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
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#
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# = bio/appl/clustalw.rb - CLUSTAL W wrapper class
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#
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# Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
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# License:: The Ruby License
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#
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# $Id: clustalw.rb,v 1.19 2007/07/16 12:27:29 ngoto Exp $
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#
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# Bio::ClustalW is a CLUSTAL W execution wrapper class.
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# It can also be called as an alignment factory.
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# CLUSTAL W is a very popular software for multiple sequence alignment.
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#
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# == References
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#
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# * Thompson,J.D., Higgins,D.G. and Gibson,T.J..
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# CLUSTAL W: improving the sensitivity of progressive multiple sequence
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# alignment through sequence weighting, position-specific gap penalties
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# and weight matrix choice. Nucleic Acids Research, 22:4673-4680, 1994.
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# http://nar.oxfordjournals.org/cgi/content/abstract/22/22/4673
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# * http://www.ebi.ac.uk/clustalw/
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# * ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/
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#
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require 'tempfile'
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require 'bio/command'
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require 'bio/sequence'
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require 'bio/alignment'
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module Bio
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# Bio::ClustalW is a CLUSTAL W execution wrapper class.
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# Its object is also called an alignment factory.
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# CLUSTAL W is a very popular software for multiple sequence alignment.
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class ClustalW
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autoload :Report, 'bio/appl/clustalw/report'
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# Creates a new CLUSTAL W execution wrapper object (alignment factory).
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def initialize(program = 'clustalw', opt = [])
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@program = program
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@options = opt
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@command = nil
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@output = nil
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@report = nil
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@data_stdout = nil
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@exit_status = nil
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@output_dnd = nil
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end
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# name of the program (usually 'clustalw' in UNIX)
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attr_accessor :program
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+
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# options
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attr_accessor :options
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+
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# option is deprecated. Instead, please use options.
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def option
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warn "Bio::ClustalW#option is deprecated. Please use options."
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options
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end
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# Returns last command-line strings executed by this factory.
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# Note that filenames described in the command-line may already
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# be removed because they are temporary files.
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# Returns an array.
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attr_reader :command
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# This method will be deprecated.
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#
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# Returns last messages of CLUSTAL W execution.
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def log
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#warn 'Bio::ClustalW#log will be deprecated.'
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@data_stdout
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end
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# Returns last raw alignment result (String or nil).
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attr_reader :output
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# Returns last alignment result.
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# Returns a Bio::ClustalW::Report object.
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attr_reader :report
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# Last exit status
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attr_reader :exit_status
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# Last output to the stdout.
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attr_accessor :data_stdout
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# Clear the internal data and status, except program and options.
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def reset
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@command = nil
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@output = nil
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@report = nil
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@exit_status = nil
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@data_stdout = nil
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@output_dnd = nil
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end
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# Executes the program(clustalw).
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# If +seqs+ is not nil, perform alignment for seqs.
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# If +seqs+ is nil, simply executes CLUSTAL W.
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#
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# Compatibility note: When seqs is nil,
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# returns true if the program exits normally, and
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# returns false if the program exits abnormally.
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def query(seqs)
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if seqs then
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query_align(seqs)
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else
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exec_local(@options)
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@exit_status.exitstatus == 0 ? true : false
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end
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end
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# Note that this method will be renamed to query_alignment.
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#
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# Performs alignment for +seqs+.
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# +seqs+ should be Bio::Alignment or Array of sequences or nil.
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#
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# Compatibility Note: Nucleic or amino is not determined by this method.
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def query_align(seqs)
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unless seqs.is_a?(Bio::Alignment)
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seqs = Bio::Alignment.new(seqs)
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end
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query_string(seqs.output_fasta(:width => 70,
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:avoid_same_name => true))
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end
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# Performs alignment for +seqs+.
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# +seqs+ should be Bio::Alignment or Array of sequences or nil.
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def query_alignment(seqs)
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query_align(seqs)
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end
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# Performs alignment for +str+.
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# +str+ should be a string that can be recognized by CLUSTAL W.
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#
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# Compatibility Note: 2nd argument is deprecated and ignored.
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def query_string(str, *arg)
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if arg.size > 0 then
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warn '2nd argument of Bio::ClustalW#query_string is ignored'
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end
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begin
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tf_in = Tempfile.open('align')
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tf_in.print str
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ensure
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tf_in.close(false)
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end
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r = query_by_filename(tf_in.path)
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tf_in.close(true)
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r
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end
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# Performs alignment of sequences in the file named +path+.
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#
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# Compatibility Note: 2nd argument (seqtype) is deprecated and ignored.
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def query_by_filename(path, *arg)
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if arg.size > 0 then
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warn '2nd argument of Bio::ClustalW#query_by_filename is ignored'
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end
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tf_out = Tempfile.open('clustalout')
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tf_out.close(false)
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tf_dnd = Tempfile.open('clustaldnd')
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tf_dnd.close(false)
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opt = [ "-align",
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"-infile=#{path}",
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"-outfile=#{tf_out.path}",
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"-newtree=#{tf_dnd.path}",
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"-outorder=input"
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]
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#opt << "-type=#{seqtype}" if seqtype
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opt.concat(@options)
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exec_local(opt)
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tf_out.open
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@output = tf_out.read
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tf_out.close(true)
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tf_dnd.open
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@output_dnd = tf_dnd.read
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tf_dnd.close(true)
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@report = Report.new(@output)
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@report
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end
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# Returns last alignment guild-tree (file.dnd).
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attr_reader :output_dnd
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#---
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# Returns last error messages (to stderr) of CLUSTAL W execution.
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#attr_reader :errorlog
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#+++
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#errorlog is deprecated (no replacement) and returns empty string.
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def errorlog
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warn "errorlog is deprecated (no replacement) and returns empty string."
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''
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end
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private
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# Executes the program in the local machine.
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def exec_local(opt)
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@command = [ @program, *opt ]
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#STDERR.print "DEBUG: ", @command.join(" "), "\n"
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@data_stdout = nil
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@exit_status = nil
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Bio::Command.call_command(@command) do |io|
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io.close_write
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@data_stdout = io.read
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end
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@exit_status = $?
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end
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end #class ClustalW
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end #module Bio
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#
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# = bio/appl/clustalw/report.rb - CLUSTAL W format data (*.aln) class
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#
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# Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
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# License:: The Ruby License
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#
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# $Id: report.rb,v 1.13 2007/07/18 08:47:39 ngoto Exp $
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#
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# Bio::ClustalW::Report is a CLUSTAL W report (*.aln file) parser.
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# CLUSTAL W is a very popular software for multiple sequence alignment.
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#
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# == References
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#
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# * Thompson,J.D., Higgins,D.G. and Gibson,T.J..
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# CLUSTAL W: improving the sensitivity of progressive multiple sequence
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# alignment through sequence weighting, position-specific gap penalties
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# and weight matrix choice. Nucleic Acids Research, 22:4673-4680, 1994.
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# http://nar.oxfordjournals.org/cgi/content/abstract/22/22/4673
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# * http://www.ebi.ac.uk/clustalw/
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# * ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/
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#
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require 'bio/sequence'
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require 'bio/db'
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require 'bio/alignment'
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require 'bio/appl/clustalw'
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module Bio
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class ClustalW
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# CLUSTAL W result data (*.aln file) parser class.
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class Report < Bio::DB
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# Delimiter of each entry. Bio::FlatFile uses it.
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# In Bio::ClustalW::Report, it it nil (1 entry 1 file).
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DELIMITER = nil
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# Creates new instance.
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# +str+ should be a CLUSTAL format string.
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# +seqclass+ should on of following:
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# * Class: Bio::Sequence::AA, Bio::Sequence::NA, ...
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# * String: 'PROTEIN', 'DNA', ...
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def initialize(str, seqclass = nil)
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@raw = str
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@align = nil
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@match_line = nil
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@header = nil
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case seqclass
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when /PROTEIN/i
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@seqclass = Bio::Sequence::AA
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when /[DR]NA/i
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@seqclass = Bio::Sequence::NA
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else
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if seqclass.is_a?(Module) then
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@seqclass = seqclass
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else
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@seqclass = Bio::Sequence
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end
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end
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end
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# string of whole result
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attr_reader :raw
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# sequence class (one of Bio::Sequence, Bio::Sequence::NA,
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# Bio::Sequence::AA, ...)
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attr_reader :seqclass
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# Shows first line of the result data, for example,
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# 'CLUSTAL W (1.82) multiple sequence alignment'.
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# Returns a string.
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def header
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@header or (do_parse or @header)
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end
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# Shows "match line" of CLUSTAL's alignment result, for example,
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# ':* :* .* * .*::*. ** :* . * . '.
|
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# Returns a string.
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def match_line
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@match_line or (do_parse or @match_line)
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end
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82
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# Gets an multiple alignment.
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# Returns a Bio::Alignment object.
|
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def alignment
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do_parse() unless @align
|
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@align
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end
|
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+
|
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# This will be deprecated. Instead, please use alignment.
|
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#
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91
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# Gets an multiple alignment.
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# Returns a Bio::Alignment object.
|
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def align
|
94
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warn "Bio::ClustalW#align will be deprecated. Please use \'alignment\'."
|
95
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alignment
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96
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end
|
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+
|
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# This will be deprecated. Instead, please use alignment.output_fasta.
|
99
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#
|
100
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# Gets an fasta-format string of the sequences.
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# Returns a string.
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def to_fasta(*arg)
|
103
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warn "Bio::ClustalW::report#to_fasta is deprecated. Please use \'alignment.output_fasta\'"
|
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alignment.output_fasta(*arg)
|
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end
|
106
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+
|
107
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# Compatibility note: Behavior of the method will be changed
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# in the future.
|
109
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#
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# Gets an array of the sequences.
|
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# Returns an array of Bio::FastaFormat objects.
|
112
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def to_a
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113
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alignment.to_fastaformat_array
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end
|
115
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+
|
116
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private
|
117
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# Parses Clustal W result text.
|
118
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def do_parse
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119
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return nil if @align
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120
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a = @raw.split(/\r?\n\r?\n/)
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@header = a.shift.to_s
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xalign = Bio::Alignment.new
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@match_line = ''
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if a.size > 0 then
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a[0].gsub!(/\A(\r?\n)+/, '')
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a.collect! { |x| x.split(/\r?\n/) }
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a.each { |x|
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x.each { |y| y.sub!(/ +\d+\s*$/, '') }} #for -SEQNOS=on option
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@tagsize = ( a[0][0].rindex(/\s/) or -1 ) + 1
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a.each do |x|
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@match_line << x.pop.to_s[@tagsize..-1]
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end
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a[0].each do |y|
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xalign.store(y[0, @tagsize].sub(/\s+\z/, ''), '')
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end
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a.each do |x|
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x.each do |y|
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name = y[0, @tagsize].sub(/\s+\z/, '')
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seq = y[@tagsize..-1]
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xalign[name] << seq
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end
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end
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xalign.collect! { |x| @seqclass.new(x) }
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end
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@align = xalign
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nil
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end
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end #class Report
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end #class ClustalW
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end #module Bio
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#
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# = bio/appl/emboss.rb - EMBOSS wrapper
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#
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# Copyright:: Copyright (C) 2002, 2005 Toshiaki Katayama<k@bioruby.org>
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# Copyright:: Copyright (C) 2006 Jan Aerts <jan.aerts@bbsrc.ac.uk>
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# License:: The Ruby License
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#
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# $Id: emboss.rb,v 1.9 2008/01/10 03:51:06 ngoto Exp $
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#
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module Bio
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# == Description
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#
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# This file holds classes pertaining to the EMBOSS software suite.
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#
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# This class provides a wrapper for the applications of the EMBOSS suite, which
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# is a mature and stable collection of open-source applications that can handle
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# a huge range of sequence formats.
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# Applications include:
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# * Sequence alignment
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# * Rapid database searching with sequence patterns
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# * Protein motif identification, including domain analysis
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# * Nucleotide sequence pattern analysis---for example to identify CpG islands or repeats
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# * Codon usage analysis for small genomes
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# * Rapid identification of sequence patterns in large scale sequence sets
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# * Presentation tools for publication
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#
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# See the emboss website for more information: http://emboss.sourceforge.net.
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#
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#
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# == Usage
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#
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# require 'bio'
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#
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# # Suppose that you could get the sequence for XLRHODOP by running
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# # the EMBOSS command +seqret embl:xlrhodop+ on the command line.
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# # Then you can get the output of that command in a String object
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# # by using Bio::EMBOSS.run method.
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# xlrhodop = Bio::EMBOSS.run('seqret', 'embl:xlrhodop')
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# puts xlrhodop
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#
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# # Or all in one go:
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# puts Bio::EMBOSS.run('seqret', 'embl:xlrhodop')
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#
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# # Similarly:
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# puts Bio::EMBOSS.run('transeq', '-sbegin', '110','-send', '1171',
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# 'embl:xlrhodop')
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# puts Bio::EMBOSS.run('showfeat', 'embl:xlrhodop')
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# puts Bio::EMBOSS.run('seqret', 'embl:xlrhodop', '-osformat', 'acedb')
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#
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# # A shortcut exists for this two-step process for +seqret+ and +entret+.
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# puts Bio::EMBOSS.seqret('embl:xlrhodop')
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# puts Bio::EMBOSS.entret('embl:xlrhodop')
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#
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# # You can use %w() syntax.
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# puts Bio::EMBOSS.run(*%w( transeq -sbegin 110 -send 1171 embl:xlrhodop ))
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#
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# # You can also use Shellwords.shellwords.
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# require 'shellwords'
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# str = 'transeq -sbegin 110 -send 1171 embl:xlrhodop'
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# cmd = Shellwords.shellwords(str)
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# puts Bio::EMBOSS.run(*cmd)
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#
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+
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#
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# == Pre-requisites
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#
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# You must have the EMBOSS suite installed locally. You can download from the
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# project website (see References below).
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#
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# = Rereferences
|
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#
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# * http://emboss.sourceforge.net
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# * Rice P, Longden I and Bleasby A. \
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# EMBOSS: the European Molecular Biology Open Software Suite. \
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+
# Trends Genet. 2000 Jun ; 16(6): 276-7
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+
#
|
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+
class EMBOSS
|
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+
|
81
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+
# Combines the initialization and execution for the emboss +seqret+ command.
|
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+
#
|
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+
# puts Bio::EMBOSS.seqret('embl:xlrhodop')
|
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+
#
|
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+
# is equivalent to:
|
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+
#
|
87
|
+
# object = Bio::EMBOSS.new('seqret embl:xlrhodop')
|
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+
# puts object.exec
|
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|
+
# ---
|
90
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+
# *Arguments*:
|
91
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+
# * (required) _arg_: argument given to the emboss seqret command
|
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+
# *Returns*:: String
|
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+
def self.seqret(arg)
|
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|
+
str = self.retrieve('seqret', arg)
|
95
|
+
end
|
96
|
+
|
97
|
+
# Combines the initialization and execution for the emboss +entret+ command.
|
98
|
+
#
|
99
|
+
# puts Bio::EMBOSS.entret('embl:xlrhodop')
|
100
|
+
#
|
101
|
+
# is equivalent to:
|
102
|
+
#
|
103
|
+
# object = Bio::EMBOSS.new('entret embl:xlrhodop')
|
104
|
+
# puts object.exec
|
105
|
+
# ---
|
106
|
+
# *Arguments*:
|
107
|
+
# * (required) _arg_: argument given to the emboss entret command
|
108
|
+
# *Returns*:: String
|
109
|
+
def self.entret(arg)
|
110
|
+
str = self.retrieve('entret', arg)
|
111
|
+
end
|
112
|
+
|
113
|
+
# WARNING: Bio::EMBOSS.new will be changed in the future because
|
114
|
+
# Bio::EMBOSS.new(cmd_line) is inconvenient and potential security hole.
|
115
|
+
# Using Bio::EMBOSS.run(program, options...) is strongly recommended.
|
116
|
+
#
|
117
|
+
# Initializes a new Bio::EMBOSS object. This provides a holder that can
|
118
|
+
# subsequently be executed (see Bio::EMBOSS.exec). The object does _not_
|
119
|
+
# hold any actual data when initialized.
|
120
|
+
#
|
121
|
+
# e = Bio::EMBOSS.new('seqret embl:xlrhodop')
|
122
|
+
#
|
123
|
+
# For e to actually hold data, it has to be executed:
|
124
|
+
# puts e.exec
|
125
|
+
#
|
126
|
+
# For an overview of commands that can be used with this method, see the
|
127
|
+
# emboss website.
|
128
|
+
# ---
|
129
|
+
# *Arguments*:
|
130
|
+
# * (required) _command_: emboss command
|
131
|
+
# *Returns*:: Bio::EMBOSS object
|
132
|
+
def initialize(cmd_line)
|
133
|
+
warn 'Bio::EMBOSS.new(cmd_line) is inconvenient and potential security hole. Using Bio::EMBOSS.run(program, options...) is strongly recommended.'
|
134
|
+
@cmd_line = cmd_line + ' -stdout -auto'
|
135
|
+
end
|
136
|
+
|
137
|
+
# A Bio::EMBOSS object has to be executed before it can return any result.
|
138
|
+
# obj_A = Bio::EMBOSS.new('transeq -sbegin 110 -send 1171 embl:xlrhodop')
|
139
|
+
# puts obj_A.result #=> nil
|
140
|
+
# obj_A.exec
|
141
|
+
# puts obj_A.result #=> a FASTA-formatted sequence
|
142
|
+
#
|
143
|
+
# obj_B = Bio::EMBOSS.new('showfeat embl:xlrhodop')
|
144
|
+
# obj_B.exec
|
145
|
+
# puts obj_B.result
|
146
|
+
def exec
|
147
|
+
begin
|
148
|
+
@io = IO.popen(@cmd_line, "w+")
|
149
|
+
@result = @io.read
|
150
|
+
return @result
|
151
|
+
ensure
|
152
|
+
@io.close
|
153
|
+
end
|
154
|
+
end
|
155
|
+
|
156
|
+
# Pipe for the command
|
157
|
+
attr_reader :io
|
158
|
+
|
159
|
+
# Result of the executed command
|
160
|
+
attr_reader :result
|
161
|
+
|
162
|
+
# Runs an emboss program and get the result as string.
|
163
|
+
# Note that "-auto -stdout" are automatically added to the options.
|
164
|
+
#
|
165
|
+
# Example 1:
|
166
|
+
#
|
167
|
+
# result = Bio::EMBOSS.run('seqret', 'embl:xlrhodop')
|
168
|
+
#
|
169
|
+
# Example 2:
|
170
|
+
#
|
171
|
+
# result = Bio::EMBOSS.run('water',
|
172
|
+
# '-asequence', 'swissprot:slpi_human',
|
173
|
+
# '-bsequence', 'swissprot:slpi_mouse')
|
174
|
+
#
|
175
|
+
# Example 3:
|
176
|
+
# options = %w( -asequence swissprot:slpi_human
|
177
|
+
# -bsequence swissprot:slpi_mouse )
|
178
|
+
# result = Bio::EMBOSS.run('needle', *options)
|
179
|
+
#
|
180
|
+
# For an overview of commands that can be used with this method, see the
|
181
|
+
# emboss website.
|
182
|
+
# ---
|
183
|
+
# *Arguments*:
|
184
|
+
# * (required) _program_: command name, or filename of an emboss program
|
185
|
+
# * _options_: options given to the emboss program
|
186
|
+
# *Returns*:: String
|
187
|
+
def self.run(program, *options)
|
188
|
+
cmd = [ program, *options ]
|
189
|
+
cmd.push '-auto'
|
190
|
+
cmd.push '-stdout'
|
191
|
+
return Bio::Command.query_command(cmd)
|
192
|
+
end
|
193
|
+
|
194
|
+
private
|
195
|
+
|
196
|
+
def self.retrieve(cmd, arg)
|
197
|
+
cmd = [ cmd, arg, '-auto', '-stdout' ]
|
198
|
+
return Bio::Command.query_command(cmd)
|
199
|
+
end
|
200
|
+
|
201
|
+
end # EMBOSS
|
202
|
+
|
203
|
+
end # Bio
|