bio::AminoAcid.names
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@table = Bio::CodonTable[number]
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@number = number
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@cuhash = cuhash
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setup_colors
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if Bio::Shell.config[:color]
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generate_colored_text
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else
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generate_mono_text
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end
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end
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attr_reader :table
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def setup_colors
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c = Bio::Shell.colors
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@colors = {
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:text => c[:none],
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:aa => c[:green],
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:start => c[:red],
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:stop => c[:red],
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:basic => c[:cyan],
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:polar => c[:blue],
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:acidic => c[:magenta],
|
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:nonpolar => c[:yellow],
|
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}
|
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+
end
|
51
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|
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def generate_mono_text
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@table.each do |codon, aa|
|
54
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if aa == '*'
|
55
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code = 'STOP'
|
56
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aa = '' unless @cuhash
|
57
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else
|
58
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code = @aacode[aa]
|
59
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+
end
|
60
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if @cuhash
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percent = @cuhash[codon].to_s.rjust(6)
|
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eval("@#{codon} = '#{aa}#{percent}'")
|
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else
|
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eval("@#{codon} = ' #{code} #{aa} '")
|
65
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end
|
66
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+
end
|
67
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|
68
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@hydrophilic = [
|
69
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+
@@properties[:basic].join(" "), "(basic),",
|
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@@properties[:polar].join(" "), "(polar),",
|
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@@properties[:acidic].join(" "), "(acidic)",
|
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+
].join(" ")
|
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@hydrophobic = @@properties[:nonpolar].join(" ") + " (nonpolar)"
|
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+
end
|
75
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|
76
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def generate_colored_text
|
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@table.each do |codon, aa|
|
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property, = @@properties.detect {|key, list| list.include?(aa)}
|
79
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+
|
80
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+
if aa == '*'
|
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+
if @cuhash
|
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color_code = "#{@colors[:stop]}STOP"
|
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color_aa = "#{@colors[:stop]}#{aa}"
|
84
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+
else
|
85
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color_code = "#{@colors[:stop]}STP"
|
86
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+
case codon
|
87
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+
when 'tga'
|
88
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color_aa = "#{@colors[:text]}U"
|
89
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when 'tag'
|
90
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color_aa = "#{@colors[:text]}O"
|
91
|
+
else
|
92
|
+
color_aa = "#{@colors[:text]}*"
|
93
|
+
end
|
94
|
+
end
|
95
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+
else
|
96
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color_code = "#{@colors[property]}#{@aacode[aa]}"
|
97
|
+
if @table.start_codon?(codon)
|
98
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+
if @cuhash
|
99
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color_aa = "#{@colors[:aa]}#{aa}"
|
100
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+
else
|
101
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+
color_aa = "#{@colors[:start]}#{aa}"
|
102
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+
end
|
103
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+
else
|
104
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+
if @cuhash
|
105
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+
color_aa = "#{@colors[property]}#{aa}"
|
106
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+
else
|
107
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+
color_aa = "#{@colors[:aa]}#{aa}"
|
108
|
+
end
|
109
|
+
end
|
110
|
+
end
|
111
|
+
|
112
|
+
if @cuhash
|
113
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+
percent = @cuhash[codon].to_s.rjust(6)
|
114
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+
eval("@#{codon} = '#{color_aa}#{@colors[:text]}#{percent}'")
|
115
|
+
else
|
116
|
+
eval("@#{codon} = ' #{color_code} #{color_aa}#{@colors[:text]} '")
|
117
|
+
end
|
118
|
+
end
|
119
|
+
|
120
|
+
@hydrophilic = [
|
121
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+
"#{@colors[:basic]}basic#{@colors[:text]},",
|
122
|
+
"#{@colors[:polar]}polar#{@colors[:text]},",
|
123
|
+
"#{@colors[:acidic]}acidic#{@colors[:text]}"
|
124
|
+
].join(" ")
|
125
|
+
@hydrophobic = "#{@colors[:nonpolar]}nonpolar"
|
126
|
+
end
|
127
|
+
|
128
|
+
def output
|
129
|
+
header = <<-END
|
130
|
+
#
|
131
|
+
# = Codon table #{@number} : #{@table.definition}
|
132
|
+
#
|
133
|
+
# hydrophilic: #{@hydrophilic}
|
134
|
+
# hydrophobic: #{@hydrophobic}
|
135
|
+
END
|
136
|
+
table = <<-END
|
137
|
+
#
|
138
|
+
# *---------------------------------------------*
|
139
|
+
# | | 2nd | |
|
140
|
+
# | 1st |-------------------------------| 3rd |
|
141
|
+
# | | U | C | A | G | |
|
142
|
+
# |-------+-------+-------+-------+-------+-----|
|
143
|
+
# | U U |#{@ttt}|#{@tct}|#{@tat}|#{@tgt}| u |
|
144
|
+
# | U U |#{@ttc}|#{@tcc}|#{@tac}|#{@tgc}| c |
|
145
|
+
# | U U |#{@tta}|#{@tca}|#{@taa}|#{@tga}| a |
|
146
|
+
# | UUU |#{@ttg}|#{@tcg}|#{@tag}|#{@tgg}| g |
|
147
|
+
# |-------+-------+-------+-------+-------+-----|
|
148
|
+
# | CCCC |#{@ctt}|#{@cct}|#{@cat}|#{@cgt}| u |
|
149
|
+
# | C |#{@ctc}|#{@ccc}|#{@cac}|#{@cgc}| c |
|
150
|
+
# | C |#{@cta}|#{@cca}|#{@caa}|#{@cga}| a |
|
151
|
+
# | CCCC |#{@ctg}|#{@ccg}|#{@cag}|#{@cgg}| g |
|
152
|
+
# |-------+-------+-------+-------+-------+-----|
|
153
|
+
# | A |#{@att}|#{@act}|#{@aat}|#{@agt}| u |
|
154
|
+
# | A A |#{@atc}|#{@acc}|#{@aac}|#{@agc}| c |
|
155
|
+
# | AAAAA |#{@ata}|#{@aca}|#{@aaa}|#{@aga}| a |
|
156
|
+
# | A A |#{@atg}|#{@acg}|#{@aag}|#{@agg}| g |
|
157
|
+
# |-------+-------+-------+-------+-------+-----|
|
158
|
+
# | GGGG |#{@gtt}|#{@gct}|#{@gat}|#{@ggt}| u |
|
159
|
+
# | G |#{@gtc}|#{@gcc}|#{@gac}|#{@ggc}| c |
|
160
|
+
# | G GGG |#{@gta}|#{@gca}|#{@gaa}|#{@gga}| a |
|
161
|
+
# | GG G |#{@gtg}|#{@gcg}|#{@gag}|#{@ggg}| g |
|
162
|
+
# *---------------------------------------------*
|
163
|
+
#
|
164
|
+
END
|
165
|
+
if @cuhash
|
166
|
+
text = table
|
167
|
+
else
|
168
|
+
text = header + table
|
169
|
+
end
|
170
|
+
if Bio::Shell.config[:color]
|
171
|
+
text.gsub(/^\s+#/, @colors[:text])
|
172
|
+
else
|
173
|
+
text.gsub(/^\s+#/, '')
|
174
|
+
end
|
175
|
+
end
|
176
|
+
|
177
|
+
end
|
178
|
+
|
179
|
+
private
|
180
|
+
|
181
|
+
def codontable(num = 1, codon_usage = nil)
|
182
|
+
cct = ColoredCodonTable.new(num, codon_usage)
|
183
|
+
if codon_usage
|
184
|
+
return cct
|
185
|
+
else
|
186
|
+
puts cct.output
|
187
|
+
return cct.table
|
188
|
+
end
|
189
|
+
end
|
190
|
+
|
191
|
+
def codontables
|
192
|
+
tables = Bio::CodonTable::DEFINITIONS
|
193
|
+
tables.sort.each do |i, definition|
|
194
|
+
puts "#{i}\t#{definition}"
|
195
|
+
end
|
196
|
+
return tables
|
197
|
+
end
|
198
|
+
|
199
|
+
def aminoacids
|
200
|
+
names = Bio::AminoAcid.names
|
201
|
+
names.sort.each do |aa, code|
|
202
|
+
if aa.length == 1
|
203
|
+
puts "#{aa}\t#{code}\t#{names[code]}"
|
204
|
+
end
|
205
|
+
end
|
206
|
+
return names
|
207
|
+
end
|
208
|
+
|
209
|
+
def nucleicacids
|
210
|
+
names = Bio::NucleicAcid.names
|
211
|
+
%w(a t g c u r y w s k m b v h d n).each do |base|
|
212
|
+
puts "#{base}\t#{names[base]}\t#{names[base.upcase]}"
|
213
|
+
end
|
214
|
+
return names
|
215
|
+
end
|
216
|
+
|
217
|
+
end
|
218
|
+
|
@@ -0,0 +1,58 @@
|
|
1
|
+
#
|
2
|
+
# = bio/shell/plugin/keggdas.rb - plugin for KEGG DAS
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2006
|
5
|
+
# Toshiaki Katayama <k@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: das.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
module Bio
|
12
|
+
|
13
|
+
class DAS
|
14
|
+
def list_sequences
|
15
|
+
result = ""
|
16
|
+
self.get_dsn.each do |dsn|
|
17
|
+
src = dsn.source_id
|
18
|
+
self.get_entry_points(src).each do |ep|
|
19
|
+
data = [src, ep.entry_id, ep.start.to_i, ep.stop.to_i, "# #{ep.description}"].join("\t") + "\n"
|
20
|
+
puts data
|
21
|
+
result += data
|
22
|
+
end
|
23
|
+
end
|
24
|
+
return result
|
25
|
+
end
|
26
|
+
end
|
27
|
+
|
28
|
+
end
|
29
|
+
|
30
|
+
module Bio::Shell
|
31
|
+
|
32
|
+
private
|
33
|
+
|
34
|
+
# http://www.biodas.org/
|
35
|
+
# http://www.dasregistry.org/
|
36
|
+
|
37
|
+
def das(url = nil)
|
38
|
+
if url
|
39
|
+
@das = Bio::DAS.new(url)
|
40
|
+
else
|
41
|
+
@das ||= keggdas
|
42
|
+
end
|
43
|
+
end
|
44
|
+
|
45
|
+
def keggdas(url = "http://das.hgc.jp/cgi-bin/")
|
46
|
+
das(url)
|
47
|
+
end
|
48
|
+
|
49
|
+
def ensembl(url = "http://das.ensembl.org/")
|
50
|
+
das(url)
|
51
|
+
end
|
52
|
+
|
53
|
+
def wormbase(url = "http://www.wormbase.org/db/")
|
54
|
+
das(url)
|
55
|
+
end
|
56
|
+
|
57
|
+
end
|
58
|
+
|
@@ -0,0 +1,23 @@
|
|
1
|
+
#
|
2
|
+
# = bio/shell/plugin/emboss.rb - methods to use EMBOSS
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2005
|
5
|
+
# Toshiaki Katayama <k@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: emboss.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
module Bio::Shell
|
12
|
+
|
13
|
+
private
|
14
|
+
|
15
|
+
def seqret(usa)
|
16
|
+
Bio::EMBOSS.seqret(usa)
|
17
|
+
end
|
18
|
+
|
19
|
+
def entret(usa)
|
20
|
+
Bio::EMBOSS.entret(usa)
|
21
|
+
end
|
22
|
+
|
23
|
+
end
|
@@ -0,0 +1,105 @@
|
|
1
|
+
#
|
2
|
+
# = bio/shell/plugin/entry.rb - extract entry and sequence
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2005
|
5
|
+
# Toshiaki Katayama <k@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: entry.rb,v 1.10 2007/04/05 23:35:41 trevor Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
module Bio::Shell
|
12
|
+
|
13
|
+
private
|
14
|
+
|
15
|
+
# Read a text file and collect the first word of each line in array
|
16
|
+
def readlist(filename)
|
17
|
+
list = []
|
18
|
+
File.open(filename).each do |line|
|
19
|
+
list << line[/^\S+/]
|
20
|
+
end
|
21
|
+
return list
|
22
|
+
end
|
23
|
+
|
24
|
+
# Obtain a Bio::Sequence::NA (DNA) or a Bio::Sequence::AA (Amino Acid)
|
25
|
+
# sequence from
|
26
|
+
# * String -- "atgcatgc" or "MQKKP"
|
27
|
+
# * IO -- io = IO.popen("gzip -dc db.gz") (first entry only)
|
28
|
+
# * "filename" -- "gbvrl.gbk" (first entry only)
|
29
|
+
# * "db:entry" -- "embl:BUM" (entry is retrieved by the ent method)
|
30
|
+
def getseq(arg)
|
31
|
+
seq = ""
|
32
|
+
if arg.kind_of?(Bio::Sequence)
|
33
|
+
seq = arg
|
34
|
+
elsif arg.respond_to?(:gets) or File.exists?(arg)
|
35
|
+
ent = flatauto(arg)
|
36
|
+
elsif arg[/:/]
|
37
|
+
ent = getobj(arg)
|
38
|
+
else
|
39
|
+
tmp = arg
|
40
|
+
end
|
41
|
+
|
42
|
+
if ent.respond_to?(:seq)
|
43
|
+
tmp = ent.seq
|
44
|
+
elsif ent.respond_to?(:naseq)
|
45
|
+
#seq = ent.naseq
|
46
|
+
tmp = ent.naseq
|
47
|
+
elsif ent.respond_to?(:aaseq)
|
48
|
+
#seq = ent.aaseq
|
49
|
+
tmp = ent.aaseq
|
50
|
+
end
|
51
|
+
|
52
|
+
if tmp and tmp.is_a?(String) and not tmp.empty?
|
53
|
+
#seq = Bio::Sequence.auto(tmp).seq
|
54
|
+
seq = Bio::Sequence.auto(tmp)
|
55
|
+
end
|
56
|
+
return seq
|
57
|
+
end
|
58
|
+
|
59
|
+
# Obtain a database entry from
|
60
|
+
# * IO -- IO object (first entry only)
|
61
|
+
# * "filename" -- local file (first entry only)
|
62
|
+
# * "db:entry" -- local BioFlat, OBDA, EMBOSS, KEGG API
|
63
|
+
def getent(arg)
|
64
|
+
entry = ""
|
65
|
+
db, entry_id = arg.to_s.strip.split(/:/)
|
66
|
+
|
67
|
+
# local file
|
68
|
+
if arg.respond_to?(:gets) or File.exists?(arg)
|
69
|
+
puts "Retrieving entry from file (#{arg})"
|
70
|
+
entry = flatfile(arg)
|
71
|
+
|
72
|
+
# BioFlat in ./.bioruby/bioflat/ or ~/.bioinformatics/.bioruby/bioflat/
|
73
|
+
elsif Bio::Shell.find_flat_dir(db)
|
74
|
+
puts "Retrieving entry from local BioFlat database (#{arg})"
|
75
|
+
entry = flatsearch(db, entry_id)
|
76
|
+
|
77
|
+
# OBDA in ~/.bioinformatics/seqdatabase.ini
|
78
|
+
elsif obdadbs.include?(db)
|
79
|
+
puts "Retrieving entry from OBDA (#{arg})"
|
80
|
+
entry = obdaentry(db, entry_id)
|
81
|
+
|
82
|
+
else
|
83
|
+
# EMBOSS USA in ~/.embossrc
|
84
|
+
str = entret(arg)
|
85
|
+
if $?.exitstatus == 0 and str.length != 0
|
86
|
+
puts "Retrieving entry from EMBOSS (#{arg})"
|
87
|
+
entry = str
|
88
|
+
|
89
|
+
# KEGG API at http://www.genome.jp/kegg/soap/
|
90
|
+
else
|
91
|
+
puts "Retrieving entry from KEGG API (#{arg})"
|
92
|
+
entry = bget(arg)
|
93
|
+
end
|
94
|
+
end
|
95
|
+
|
96
|
+
return entry
|
97
|
+
end
|
98
|
+
|
99
|
+
# Obtain a parsed object from sources that ent() supports.
|
100
|
+
def getobj(arg)
|
101
|
+
str = getent(arg)
|
102
|
+
flatparse(str)
|
103
|
+
end
|
104
|
+
|
105
|
+
end
|