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 +1,374 @@
|
|
1
|
+
#
|
2
|
+
# = bio/appl/iprscan/report.rb - a class for iprscan output.
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2006
|
5
|
+
# Mitsuteru C. Nakao <mn@kazusa.or.jp>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: report.rb,v 1.9 2007/07/18 11:11:57 nakao Exp $
|
9
|
+
#
|
10
|
+
# == Report classes for the iprscan program.
|
11
|
+
#
|
12
|
+
|
13
|
+
|
14
|
+
module Bio
|
15
|
+
|
16
|
+
class Iprscan
|
17
|
+
|
18
|
+
# = DESCRIPTION
|
19
|
+
# Class for InterProScan report. It is used to parse results and reformat
|
20
|
+
# results from (raw|xml|txt) into (html, xml, ebihtml, txt, gff3) format.
|
21
|
+
#
|
22
|
+
# See ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/README.html
|
23
|
+
#
|
24
|
+
# == USAGE
|
25
|
+
# # Read a marged.txt and split each entry.
|
26
|
+
# Bio::Iprscan::Report.parse_txt(File.read("marged.txt")) do |report|
|
27
|
+
# report.query_id
|
28
|
+
# report.matches.size
|
29
|
+
# report.matches.each do |match|
|
30
|
+
# match.ipr_id #=> 'IPR...'
|
31
|
+
# match.ipr_description
|
32
|
+
# match.method
|
33
|
+
# match.accession
|
34
|
+
# match.description
|
35
|
+
# match.match_start
|
36
|
+
# match.match_end
|
37
|
+
# match.evalue
|
38
|
+
# end
|
39
|
+
# # report.to_gff3
|
40
|
+
# # report.to_html
|
41
|
+
# end
|
42
|
+
#
|
43
|
+
# Bio::Iprscan::Report.parse_raw(File.read("marged.raw")) do |report|
|
44
|
+
# report.class #=> Bio::Iprscan::Report
|
45
|
+
# end
|
46
|
+
#
|
47
|
+
class Report
|
48
|
+
# Entry delimiter pattern.
|
49
|
+
RS = DELIMITER = "\n\/\/\n"
|
50
|
+
|
51
|
+
# Qeury sequence name (entry_id).
|
52
|
+
attr_accessor :query_id
|
53
|
+
alias :entry_id :query_id
|
54
|
+
|
55
|
+
# Qeury sequence length.
|
56
|
+
attr_accessor :query_length
|
57
|
+
|
58
|
+
# CRC64 checksum of query sequence.
|
59
|
+
attr_accessor :crc64
|
60
|
+
|
61
|
+
# Matched InterPro motifs in Hash. Each InterPro motif have :name,
|
62
|
+
# :definition, :accession and :motifs keys. And :motifs key contains
|
63
|
+
# motifs in Array. Each motif have :method, :accession, :definition,
|
64
|
+
# :score, :location_from and :location_to keys.
|
65
|
+
attr_accessor :matches
|
66
|
+
|
67
|
+
# == USAGE
|
68
|
+
# Bio::Iprscan::Report.parse_raw(File.open("merged.raw")) do |report|
|
69
|
+
# report
|
70
|
+
# end
|
71
|
+
#
|
72
|
+
def self.parse_raw(io)
|
73
|
+
entry = ''
|
74
|
+
while line = io.gets
|
75
|
+
if entry != '' and entry.split("\t").first == line.split("\t").first
|
76
|
+
entry << line
|
77
|
+
elsif entry != ''
|
78
|
+
yield Bio::Iprscan::Report.parse_raw_entry(entry)
|
79
|
+
entry = line
|
80
|
+
else
|
81
|
+
entry << line
|
82
|
+
end
|
83
|
+
end
|
84
|
+
yield Bio::Iprscan::Report.parse_raw_entry(entry) if entry != ''
|
85
|
+
end
|
86
|
+
|
87
|
+
# Parser method for a raw formated entry. Retruns a Bio::Iprscan::Report
|
88
|
+
# object.
|
89
|
+
def self.parse_raw_entry(str)
|
90
|
+
report = self.new
|
91
|
+
str.split(/\n/).each do |line|
|
92
|
+
line = line.split("\t")
|
93
|
+
report.matches << Match.new(:query_id => line[0],
|
94
|
+
:crc64 => line[1],
|
95
|
+
:query_length => line[2].to_i,
|
96
|
+
:method => line[3],
|
97
|
+
:accession => line[4],
|
98
|
+
:description => line[5],
|
99
|
+
:match_start => line[6].to_i,
|
100
|
+
:match_end => line[7].to_i,
|
101
|
+
:evalue => line[8],
|
102
|
+
:status => line[9],
|
103
|
+
:date => line[10])
|
104
|
+
if line[11]
|
105
|
+
report.matches.last.ipr_id = line[11]
|
106
|
+
report.matches.last.ipr_description = line[12]
|
107
|
+
end
|
108
|
+
report.matches.last.go_terms = line[13].scan(/(\w+ \w+\:.+? \(GO:\d+\))/).flatten if line[13]
|
109
|
+
end
|
110
|
+
report.query_id = report.matches.first.query_id
|
111
|
+
report.query_length = report.matches.first.query_length
|
112
|
+
report
|
113
|
+
end
|
114
|
+
|
115
|
+
|
116
|
+
|
117
|
+
# Parser method for a xml formated entry. Retruns a Bio::Iprscan::Report
|
118
|
+
# object.
|
119
|
+
# def self.parse_xml(str)
|
120
|
+
# end
|
121
|
+
|
122
|
+
# Splits the entry stream.
|
123
|
+
#
|
124
|
+
# == Usage
|
125
|
+
#
|
126
|
+
# Bio::Iprscan::Report.reports_txt(File.open("merged.txt")) do |report|
|
127
|
+
# report.class #=> Bio::Iprscan::Report
|
128
|
+
# end
|
129
|
+
#
|
130
|
+
def self.parse_txt(io)
|
131
|
+
io.each("\n\nSequence") do |entry|
|
132
|
+
if entry =~ /Sequence$/
|
133
|
+
entry = entry.sub(/Sequence$/, '')
|
134
|
+
end
|
135
|
+
unless entry =~ /^Sequence/
|
136
|
+
entry = 'Sequence' + entry
|
137
|
+
end
|
138
|
+
yield self.parse_txt_entry(entry)
|
139
|
+
end
|
140
|
+
end
|
141
|
+
|
142
|
+
|
143
|
+
|
144
|
+
# Parser method for a txt formated entry. Returns a Bio::Iprscan::Report
|
145
|
+
# object.
|
146
|
+
#
|
147
|
+
def self.parse_txt_entry(str)
|
148
|
+
unless str =~ /^Sequence /
|
149
|
+
raise ArgumentError, "Invalid format: \n\n#{str}"
|
150
|
+
end
|
151
|
+
header, *matches = str.split(/\n\n/)
|
152
|
+
report = self.new
|
153
|
+
report.query_id = if header =~ /Sequence \"(.+)\" / then $1 else '' end
|
154
|
+
report.query_length = if header =~ /length: (\d+) aa./ then $1.to_i else nil end
|
155
|
+
report.crc64 = if header =~ /crc64 checksum: (\S+) / then $1 else nil end
|
156
|
+
ipr_line = ''
|
157
|
+
go_annotation = ''
|
158
|
+
matches.each do |m|
|
159
|
+
m = m.split(/\n/).map {|x| x.split(/ +/) }
|
160
|
+
m.each do |match|
|
161
|
+
case match[0]
|
162
|
+
when 'method'
|
163
|
+
when /(Molecular Function|Cellular Component|Biological Process):/
|
164
|
+
go_annotation = match[0].scan(/([MCB]\w+ \w+): (\S.+?\S) \((GO:\d+)\),*/)
|
165
|
+
when 'InterPro'
|
166
|
+
ipr_line = match
|
167
|
+
else
|
168
|
+
pos_scores = match[3].scan(/(\S)\[(\d+)-(\d+)\] (\S+) */)
|
169
|
+
pos_scores.each do |pos_score|
|
170
|
+
report.matches << Match.new(:ipr_id => ipr_line[1],
|
171
|
+
:ipr_description => ipr_line[2],
|
172
|
+
:method => match[0],
|
173
|
+
:accession => match[1],
|
174
|
+
:description => match[2],
|
175
|
+
:evalue => pos_score[3],
|
176
|
+
:status => pos_score[0],
|
177
|
+
:match_start => pos_score[1].to_i,
|
178
|
+
:match_end => pos_score[2].to_i,
|
179
|
+
:go_terms => go_annotation)
|
180
|
+
end
|
181
|
+
end
|
182
|
+
end
|
183
|
+
end
|
184
|
+
return report
|
185
|
+
end
|
186
|
+
|
187
|
+
|
188
|
+
# Splits entry stream.
|
189
|
+
#
|
190
|
+
# == Usage
|
191
|
+
# Bio::Iprscan::Report.parse_ptxt(File.open("merged.txt")) do |report|
|
192
|
+
# report
|
193
|
+
# end
|
194
|
+
def self.parse_ptxt(io)
|
195
|
+
io.each("\n\/\/\n") do |entry|
|
196
|
+
yield self.parse_ptxt_entry(entry)
|
197
|
+
end
|
198
|
+
end
|
199
|
+
|
200
|
+
# Parser method for a pseudo-txt formated entry. Retruns a Bio::Iprscan::Report
|
201
|
+
# object.
|
202
|
+
#
|
203
|
+
# == Usage
|
204
|
+
#
|
205
|
+
# File.read("marged.txt").each(Bio::Iprscan::Report::RS) do |e|
|
206
|
+
# report = Bio::Iprscan::Report.parse_ptxt_entry(e)
|
207
|
+
# end
|
208
|
+
#
|
209
|
+
def self.parse_ptxt_entry(str)
|
210
|
+
report = self.new
|
211
|
+
ipr_line = ''
|
212
|
+
str.split(/\n/).each do |line|
|
213
|
+
line = line.split("\t")
|
214
|
+
if line.size == 2
|
215
|
+
report.query_id = line[0]
|
216
|
+
report.query_length = line[1].to_i
|
217
|
+
elsif line.first == '//'
|
218
|
+
elsif line.first == 'InterPro'
|
219
|
+
ipr_line = line
|
220
|
+
else
|
221
|
+
startp, endp = line[4].split("-")
|
222
|
+
report.matches << Match.new(:ipr_id => ipr_line[1],
|
223
|
+
:ipr_description => ipr_line[2],
|
224
|
+
:method => line[0],
|
225
|
+
:accession => line[1],
|
226
|
+
:description => line[2],
|
227
|
+
:evalue => line[3],
|
228
|
+
:match_start => startp.to_i,
|
229
|
+
:match_end => endp.to_i)
|
230
|
+
end
|
231
|
+
end
|
232
|
+
report
|
233
|
+
end
|
234
|
+
|
235
|
+
#
|
236
|
+
def initialize
|
237
|
+
@query_id = nil
|
238
|
+
@query_length = nil
|
239
|
+
@crc64 = nil
|
240
|
+
@matches = []
|
241
|
+
end
|
242
|
+
|
243
|
+
|
244
|
+
# Output interpro matches in the format_type.
|
245
|
+
def output(format_type)
|
246
|
+
case format_type
|
247
|
+
when 'raw', :raw
|
248
|
+
format_raw
|
249
|
+
else
|
250
|
+
raise NameError, "Invalid format_type."
|
251
|
+
end
|
252
|
+
end
|
253
|
+
|
254
|
+
# def format_html
|
255
|
+
# end
|
256
|
+
|
257
|
+
# def format_xml
|
258
|
+
# end
|
259
|
+
|
260
|
+
# def format_ebixml
|
261
|
+
# end
|
262
|
+
|
263
|
+
# def format_txt
|
264
|
+
# end
|
265
|
+
|
266
|
+
def format_raw
|
267
|
+
@matches.map { |match|
|
268
|
+
[self.query_id,
|
269
|
+
self.crc64,
|
270
|
+
self.query_length,
|
271
|
+
match.method_name,
|
272
|
+
match.accession,
|
273
|
+
match.description,
|
274
|
+
match.match_start,
|
275
|
+
match.match_end,
|
276
|
+
match.evalue,
|
277
|
+
match.status,
|
278
|
+
match.date,
|
279
|
+
match.ipr_id,
|
280
|
+
match.ipr_description,
|
281
|
+
match.go_terms.map {|x| x[0] + ': ' + x[1] + ' (' + x[2] + ')' }.join(', ')
|
282
|
+
].join("\t")
|
283
|
+
}.join("\n")
|
284
|
+
end
|
285
|
+
|
286
|
+
# def format_gff3
|
287
|
+
# end
|
288
|
+
|
289
|
+
|
290
|
+
# Returns a Hash (key as an Interpro ID and value as a Match).
|
291
|
+
#
|
292
|
+
# report.to_hash.each do |ipr_id, matches|
|
293
|
+
# matches.each do |match|
|
294
|
+
# report.matches.ipr_id == ipr_id #=> true
|
295
|
+
# end
|
296
|
+
# end
|
297
|
+
#
|
298
|
+
def to_hash
|
299
|
+
unless @ipr_ids
|
300
|
+
@ipr_ids = {}
|
301
|
+
@matches.each_with_index do |match, i|
|
302
|
+
@ipr_ids[match.ipr_id] ||= []
|
303
|
+
@ipr_ids[match.ipr_id] << match
|
304
|
+
end
|
305
|
+
return @ipr_ids
|
306
|
+
else
|
307
|
+
return @ipr_ids
|
308
|
+
end
|
309
|
+
end
|
310
|
+
|
311
|
+
|
312
|
+
|
313
|
+
# == Description
|
314
|
+
# Container class for InterProScan matches.
|
315
|
+
#
|
316
|
+
# == Usage
|
317
|
+
# match = Match.new(:query_id => ...)
|
318
|
+
#
|
319
|
+
# match.ipr_id = 'IPR001234'
|
320
|
+
# match.ipr_id #=> 'IPR001234'
|
321
|
+
#
|
322
|
+
class Match
|
323
|
+
def initialize(hash)
|
324
|
+
@data = Hash.new
|
325
|
+
hash.each do |key, value|
|
326
|
+
@data[key.to_sym] = value
|
327
|
+
end
|
328
|
+
end
|
329
|
+
|
330
|
+
# Date for computation.
|
331
|
+
def date; @data[:date]; end
|
332
|
+
# CRC64 checksum of query sequence.
|
333
|
+
def crc64; @data[:crc64]; end
|
334
|
+
# E-value of the match
|
335
|
+
def evalue; @data[:evalue]; end
|
336
|
+
# Status of the match (T for true / M for marginal).
|
337
|
+
def status; @data[:status]; end
|
338
|
+
# the corresponding InterPro entry (if any).
|
339
|
+
def ipr_id; @data[:ipr_id]; end
|
340
|
+
# the length of the sequence in AA.
|
341
|
+
def length; @data[:length]; end
|
342
|
+
# the analysis method launched.
|
343
|
+
def method_name; @data[:method]; end
|
344
|
+
# the Gene Ontology description for the InterPro entry, in "Aspect :term (ID)" format.
|
345
|
+
def go_terms; @data[:go_terms]; end
|
346
|
+
# Id of the input sequence.
|
347
|
+
def query_id; @data[:query_id]; end
|
348
|
+
# the end of the domain match.
|
349
|
+
def match_end; @data[:match_end]; end
|
350
|
+
# the database members entry for this match.
|
351
|
+
def accession; @data[:accession]; end
|
352
|
+
# the database mambers description for this match.
|
353
|
+
def description; @data[:description]; end
|
354
|
+
# the start of the domain match.
|
355
|
+
def match_start; @data[:match_start]; end
|
356
|
+
# the descriotion of the InterPro entry.
|
357
|
+
def ipr_odescription; @data[:ipr_description]; end
|
358
|
+
|
359
|
+
def method_missing(name, arg = nil)
|
360
|
+
if arg
|
361
|
+
name = name.to_s.sub(/=$/, '')
|
362
|
+
@data[name.to_sym] = arg
|
363
|
+
else
|
364
|
+
@data[name.to_sym]
|
365
|
+
end
|
366
|
+
end
|
367
|
+
|
368
|
+
end # class Match
|
369
|
+
|
370
|
+
end # class Report
|
371
|
+
|
372
|
+
end # class Iprscan
|
373
|
+
|
374
|
+
end # module Bio
|
@@ -0,0 +1,259 @@
|
|
1
|
+
#
|
2
|
+
# = bio/appl/mafft.rb - MAFFT wrapper class
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
|
5
|
+
# License:: The Ruby License
|
6
|
+
#
|
7
|
+
# $Id: mafft.rb,v 1.18 2007/07/16 12:27:29 ngoto Exp $
|
8
|
+
#
|
9
|
+
# Bio::MAFFT is a wrapper class to execute MAFFT.
|
10
|
+
# MAFFT is a very fast multiple sequence alignment software.
|
11
|
+
#
|
12
|
+
# = Important Notes
|
13
|
+
#
|
14
|
+
# Though Bio::MAFFT class currently supports only MAFFT version 3,
|
15
|
+
# you can use MAFFT version 5 because the class is a wrapper class.
|
16
|
+
#
|
17
|
+
# == References
|
18
|
+
#
|
19
|
+
# * K. Katoh, K. Misawa, K. Kuma and T. Miyata.
|
20
|
+
# MAFFT: a novel method for rapid multiple sequence alignment based
|
21
|
+
# on fast Fourier transform. Nucleic Acids Res. 30: 3059-3066, 2002.
|
22
|
+
# http://nar.oupjournals.org/cgi/content/abstract/30/14/3059
|
23
|
+
# * http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/
|
24
|
+
#
|
25
|
+
|
26
|
+
require 'tempfile'
|
27
|
+
|
28
|
+
require 'bio/command'
|
29
|
+
|
30
|
+
require 'bio/db/fasta'
|
31
|
+
require 'bio/io/flatfile'
|
32
|
+
|
33
|
+
module Bio
|
34
|
+
|
35
|
+
# Bio::MAFFT is a wrapper class to execute MAFFT.
|
36
|
+
# MAFFT is a very fast multiple sequence alignment software.
|
37
|
+
#
|
38
|
+
# Though Bio::MAFFT class currently supports only MAFFT version 3,
|
39
|
+
# you can use MAFFT version 5 because the class is a wrapper class.
|
40
|
+
class MAFFT
|
41
|
+
|
42
|
+
autoload :Report, 'bio/appl/mafft/report'
|
43
|
+
|
44
|
+
# Creates a new alignment factory.
|
45
|
+
# When +n+ is a number (1,2,3, ...), performs 'fftns n'.
|
46
|
+
# When +n+ is :i or 'i', performs 'fftnsi'.
|
47
|
+
def self.fftns(n = nil)
|
48
|
+
opt = []
|
49
|
+
if n.to_s == 'i' then
|
50
|
+
self.new2(nil, 'fftnsi', *opt)
|
51
|
+
else
|
52
|
+
opt << n.to_s if n
|
53
|
+
self.new2(nil, 'fftns', *opt)
|
54
|
+
end
|
55
|
+
end
|
56
|
+
|
57
|
+
# Creates a new alignment factory.
|
58
|
+
# Performs 'fftnsi'.
|
59
|
+
def self.fftnsi
|
60
|
+
self.new2(nil, 'fftnsi')
|
61
|
+
end
|
62
|
+
|
63
|
+
# Creates a new alignment factory.
|
64
|
+
# When +n+ is a number (1,2,3, ...), performs 'nwns n'.
|
65
|
+
# When +n+ is :i or 'i', performs 'nwnsi'.
|
66
|
+
# In both case, if all_positive is true, add option '--all-positive'.
|
67
|
+
def self.nwns(n = nil, ap = nil)
|
68
|
+
opt = []
|
69
|
+
opt << '--all-positive' if ap
|
70
|
+
if n.to_s == 'i' then
|
71
|
+
self.new2(nil, 'nwnsi', *opt)
|
72
|
+
else
|
73
|
+
opt << n.to_s if n
|
74
|
+
self.new2(nil, 'nwns', *opt)
|
75
|
+
end
|
76
|
+
end
|
77
|
+
|
78
|
+
# Creates a new alignment factory.
|
79
|
+
# Performs 'nwnsi'.
|
80
|
+
# If +all_positive+ is true, add option '--all-positive'.
|
81
|
+
def self.nwnsi(all_positive = nil)
|
82
|
+
opt = []
|
83
|
+
opt << '--all-positive' if all_positive
|
84
|
+
self.new2(nil, 'nwnsi', *opt)
|
85
|
+
end
|
86
|
+
|
87
|
+
# Creates a new alignment factory.
|
88
|
+
# Performs 'nwns --all-positive n' or 'nwnsi --all-positive'.
|
89
|
+
# Same as Bio::MAFFT.nwap(n, true).
|
90
|
+
def self.nwap(n = nil)
|
91
|
+
self.nwns(n, true)
|
92
|
+
end
|
93
|
+
|
94
|
+
# Creates a new alignment factory.
|
95
|
+
# +dir+ is the path of the MAFFT program.
|
96
|
+
# +prog+ is the name of the program.
|
97
|
+
# +opt+ is options of the program.
|
98
|
+
def self.new2(dir, prog, *opt)
|
99
|
+
if dir then
|
100
|
+
prog = File.join(dir, prog)
|
101
|
+
end
|
102
|
+
self.new(prog, opt)
|
103
|
+
end
|
104
|
+
|
105
|
+
# Creates a new alignment factory.
|
106
|
+
# +program+ is the name of the program.
|
107
|
+
# +opt+ is options of the program.
|
108
|
+
def initialize(program = 'mafft', opt = [])
|
109
|
+
@program = program
|
110
|
+
@options = opt
|
111
|
+
@command = nil
|
112
|
+
@output = nil
|
113
|
+
@report = nil
|
114
|
+
@data_stdout = nil
|
115
|
+
@exit_status = nil
|
116
|
+
end
|
117
|
+
|
118
|
+
# program name (usually 'mafft' in UNIX)
|
119
|
+
attr_accessor :program
|
120
|
+
|
121
|
+
# options
|
122
|
+
attr_accessor :options
|
123
|
+
|
124
|
+
# option is deprecated. Instead, please use options.
|
125
|
+
def option
|
126
|
+
warn "Bio::MAFFT#option is deprecated. Please use options."
|
127
|
+
options
|
128
|
+
end
|
129
|
+
|
130
|
+
# Shows last command-line string. Returns nil or an array of String.
|
131
|
+
# Note that filenames described in the command-line may already
|
132
|
+
# be removed because they are temporary files.
|
133
|
+
attr_reader :command
|
134
|
+
|
135
|
+
#---
|
136
|
+
# last message to STDERR when executing the program.
|
137
|
+
#attr_reader :log
|
138
|
+
#+++
|
139
|
+
|
140
|
+
#log is deprecated (no replacement) and returns empty string.
|
141
|
+
def log
|
142
|
+
warn "Bio::MAFFT#log is deprecated (no replacement) and returns empty string."
|
143
|
+
''
|
144
|
+
end
|
145
|
+
|
146
|
+
# Shows latest raw alignment result.
|
147
|
+
# Return a string. (Changed in bioruby-1.1.0).
|
148
|
+
# Compatibility note:
|
149
|
+
# If you want an array of Bio::FastaFormat instances,
|
150
|
+
# you should use report.data instead.
|
151
|
+
attr_reader :output
|
152
|
+
|
153
|
+
# Shows last alignment result (instance of Bio::MAFFT::Report class)
|
154
|
+
# performed by the factory.
|
155
|
+
attr_reader :report
|
156
|
+
|
157
|
+
# Last exit status
|
158
|
+
attr_reader :exit_status
|
159
|
+
|
160
|
+
# Last output to the stdout.
|
161
|
+
attr_accessor :data_stdout
|
162
|
+
|
163
|
+
# Clear the internal data and status, except program and options.
|
164
|
+
def reset
|
165
|
+
@command = nil
|
166
|
+
@output = nil
|
167
|
+
@report = nil
|
168
|
+
@exit_status = nil
|
169
|
+
@data_stdout = nil
|
170
|
+
end
|
171
|
+
|
172
|
+
# Executes the program.
|
173
|
+
# If +seqs+ is not nil, perform alignment for seqs.
|
174
|
+
# If +seqs+ is nil, simply executes the program.
|
175
|
+
#
|
176
|
+
# Compatibility note: When seqs is nil,
|
177
|
+
# returns true if the program exits normally, and
|
178
|
+
# returns false if the program exits abnormally.
|
179
|
+
def query(seqs)
|
180
|
+
if seqs then
|
181
|
+
query_align(seqs)
|
182
|
+
else
|
183
|
+
exec_local(@options)
|
184
|
+
@exit_status.exitstatus == 0 ? true : false
|
185
|
+
end
|
186
|
+
end
|
187
|
+
|
188
|
+
# Note that this method will be renamed to query_alignment.
|
189
|
+
#
|
190
|
+
# Performs alignment for seqs.
|
191
|
+
# +seqs+ should be Bio::Alignment or Array of sequences or nil.
|
192
|
+
#
|
193
|
+
# Compatibility Note: arg is deprecated and ignored.
|
194
|
+
def query_align(seqs, *arg)
|
195
|
+
if arg.size > 0 then
|
196
|
+
warn '2nd and other arguments of Bio::MAFFT#query_align is ignored'
|
197
|
+
end
|
198
|
+
unless seqs.is_a?(Bio::Alignment)
|
199
|
+
seqs = Bio::Alignment.new(seqs)
|
200
|
+
end
|
201
|
+
query_string(seqs.output_fasta(:width => 70))
|
202
|
+
end
|
203
|
+
|
204
|
+
# Performs alignment for seqs.
|
205
|
+
# +seqs+ should be Bio::Alignment or Array of sequences or nil.
|
206
|
+
def query_alignment(seqs)
|
207
|
+
query_align(seqs)
|
208
|
+
end
|
209
|
+
|
210
|
+
# Performs alignment for +str+.
|
211
|
+
# Str should be a string that can be recognized by the program.
|
212
|
+
#
|
213
|
+
# Compatibility Note: arg is deprecated and ignored.
|
214
|
+
def query_string(str, *arg)
|
215
|
+
if arg.size > 0 then
|
216
|
+
warn '2nd and other arguments of Bio::MAFFT#query_string is ignored'
|
217
|
+
end
|
218
|
+
begin
|
219
|
+
tf_in = Tempfile.open('align')
|
220
|
+
tf_in.print str
|
221
|
+
ensure
|
222
|
+
tf_in.close(false)
|
223
|
+
end
|
224
|
+
r = query_by_filename(tf_in.path, *arg)
|
225
|
+
tf_in.close(true)
|
226
|
+
r
|
227
|
+
end
|
228
|
+
|
229
|
+
# Performs alignment of sequences in the file named +fn+.
|
230
|
+
#
|
231
|
+
# Compatibility Note: 2nd argument (seqtype) is deprecated and ignored.
|
232
|
+
def query_by_filename(fn, *arg)
|
233
|
+
if arg.size > 0 then
|
234
|
+
warn '2nd argument of Bio::MAFFT#query_filename is ignored'
|
235
|
+
end
|
236
|
+
opt = @options + [ fn ]
|
237
|
+
exec_local(opt)
|
238
|
+
@report = Report.new(@output)
|
239
|
+
@report
|
240
|
+
end
|
241
|
+
|
242
|
+
private
|
243
|
+
# Executes a program in the local machine.
|
244
|
+
def exec_local(opt)
|
245
|
+
@command = [ @program, *opt ]
|
246
|
+
#STDERR.print "DEBUG: ", @command.join(" "), "\n"
|
247
|
+
@data_stdout = nil
|
248
|
+
@exit_status = nil
|
249
|
+
Bio::Command.call_command(@command) do |io|
|
250
|
+
io.close_write
|
251
|
+
@data_stdout = io.read
|
252
|
+
end
|
253
|
+
@output = @data_stdout
|
254
|
+
@exit_status = $?
|
255
|
+
end
|
256
|
+
|
257
|
+
end #class MAFFT
|
258
|
+
end #module Bio
|
259
|
+
|