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 +1,253 @@
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#
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# bio/io/flatfile/bdb.rb - OBDA flatfile index by Berkley DB
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#
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# Copyright:: Copyright (C) 2002 GOTO Naohisa <ng@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: bdb.rb,v 1.10 2007/04/05 23:35:41 trevor Exp $
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#
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begin
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require 'bdb'
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rescue LoadError,NotImplementedError
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end
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require 'bio/io/flatfile/index'
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require 'bio/io/flatfile/indexer'
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module Bio
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class FlatFileIndex
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module BDBdefault
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def permission
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(0666 & (0777 ^ File.umask))
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end
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module_function :permission
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def flag_read
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BDB::RDONLY
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end
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module_function :flag_read
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def flag_write
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(BDB::CREATE | BDB::TRUNCATE)
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end
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module_function :flag_write
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def flag_append
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'r+'
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end
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module_function :flag_append
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end #module BDBdefault
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class BDBwrapper
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def initialize(name, filename, *arg)
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@dbname = name
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@file = nil
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@filename = filename
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#self.open(*arg)
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end
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def filename
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File.join(@dbname, @filename)
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end
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def open(flag = BDBdefault.flag_read,
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permission = BDBdefault.permission)
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unless @file then
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DEBUG.print "BDBwrapper: open #{filename}\n"
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@file = BDB::Btree.open(filename, nil, flag, permission)
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end
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true
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end
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def close
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if @file
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DEBUG.print "BDBwrapper: close #{filename}\n"
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@file.close
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@file = nil
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end
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nil
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end
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def [](arg)
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#self.open
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if @file then
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@file[arg]
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else
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nil
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end
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end
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def []=(key, val)
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#self.open
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@file[key.to_s] = val.to_s
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end
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def writeback_array(prefix, array, *arg)
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self.close
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self.open(*arg)
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array.each_with_index do |val, key|
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@file["#{prefix}#{key}"] = val.to_s
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end
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end
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def keys
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if @file then
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@file.keys
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else
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[]
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end
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end
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end #class BDBwrapper
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module BDB_1
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class BDBMappingFile
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def self.open(*arg)
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self.new(*arg)
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end
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def initialize(filename, flag = BDBdefault.flag_read,
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permission = BDBdefault.permission)
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@filename = filename
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@flag = flag
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@permission = permission
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#@bdb = BDB::Btree.open(@filename, nil, @flag, @permission)
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end
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attr_reader :filename
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attr_accessor :flag, :permission
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def open
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unless @bdb then
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DEBUG.print "BDBMappingFile: open #{@filename}\n"
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@bdb = BDB::Btree.open(@filename, nil, @flag, @permission)
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true
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else
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nil
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end
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end
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def close
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if @bdb then
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DEBUG.print "BDBMappingFile: close #{@filename}\n"
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@bdb.close
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@bdb = nil
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end
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nil
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end
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def records
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@bdb.size
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end
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alias size records
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# methods for writing
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def add(key, val)
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open
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val = val.to_a.join("\t")
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s = @bdb[key]
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if s then
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s << "\t"
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s << val
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val = s
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end
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@bdb[key] = val
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#DEBUG.print "add: key=#{key.inspect}, val=#{val.inspect}\n"
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val
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end
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def add_exclusive(key, val)
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open
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val = val.to_a.join("\t")
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s = @bdb[key]
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if s then
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raise RuntimeError, "keys must be unique, but key #{key.inspect} already exists"
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end
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@bdb[key] = val
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#DEBUG.print "add_exclusive: key=#{key.inspect}, val=#{val.inspect}\n"
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val
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end
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def add_overwrite(key, val)
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open
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val = val.to_a.join("\t")
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s = @bdb[key]
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if s then
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DEBUG.print "Warining: overwrote unique id #{key.inspect}\n"
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end
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@bdb[key] = val
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#DEBUG.print "add_overwrite: key=#{key.inspect}, val=#{val.inspect}\n"
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val
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end
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def add_nr(key, val)
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open
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s = @bdb[key]
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if s then
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a = s.split("\t")
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else
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a = []
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end
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a.concat val.to_a
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a.sort!
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a.uniq!
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str = a.join("\t")
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@bdb[key] = str
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#DEBUG.print "add_nr: key=#{key.inspect}, val=#{str.inspect}\n"
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str
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end
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# methods for searching
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def search(key)
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open
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s = @bdb[key]
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if s then
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a = s.split("\t")
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a
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else
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[]
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end
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end
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end #class BDBMappingFile
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class PrimaryNameSpace < Template::NameSpace
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def mapping(filename)
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BDBMappingFile.new(filename)
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end
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def filename
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File.join(dbname, "key_#{name}")
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end
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def search(key)
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r = super(key)
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unless r.empty? then
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[ r ]
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else
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r
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end
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end
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end #class PrimaryNameSpace
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class SecondaryNameSpace < Template::NameSpace
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def mapping(filename)
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BDBMappingFile.new(filename)
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end
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def filename
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File.join(dbname, "id_#{name}")
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end #class SecondaryNameSpaces
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def search(key)
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r = super(key)
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file.close
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r
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end
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end #class SecondaryNameSpace
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end #module BDB_1
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end #class FlatFileIndex
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end #module Bio
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=begin
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* Classes/modules in this file are internal use only.
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=end
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@@ -0,0 +1,237 @@
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#
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# = bio/io/flatfile/buffer.rb - Input stream buffer for FlatFile
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#
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# Copyright (C) 2001-2006 Naohisa Goto <ng@bioruby.org>
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#
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# License:: The Ruby License
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#
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# $Id:$
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#
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#
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# See documents for Bio::FlatFile::BufferedInputStream and Bio::FlatFile.
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#
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require 'bio/io/flatfile'
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module Bio
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class FlatFile
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# Wrapper for a IO (or IO-like) object.
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# It can input with a buffer.
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class BufferedInputStream
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# Creates a new input stream wrapper
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def initialize(io, path)
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@io = io
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@path = path
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# initialize prefetch buffer
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@buffer = ''
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end
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# Creates a new input stream wrapper from the given IO object.
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def self.for_io(io)
|
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begin
|
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path = io.path
|
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rescue NameError
|
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path = nil
|
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end
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self.new(io, path)
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end
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41
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# Creates a new input stream wrapper to open file _filename_
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# by using File.open.
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# *arg is passed to File.open.
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44
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#
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# Like File.open, a block can be accepted.
|
46
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def self.open_file(filename, *arg)
|
47
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if block_given? then
|
48
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File.open(filename, *arg) do |fobj|
|
49
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yield self.new(fobj, filename)
|
50
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end
|
51
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else
|
52
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fobj = File.open(filename, *arg)
|
53
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self.new(fobj, filename)
|
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end
|
55
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end
|
56
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|
57
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# Creates a new input stream wrapper from URI specified as _uri_.
|
58
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# by using OpenURI.open_uri or URI#open.
|
59
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# _uri_ must be a String or URI object.
|
60
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# *arg is passed to OpenURI.open_uri or URI#open.
|
61
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#
|
62
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# Like OpenURI.open_uri, it can accept a block.
|
63
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+
def self.open_uri(uri, *arg)
|
64
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+
if uri.kind_of?(URI)
|
65
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+
if block_given?
|
66
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uri.open(*arg) do |fobj|
|
67
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+
yield self.new(fobj, uri.to_s)
|
68
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+
end
|
69
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else
|
70
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fobj = uri.open(*arg)
|
71
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+
self.new(fobj, uri.to_s)
|
72
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+
end
|
73
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+
else
|
74
|
+
if block_given?
|
75
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+
OpenURI.open_uri(uri, *arg) do |fobj|
|
76
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+
yield self.new(fobj, uri)
|
77
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+
end
|
78
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+
else
|
79
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fobj = OpenURI.open_uri(uri, *arg)
|
80
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+
self.new(fobj, uri)
|
81
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+
end
|
82
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+
end
|
83
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+
end
|
84
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+
|
85
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+
# Pathname, filename or URI to open the object.
|
86
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+
# Like File#path, returned value isn't normalized.
|
87
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attr_reader :path
|
88
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+
|
89
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+
# Converts to IO object if possible
|
90
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+
def to_io
|
91
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+
@io.to_io
|
92
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+
end
|
93
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+
|
94
|
+
# Closes the IO object if possible
|
95
|
+
def close
|
96
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+
@io.close
|
97
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+
end
|
98
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|
99
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# Rewinds the IO object if possible
|
100
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# Internal buffer in this wrapper is cleared.
|
101
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def rewind
|
102
|
+
r = @io.rewind
|
103
|
+
@buffer = ''
|
104
|
+
r
|
105
|
+
end
|
106
|
+
|
107
|
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# Returns current file position
|
108
|
+
def pos
|
109
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+
@io.pos - @buffer.size
|
110
|
+
end
|
111
|
+
|
112
|
+
# Sets current file position if possible
|
113
|
+
# Internal buffer in this wrapper is cleared.
|
114
|
+
def pos=(p)
|
115
|
+
r = (@io.pos = p)
|
116
|
+
@buffer = ''
|
117
|
+
r
|
118
|
+
end
|
119
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+
|
120
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+
# Returns true if end-of-file. Otherwise, returns false.
|
121
|
+
#
|
122
|
+
# Note that it returns false if internal buffer is this wrapper
|
123
|
+
# is not empty,
|
124
|
+
def eof?
|
125
|
+
if @buffer.size > 0
|
126
|
+
false
|
127
|
+
else
|
128
|
+
@io.eof?
|
129
|
+
end
|
130
|
+
end
|
131
|
+
|
132
|
+
# Same as IO#gets.
|
133
|
+
#
|
134
|
+
# Compatibility note: the bahavior of paragraph mode (io_rs = '')
|
135
|
+
# may differ from that of IO#gets('').
|
136
|
+
def gets(io_rs = $/)
|
137
|
+
if @buffer.size > 0
|
138
|
+
if io_rs == nil then
|
139
|
+
r = @buffer + @io.gets(nil).to_s
|
140
|
+
@buffer = ''
|
141
|
+
else
|
142
|
+
if io_rs == '' then # io_rs.empty?
|
143
|
+
sp_rs = /((?:\r?\n){2,})/n
|
144
|
+
else
|
145
|
+
sp_rs = io_rs
|
146
|
+
end
|
147
|
+
a = @buffer.split(sp_rs, 2)
|
148
|
+
if a.size > 1 then
|
149
|
+
r = a.shift
|
150
|
+
r += (io_rs.empty? ? a.shift : io_rs)
|
151
|
+
@buffer = a.shift.to_s
|
152
|
+
else
|
153
|
+
@buffer << @io.gets(io_rs).to_s
|
154
|
+
a = @buffer.split(sp_rs, 2)
|
155
|
+
if a.size > 1 then
|
156
|
+
r = a.shift
|
157
|
+
r += (io_rs.empty? ? a.shift : io_rs)
|
158
|
+
@buffer = a.shift.to_s
|
159
|
+
else
|
160
|
+
r = @buffer
|
161
|
+
@buffer = ''
|
162
|
+
end
|
163
|
+
end
|
164
|
+
end
|
165
|
+
r
|
166
|
+
else
|
167
|
+
@io.gets(io_rs)
|
168
|
+
end
|
169
|
+
end
|
170
|
+
|
171
|
+
# Pushes back given str to the internal buffer.
|
172
|
+
# Returns nil.
|
173
|
+
# str must be read previously with the wrapper object.
|
174
|
+
#
|
175
|
+
# Note that in current implementation, the str can be everything,
|
176
|
+
# but please don't depend on it.
|
177
|
+
#
|
178
|
+
def ungets(str)
|
179
|
+
@buffer = str + @buffer
|
180
|
+
nil
|
181
|
+
end
|
182
|
+
|
183
|
+
# Same as IO#getc.
|
184
|
+
def getc
|
185
|
+
if @buffer.size > 0 then
|
186
|
+
r = @buffer[0]
|
187
|
+
@buffer = @buffer[1..-1]
|
188
|
+
else
|
189
|
+
r = @io.getc
|
190
|
+
end
|
191
|
+
r
|
192
|
+
end
|
193
|
+
|
194
|
+
# Pushes back one character into the internal buffer.
|
195
|
+
# Unlike IO#getc, it can be called more than one time.
|
196
|
+
def ungetc(c)
|
197
|
+
@buffer = sprintf("%c", c) + @buffer
|
198
|
+
nil
|
199
|
+
end
|
200
|
+
|
201
|
+
# Gets current prefetch buffer
|
202
|
+
def prefetch_buffer
|
203
|
+
@buffer
|
204
|
+
end
|
205
|
+
|
206
|
+
# It does @io.gets, and addes returned string
|
207
|
+
# to the internal buffer, and returns the string.
|
208
|
+
def prefetch_gets(*arg)
|
209
|
+
r = @io.gets(*arg)
|
210
|
+
@buffer << r if r
|
211
|
+
r
|
212
|
+
end
|
213
|
+
|
214
|
+
# It does @io.readpartial, and addes returned string
|
215
|
+
# to the internal buffer, and returns the string.
|
216
|
+
def prefetch_readpartial(*arg)
|
217
|
+
r = @io.readpartial(*arg)
|
218
|
+
@buffer << r if r
|
219
|
+
r
|
220
|
+
end
|
221
|
+
|
222
|
+
# Skips space characters in the stream.
|
223
|
+
# returns nil.
|
224
|
+
def skip_spaces
|
225
|
+
ws = { ?\s => true, ?\n => true, ?\r => true, ?\t => true }
|
226
|
+
while r = self.getc
|
227
|
+
unless ws[r] then
|
228
|
+
self.ungetc(r)
|
229
|
+
break
|
230
|
+
end
|
231
|
+
end
|
232
|
+
nil
|
233
|
+
end
|
234
|
+
end #class BufferedInputStream
|
235
|
+
|
236
|
+
end #class FlatFile
|
237
|
+
end #module Bio
|