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 +1,45 @@
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#
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# = bio/shell/plugin/obda.rb - plugin for OBDA
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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: obda.rb,v 1.10 2007/04/05 23:45:11 trevor Exp $
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#
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module Bio::Shell
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private
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def obda
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@obda ||= Bio::Registry.new
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end
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def obdaentry(dbname, entry_id)
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db = obda.get_database(dbname)
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unless db
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warn "Error: No such database (#{dbname})"
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return
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end
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entry = db.get_by_id(entry_id)
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if block_given?
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yield entry
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else
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return entry
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end
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end
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def obdadbs
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result = obda.databases.map {|db| db.database}
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return result
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end
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def biofetch(db, id, style = 'raw', format = 'default')
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serv = Bio::Fetch.new("http://www.ebi.ac.uk/cgi-bin/dbfetch")
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result = serv.fetch(db, id, style, format)
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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/psort.rb - plugin for PSORT
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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: psort.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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def psort1(str)
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seq = getseq(str)
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if seq.is_a?(Bio::Sequence::NA)
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seq = seq.translate
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end
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psort = Bio::PSORT::PSORT1.imsut
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fasta = seq.to_fasta
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results = psort.exec(fasta).final_result
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results.each do |result|
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puts "#{result["certainty"].to_f*100.0}\t#{result["prediction"]}"
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end
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return results.first["prediction"]
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end
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def psort2(str)
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seq = getseq(str)
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if seq.is_a?(Bio::Sequence::NA)
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seq = seq.translate
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end
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psort = Bio::PSORT::PSORT2.imsut
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fasta = seq.to_fasta
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results = psort.exec(fasta).prob.sort_by{|x, y| y}.reverse
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results.each do |loc, prob|
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next if prob <= 0.0
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puts "#{prob}\t#{Bio::PSORT::PSORT2::SclNames[loc]}"
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end
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return results.first.first
|
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end
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def psort2locations
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names = Bio::PSORT::PSORT2::SclNames
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names.sort.each do |loc, desc|
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puts "#{loc}\t#{desc}"
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end
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return names
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end
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end
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@@ -0,0 +1,247 @@
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#
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# = bio/shell/plugin/seq.rb - plugin for biological sequence manipulations
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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: seq.rb,v 1.21 2007/04/05 23:35:41 trevor Exp $
|
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#
|
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|
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module Bio::Shell
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private
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# Convert sequence to colored HTML string
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def htmlseq(str)
|
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if str.kind_of?(Bio::Sequence)
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seq = str
|
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else
|
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seq = getseq(str)
|
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end
|
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|
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if seq.is_a?(Bio::Sequence::AA)
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scheme = Bio::ColorScheme::Taylor
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else
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scheme = Bio::ColorScheme::Nucleotide
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end
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html = %Q[<div style="font-family:monospace;">\n]
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seq.fold(50).each_byte do |c|
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case c.chr
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when "\n"
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html += "<br>\n"
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else
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color = scheme[c.chr]
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html += %Q[<span style="background:\##{color};">#{c.chr}</span>\n]
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end
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end
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html += "</div>\n"
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return html
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end
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def sixtrans(str)
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seq = getseq(str)
|
46
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[ 1, 2, 3, -1, -2, -3 ].each do |frame|
|
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title = "Translation #{frame.to_s.rjust(2)}"
|
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puts seq.translate(frame).to_fasta(title, 60)
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end
|
50
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end
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|
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# Displays some basic properties of the sequence.
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def seqstat(str)
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max = 150
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seq = getseq(str)
|
57
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rep = "\n* * * Sequence statistics * * *\n\n"
|
58
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+
if seq.moltype == Bio::Sequence::NA
|
59
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fwd = seq
|
60
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rev = seq.complement
|
61
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if seq.length > max
|
62
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dot = " ..."
|
63
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+
fwd = fwd.subseq(1, max)
|
64
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+
rev = rev.subseq(1, max)
|
65
|
+
end
|
66
|
+
rep << "5'->3' sequence : #{fwd.fold(70,20).strip}#{dot}\n"
|
67
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+
rep << "3'->5' sequence : #{rev.fold(70,20).strip}#{dot}\n"
|
68
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+
[ 1, 2, 3, -1, -2, -3 ].each do |frame|
|
69
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pep = seq.subseq(1, max+2).translate(frame).fold(70,20).strip
|
70
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+
rep << "Translation #{frame.to_s.rjust(2)} : #{pep}#{dot}\n"
|
71
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+
end
|
72
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rep << "Length : #{seq.length} bp\n"
|
73
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+
rep << "GC percent : #{seq.gc_percent} %\n"
|
74
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+
|
75
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ary = []
|
76
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seq.composition.sort.each do |base, num|
|
77
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percent = format("%.2f", 100.0 * num / seq.length).rjust(6)
|
78
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+
count = num.to_s.rjust(seq.length.to_s.length)
|
79
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ary << " #{base} - #{count} (#{percent} %)\n"
|
80
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+
end
|
81
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rep << "Composition : #{ary.join.strip}\n"
|
82
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+
|
83
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rep << "Codon usage :\n"
|
84
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+
hash = Hash.new("0.0%")
|
85
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+
seq.codon_usage.sort.each do |codon, num|
|
86
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percent = format("%.1f%", 100.0 * num / (seq.length / 3))
|
87
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hash[codon] = percent
|
88
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+
end
|
89
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+
rep << codontable(1, hash).output
|
90
|
+
|
91
|
+
begin
|
92
|
+
rep << "Molecular weight : #{seq.molecular_weight}\n"
|
93
|
+
rescue
|
94
|
+
rep << "Molecular weight : #{$!}\n"
|
95
|
+
end
|
96
|
+
begin
|
97
|
+
rep << "Protein weight : #{seq.translate.chomp('*').molecular_weight}\n"
|
98
|
+
rescue
|
99
|
+
rep << "Protein weight : #{$!}\n"
|
100
|
+
end
|
101
|
+
else
|
102
|
+
pep = seq
|
103
|
+
if seq.length > max
|
104
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+
dot = " ..."
|
105
|
+
pep = seq.subseq(1, max)
|
106
|
+
end
|
107
|
+
rep << "N->C sequence : #{pep.fold(70,20).strip}#{dot}\n"
|
108
|
+
rep << "Length : #{seq.length} aa\n"
|
109
|
+
|
110
|
+
names = Bio::AminoAcid.names
|
111
|
+
ary = []
|
112
|
+
seq.composition.sort.each do |aa, num|
|
113
|
+
percent = format("%.2f", 100.0 * num / seq.length).rjust(6)
|
114
|
+
count = num.to_s.rjust(seq.length.to_s.length)
|
115
|
+
code = names[aa]
|
116
|
+
name = names[names[aa]]
|
117
|
+
ary << " #{aa} #{code} - #{count} (#{percent} %) #{name}\n"
|
118
|
+
end
|
119
|
+
rep << "Composition : #{ary.join.strip}\n"
|
120
|
+
|
121
|
+
begin
|
122
|
+
rep << "Protein weight : #{seq.molecular_weight}\n"
|
123
|
+
rescue
|
124
|
+
rep << "Protein weight : #{$!}\n"
|
125
|
+
end
|
126
|
+
end
|
127
|
+
rep << "//\n"
|
128
|
+
puts rep
|
129
|
+
return rep
|
130
|
+
end
|
131
|
+
|
132
|
+
# Displays a DNA sequence by ascii art in B-type double helix.
|
133
|
+
# Argument need to be at least 16 bases in length.
|
134
|
+
def doublehelix(str)
|
135
|
+
seq = getseq(str)
|
136
|
+
if seq.length < 16
|
137
|
+
warn "Error: Sequence must be longer than 16 bases."
|
138
|
+
return
|
139
|
+
end
|
140
|
+
if seq.moltype != Bio::Sequence::NA
|
141
|
+
warn "Error: Sequence must be a DNA sequence."
|
142
|
+
return
|
143
|
+
end
|
144
|
+
pairs = [ [5, 0], [4, 2], [3, 3], [2, 4],
|
145
|
+
[1, 4], [0, 3], [0, 2], [1, 0] ]
|
146
|
+
seq.window_search(16, 16) do |subseq|
|
147
|
+
pairs.each_with_index do |ij, x|
|
148
|
+
base = subseq[x, 1]
|
149
|
+
puts ' ' * ij[0] + base + '-' * ij[1] + base.complement + "\n"
|
150
|
+
end
|
151
|
+
pairs.reverse.each_with_index do |ij, x|
|
152
|
+
base = subseq[x + 8, 1]
|
153
|
+
puts ' ' * ij[0] + base.complement + '-' * ij[1] + base + "\n"
|
154
|
+
end
|
155
|
+
end
|
156
|
+
end
|
157
|
+
|
158
|
+
end
|
159
|
+
|
160
|
+
|
161
|
+
class String
|
162
|
+
|
163
|
+
def step(window_size)
|
164
|
+
i = 0
|
165
|
+
0.step(self.length - window_size, window_size) do |i|
|
166
|
+
yield self[i, window_size]
|
167
|
+
end
|
168
|
+
yield self[i + window_size .. -1] if i + window_size < self.length
|
169
|
+
end
|
170
|
+
|
171
|
+
def skip(window_size, step_size = 1)
|
172
|
+
i = 0
|
173
|
+
0.step(self.length - window_size, step_size) do |i|
|
174
|
+
yield [self[i, window_size], i + 1, i + window_size]
|
175
|
+
end
|
176
|
+
from = i + step_size
|
177
|
+
to = [self.length, i + step_size + window_size].min
|
178
|
+
yield [self[from, window_size], from + 1, to] if from + 1 <= to
|
179
|
+
end
|
180
|
+
|
181
|
+
def to_naseq
|
182
|
+
Bio::Sequence::NA.new(self)
|
183
|
+
end
|
184
|
+
|
185
|
+
def to_aaseq
|
186
|
+
Bio::Sequence::AA.new(self)
|
187
|
+
end
|
188
|
+
|
189
|
+
# folding both line end justified
|
190
|
+
def fold(fill_column = 72, indent = 0)
|
191
|
+
str = ''
|
192
|
+
|
193
|
+
# size : allowed length of the actual text
|
194
|
+
unless (size = fill_column - indent) > 0
|
195
|
+
warn "Error: indent > fill_column (indent is set to 0)"
|
196
|
+
size = fill_column
|
197
|
+
indent = 0
|
198
|
+
end
|
199
|
+
|
200
|
+
0.step(self.length - 1, size) do |n|
|
201
|
+
str << ' ' * indent + self[n, size] + "\n"
|
202
|
+
end
|
203
|
+
|
204
|
+
return str
|
205
|
+
end
|
206
|
+
|
207
|
+
# folding with conscious about word boundaries with prefix string
|
208
|
+
def fill(fill_column = 80, indent = 0, separater = ' ', prefix = '', first_line_only = true)
|
209
|
+
|
210
|
+
# size : allowed length of the actual text
|
211
|
+
unless (size = fill_column - indent) > 0
|
212
|
+
warn "Error: indent > fill_column (indent is set to 0)"
|
213
|
+
size = fill_column
|
214
|
+
indent = 0
|
215
|
+
end
|
216
|
+
|
217
|
+
n = pos = 0
|
218
|
+
ary = []
|
219
|
+
while n < self.length
|
220
|
+
pos = self[n, size].rindex(separater)
|
221
|
+
|
222
|
+
if self[n, size].length < size # last line of the folded str
|
223
|
+
pos = nil
|
224
|
+
end
|
225
|
+
|
226
|
+
if pos
|
227
|
+
ary << self[n, pos+separater.length]
|
228
|
+
n += pos + separater.length
|
229
|
+
else # line too long or the last line
|
230
|
+
ary << self[n, size]
|
231
|
+
n += size
|
232
|
+
end
|
233
|
+
end
|
234
|
+
str = ary.join("\n")
|
235
|
+
|
236
|
+
str[0,0] = prefix + ' ' * (indent - prefix.length)
|
237
|
+
if first_line_only
|
238
|
+
head = ' ' * indent
|
239
|
+
else
|
240
|
+
head = prefix + ' ' * (indent - prefix.length)
|
241
|
+
end
|
242
|
+
str.gsub!("\n", "\n#{head}")
|
243
|
+
|
244
|
+
return str.chomp
|
245
|
+
end
|
246
|
+
end
|
247
|
+
|
@@ -0,0 +1,87 @@
|
|
1
|
+
#
|
2
|
+
# = bio/shell/plugin/soap.rb - web services
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2006
|
5
|
+
# Toshiaki Katayama <k@bioruby.org>
|
6
|
+
# License:: Ruby's
|
7
|
+
#
|
8
|
+
# $Id: soap.rb,v 1.1 2007/07/09 11:17:09 k Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
module Bio::Shell
|
12
|
+
|
13
|
+
private
|
14
|
+
|
15
|
+
def ncbisoap(wsdl = nil)
|
16
|
+
if wsdl
|
17
|
+
@ncbisoap = Bio::NCBI::SOAP.new(wsdl)
|
18
|
+
else
|
19
|
+
@ncbisoap ||= Bio::NCBI::SOAP.new
|
20
|
+
end
|
21
|
+
return @ncbisoap
|
22
|
+
end
|
23
|
+
|
24
|
+
def ebisoap(wsdl = nil)
|
25
|
+
case wsdl
|
26
|
+
when :ipscan
|
27
|
+
@ebisoap = Bio::EBI::SOAP::InterProScan.new(wsdl)
|
28
|
+
when :emboss
|
29
|
+
@ebisoap = Bio::EBI::SOAP::Emboss.new(wsdl)
|
30
|
+
when :clustalw
|
31
|
+
@ebisoap = Bio::EBI::SOAP::ClustalW.new(wsdl)
|
32
|
+
when :tcoffee
|
33
|
+
@ebisoap = Bio::EBI::SOAP::TCoffee.new(wsdl)
|
34
|
+
when :muscle
|
35
|
+
@ebisoap = Bio::EBI::SOAP::Muscle.new(wsdl)
|
36
|
+
when :fasta
|
37
|
+
@ebisoap = Bio::EBI::SOAP::Fasta.new(wsdl)
|
38
|
+
when :wublast
|
39
|
+
@ebisoap = Bio::EBI::SOAP::WUBlast.new(wsdl)
|
40
|
+
when :mpsrch
|
41
|
+
@ebisoap = Bio::EBI::SOAP::MPsrch.new(wsdl)
|
42
|
+
when :scanps
|
43
|
+
@ebisoap = Bio::EBI::SOAP::ScanPS.new(wsdl)
|
44
|
+
when :msd
|
45
|
+
@ebisoap = Bio::EBI::SOAP::MSD.new(wsdl)
|
46
|
+
when :ontology
|
47
|
+
@ebisoap = Bio::EBI::SOAP::Ontology.new(wsdl)
|
48
|
+
when :citation
|
49
|
+
@ebisoap = Bio::EBI::SOAP::Citation.new(wsdl)
|
50
|
+
when /^http/
|
51
|
+
@ebisoap = Bio::EBI::SOAP.new(wsdl)
|
52
|
+
else
|
53
|
+
@ebisoap ||= Bio::EBI::SOAP.new
|
54
|
+
end
|
55
|
+
return @ebisoap
|
56
|
+
end
|
57
|
+
|
58
|
+
def ddbjsoap(wsdl = nil)
|
59
|
+
case wsdl
|
60
|
+
when :blast
|
61
|
+
@ddbjsoap = Bio::DDBJ::XML::Blast.new
|
62
|
+
when :fasta
|
63
|
+
@ddbjsoap = Bio::DDBJ::XML::Fasta.new
|
64
|
+
when :clustalw
|
65
|
+
@ddbjsoap = Bio::DDBJ::XML::ClustalW.new
|
66
|
+
when :ddbj
|
67
|
+
@ddbjsoap = Bio::DDBJ::XML::DDBJ.new
|
68
|
+
when :gib
|
69
|
+
@ddbjsoap = Bio::DDBJ::XML::Gib.new
|
70
|
+
when :gtop
|
71
|
+
@ddbjsoap = Bio::DDBJ::XML::Gtop.new
|
72
|
+
when :pml
|
73
|
+
@ddbjsoap = Bio::DDBJ::XML::PML.new
|
74
|
+
when :srs
|
75
|
+
@ddbjsoap = Bio::DDBJ::XML::SRS.new
|
76
|
+
when :txsearch
|
77
|
+
@ddbjsoap = Bio::DDBJ::XML::TxSearch.new
|
78
|
+
when /^http/
|
79
|
+
@ddbjsoap = Bio::DDBJ::XML.new(wsdl)
|
80
|
+
else
|
81
|
+
@ddbjsoap ||= Bio::DDBJ::XML.new
|
82
|
+
end
|
83
|
+
return @ddbjsoap
|
84
|
+
end
|
85
|
+
|
86
|
+
end
|
87
|
+
|
@@ -0,0 +1,29 @@
|
|
1
|
+
class BiorubyGenerator < Rails::Generator::Base
|
2
|
+
def manifest
|
3
|
+
record do |m|
|
4
|
+
m.directory 'app/controllers'
|
5
|
+
m.directory 'app/helpers'
|
6
|
+
m.directory 'app/views/bioruby'
|
7
|
+
m.directory 'app/views/layouts'
|
8
|
+
m.directory 'public/images/bioruby'
|
9
|
+
m.directory 'public/stylesheets'
|
10
|
+
m.file 'bioruby_controller.rb', 'app/controllers/bioruby_controller.rb'
|
11
|
+
m.file 'bioruby_helper.rb', 'app/helpers/bioruby_helper.rb'
|
12
|
+
m.file '_methods.rhtml', 'app/views/bioruby/_methods.rhtml'
|
13
|
+
m.file '_classes.rhtml', 'app/views/bioruby/_classes.rhtml'
|
14
|
+
m.file '_modules.rhtml', 'app/views/bioruby/_modules.rhtml'
|
15
|
+
m.file '_log.rhtml', 'app/views/bioruby/_log.rhtml'
|
16
|
+
m.file '_variables.rhtml', 'app/views/bioruby/_variables.rhtml'
|
17
|
+
m.file 'commands.rhtml', 'app/views/bioruby/commands.rhtml'
|
18
|
+
m.file 'history.rhtml', 'app/views/bioruby/history.rhtml'
|
19
|
+
m.file 'index.rhtml', 'app/views/bioruby/index.rhtml'
|
20
|
+
m.file 'bioruby.rhtml', 'app/views/layouts/bioruby.rhtml'
|
21
|
+
m.file 'spinner.gif', 'public/images/bioruby/spinner.gif'
|
22
|
+
m.file 'bioruby-gem.png', 'public/images/bioruby/gem.png'
|
23
|
+
m.file 'bioruby-link.gif', 'public/images/bioruby/link.gif'
|
24
|
+
m.file 'bioruby-bg.gif', 'public/images/bioruby/bg.gif'
|
25
|
+
m.file 'bioruby.css', 'public/stylesheets/bioruby.css'
|
26
|
+
end
|
27
|
+
end
|
28
|
+
end
|
29
|
+
|