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 +1,146 @@
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#
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# = bio/shell/demo.rb - demo mode for the BioRuby shell
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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: demo.rb,v 1.4 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 demo(part = nil)
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demo = Demo.new
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if part
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demo.send(part)
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else
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demo.all
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end
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end
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class Demo
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def initialize
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@bind = Bio::Shell.cache[:binding]
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end
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def all
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sequence &&
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entry &&
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shell &&
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pdb &&
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true
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end
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def tutorial
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end
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def aldh2
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end
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def mito
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run(%q[entry = getent("data/kumamushi.gb")], "Load kumamushi gene from GenBank database entry ...", false) &&
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run(%q[disp entry], "Check the contents ...", false) &&
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run(%q[kuma = flatparse(entry)], "Parse the database entry ...", true) &&
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run(%q[web], "Start BioRuby on Rails...", false) &&
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run(%q[puts kuma.entry_id], "Extract entry ID ...", false) &&
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run(%q[puts kuma.definition], "Extract definition ...", false) &&
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run(%q[gene = kuma.seq], "Extract DNA sequence of the gene ...", true) &&
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run(%q[doublehelix(gene)], "Show the sequence in ascii art ...", false) &&
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run(%q[seqstat(gene)], "Statistics of the gene ...", false) &&
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run(%q[config :color], "Change to color mode...", false) &&
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run(%q[seqstat(gene)], "Statistics of the gene ...", false) &&
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#run(%q[codontable], "Codontalble ...", false) &&
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run(%q[protein = gene.translate], "Translate DNA into protein ...", true) &&
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run(%q[comp = protein.composition], "Composition of the amino acids ...", false) &&
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run(%q[pp comp], "Check the composition ...", false) &&
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run(%q[puts protein.molecular_weight], "Molecular weight ...", false) &&
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run(%q[midifile("data/kumamushi.mid", gene)], "Gene to music ...", false) &&
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run(%q[`open "data/kumamushi.mid"`], "Let's listen ...", false) &&
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true
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end
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def sequence
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run(%q[dna = getseq("atgc" * 100)], "Generating DNA sequence ...", true) &&
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run(%q[doublehelix dna], "Double helix representation", false) &&
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run(%q[protein = dna.translate], "Translate DNA into Protein ...", true) &&
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run(%q[protein.molecular_weight], "Calculating molecular weight ...", true) &&
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run(%q[protein.composition], "Amino acid composition ...", true) &&
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true
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end
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def entry
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run(%q[kuma = getobj("gb:AF237819")], "Obtain an entry from GenBank database", false) &&
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run(%q[kuma.definition], "Definition of the entry", true) &&
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run(%q[kuma.naseq], "Sequence of the entry", true) &&
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run(%q[kuma.naseq.translate], "Translate the sequence to protein", true) &&
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run(%q[midifile("data/AF237819.mid", kuma.naseq)], "Generate gene music ...", false) &&
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true
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end
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def shell
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run(%q[pwd], "Show current working directory ...", false) &&
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run(%q[dir], "Show directory contents ...", false) &&
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run(%q[dir "shell/session"], "Show directory contents ...", false) &&
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true
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end
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def pdb
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run(%q[ent_1bl8 = getent("pdb:1bl8")], "Retrieving PDB entry 1BL8 ...", false) &&
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run(%q[head ent_1bl8], "Head part of the entry ...", false) &&
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run(%q[savefile("1bl8.pdb", ent_1bl8)], "Saving the original entry in file ...", false) &&
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run(%q[disp "data/1bl8.pdb"], "Look through the entire entry ...", false) &&
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run(%q[pdb_1bl8 = flatparse(ent_1bl8)], "Parsing the entry ...", false) &&
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run(%q[pdb_1bl8.entry_id], "Showing the entry ID ...", true) &&
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run(%q[pdb_1bl8.each_heterogen { |heterogen| p heterogen.resName }], "Showing each heterogen object ...", false) &&
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true
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end
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def pdb_hetdic
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# run(%q[het_dic = open("http://deposit.pdb.org/het_dictionary.txt").read],
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# "Retrieving the het_dic database ...", false) &&
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# run(%q[savefile("data/het_dictionary.txt", het_dic)],
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# "Saving the file ... ", false) &&
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run(%q[het_dic.size], "Bytes of the file ...", true) &&
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run(%q[disp "data/het_dictionary.txt"], "Take a look on the contents ...", true) &&
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run(%q[flatindex("het_dic", "data/het_dictionary.txt")],
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"Creating index to make the seaarchable database ...", false) &&
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run(%q[ethanol = flatsearch("het_dic", "EOH")], "Search an ethanol entry ...", true) &&
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run(%q[osake = flatparse(ethanol)], "Parse the entry ...", true) &&
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run(%q[osake.conect], "Showing connect table (conect) of the molecule ...", true) &&
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true
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end
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private
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def run(cmd, msg, echo)
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comment(msg)
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splash(cmd)
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result = eval(cmd, @bind)
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if echo
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pp result
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end
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continue?
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end
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def comment(msg)
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puts "### #{msg}"
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end
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def splash(msg)
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Bio::Shell.splash_message_action("bioruby> #{msg}")
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print "bioruby> #{msg}"
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gets
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end
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def continue?
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Bio::Shell.ask_yes_or_no("Continue? [y/n] ")
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end
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end
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end
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@@ -0,0 +1,218 @@
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#
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# = bio/shell/interface.rb - core user interface of the BioRuby shell
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#
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4
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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: interface.rb,v 1.19 2007/11/15 07:08:49 k Exp $
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#
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module Bio::Shell
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private
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### work space
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def ls
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bind = Bio::Shell.cache[:binding]
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list = eval("local_variables", bind).reject { |x|
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eval(x, bind).nil?
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}
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puts list.inspect
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return list
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end
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def rm(name)
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bind = Bio::Shell.cache[:binding]
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list = eval("local_variables", bind).reject { |x|
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eval(x, bind).nil?
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}
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begin
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if list.include?(name.to_s)
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eval("#{name} = nil", bind)
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else
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raise
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end
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rescue
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warn "Usage: rm :var or rm 'var' (rm var is not valid)"
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end
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end
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|
42
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### script
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def script(mode = nil)
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Bio::Shell.script(mode)
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end
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### object
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|
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def reload_object
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Bio::Shell.load_object
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end
|
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|
54
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### plugin
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55
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|
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def reload_plugin
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Bio::Shell.load_plugin
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end
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|
60
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### config
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61
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|
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def config(mode = :show, *opts)
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case mode
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64
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when :show, "show"
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Bio::Shell.config_show
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when :echo, "echo"
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Bio::Shell.config_echo
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when :color, "color"
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Bio::Shell.config_color
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70
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when :splash, "splash"
|
71
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Bio::Shell.config_splash
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72
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when :pager, "pager"
|
73
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Bio::Shell.config_pager(*opts)
|
74
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when :message, "message"
|
75
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Bio::Shell.config_message(*opts)
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else
|
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puts "Invalid mode (#{mode}) - :show, :echo, :color, :splash, :massage"
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end
|
79
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end
|
80
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+
|
81
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def reload_config
|
82
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Bio::Shell.load_config
|
83
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end
|
84
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|
85
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### pager
|
86
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+
|
87
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def pager(cmd = nil)
|
88
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unless Bio::Shell.config[:pager]
|
89
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cmd ||= ENV['PAGER']
|
90
|
+
end
|
91
|
+
Bio::Shell.config_pager(cmd)
|
92
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+
puts "Pager is set to '#{cmd ? cmd : 'off'}'"
|
93
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+
end
|
94
|
+
|
95
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def disp(*objs)
|
96
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# The original idea is from http://sheepman.parfait.ne.jp/20050215.html
|
97
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if cmd = Bio::Shell.config[:pager]
|
98
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+
pg = IO.popen(cmd, "w")
|
99
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+
begin
|
100
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stdout_save = STDOUT.clone
|
101
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STDOUT.reopen(pg)
|
102
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objs.each do |obj|
|
103
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if obj.is_a?(String)
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104
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if File.exists?(obj)
|
105
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system("#{cmd} #{obj}")
|
106
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+
else
|
107
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obj.display
|
108
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+
end
|
109
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else
|
110
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pp obj
|
111
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+
end
|
112
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+
end
|
113
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ensure
|
114
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STDOUT.reopen(stdout_save)
|
115
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stdout_save.close
|
116
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pg.close
|
117
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+
end
|
118
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else
|
119
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+
objs.each do |obj|
|
120
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if obj.is_a?(String)
|
121
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obj.display
|
122
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else
|
123
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pp obj
|
124
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end
|
125
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end
|
126
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+
end
|
127
|
+
end
|
128
|
+
|
129
|
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def head(arg, num = 10)
|
130
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str = ""
|
131
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+
if File.exists?(arg)
|
132
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File.open(arg) do |file|
|
133
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num.times do
|
134
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if line = file.gets
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135
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str << line
|
136
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+
end
|
137
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end
|
138
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end
|
139
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else
|
140
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arg.to_s.each_with_index do |line, i|
|
141
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break if i >= num
|
142
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str << line
|
143
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+
end
|
144
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end
|
145
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puts str
|
146
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return str
|
147
|
+
end
|
148
|
+
|
149
|
+
### file save
|
150
|
+
|
151
|
+
def savefile(file, *objs)
|
152
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+
datadir = Bio::Shell.data_dir
|
153
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message = "Save file '#{file}' in '#{datadir}' directory? [y/n] "
|
154
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if ! file[/^#{datadir}/] and Bio::Shell.ask_yes_or_no(message)
|
155
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file = File.join(datadir, file)
|
156
|
+
end
|
157
|
+
if File.exists?(file)
|
158
|
+
message = "Overwrite existing '#{file}' file? [y/n] "
|
159
|
+
if ! Bio::Shell.ask_yes_or_no(message)
|
160
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puts " ... save aborted."
|
161
|
+
return
|
162
|
+
end
|
163
|
+
end
|
164
|
+
begin
|
165
|
+
print "Saving file (#{file}) ... "
|
166
|
+
File.open(file, "w") do |f|
|
167
|
+
objs.each do |obj|
|
168
|
+
f.puts obj.to_s
|
169
|
+
end
|
170
|
+
end
|
171
|
+
puts "done"
|
172
|
+
rescue
|
173
|
+
warn "Error: Failed to save (#{file}) : #{$!}"
|
174
|
+
end
|
175
|
+
end
|
176
|
+
|
177
|
+
### file system
|
178
|
+
|
179
|
+
def cd(dir = ENV['HOME'])
|
180
|
+
if dir
|
181
|
+
Dir.chdir(dir)
|
182
|
+
end
|
183
|
+
puts Dir.pwd.inspect
|
184
|
+
end
|
185
|
+
|
186
|
+
def pwd
|
187
|
+
puts Dir.pwd.inspect
|
188
|
+
end
|
189
|
+
|
190
|
+
def dir(file = nil)
|
191
|
+
if file
|
192
|
+
if File.directory?(file)
|
193
|
+
files = Dir.glob("#{file}/*")
|
194
|
+
else
|
195
|
+
files = Dir.glob(file)
|
196
|
+
end
|
197
|
+
else
|
198
|
+
files = Dir.glob("*")
|
199
|
+
end
|
200
|
+
if files
|
201
|
+
str = " UGO Date Byte File\n"
|
202
|
+
str << "------ ------------------------------ ----------- ------------\n"
|
203
|
+
files.sort.each { |f|
|
204
|
+
stat = File.lstat(f)
|
205
|
+
mode = format("%6o", stat.mode)
|
206
|
+
date = stat.mtime
|
207
|
+
byte = stat.size
|
208
|
+
name = f.inspect
|
209
|
+
str << format("%s %30s%13d %s\n", mode, date, byte, name)
|
210
|
+
}
|
211
|
+
puts str
|
212
|
+
return files.sort
|
213
|
+
end
|
214
|
+
end
|
215
|
+
|
216
|
+
end
|
217
|
+
|
218
|
+
|
@@ -0,0 +1,95 @@
|
|
1
|
+
#
|
2
|
+
# = bio/shell/irb.rb - CUI for the BioRuby shell
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2006
|
5
|
+
# Toshiaki Katayama <k@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: irb.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
module Bio::Shell
|
12
|
+
|
13
|
+
class Irb
|
14
|
+
|
15
|
+
def initialize
|
16
|
+
require 'irb'
|
17
|
+
begin
|
18
|
+
require 'irb/completion'
|
19
|
+
Bio::Shell.cache[:readline] = true
|
20
|
+
rescue LoadError
|
21
|
+
Bio::Shell.cache[:readline] = false
|
22
|
+
end
|
23
|
+
IRB.setup(nil)
|
24
|
+
setup_irb
|
25
|
+
start_irb
|
26
|
+
end
|
27
|
+
|
28
|
+
def start_irb
|
29
|
+
Bio::Shell.cache[:irb] = IRB::Irb.new
|
30
|
+
|
31
|
+
# needed for method completion
|
32
|
+
IRB.conf[:MAIN_CONTEXT] = Bio::Shell.cache[:irb].context
|
33
|
+
|
34
|
+
# store binding for evaluation
|
35
|
+
Bio::Shell.cache[:binding] = IRB.conf[:MAIN_CONTEXT].workspace.binding
|
36
|
+
|
37
|
+
# overwrite gets to store history with time stamp
|
38
|
+
io = IRB.conf[:MAIN_CONTEXT].io
|
39
|
+
io.class.class_eval do
|
40
|
+
alias_method :irb_original_gets, :gets
|
41
|
+
end
|
42
|
+
|
43
|
+
def io.gets
|
44
|
+
line = irb_original_gets
|
45
|
+
if line
|
46
|
+
Bio::Shell.store_history(line)
|
47
|
+
end
|
48
|
+
return line
|
49
|
+
end
|
50
|
+
|
51
|
+
if File.exists?("./config/boot.rb")
|
52
|
+
require "./config/boot"
|
53
|
+
require "./config/environment"
|
54
|
+
#require 'commands/console'
|
55
|
+
end
|
56
|
+
end
|
57
|
+
|
58
|
+
def setup_irb
|
59
|
+
# set application name
|
60
|
+
IRB.conf[:AP_NAME] = 'bioruby'
|
61
|
+
|
62
|
+
# change prompt for bioruby
|
63
|
+
$_ = Bio::Shell.colors
|
64
|
+
IRB.conf[:PROMPT][:BIORUBY_COLOR] = {
|
65
|
+
:PROMPT_I => "bio#{$_[:ruby]}ruby#{$_[:none]}> ",
|
66
|
+
:PROMPT_S => "bio#{$_[:ruby]}ruby#{$_[:none]}%l ",
|
67
|
+
:PROMPT_C => "bio#{$_[:ruby]}ruby#{$_[:none]}+ ",
|
68
|
+
:RETURN => " ==> %s\n"
|
69
|
+
}
|
70
|
+
IRB.conf[:PROMPT][:BIORUBY] = {
|
71
|
+
:PROMPT_I => "bioruby> ",
|
72
|
+
:PROMPT_S => "bioruby%l ",
|
73
|
+
:PROMPT_C => "bioruby+ ",
|
74
|
+
:RETURN => " ==> %s\n"
|
75
|
+
}
|
76
|
+
if Bio::Shell.config[:color]
|
77
|
+
IRB.conf[:PROMPT_MODE] = :BIORUBY_COLOR
|
78
|
+
else
|
79
|
+
IRB.conf[:PROMPT_MODE] = :BIORUBY
|
80
|
+
end
|
81
|
+
|
82
|
+
# echo mode (uncomment to off by default)
|
83
|
+
#IRB.conf[:ECHO] = Bio::Shell.config[:echo] || false
|
84
|
+
|
85
|
+
# irb/input-method.rb >= v1.5 (not in 1.8.2)
|
86
|
+
#IRB.conf[:SAVE_HISTORY] = 100000
|
87
|
+
|
88
|
+
# not nicely works
|
89
|
+
#IRB.conf[:AUTO_INDENT] = true
|
90
|
+
end
|
91
|
+
|
92
|
+
end # Irb
|
93
|
+
|
94
|
+
end
|
95
|
+
|