wwood-bioruby 1.2.11
Sign up to get free protection for your applications and to get access to all the features.
- 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
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +11 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +7 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +47 -0
- 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
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +10 -0
- 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
- data/test/data/blast/b0002.faa.m0 +128 -0
- data/test/data/blast/b0002.faa.m7 +65 -0
- 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 +1,256 @@
|
|
1
|
+
#
|
2
|
+
# = bio/db/kegg/kgml.rb - KEGG KGML parser class
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2005
|
5
|
+
# Toshiaki Katayama <k@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: kgml.rb,v 1.7 2007/04/05 23:35:41 trevor Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
autoload :REXML, 'rexml/document'
|
12
|
+
|
13
|
+
module Bio
|
14
|
+
class KEGG
|
15
|
+
|
16
|
+
# == KGML (KEGG XML) parser
|
17
|
+
#
|
18
|
+
# See http://www.genome.jp/kegg/xml/ for more details on KGML.
|
19
|
+
#
|
20
|
+
# === Incompatible attribute names with KGML tags
|
21
|
+
#
|
22
|
+
# <entry>
|
23
|
+
# :id -> :entry_id
|
24
|
+
# :type -> :category
|
25
|
+
# :map -> :pathway
|
26
|
+
# names()
|
27
|
+
# <graphics>
|
28
|
+
# :name -> :label
|
29
|
+
# :type -> :shape
|
30
|
+
# <relation>
|
31
|
+
# :entry1 -> :node1
|
32
|
+
# :entry2 -> :node2
|
33
|
+
# :type -> :rel
|
34
|
+
# <subtype>
|
35
|
+
# edge()
|
36
|
+
# <reaction>
|
37
|
+
# :name -> :entry_id
|
38
|
+
# :type -> :direction
|
39
|
+
#
|
40
|
+
# === Examples
|
41
|
+
#
|
42
|
+
# file = File.read("kgml/hsa/hsa00010.xml")
|
43
|
+
# kgml = Bio::KEGG::KGML.new(file)
|
44
|
+
#
|
45
|
+
# # <pathway> attributes
|
46
|
+
# puts kgml.name
|
47
|
+
# puts kgml.org
|
48
|
+
# puts kgml.number
|
49
|
+
# puts kgml.title
|
50
|
+
# puts kgml.image
|
51
|
+
# puts kgml.link
|
52
|
+
#
|
53
|
+
# kgml.entries.each do |entry|
|
54
|
+
# # <entry> attributes
|
55
|
+
# puts entry.entry_id
|
56
|
+
# puts entry.name
|
57
|
+
# puts entry.category
|
58
|
+
# puts entry.link
|
59
|
+
# puts entry.reaction
|
60
|
+
# puts entry.pathway
|
61
|
+
# # <graphics> attributes
|
62
|
+
# puts entry.label # name
|
63
|
+
# puts entry.shape # type
|
64
|
+
# puts entry.x
|
65
|
+
# puts entry.y
|
66
|
+
# puts entry.width
|
67
|
+
# puts entry.height
|
68
|
+
# puts entry.fgcolor
|
69
|
+
# puts entry.bgcolor
|
70
|
+
# # <component> attributes
|
71
|
+
# puts entry.components
|
72
|
+
# # methood
|
73
|
+
# puts entry.names
|
74
|
+
# end
|
75
|
+
#
|
76
|
+
# kgml.relations.each do |relation|
|
77
|
+
# # <relation> attributes
|
78
|
+
# puts relation.node1 # entry1
|
79
|
+
# puts relation.node2 # entry2
|
80
|
+
# puts relation.rel # type
|
81
|
+
# # method
|
82
|
+
# puts relation.edge
|
83
|
+
# # <subtype> attributes
|
84
|
+
# puts relation.name
|
85
|
+
# puts relation.value
|
86
|
+
# end
|
87
|
+
#
|
88
|
+
# kgml.reactions.each do |reaction|
|
89
|
+
# # <reaction> attributes
|
90
|
+
# puts reaction.entry_id # name
|
91
|
+
# puts reaction.direction # type
|
92
|
+
# # <substrate> attributes
|
93
|
+
# reaction.substrates.each do |entry_id|
|
94
|
+
# puts entry_id
|
95
|
+
# # <alt> attributes
|
96
|
+
# altnames = reaction.alt[entry_id]
|
97
|
+
# altnames.each do |name|
|
98
|
+
# puts name
|
99
|
+
# end
|
100
|
+
# end
|
101
|
+
# # <product> attributes
|
102
|
+
# reaction.products.each do |entry_id|
|
103
|
+
# puts entry_id
|
104
|
+
# # <alt> attributes
|
105
|
+
# altnames = reaction.alt[entry_id]
|
106
|
+
# altnames.each do |name|
|
107
|
+
# puts name
|
108
|
+
# end
|
109
|
+
# end
|
110
|
+
# end
|
111
|
+
#
|
112
|
+
class KGML
|
113
|
+
|
114
|
+
def initialize(xml)
|
115
|
+
dom = REXML::Document.new(xml)
|
116
|
+
parse_root(dom)
|
117
|
+
parse_entry(dom)
|
118
|
+
parse_relation(dom)
|
119
|
+
parse_reaction(dom)
|
120
|
+
end
|
121
|
+
attr_reader :name, :org, :number, :title, :image, :link
|
122
|
+
attr_accessor :entries, :relations, :reactions
|
123
|
+
|
124
|
+
class Entry
|
125
|
+
attr_accessor :entry_id, :name, :category, :link, :reaction, :pathway
|
126
|
+
attr_accessor :label, :shape, :x, :y, :width, :height, :fgcolor, :bgcolor
|
127
|
+
attr_accessor :components
|
128
|
+
def names
|
129
|
+
@name.split(/\s+/)
|
130
|
+
end
|
131
|
+
end
|
132
|
+
|
133
|
+
class Relation
|
134
|
+
attr_accessor :node1, :node2, :rel
|
135
|
+
attr_accessor :name, :value
|
136
|
+
def edge
|
137
|
+
@value.to_i
|
138
|
+
end
|
139
|
+
end
|
140
|
+
|
141
|
+
class Reaction
|
142
|
+
attr_accessor :entry_id, :direction
|
143
|
+
attr_accessor :substrates, :products # Array
|
144
|
+
attr_accessor :alt # Hash
|
145
|
+
end
|
146
|
+
|
147
|
+
private
|
148
|
+
|
149
|
+
def parse_root(dom)
|
150
|
+
root = dom.root.attributes
|
151
|
+
@name = root["name"]
|
152
|
+
@org = root["org"]
|
153
|
+
@number = root["number"]
|
154
|
+
@title = root["title"]
|
155
|
+
@image = root["image"]
|
156
|
+
@link = root["link"]
|
157
|
+
end
|
158
|
+
|
159
|
+
def parse_entry(dom)
|
160
|
+
@entries = Array.new
|
161
|
+
|
162
|
+
dom.elements.each("/pathway/entry") { |node|
|
163
|
+
attr = node.attributes
|
164
|
+
entry = Entry.new
|
165
|
+
entry.entry_id = attr["id"].to_i
|
166
|
+
entry.name = attr["name"]
|
167
|
+
entry.category = attr["type"]
|
168
|
+
# implied
|
169
|
+
entry.link = attr["link"]
|
170
|
+
entry.reaction = attr["reaction"]
|
171
|
+
entry.pathway = attr["map"]
|
172
|
+
|
173
|
+
node.elements.each("graphics") { |graphics|
|
174
|
+
attr = graphics.attributes
|
175
|
+
entry.x = attr["x"].to_i
|
176
|
+
entry.y = attr["y"].to_i
|
177
|
+
entry.shape = attr["type"]
|
178
|
+
entry.label = attr["name"]
|
179
|
+
entry.width = attr["width"].to_i
|
180
|
+
entry.height = attr["height"].to_i
|
181
|
+
entry.fgcolor = attr["fgcolor"]
|
182
|
+
entry.bgcolor = attr["bgcolor"]
|
183
|
+
}
|
184
|
+
|
185
|
+
node.elements.each("component") { |component|
|
186
|
+
attr = component.attributes
|
187
|
+
entry.components ||= []
|
188
|
+
entry.components << attr["id"].to_i
|
189
|
+
}
|
190
|
+
|
191
|
+
@entries << entry
|
192
|
+
}
|
193
|
+
end
|
194
|
+
|
195
|
+
def parse_relation(dom)
|
196
|
+
@relations = Array.new
|
197
|
+
|
198
|
+
dom.elements.each("/pathway/relation") { |node|
|
199
|
+
attr = node.attributes
|
200
|
+
relation = Relation.new
|
201
|
+
relation.node1 = attr["entry1"].to_i
|
202
|
+
relation.node2 = attr["entry2"].to_i
|
203
|
+
relation.rel = attr["type"]
|
204
|
+
|
205
|
+
node.elements.each("subtype") { |subtype|
|
206
|
+
attr = subtype.attributes
|
207
|
+
relation.name = attr["name"]
|
208
|
+
relation.value = attr["value"]
|
209
|
+
}
|
210
|
+
@relations << relation
|
211
|
+
}
|
212
|
+
end
|
213
|
+
|
214
|
+
def parse_reaction(dom)
|
215
|
+
@reactions = Array.new
|
216
|
+
|
217
|
+
dom.elements.each("/pathway/reaction") { |node|
|
218
|
+
attr = node.attributes
|
219
|
+
reaction = Reaction.new
|
220
|
+
reaction.entry_id = attr["name"]
|
221
|
+
reaction.direction = attr["type"]
|
222
|
+
|
223
|
+
substrates = Array.new
|
224
|
+
products = Array.new
|
225
|
+
hash = Hash.new
|
226
|
+
|
227
|
+
node.elements.each("substrate") { |substrate|
|
228
|
+
name = substrate.attributes["name"]
|
229
|
+
substrates << name
|
230
|
+
substrate.elements.each("alt") { |alt|
|
231
|
+
hash[name] ||= Array.new
|
232
|
+
hash[name] << alt.attributes["name"]
|
233
|
+
}
|
234
|
+
}
|
235
|
+
node.elements.each("product") { |product|
|
236
|
+
name = product.attributes["name"]
|
237
|
+
products << name
|
238
|
+
product.elements.each("alt") { |alt|
|
239
|
+
hash[name] ||= Array.new
|
240
|
+
hash[name] << alt.attributes["name"]
|
241
|
+
}
|
242
|
+
}
|
243
|
+
reaction.substrates = substrates
|
244
|
+
reaction.products = products
|
245
|
+
reaction.alt = hash
|
246
|
+
|
247
|
+
@reactions << reaction
|
248
|
+
}
|
249
|
+
end
|
250
|
+
|
251
|
+
end # KGML
|
252
|
+
|
253
|
+
end # KEGG
|
254
|
+
end # Bio
|
255
|
+
|
256
|
+
|
@@ -0,0 +1,136 @@
|
|
1
|
+
#
|
2
|
+
# = bio/db/kegg/orthology.rb - KEGG ORTHOLOGY database class
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2003-2007 Toshiaki Katayama <k@bioruby.org>
|
5
|
+
# Copyright:: Copyright (C) 2003 Masumi Itoh <m@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: orthology.rb,v 1.10 2007/12/14 16:19:54 k Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
require 'bio/db'
|
12
|
+
|
13
|
+
module Bio
|
14
|
+
class KEGG
|
15
|
+
|
16
|
+
# == Description
|
17
|
+
#
|
18
|
+
# KO (KEGG Orthology) entry parser.
|
19
|
+
#
|
20
|
+
# == References
|
21
|
+
#
|
22
|
+
# * http://www.genome.jp/dbget-bin/get_htext?KO
|
23
|
+
# * ftp://ftp.genome.jp/pub/kegg/genes/ko
|
24
|
+
#
|
25
|
+
class ORTHOLOGY < KEGGDB
|
26
|
+
|
27
|
+
DELIMITER = RS = "\n///\n"
|
28
|
+
TAGSIZE = 12
|
29
|
+
|
30
|
+
# Reads a flat file format entry of the KO database.
|
31
|
+
def initialize(entry)
|
32
|
+
super(entry, TAGSIZE)
|
33
|
+
end
|
34
|
+
|
35
|
+
# Returns ID of the entry.
|
36
|
+
def entry_id
|
37
|
+
field_fetch('ENTRY')[/\S+/]
|
38
|
+
end
|
39
|
+
|
40
|
+
# Returns NAME field of the entry.
|
41
|
+
def name
|
42
|
+
field_fetch('NAME')
|
43
|
+
end
|
44
|
+
|
45
|
+
# Returns an Array of names in NAME field.
|
46
|
+
def names
|
47
|
+
name.split(', ')
|
48
|
+
end
|
49
|
+
|
50
|
+
# Returns DEFINITION field of the entry.
|
51
|
+
def definition
|
52
|
+
field_fetch('DEFINITION')
|
53
|
+
end
|
54
|
+
|
55
|
+
# Returns CLASS field of the entry.
|
56
|
+
def keggclass
|
57
|
+
field_fetch('CLASS')
|
58
|
+
end
|
59
|
+
|
60
|
+
# Returns an Array of biological classes in CLASS field.
|
61
|
+
def keggclasses
|
62
|
+
keggclass.gsub(/ \[[^\]]+/, '').split(/\] ?/)
|
63
|
+
end
|
64
|
+
|
65
|
+
# Returns an Array of KEGG/PATHWAY ID in CLASS field.
|
66
|
+
def pathways
|
67
|
+
keggclass.scan(/\[PATH:(.*?)\]/).flatten
|
68
|
+
end
|
69
|
+
|
70
|
+
# Returns an Array of a database name and entry IDs in DBLINKS field.
|
71
|
+
def dblinks
|
72
|
+
unless @data['DBLINKS']
|
73
|
+
@data['DBLINKS'] = lines_fetch('DBLINKS')
|
74
|
+
end
|
75
|
+
@data['DBLINKS']
|
76
|
+
end
|
77
|
+
|
78
|
+
# Returns a Hash of the DB name and an Array of entry IDs in DBLINKS field.
|
79
|
+
def dblinks_as_hash
|
80
|
+
hash = {}
|
81
|
+
dblinks.each do |line|
|
82
|
+
name, *list = line.split(/\s+/)
|
83
|
+
db = name.downcase.sub(/:/, '')
|
84
|
+
hash[db] = list
|
85
|
+
end
|
86
|
+
return hash
|
87
|
+
end
|
88
|
+
|
89
|
+
# Returns an Array of the organism ID and entry IDs in GENES field.
|
90
|
+
def genes
|
91
|
+
unless @data['GENES']
|
92
|
+
@data['GENES'] = lines_fetch('GENES')
|
93
|
+
end
|
94
|
+
@data['GENES']
|
95
|
+
end
|
96
|
+
|
97
|
+
# Returns a Hash of the organism ID and an Array of entry IDs in GENES field.
|
98
|
+
def genes_as_hash
|
99
|
+
hash = {}
|
100
|
+
genes.each do |line|
|
101
|
+
name, *list = line.split(/\s+/)
|
102
|
+
org = name.downcase.sub(/:/, '')
|
103
|
+
genes = list.map {|x| x.sub(/\(.*\)/, '')}
|
104
|
+
#names = list.map {|x| x.scan(/.*\((.*)\)/)}
|
105
|
+
hash[org] = genes
|
106
|
+
end
|
107
|
+
return hash
|
108
|
+
end
|
109
|
+
|
110
|
+
end # ORTHOLOGY
|
111
|
+
|
112
|
+
end # KEGG
|
113
|
+
end # Bio
|
114
|
+
|
115
|
+
|
116
|
+
|
117
|
+
if __FILE__ == $0
|
118
|
+
|
119
|
+
require 'bio/io/fetch'
|
120
|
+
|
121
|
+
flat = Bio::Fetch.query('ko', 'K00001')
|
122
|
+
entry = Bio::KEGG::ORTHOLOGY.new(flat)
|
123
|
+
|
124
|
+
p entry.entry_id
|
125
|
+
p entry.name
|
126
|
+
p entry.names
|
127
|
+
p entry.definition
|
128
|
+
p entry.keggclass
|
129
|
+
p entry.keggclasses
|
130
|
+
p entry.pathways
|
131
|
+
p entry.dblinks
|
132
|
+
p entry.genes
|
133
|
+
|
134
|
+
end
|
135
|
+
|
136
|
+
|
@@ -0,0 +1,82 @@
|
|
1
|
+
#
|
2
|
+
# = bio/db/kegg/reaction.rb - KEGG REACTION database class
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2004 Toshiaki Katayama <k@bioruby.org>
|
5
|
+
# License:: The Ruby License
|
6
|
+
#
|
7
|
+
# $Id: reaction.rb,v 1.6 2007/06/28 11:27:24 k Exp $
|
8
|
+
#
|
9
|
+
|
10
|
+
require 'bio/db'
|
11
|
+
|
12
|
+
module Bio
|
13
|
+
class KEGG
|
14
|
+
|
15
|
+
class REACTION < KEGGDB
|
16
|
+
|
17
|
+
DELIMITER = RS = "\n///\n"
|
18
|
+
TAGSIZE = 12
|
19
|
+
|
20
|
+
def initialize(entry)
|
21
|
+
super(entry, TAGSIZE)
|
22
|
+
end
|
23
|
+
|
24
|
+
# ENTRY
|
25
|
+
def entry_id
|
26
|
+
field_fetch('ENTRY')[/\S+/]
|
27
|
+
end
|
28
|
+
|
29
|
+
# NAME
|
30
|
+
def name
|
31
|
+
field_fetch('NAME')
|
32
|
+
end
|
33
|
+
|
34
|
+
# DEFINITION
|
35
|
+
def definition
|
36
|
+
field_fetch('DEFINITION')
|
37
|
+
end
|
38
|
+
|
39
|
+
# EQUATION
|
40
|
+
def equation
|
41
|
+
field_fetch('EQUATION')
|
42
|
+
end
|
43
|
+
|
44
|
+
# RPAIR
|
45
|
+
def rpairs
|
46
|
+
unless @data['RPAIR']
|
47
|
+
@data['RPAIR'] = fetch('RPAIR').split(/\s+/)
|
48
|
+
end
|
49
|
+
@data['RPAIR']
|
50
|
+
end
|
51
|
+
|
52
|
+
# PATHWAY
|
53
|
+
def pathways
|
54
|
+
lines_fetch('PATHWAY')
|
55
|
+
end
|
56
|
+
|
57
|
+
# ENZYME
|
58
|
+
def enzymes
|
59
|
+
unless @data['ENZYME']
|
60
|
+
@data['ENZYME'] = fetch('ENZYME').scan(/\S+/)
|
61
|
+
end
|
62
|
+
@data['ENZYME']
|
63
|
+
end
|
64
|
+
|
65
|
+
end # REACTION
|
66
|
+
|
67
|
+
end # KEGG
|
68
|
+
end # Bio
|
69
|
+
|
70
|
+
|
71
|
+
if __FILE__ == $0
|
72
|
+
entry = ARGF.read
|
73
|
+
rn = Bio::KEGG::REACTION.new(entry)
|
74
|
+
p rn.entry_id
|
75
|
+
p rn.name
|
76
|
+
p rn.definition
|
77
|
+
p rn.equation
|
78
|
+
p rn.rpairs
|
79
|
+
p rn.pathways
|
80
|
+
p rn.enzymes
|
81
|
+
end
|
82
|
+
|