wwood-bioruby 1.2.11
Sign up to get free protection for your applications and to get access to all the features.
- data/README.rdoc +205 -0
- data/README_DEV.rdoc +285 -0
- data/VERSION.yml +4 -0
- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +293 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/lib/bio.rb +306 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +505 -0
- data/lib/bio/appl/blast/ddbj.rb +142 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/genomenet.rb +263 -0
- data/lib/bio/appl/blast/ncbioptions.rb +220 -0
- data/lib/bio/appl/blast/remote.rb +105 -0
- data/lib/bio/appl/blast/report.rb +767 -0
- data/lib/bio/appl/blast/rexml.rb +144 -0
- data/lib/bio/appl/blast/rpsblast.rb +277 -0
- data/lib/bio/appl/blast/wublast.rb +635 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blat/report.rb +530 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta.rb +235 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/gcg/msf.rb +212 -0
- data/lib/bio/appl/gcg/seq.rb +195 -0
- data/lib/bio/appl/genscan/report.rb +552 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/hmmer/report.rb +683 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/paml/baseml.rb +95 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/codeml.rb +242 -0
- data/lib/bio/appl/paml/codeml/rates.rb +67 -0
- data/lib/bio/appl/paml/codeml/report.rb +67 -0
- data/lib/bio/appl/paml/common.rb +348 -0
- data/lib/bio/appl/paml/common_report.rb +38 -0
- data/lib/bio/appl/paml/yn00.rb +103 -0
- data/lib/bio/appl/paml/yn00/report.rb +32 -0
- data/lib/bio/appl/phylip/alignment.rb +133 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/psort/report.rb +542 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +124 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sosui/report.rb +151 -0
- data/lib/bio/appl/spidey/report.rb +593 -0
- data/lib/bio/appl/targetp/report.rb +267 -0
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +231 -0
- data/lib/bio/command.rb +593 -0
- data/lib/bio/compat/features.rb +157 -0
- data/lib/bio/compat/references.rb +128 -0
- data/lib/bio/data/aa.rb +353 -0
- data/lib/bio/data/codontable.rb +722 -0
- data/lib/bio/data/na.rb +223 -0
- data/lib/bio/db.rb +329 -0
- data/lib/bio/db/aaindex.rb +357 -0
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +67 -0
- data/lib/bio/db/biosql/sequence.rb +508 -0
- data/lib/bio/db/embl/common.rb +352 -0
- data/lib/bio/db/embl/embl.rb +500 -0
- data/lib/bio/db/embl/embl_to_biosequence.rb +85 -0
- data/lib/bio/db/embl/format_embl.rb +190 -0
- data/lib/bio/db/embl/sptr.rb +1283 -0
- data/lib/bio/db/embl/swissprot.rb +42 -0
- data/lib/bio/db/embl/trembl.rb +41 -0
- data/lib/bio/db/embl/uniprot.rb +42 -0
- data/lib/bio/db/fantom.rb +597 -0
- data/lib/bio/db/fasta.rb +410 -0
- data/lib/bio/db/fasta/defline.rb +532 -0
- data/lib/bio/db/fasta/fasta_to_biosequence.rb +63 -0
- data/lib/bio/db/fasta/format_fasta.rb +97 -0
- data/lib/bio/db/genbank/common.rb +307 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/format_genbank.rb +187 -0
- data/lib/bio/db/genbank/genbank.rb +250 -0
- data/lib/bio/db/genbank/genbank_to_biosequence.rb +86 -0
- data/lib/bio/db/genbank/genpept.rb +60 -0
- data/lib/bio/db/genbank/refseq.rb +18 -0
- data/lib/bio/db/gff.rb +1846 -0
- data/lib/bio/db/go.rb +481 -0
- data/lib/bio/db/kegg/brite.rb +41 -0
- data/lib/bio/db/kegg/compound.rb +131 -0
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +148 -0
- data/lib/bio/db/kegg/expression.rb +155 -0
- data/lib/bio/db/kegg/genes.rb +263 -0
- data/lib/bio/db/kegg/genome.rb +241 -0
- data/lib/bio/db/kegg/glycan.rb +166 -0
- data/lib/bio/db/kegg/keggtab.rb +357 -0
- data/lib/bio/db/kegg/kgml.rb +256 -0
- data/lib/bio/db/kegg/orthology.rb +136 -0
- data/lib/bio/db/kegg/reaction.rb +82 -0
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +107 -0
- data/lib/bio/db/medline.rb +326 -0
- data/lib/bio/db/nbrf.rb +191 -0
- data/lib/bio/db/newick.rb +658 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +29 -0
- data/lib/bio/db/pdb/atom.rb +77 -0
- data/lib/bio/db/pdb/chain.rb +210 -0
- data/lib/bio/db/pdb/chemicalcomponent.rb +224 -0
- data/lib/bio/db/pdb/model.rb +148 -0
- data/lib/bio/db/pdb/pdb.rb +1911 -0
- data/lib/bio/db/pdb/residue.rb +176 -0
- data/lib/bio/db/pdb/utils.rb +399 -0
- data/lib/bio/db/prosite.rb +597 -0
- data/lib/bio/db/rebase.rb +456 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/db/url.rb +42 -0
- data/lib/bio/feature.rb +139 -0
- data/lib/bio/io/biosql/biodatabase.rb +64 -0
- data/lib/bio/io/biosql/bioentry.rb +29 -0
- data/lib/bio/io/biosql/bioentry_dbxref.rb +11 -0
- data/lib/bio/io/biosql/bioentry_path.rb +12 -0
- data/lib/bio/io/biosql/bioentry_qualifier_value.rb +10 -0
- data/lib/bio/io/biosql/bioentry_reference.rb +10 -0
- data/lib/bio/io/biosql/bioentry_relationship.rb +10 -0
- data/lib/bio/io/biosql/biosequence.rb +11 -0
- data/lib/bio/io/biosql/comment.rb +7 -0
- data/lib/bio/io/biosql/config/database.yml +20 -0
- data/lib/bio/io/biosql/dbxref.rb +13 -0
- data/lib/bio/io/biosql/dbxref_qualifier_value.rb +12 -0
- data/lib/bio/io/biosql/location.rb +32 -0
- data/lib/bio/io/biosql/location_qualifier_value.rb +11 -0
- data/lib/bio/io/biosql/ontology.rb +10 -0
- data/lib/bio/io/biosql/reference.rb +9 -0
- data/lib/bio/io/biosql/seqfeature.rb +32 -0
- data/lib/bio/io/biosql/seqfeature_dbxref.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_path.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_qualifier_value.rb +20 -0
- data/lib/bio/io/biosql/seqfeature_relationship.rb +11 -0
- data/lib/bio/io/biosql/taxon.rb +12 -0
- data/lib/bio/io/biosql/taxon_name.rb +9 -0
- data/lib/bio/io/biosql/term.rb +27 -0
- data/lib/bio/io/biosql/term_dbxref.rb +11 -0
- data/lib/bio/io/biosql/term_path.rb +12 -0
- data/lib/bio/io/biosql/term_relationship.rb +13 -0
- data/lib/bio/io/biosql/term_relationship_term.rb +11 -0
- data/lib/bio/io/biosql/term_synonym.rb +10 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +638 -0
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +163 -0
- data/lib/bio/io/fetch.rb +195 -0
- data/lib/bio/io/flatfile.rb +482 -0
- data/lib/bio/io/flatfile/autodetection.rb +545 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/buffer.rb +237 -0
- data/lib/bio/io/flatfile/index.rb +1381 -0
- data/lib/bio/io/flatfile/indexer.rb +805 -0
- data/lib/bio/io/flatfile/splitter.rb +297 -0
- data/lib/bio/io/higet.rb +73 -0
- data/lib/bio/io/hinv.rb +442 -0
- data/lib/bio/io/keggapi.rb +805 -0
- data/lib/bio/io/ncbirest.rb +733 -0
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +307 -0
- data/lib/bio/io/registry.rb +292 -0
- data/lib/bio/io/soapwsdl.rb +119 -0
- data/lib/bio/io/sql.rb +186 -0
- data/lib/bio/location.rb +867 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +960 -0
- data/lib/bio/reference.rb +602 -0
- data/lib/bio/sequence.rb +456 -0
- data/lib/bio/sequence/aa.rb +152 -0
- data/lib/bio/sequence/adapter.rb +108 -0
- data/lib/bio/sequence/common.rb +310 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/dblink.rb +54 -0
- data/lib/bio/sequence/format.rb +358 -0
- data/lib/bio/sequence/format_raw.rb +23 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +491 -0
- data/lib/bio/shell.rb +44 -0
- data/lib/bio/shell/core.rb +578 -0
- data/lib/bio/shell/demo.rb +146 -0
- data/lib/bio/shell/interface.rb +218 -0
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +71 -0
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +218 -0
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +105 -0
- data/lib/bio/shell/plugin/flatfile.rb +101 -0
- data/lib/bio/shell/plugin/keggapi.rb +181 -0
- data/lib/bio/shell/plugin/midi.rb +430 -0
- data/lib/bio/shell/plugin/obda.rb +45 -0
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +247 -0
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +11 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +7 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +10 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +102 -0
- data/lib/bio/tree.rb +852 -0
- data/lib/bio/util/color_scheme.rb +191 -0
- data/lib/bio/util/color_scheme/buried.rb +59 -0
- data/lib/bio/util/color_scheme/helix.rb +59 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +64 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +31 -0
- data/lib/bio/util/color_scheme/strand.rb +59 -0
- data/lib/bio/util/color_scheme/taylor.rb +50 -0
- data/lib/bio/util/color_scheme/turn.rb +59 -0
- data/lib/bio/util/color_scheme/zappo.rb +50 -0
- data/lib/bio/util/contingency_table.rb +370 -0
- data/lib/bio/util/restriction_enzyme.rb +228 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
- data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +200 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/aaindex/DAYM780301 +30 -0
- data/test/data/aaindex/PRAM900102 +20 -0
- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
- data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
- data/test/data/blast/2.2.15.blastp.m7 +876 -0
- data/test/data/blast/b0002.faa +15 -0
- data/test/data/blast/b0002.faa.m0 +128 -0
- data/test/data/blast/b0002.faa.m7 +65 -0
- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/blast/blastp-multi.m7 +188 -0
- data/test/data/command/echoarg2.bat +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/embl/AB090716.embl.rel89 +63 -0
- data/test/data/fasta/example1.txt +75 -0
- data/test/data/fasta/example2.txt +21 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/paml/codeml/control_file.txt +30 -0
- data/test/data/paml/codeml/output.txt +78 -0
- data/test/data/paml/codeml/rates +217 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/rpsblast/misc.rpsblast +193 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/functional/bio/appl/test_pts1.rb +115 -0
- data/test/functional/bio/io/test_ensembl.rb +229 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -0
- data/test/functional/bio/sequence/test_output_embl.rb +51 -0
- data/test/functional/bio/test_command.rb +301 -0
- data/test/runner.rb +14 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_ncbioptions.rb +112 -0
- data/test/unit/bio/appl/blast/test_report.rb +1135 -0
- data/test/unit/bio/appl/blast/test_rpsblast.rb +398 -0
- data/test/unit/bio/appl/genscan/test_report.rb +182 -0
- data/test/unit/bio/appl/hmmer/test_report.rb +342 -0
- data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
- data/test/unit/bio/appl/mafft/test_report.rb +63 -0
- data/test/unit/bio/appl/paml/codeml/test_rates.rb +45 -0
- data/test/unit/bio/appl/paml/codeml/test_report.rb +45 -0
- data/test/unit/bio/appl/paml/test_codeml.rb +174 -0
- data/test/unit/bio/appl/sosui/test_report.rb +81 -0
- data/test/unit/bio/appl/targetp/test_report.rb +146 -0
- data/test/unit/bio/appl/test_blast.rb +277 -0
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_psort.rb +57 -0
- data/test/unit/bio/appl/test_pts1.rb +77 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +126 -0
- data/test/unit/bio/data/test_aa.rb +90 -0
- data/test/unit/bio/data/test_codontable.rb +107 -0
- data/test/unit/bio/data/test_na.rb +80 -0
- data/test/unit/bio/db/embl/test_common.rb +117 -0
- data/test/unit/bio/db/embl/test_embl.rb +214 -0
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +203 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1812 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +31 -0
- data/test/unit/bio/db/kegg/test_genes.rb +45 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +152 -0
- data/test/unit/bio/db/test_aaindex.rb +197 -0
- data/test/unit/bio/db/test_fasta.rb +250 -0
- data/test/unit/bio/db/test_gff.rb +1190 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_medline.rb +127 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +364 -0
- data/test/unit/bio/db/test_prosite.rb +1437 -0
- data/test/unit/bio/db/test_rebase.rb +101 -0
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/db/test_url.rb +36 -0
- data/test/unit/bio/io/flatfile/test_autodetection.rb +375 -0
- data/test/unit/bio/io/flatfile/test_buffer.rb +251 -0
- data/test/unit/bio/io/flatfile/test_splitter.rb +369 -0
- data/test/unit/bio/io/test_ddbjxml.rb +80 -0
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +42 -0
- data/test/unit/bio/io/test_flatfile.rb +505 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +115 -0
- data/test/unit/bio/sequence/test_common.rb +373 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -0
- data/test/unit/bio/sequence/test_dblink.rb +58 -0
- data/test/unit/bio/sequence/test_na.rb +330 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +185 -0
- data/test/unit/bio/test_alignment.rb +1025 -0
- data/test/unit/bio/test_command.rb +349 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +144 -0
- data/test/unit/bio/test_location.rb +599 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +499 -0
- data/test/unit/bio/test_reference.rb +252 -0
- data/test/unit/bio/test_sequence.rb +329 -0
- data/test/unit/bio/test_shell.rb +18 -0
- data/test/unit/bio/test_tree.rb +593 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +101 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
- data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
- data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
- data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
- data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
- data/test/unit/bio/util/test_color_scheme.rb +33 -0
- data/test/unit/bio/util/test_contingency_table.rb +94 -0
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +245 -0
- metadata +543 -0
@@ -0,0 +1,83 @@
|
|
1
|
+
#
|
2
|
+
# = bio/appl/blast/format8.rb - BLAST tab-delimited output (-m 8) parser
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2002, 2003, 2007 Toshiaki Katayama <k@bioruby.org>
|
5
|
+
# License:: The Ruby License
|
6
|
+
#
|
7
|
+
# $Id:$
|
8
|
+
#
|
9
|
+
# == Note
|
10
|
+
#
|
11
|
+
# This file is automatically loaded by bio/appl/blast/report.rb
|
12
|
+
#
|
13
|
+
|
14
|
+
module Bio
|
15
|
+
class Blast
|
16
|
+
class Report
|
17
|
+
|
18
|
+
private
|
19
|
+
|
20
|
+
def tab_parse(data)
|
21
|
+
iteration = Iteration.new
|
22
|
+
@iterations.push(iteration)
|
23
|
+
@query_id = @query_def = data[/\S+/]
|
24
|
+
|
25
|
+
query_prev = ''
|
26
|
+
target_prev = ''
|
27
|
+
hit_num = 1
|
28
|
+
hsp_num = 1
|
29
|
+
hit = ''
|
30
|
+
data.each_line do |line|
|
31
|
+
ary = line.chomp.split("\t")
|
32
|
+
query_id, target_id, hsp = tab_parse_hsp(ary)
|
33
|
+
if query_prev != query_id or target_prev != target_id
|
34
|
+
hit = Hit.new
|
35
|
+
hit.num = hit_num
|
36
|
+
hit_num += 1
|
37
|
+
hit.query_id = hit.query_def = query_id
|
38
|
+
hit.accession = hit.definition = target_id
|
39
|
+
iteration.hits.push(hit)
|
40
|
+
hsp_num = 1
|
41
|
+
end
|
42
|
+
hsp.num = hsp_num
|
43
|
+
hsp_num += 1
|
44
|
+
hit.hsps.push(hsp)
|
45
|
+
query_prev = query_id
|
46
|
+
target_prev = target_id
|
47
|
+
end
|
48
|
+
end
|
49
|
+
|
50
|
+
def tab_parse_hsp(ary)
|
51
|
+
query_id, target_id,
|
52
|
+
percent_identity,
|
53
|
+
align_len,
|
54
|
+
mismatch_count,
|
55
|
+
gaps,
|
56
|
+
query_from,
|
57
|
+
query_to,
|
58
|
+
hit_from,
|
59
|
+
hit_to,
|
60
|
+
evalue,
|
61
|
+
bit_score = *ary
|
62
|
+
|
63
|
+
hsp = Hsp.new
|
64
|
+
hsp.align_len = align_len.to_i
|
65
|
+
hsp.gaps = gaps.to_i
|
66
|
+
hsp.query_from = query_from.to_i
|
67
|
+
hsp.query_to = query_to.to_i
|
68
|
+
hsp.hit_from = hit_from.to_i
|
69
|
+
hsp.hit_to = hit_to.to_i
|
70
|
+
hsp.evalue = evalue.strip.to_f
|
71
|
+
hsp.bit_score = bit_score.to_f
|
72
|
+
|
73
|
+
hsp.percent_identity = percent_identity.to_f
|
74
|
+
hsp.mismatch_count = mismatch_count.to_i
|
75
|
+
|
76
|
+
return query_id, target_id, hsp
|
77
|
+
end
|
78
|
+
|
79
|
+
end
|
80
|
+
end
|
81
|
+
end
|
82
|
+
|
83
|
+
|
@@ -0,0 +1,263 @@
|
|
1
|
+
#
|
2
|
+
# = bio/appl/blast/genomenet.rb - Remote BLAST wrapper using GenomeNet
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2001,2008 Mitsuteru C. Nakao <n@bioruby.org>
|
5
|
+
# Copyright:: Copyright (C) 2002,2003 Toshiaki Katayama <k@bioruby.org>
|
6
|
+
# Copyright:: Copyright (C) 2006 Jan Aerts <jan.aerts@bbsrc.ac.uk>
|
7
|
+
# Copyright:: Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>
|
8
|
+
# License:: The Ruby License
|
9
|
+
#
|
10
|
+
# $Id:$
|
11
|
+
#
|
12
|
+
|
13
|
+
require 'net/http'
|
14
|
+
require 'uri'
|
15
|
+
require 'bio/command'
|
16
|
+
require 'shellwords'
|
17
|
+
require 'bio/appl/blast/remote'
|
18
|
+
|
19
|
+
module Bio::Blast::Remote
|
20
|
+
|
21
|
+
# == Description
|
22
|
+
#
|
23
|
+
# The Bio::Blast::Remote::GenomeNet class contains methods for running
|
24
|
+
# remote BLAST searches on GenomeNet (http://blast.genome.jp/).
|
25
|
+
#
|
26
|
+
# == Usage
|
27
|
+
#
|
28
|
+
# require 'bio'
|
29
|
+
#
|
30
|
+
# # To run an actual BLAST analysis:
|
31
|
+
# # 1. create a BLAST factory
|
32
|
+
# blast_factory = Bio::Blast.remote('blastp', 'nr-aa',
|
33
|
+
# '-e 0.0001', 'genomenet')
|
34
|
+
# #or:
|
35
|
+
# blast_factory = Bio::Blast::Remote.genomenet('blastp', 'nr-aa',
|
36
|
+
# '-e 0.0001')
|
37
|
+
#
|
38
|
+
# # 2. run the actual BLAST by querying the factory
|
39
|
+
# report = blast_factory.query(sequence_text)
|
40
|
+
#
|
41
|
+
# # Then, to parse the report, see Bio::Blast::Report
|
42
|
+
#
|
43
|
+
# === Available databases for Bio::Blast::Remote::GenomeNet
|
44
|
+
#
|
45
|
+
# Up-to-date available databases can be obtained by using
|
46
|
+
# Bio::Blast::Remote::GenomeNet.databases(program).
|
47
|
+
# Short descriptions of databases
|
48
|
+
#
|
49
|
+
# ----------+-------+---------------------------------------------------
|
50
|
+
# program | query | db (supported in GenomeNet)
|
51
|
+
# ----------+-------+---------------------------------------------------
|
52
|
+
# blastp | AA | nr-aa, genes, vgenes.pep, swissprot, swissprot-upd,
|
53
|
+
# ----------+-------+ pir, prf, pdbstr
|
54
|
+
# blastx | NA |
|
55
|
+
# ----------+-------+---------------------------------------------------
|
56
|
+
# blastn | NA | nr-nt, genbank-nonst, gbnonst-upd, dbest, dbgss,
|
57
|
+
# ----------+-------+ htgs, dbsts, embl-nonst, embnonst-upd, epd,
|
58
|
+
# tblastn | AA | genes-nt, genome, vgenes.nuc
|
59
|
+
# ----------+-------+---------------------------------------------------
|
60
|
+
#
|
61
|
+
# == See also
|
62
|
+
#
|
63
|
+
# * Bio::Blast
|
64
|
+
# * Bio::Blast::Report
|
65
|
+
# * Bio::Blast::Report::Hit
|
66
|
+
# * Bio::Blast::Report::Hsp
|
67
|
+
#
|
68
|
+
# == References
|
69
|
+
#
|
70
|
+
# * http://www.ncbi.nlm.nih.gov/blast/
|
71
|
+
# * http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/similarity.html
|
72
|
+
# * http://blast.genome.jp/ideas/ideas.html#blast
|
73
|
+
#
|
74
|
+
module GenomeNet
|
75
|
+
|
76
|
+
Host = "blast.genome.jp".freeze
|
77
|
+
|
78
|
+
# Creates a remote BLAST factory using GenomeNet.
|
79
|
+
# Returns Bio::Blast object.
|
80
|
+
#
|
81
|
+
# Note for future improvement: In the future, it might return
|
82
|
+
# Bio::Blast::Remote::GenomeNet or other object.
|
83
|
+
#
|
84
|
+
def self.new(program, db, options = [])
|
85
|
+
Bio::Blast.new(program, db, options, 'genomenet')
|
86
|
+
end
|
87
|
+
|
88
|
+
# Information for GenomeNet BLAST search.
|
89
|
+
module Information
|
90
|
+
|
91
|
+
include Bio::Blast::Remote::Information
|
92
|
+
|
93
|
+
# gets information from remote host and parses database information
|
94
|
+
def _parse_databases
|
95
|
+
if defined? @parse_databases
|
96
|
+
return nil if @parse_databases
|
97
|
+
end
|
98
|
+
databases = {}
|
99
|
+
dbdescs = {}
|
100
|
+
key = nil
|
101
|
+
host = Bio::Blast::Remote::Genomenet::Host
|
102
|
+
http = Bio::Command.new_http(host)
|
103
|
+
result = http.get('/')
|
104
|
+
#p result.body
|
105
|
+
result.body.each_line do |line|
|
106
|
+
case line
|
107
|
+
when /\"set\_dbtype\(this\.form\,\'(prot|nucl)\'\)\"/
|
108
|
+
key = $1
|
109
|
+
databases[key] ||= []
|
110
|
+
dbdescs[key] ||= {}
|
111
|
+
when /\<input *type\=\"radio\" *name\=\"dbname\" *value\=\"([^\"]+)\"[^\>]*\>([^\<\>]+)/
|
112
|
+
db = $1.freeze
|
113
|
+
desc = $2.strip.freeze
|
114
|
+
databases[key].push db
|
115
|
+
dbdescs[key][db] = desc
|
116
|
+
end
|
117
|
+
end
|
118
|
+
|
119
|
+
# mine-aa and mine-nt should be removed
|
120
|
+
[ 'prot', 'nucl' ].each do |mol|
|
121
|
+
ary = databases[mol] || []
|
122
|
+
hash = dbdescs[mol] || {}
|
123
|
+
[ 'mine-aa', 'mine-nt' ].each do |k|
|
124
|
+
ary.delete(k)
|
125
|
+
hash.delete(k)
|
126
|
+
end
|
127
|
+
databases[mol] = ary.freeze
|
128
|
+
dbdescs[mol] = hash
|
129
|
+
end
|
130
|
+
|
131
|
+
[ databases, dbdescs ].each do |h|
|
132
|
+
prot = h['prot']
|
133
|
+
nucl = h['nucl']
|
134
|
+
h.delete('prot')
|
135
|
+
h.delete('nucl')
|
136
|
+
h['blastp'] = prot
|
137
|
+
h['blastx'] = prot
|
138
|
+
h['blastn'] = nucl
|
139
|
+
h['tblastn'] = nucl
|
140
|
+
h['tblastx'] = nucl
|
141
|
+
end
|
142
|
+
|
143
|
+
@databases = databases
|
144
|
+
@database_descriptions = dbdescs
|
145
|
+
@parse_databases = true
|
146
|
+
true
|
147
|
+
end
|
148
|
+
private :_parse_databases
|
149
|
+
|
150
|
+
end #module Information
|
151
|
+
|
152
|
+
extend Information
|
153
|
+
|
154
|
+
private
|
155
|
+
|
156
|
+
# executes BLAST and returns result as a string
|
157
|
+
def exec_genomenet(query)
|
158
|
+
host = Host
|
159
|
+
#host = "blast.genome.jp"
|
160
|
+
#path = "/sit-bin/nph-blast"
|
161
|
+
path = "/sit-bin/blast" #2005.08.12
|
162
|
+
|
163
|
+
options = make_command_line_options
|
164
|
+
opt = Bio::Blast::NCBIOptions.new(options)
|
165
|
+
|
166
|
+
program = opt.delete('-p')
|
167
|
+
db = opt.delete('-d')
|
168
|
+
|
169
|
+
matrix = opt.delete('-M') || 'blosum62'
|
170
|
+
filter = opt.delete('-F') || 'T'
|
171
|
+
|
172
|
+
opt_V = opt.delete('-V') || 500 # default value for GenomeNet
|
173
|
+
opt_B = opt.delete('-B') || 250 # default value for GenomeNet
|
174
|
+
|
175
|
+
# format, not for form parameters, but included in option string
|
176
|
+
opt_m = opt.get('-m') || '7' # default of BioRuby GenomeNet factory
|
177
|
+
opt.set('-m', opt_m)
|
178
|
+
|
179
|
+
optstr = Bio::Command.make_command_line_unix(opt.options)
|
180
|
+
|
181
|
+
form = {
|
182
|
+
'style' => 'raw',
|
183
|
+
'prog' => program,
|
184
|
+
'dbname' => db,
|
185
|
+
'sequence' => query,
|
186
|
+
'other_param' => optstr,
|
187
|
+
'matrix' => matrix,
|
188
|
+
'filter' => filter,
|
189
|
+
'V_value' => opt_V,
|
190
|
+
'B_value' => opt_B,
|
191
|
+
'alignment_view' => 0,
|
192
|
+
}
|
193
|
+
|
194
|
+
form.keys.each do |k|
|
195
|
+
form.delete(k) unless form[k]
|
196
|
+
end
|
197
|
+
|
198
|
+
begin
|
199
|
+
http = Bio::Command.new_http(host)
|
200
|
+
http.open_timeout = 300
|
201
|
+
http.read_timeout = 600
|
202
|
+
result = Bio::Command.http_post_form(http, path, form)
|
203
|
+
@output = result.body
|
204
|
+
|
205
|
+
# workaround 2008.8.13
|
206
|
+
if result.code == '302' then
|
207
|
+
newuri = URI.parse(result['location'])
|
208
|
+
newpath = newuri.path
|
209
|
+
result = http.get(newpath)
|
210
|
+
@output = result.body
|
211
|
+
# waiting for BLAST finished
|
212
|
+
while /Your job ID is/ =~ @output and
|
213
|
+
/Your result will be displayed here\<br\>/ =~ @output
|
214
|
+
if /This page will be reloaded automatically in\s*((\d+)\s*min\.)?\s*(\d+)\s*sec\./ =~ @output then
|
215
|
+
reloadtime = $2.to_i * 60 + $3.to_i
|
216
|
+
reloadtime = 300 if reloadtime > 300
|
217
|
+
reloadtime = 1 if reloadtime < 1
|
218
|
+
else
|
219
|
+
reloadtime = 5
|
220
|
+
end
|
221
|
+
if $VERBOSE then
|
222
|
+
$stderr.puts "waiting #{reloadtime} sec to reload #{newuri.to_s}"
|
223
|
+
end
|
224
|
+
sleep(reloadtime)
|
225
|
+
result = http.get(newpath)
|
226
|
+
@output = result.body
|
227
|
+
end
|
228
|
+
end
|
229
|
+
|
230
|
+
# workaround 2005.08.12
|
231
|
+
if /\<A +HREF=\"(http\:\/\/blast\.genome\.jp(\/tmp\/[^\"]+))\"\>Show all result\<\/A\>/i =~ @output.to_s then
|
232
|
+
result = http.get($2)
|
233
|
+
@output = result.body
|
234
|
+
txt = @output.to_s.split(/\<pre\>/)[1]
|
235
|
+
raise 'cannot understand response' unless txt
|
236
|
+
txt.sub!(/\<\/pre\>.*\z/m, '')
|
237
|
+
txt.sub!(/.*^ \-{20,}\s*/m, '')
|
238
|
+
@output = txt.gsub(/\<\;/, '<')
|
239
|
+
else
|
240
|
+
raise 'cannot understand response'
|
241
|
+
end
|
242
|
+
end
|
243
|
+
|
244
|
+
# for -m 0 (NCBI BLAST default) output, html tags are removed.
|
245
|
+
if opt_m.to_i == 0 then
|
246
|
+
#@output_bak = @output
|
247
|
+
txt = @output.gsub(/^\s*\<img +src\=\"\/Fig\/arrow\_top\.gif\"\>.+$\r?\n/, '')
|
248
|
+
txt.gsub!(/^.+\<\/form\>$/, '')
|
249
|
+
txt.gsub!(/^\<form *method\=\"POST\" name\=\"clust\_check\"\>.+$\r?\n/, '')
|
250
|
+
txt.gsub!(/\<[^\>\<]+\>/m, '')
|
251
|
+
@output = txt
|
252
|
+
end
|
253
|
+
|
254
|
+
return @output
|
255
|
+
end
|
256
|
+
|
257
|
+
end # class GenomeNet
|
258
|
+
|
259
|
+
# alias for lazy load
|
260
|
+
Genomenet = GenomeNet
|
261
|
+
|
262
|
+
end # module Bio::Blast::Remote
|
263
|
+
|
@@ -0,0 +1,220 @@
|
|
1
|
+
#
|
2
|
+
# = bio/appl/blast/ncbioptions.rb - NCBI Tools-style options parser
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>
|
5
|
+
# License:: The Ruby License
|
6
|
+
#
|
7
|
+
# $Id:$
|
8
|
+
#
|
9
|
+
# == Description
|
10
|
+
#
|
11
|
+
# Bio::Blast::NCBIOptions is a class to parse and store NCBI Tools-style
|
12
|
+
# command-line options.
|
13
|
+
# It is internally used in Bio::Blast and some other classes.
|
14
|
+
#
|
15
|
+
|
16
|
+
require 'bio/appl/blast'
|
17
|
+
require 'shellwords'
|
18
|
+
|
19
|
+
class Bio::Blast
|
20
|
+
|
21
|
+
# A class to parse and store NCBI-tools style command-line options.
|
22
|
+
# It is internally used in Bio::Blast and some other classes.
|
23
|
+
#
|
24
|
+
class NCBIOptions
|
25
|
+
|
26
|
+
# creates a new object from an array
|
27
|
+
def initialize(options = [])
|
28
|
+
#@option_pairs = []
|
29
|
+
@option_pairs = _parse_options(options)
|
30
|
+
end
|
31
|
+
|
32
|
+
# (protected) option pairs. internal use only.
|
33
|
+
attr_reader :option_pairs
|
34
|
+
protected :option_pairs
|
35
|
+
|
36
|
+
# (private) parse options from given array
|
37
|
+
def _parse_options(options)
|
38
|
+
i = 0
|
39
|
+
pairs = []
|
40
|
+
while i < options.size
|
41
|
+
opt = options[i].to_s
|
42
|
+
if m = /\A(\-.)/.match(opt) then
|
43
|
+
key = m[1]
|
44
|
+
if m.post_match.empty? then
|
45
|
+
i += 1
|
46
|
+
val = options.fetch(i) rescue ''
|
47
|
+
else
|
48
|
+
val = m.post_match
|
49
|
+
end
|
50
|
+
pairs.push([ key, val ])
|
51
|
+
elsif '-' == opt then
|
52
|
+
pairs.push [ opt ]
|
53
|
+
else
|
54
|
+
#warn "Arguments must start with \'-\'" if $VERBOSE
|
55
|
+
pairs.push [ opt ]
|
56
|
+
end
|
57
|
+
i += 1
|
58
|
+
end
|
59
|
+
pairs
|
60
|
+
end
|
61
|
+
private :_parse_options
|
62
|
+
|
63
|
+
# Normalize options.
|
64
|
+
# For two or more same options (e.g. '-p blastn -p blastp'),
|
65
|
+
# only the last option is used. (e.g. '-p blastp' for above example).
|
66
|
+
#
|
67
|
+
# Note that completely illegal options are left untouched.
|
68
|
+
#
|
69
|
+
# ---
|
70
|
+
# *Returns*:: self
|
71
|
+
def normalize!
|
72
|
+
hash = {}
|
73
|
+
newpairs = []
|
74
|
+
@option_pairs.reverse_each do |pair|
|
75
|
+
if pair.size == 2 then
|
76
|
+
key = pair[0]
|
77
|
+
unless hash[key] then
|
78
|
+
newpairs.push pair
|
79
|
+
hash[key] = pair
|
80
|
+
end
|
81
|
+
else
|
82
|
+
newpairs.push pair
|
83
|
+
end
|
84
|
+
end
|
85
|
+
newpairs.reverse!
|
86
|
+
@option_pairs = newpairs
|
87
|
+
self
|
88
|
+
end
|
89
|
+
|
90
|
+
# current options as an array of strings
|
91
|
+
def options
|
92
|
+
@option_pairs.flatten
|
93
|
+
end
|
94
|
+
|
95
|
+
# parses a string and returns a new object
|
96
|
+
def self.parse(str)
|
97
|
+
options = Shellwords.shellwords(str)
|
98
|
+
self.new(options)
|
99
|
+
end
|
100
|
+
|
101
|
+
# (private) key string to regexp
|
102
|
+
def _key_to_regexp(key)
|
103
|
+
key = key.sub(/\A\-/, '')
|
104
|
+
Regexp.new('\A\-' + Regexp.escape(key) + '\z')
|
105
|
+
end
|
106
|
+
private :_key_to_regexp
|
107
|
+
|
108
|
+
# Return the option.
|
109
|
+
# ---
|
110
|
+
# *Arguments*:
|
111
|
+
# * _key_: option name as a string, e.g. 'm', 'p', or '-m', '-p'.
|
112
|
+
# *Returns*:: String or nil
|
113
|
+
def get(key)
|
114
|
+
re = _key_to_regexp(key)
|
115
|
+
|
116
|
+
# Note: the last option is used when two or more same option exist.
|
117
|
+
value = nil
|
118
|
+
@option_pairs.reverse_each do |pair|
|
119
|
+
if re =~ pair[0] then
|
120
|
+
value = pair[1]
|
121
|
+
break
|
122
|
+
end
|
123
|
+
end
|
124
|
+
return value
|
125
|
+
end
|
126
|
+
|
127
|
+
# Delete the given option.
|
128
|
+
# ---
|
129
|
+
# *Arguments*:
|
130
|
+
# * _key_: option name as a string, e.g. 'm', 'p', or '-m', '-p'.
|
131
|
+
# *Returns*:: String or nil
|
132
|
+
def delete(key)
|
133
|
+
re = _key_to_regexp(key)
|
134
|
+
|
135
|
+
# Note: the last option is used for return value
|
136
|
+
# when two or more same option exist.
|
137
|
+
oldvalue = nil
|
138
|
+
@option_pairs = @option_pairs.delete_if do |pair|
|
139
|
+
if re =~ pair[0] then
|
140
|
+
oldvalue = pair[1]
|
141
|
+
true
|
142
|
+
else
|
143
|
+
false
|
144
|
+
end
|
145
|
+
end
|
146
|
+
return oldvalue
|
147
|
+
end
|
148
|
+
|
149
|
+
# Sets the option to given value.
|
150
|
+
#
|
151
|
+
# For example, if you want to set '-p blastall' option,
|
152
|
+
# obj.set('p', 'blastall')
|
153
|
+
# or
|
154
|
+
# obj.set('-p', 'blastall')
|
155
|
+
# (above two are equivalent).
|
156
|
+
#
|
157
|
+
# ---
|
158
|
+
# *Arguments*:
|
159
|
+
# * _key_: option name as a string, e.g. 'm', 'p'.
|
160
|
+
# * _value_: value as a string, e.g. '7', 'blastp'.
|
161
|
+
# *Returns*:: previous value; String or nil
|
162
|
+
def set(key, value)
|
163
|
+
re = _key_to_regexp(key)
|
164
|
+
oldvalue = nil
|
165
|
+
flag = false
|
166
|
+
# Note: only the last options is modified for multiple same options.
|
167
|
+
@option_pairs.reverse_each do |pair|
|
168
|
+
if re =~ pair[0] then
|
169
|
+
oldvalue = pair[1]
|
170
|
+
pair[1] = value
|
171
|
+
flag = true
|
172
|
+
break
|
173
|
+
end
|
174
|
+
end
|
175
|
+
unless flag then
|
176
|
+
key = "-#{key}" unless key[0, 1] == '-'
|
177
|
+
@option_pairs.push([ key, value ])
|
178
|
+
end
|
179
|
+
oldvalue
|
180
|
+
end
|
181
|
+
|
182
|
+
# Adds options from given array.
|
183
|
+
# Note that existing options will also be normalized.
|
184
|
+
# ---
|
185
|
+
# *Arguments*:
|
186
|
+
# * _options_: options as an Array of String objects.
|
187
|
+
# *Returns*:: self
|
188
|
+
def add_options(options)
|
189
|
+
@option_pairs.concat _parse_options(options)
|
190
|
+
self.normalize!
|
191
|
+
self
|
192
|
+
end
|
193
|
+
|
194
|
+
# If self == other, returns true. Otherwise, returns false.
|
195
|
+
def ==(other)
|
196
|
+
return true if super(other)
|
197
|
+
begin
|
198
|
+
oopts = other.options
|
199
|
+
rescue
|
200
|
+
return false
|
201
|
+
end
|
202
|
+
return self.options == oopts
|
203
|
+
end
|
204
|
+
|
205
|
+
# Returns an array for command-line options.
|
206
|
+
# prior_options are preferred to be used.
|
207
|
+
def make_command_line_options(prior_options = [])
|
208
|
+
newopts = self.class.new(self.options)
|
209
|
+
#newopts.normalize!
|
210
|
+
prior_pairs = _parse_options(prior_options)
|
211
|
+
prior_pairs.each do |pair|
|
212
|
+
newopts.delete(pair[0])
|
213
|
+
end
|
214
|
+
newopts.option_pairs[0, 0] = prior_pairs
|
215
|
+
newopts.options
|
216
|
+
end
|
217
|
+
|
218
|
+
end #class NCBIOptions
|
219
|
+
|
220
|
+
end #class Bio::Blast
|