wwood-bioruby 1.2.11
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- data/README.rdoc +205 -0
- data/README_DEV.rdoc +285 -0
- data/VERSION.yml +4 -0
- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +293 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/lib/bio.rb +306 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +505 -0
- data/lib/bio/appl/blast/ddbj.rb +142 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/genomenet.rb +263 -0
- data/lib/bio/appl/blast/ncbioptions.rb +220 -0
- data/lib/bio/appl/blast/remote.rb +105 -0
- data/lib/bio/appl/blast/report.rb +767 -0
- data/lib/bio/appl/blast/rexml.rb +144 -0
- data/lib/bio/appl/blast/rpsblast.rb +277 -0
- data/lib/bio/appl/blast/wublast.rb +635 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blat/report.rb +530 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta.rb +235 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/gcg/msf.rb +212 -0
- data/lib/bio/appl/gcg/seq.rb +195 -0
- data/lib/bio/appl/genscan/report.rb +552 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/hmmer/report.rb +683 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/paml/baseml.rb +95 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/codeml.rb +242 -0
- data/lib/bio/appl/paml/codeml/rates.rb +67 -0
- data/lib/bio/appl/paml/codeml/report.rb +67 -0
- data/lib/bio/appl/paml/common.rb +348 -0
- data/lib/bio/appl/paml/common_report.rb +38 -0
- data/lib/bio/appl/paml/yn00.rb +103 -0
- data/lib/bio/appl/paml/yn00/report.rb +32 -0
- data/lib/bio/appl/phylip/alignment.rb +133 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/psort/report.rb +542 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +124 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sosui/report.rb +151 -0
- data/lib/bio/appl/spidey/report.rb +593 -0
- data/lib/bio/appl/targetp/report.rb +267 -0
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +231 -0
- data/lib/bio/command.rb +593 -0
- data/lib/bio/compat/features.rb +157 -0
- data/lib/bio/compat/references.rb +128 -0
- data/lib/bio/data/aa.rb +353 -0
- data/lib/bio/data/codontable.rb +722 -0
- data/lib/bio/data/na.rb +223 -0
- data/lib/bio/db.rb +329 -0
- data/lib/bio/db/aaindex.rb +357 -0
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +67 -0
- data/lib/bio/db/biosql/sequence.rb +508 -0
- data/lib/bio/db/embl/common.rb +352 -0
- data/lib/bio/db/embl/embl.rb +500 -0
- data/lib/bio/db/embl/embl_to_biosequence.rb +85 -0
- data/lib/bio/db/embl/format_embl.rb +190 -0
- data/lib/bio/db/embl/sptr.rb +1283 -0
- data/lib/bio/db/embl/swissprot.rb +42 -0
- data/lib/bio/db/embl/trembl.rb +41 -0
- data/lib/bio/db/embl/uniprot.rb +42 -0
- data/lib/bio/db/fantom.rb +597 -0
- data/lib/bio/db/fasta.rb +410 -0
- data/lib/bio/db/fasta/defline.rb +532 -0
- data/lib/bio/db/fasta/fasta_to_biosequence.rb +63 -0
- data/lib/bio/db/fasta/format_fasta.rb +97 -0
- data/lib/bio/db/genbank/common.rb +307 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/format_genbank.rb +187 -0
- data/lib/bio/db/genbank/genbank.rb +250 -0
- data/lib/bio/db/genbank/genbank_to_biosequence.rb +86 -0
- data/lib/bio/db/genbank/genpept.rb +60 -0
- data/lib/bio/db/genbank/refseq.rb +18 -0
- data/lib/bio/db/gff.rb +1846 -0
- data/lib/bio/db/go.rb +481 -0
- data/lib/bio/db/kegg/brite.rb +41 -0
- data/lib/bio/db/kegg/compound.rb +131 -0
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +148 -0
- data/lib/bio/db/kegg/expression.rb +155 -0
- data/lib/bio/db/kegg/genes.rb +263 -0
- data/lib/bio/db/kegg/genome.rb +241 -0
- data/lib/bio/db/kegg/glycan.rb +166 -0
- data/lib/bio/db/kegg/keggtab.rb +357 -0
- data/lib/bio/db/kegg/kgml.rb +256 -0
- data/lib/bio/db/kegg/orthology.rb +136 -0
- data/lib/bio/db/kegg/reaction.rb +82 -0
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +107 -0
- data/lib/bio/db/medline.rb +326 -0
- data/lib/bio/db/nbrf.rb +191 -0
- data/lib/bio/db/newick.rb +658 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +29 -0
- data/lib/bio/db/pdb/atom.rb +77 -0
- data/lib/bio/db/pdb/chain.rb +210 -0
- data/lib/bio/db/pdb/chemicalcomponent.rb +224 -0
- data/lib/bio/db/pdb/model.rb +148 -0
- data/lib/bio/db/pdb/pdb.rb +1911 -0
- data/lib/bio/db/pdb/residue.rb +176 -0
- data/lib/bio/db/pdb/utils.rb +399 -0
- data/lib/bio/db/prosite.rb +597 -0
- data/lib/bio/db/rebase.rb +456 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/db/url.rb +42 -0
- data/lib/bio/feature.rb +139 -0
- data/lib/bio/io/biosql/biodatabase.rb +64 -0
- data/lib/bio/io/biosql/bioentry.rb +29 -0
- data/lib/bio/io/biosql/bioentry_dbxref.rb +11 -0
- data/lib/bio/io/biosql/bioentry_path.rb +12 -0
- data/lib/bio/io/biosql/bioentry_qualifier_value.rb +10 -0
- data/lib/bio/io/biosql/bioentry_reference.rb +10 -0
- data/lib/bio/io/biosql/bioentry_relationship.rb +10 -0
- data/lib/bio/io/biosql/biosequence.rb +11 -0
- data/lib/bio/io/biosql/comment.rb +7 -0
- data/lib/bio/io/biosql/config/database.yml +20 -0
- data/lib/bio/io/biosql/dbxref.rb +13 -0
- data/lib/bio/io/biosql/dbxref_qualifier_value.rb +12 -0
- data/lib/bio/io/biosql/location.rb +32 -0
- data/lib/bio/io/biosql/location_qualifier_value.rb +11 -0
- data/lib/bio/io/biosql/ontology.rb +10 -0
- data/lib/bio/io/biosql/reference.rb +9 -0
- data/lib/bio/io/biosql/seqfeature.rb +32 -0
- data/lib/bio/io/biosql/seqfeature_dbxref.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_path.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_qualifier_value.rb +20 -0
- data/lib/bio/io/biosql/seqfeature_relationship.rb +11 -0
- data/lib/bio/io/biosql/taxon.rb +12 -0
- data/lib/bio/io/biosql/taxon_name.rb +9 -0
- data/lib/bio/io/biosql/term.rb +27 -0
- data/lib/bio/io/biosql/term_dbxref.rb +11 -0
- data/lib/bio/io/biosql/term_path.rb +12 -0
- data/lib/bio/io/biosql/term_relationship.rb +13 -0
- data/lib/bio/io/biosql/term_relationship_term.rb +11 -0
- data/lib/bio/io/biosql/term_synonym.rb +10 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +638 -0
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +163 -0
- data/lib/bio/io/fetch.rb +195 -0
- data/lib/bio/io/flatfile.rb +482 -0
- data/lib/bio/io/flatfile/autodetection.rb +545 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/buffer.rb +237 -0
- data/lib/bio/io/flatfile/index.rb +1381 -0
- data/lib/bio/io/flatfile/indexer.rb +805 -0
- data/lib/bio/io/flatfile/splitter.rb +297 -0
- data/lib/bio/io/higet.rb +73 -0
- data/lib/bio/io/hinv.rb +442 -0
- data/lib/bio/io/keggapi.rb +805 -0
- data/lib/bio/io/ncbirest.rb +733 -0
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +307 -0
- data/lib/bio/io/registry.rb +292 -0
- data/lib/bio/io/soapwsdl.rb +119 -0
- data/lib/bio/io/sql.rb +186 -0
- data/lib/bio/location.rb +867 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +960 -0
- data/lib/bio/reference.rb +602 -0
- data/lib/bio/sequence.rb +456 -0
- data/lib/bio/sequence/aa.rb +152 -0
- data/lib/bio/sequence/adapter.rb +108 -0
- data/lib/bio/sequence/common.rb +310 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/dblink.rb +54 -0
- data/lib/bio/sequence/format.rb +358 -0
- data/lib/bio/sequence/format_raw.rb +23 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +491 -0
- data/lib/bio/shell.rb +44 -0
- data/lib/bio/shell/core.rb +578 -0
- data/lib/bio/shell/demo.rb +146 -0
- data/lib/bio/shell/interface.rb +218 -0
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +71 -0
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +218 -0
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +105 -0
- data/lib/bio/shell/plugin/flatfile.rb +101 -0
- data/lib/bio/shell/plugin/keggapi.rb +181 -0
- data/lib/bio/shell/plugin/midi.rb +430 -0
- data/lib/bio/shell/plugin/obda.rb +45 -0
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +247 -0
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +102 -0
- data/lib/bio/tree.rb +852 -0
- data/lib/bio/util/color_scheme.rb +191 -0
- data/lib/bio/util/color_scheme/buried.rb +59 -0
- data/lib/bio/util/color_scheme/helix.rb +59 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +64 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +31 -0
- data/lib/bio/util/color_scheme/strand.rb +59 -0
- data/lib/bio/util/color_scheme/taylor.rb +50 -0
- data/lib/bio/util/color_scheme/turn.rb +59 -0
- data/lib/bio/util/color_scheme/zappo.rb +50 -0
- data/lib/bio/util/contingency_table.rb +370 -0
- data/lib/bio/util/restriction_enzyme.rb +228 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
- data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +200 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/aaindex/DAYM780301 +30 -0
- data/test/data/aaindex/PRAM900102 +20 -0
- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
- data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
- data/test/data/blast/2.2.15.blastp.m7 +876 -0
- data/test/data/blast/b0002.faa +15 -0
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- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/blast/blastp-multi.m7 +188 -0
- data/test/data/command/echoarg2.bat +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/embl/AB090716.embl.rel89 +63 -0
- data/test/data/fasta/example1.txt +75 -0
- data/test/data/fasta/example2.txt +21 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/paml/codeml/control_file.txt +30 -0
- data/test/data/paml/codeml/output.txt +78 -0
- data/test/data/paml/codeml/rates +217 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/rpsblast/misc.rpsblast +193 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/functional/bio/appl/test_pts1.rb +115 -0
- data/test/functional/bio/io/test_ensembl.rb +229 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -0
- data/test/functional/bio/sequence/test_output_embl.rb +51 -0
- data/test/functional/bio/test_command.rb +301 -0
- data/test/runner.rb +14 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_ncbioptions.rb +112 -0
- data/test/unit/bio/appl/blast/test_report.rb +1135 -0
- data/test/unit/bio/appl/blast/test_rpsblast.rb +398 -0
- data/test/unit/bio/appl/genscan/test_report.rb +182 -0
- data/test/unit/bio/appl/hmmer/test_report.rb +342 -0
- data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
- data/test/unit/bio/appl/mafft/test_report.rb +63 -0
- data/test/unit/bio/appl/paml/codeml/test_rates.rb +45 -0
- data/test/unit/bio/appl/paml/codeml/test_report.rb +45 -0
- data/test/unit/bio/appl/paml/test_codeml.rb +174 -0
- data/test/unit/bio/appl/sosui/test_report.rb +81 -0
- data/test/unit/bio/appl/targetp/test_report.rb +146 -0
- data/test/unit/bio/appl/test_blast.rb +277 -0
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_psort.rb +57 -0
- data/test/unit/bio/appl/test_pts1.rb +77 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +126 -0
- data/test/unit/bio/data/test_aa.rb +90 -0
- data/test/unit/bio/data/test_codontable.rb +107 -0
- data/test/unit/bio/data/test_na.rb +80 -0
- data/test/unit/bio/db/embl/test_common.rb +117 -0
- data/test/unit/bio/db/embl/test_embl.rb +214 -0
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +203 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1812 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +31 -0
- data/test/unit/bio/db/kegg/test_genes.rb +45 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +152 -0
- data/test/unit/bio/db/test_aaindex.rb +197 -0
- data/test/unit/bio/db/test_fasta.rb +250 -0
- data/test/unit/bio/db/test_gff.rb +1190 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_medline.rb +127 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +364 -0
- data/test/unit/bio/db/test_prosite.rb +1437 -0
- data/test/unit/bio/db/test_rebase.rb +101 -0
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/db/test_url.rb +36 -0
- data/test/unit/bio/io/flatfile/test_autodetection.rb +375 -0
- data/test/unit/bio/io/flatfile/test_buffer.rb +251 -0
- data/test/unit/bio/io/flatfile/test_splitter.rb +369 -0
- data/test/unit/bio/io/test_ddbjxml.rb +80 -0
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +42 -0
- data/test/unit/bio/io/test_flatfile.rb +505 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +115 -0
- data/test/unit/bio/sequence/test_common.rb +373 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -0
- data/test/unit/bio/sequence/test_dblink.rb +58 -0
- data/test/unit/bio/sequence/test_na.rb +330 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +185 -0
- data/test/unit/bio/test_alignment.rb +1025 -0
- data/test/unit/bio/test_command.rb +349 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +144 -0
- data/test/unit/bio/test_location.rb +599 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +499 -0
- data/test/unit/bio/test_reference.rb +252 -0
- data/test/unit/bio/test_sequence.rb +329 -0
- data/test/unit/bio/test_shell.rb +18 -0
- data/test/unit/bio/test_tree.rb +593 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +101 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
- data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
- data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
- data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
- data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
- data/test/unit/bio/util/test_color_scheme.rb +33 -0
- data/test/unit/bio/util/test_contingency_table.rb +94 -0
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +245 -0
- metadata +543 -0
@@ -0,0 +1,235 @@
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#
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# = bio/appl/fasta.rb - FASTA wrapper
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#
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# Copyright:: Copyright (C) 2001, 2002 Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
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# $Id:$
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#
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require 'net/http'
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require 'uri'
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require 'bio/command'
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require 'shellwords'
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module Bio
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class Fasta
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#autoload :Report, 'bio/appl/fasta/format10'
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#autoload :?????, 'bio/appl/fasta/format6'
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# Returns a FASTA factory object (Bio::Fasta).
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def initialize(program, db, opt = [], server = 'local')
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@format = 10
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@program = program
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@db = db
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@server = server
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@ktup = nil
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@matrix = nil
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@output = ''
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begin
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a = opt.to_ary
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rescue NameError #NoMethodError
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# backward compatibility
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a = Shellwords.shellwords(opt)
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end
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@options = [ '-Q', '-H', '-m', @format.to_s, *a ] # need -a ?
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end
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attr_accessor :program, :db, :options, :server, :ktup, :matrix
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# Returns a String containing fasta execution output in as is format.
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attr_reader :output
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def option
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# backward compatibility
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Bio::Command.make_command_line(@options)
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end
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def option=(str)
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# backward compatibility
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@options = Shellwords.shellwords(str)
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end
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# Accessors for the -m option.
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def format=(num)
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@format = num.to_i
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if i = @options.index('-m') then
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@options[i+1, 1] = @format.to_s
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else
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@options << '-m' << @format.to_s
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end
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end
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attr_reader :format
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# Select parser to use ('format6' and 'format10' is acceptable for now)
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#
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# This method will import Bio::Fasta::Report class by requiring specified
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# parser and will be useful when you already have fasta output files and
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# want to use appropriate Report class for parsing.
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#
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def self.parser(parser)
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require "bio/appl/fasta/#{parser}"
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end
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# Returns a FASTA factory object (Bio::Fasta) to run FASTA search on
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# local computer.
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def self.local(program, db, option = '')
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self.new(program, db, option, 'local')
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end
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# Returns a FASTA factory object (Bio::Fasta) to execute FASTA search on
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# remote server.
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#
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# For the develpper, you can add server 'hoge' by adding
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# exec_hoge(query) method.
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#
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def self.remote(program, db, option = '', server = 'genomenet')
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self.new(program, db, option, server)
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end
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# Execute FASTA search and returns Report object (Bio::Fasta::Report).
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def query(query)
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return self.send("exec_#{@server}", query.to_s)
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end
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private
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def parse_result(data)
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case @format
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when 6
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require 'bio/appl/fasta/format6'
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when 10
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require 'bio/appl/fasta/format10'
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end
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Report.new(data)
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end
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def exec_local(query)
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cmd = [ @program, *@options ]
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cmd.concat([ '@', @db ])
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cmd.push(@ktup) if @ktup
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report = nil
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@output = Bio::Command.query_command(cmd, query)
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report = parse_result(@output)
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return report
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end
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# == Available databases for Fasta.remote(@program, @db, option, 'genomenet')
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#
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# See http://fasta.genome.jp/ideas/ideas.html#fasta for more details.
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#
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# ----------+-------+---------------------------------------------------
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# @program | query | @db (supported in GenomeNet)
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# ----------+-------+---------------------------------------------------
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# fasta | AA | nr-aa, genes, vgenes.pep, swissprot, swissprot-upd,
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# | | pir, prf, pdbstr
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# +-------+---------------------------------------------------
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# | NA | nr-nt, genbank-nonst, gbnonst-upd, dbest, dbgss,
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# | | htgs, dbsts, embl-nonst, embnonst-upd, epd,
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# | | genes-nt, genome, vgenes.nuc
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# ----------+-------+---------------------------------------------------
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# tfasta | AA | nr-nt, genbank-nonst, gbnonst-upd, dbest, dbgss,
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# | | htgs, dbsts, embl-nonst, embnonst-upd,
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# | | genes-nt, genome, vgenes.nuc
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# ----------+-------+---------------------------------------------------
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#
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def exec_genomenet(query)
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host = "fasta.genome.jp"
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#path = "/sit-bin/nph-fasta"
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path = "/sit-bin/fasta" # 2005.08.12
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form = {
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'style' => 'raw',
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'prog' => @program,
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'dbname' => @db,
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'sequence' => query,
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'other_param' => Bio::Command.make_command_line_unix(@options),
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'ktup_value' => @ktup,
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'matrix' => @matrix,
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}
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form.keys.each do |k|
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form.delete(k) unless form[k]
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end
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report = nil
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begin
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http = Bio::Command.new_http(host)
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http.open_timeout = 3000
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http.read_timeout = 6000
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result = Bio::Command.http_post_form(http, path, form)
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# workaround 2006.8.1 - fixed for new batch queuing system
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case result.code
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when "302"
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result_location = result.header['location']
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result_uri = URI.parse(result_location)
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result_path = result_uri.path
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done = false
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until done
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result = http.get(result_path)
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if result.body[/Your job ID is/]
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sleep 15
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else
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done = true
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end
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end
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end
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@output = result.body.to_s
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# workaround 2005.08.12
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re = %r{<A HREF="http://#{host}(/tmp/[^"]+)">Show all result</A>}i # "
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if path = @output[re, 1]
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result = http.get(path)
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@output = result.body
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txt = @output.to_s.split(/\<pre\>/)[1]
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raise 'cannot understand response' unless txt
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txt.sub!(/\<\/pre\>.*\z/m, '')
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txt.sub!(/.*^((T?FASTA|SSEARCH) (searches|compares))/m, '\1')
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txt.sub!(/^\<form method\=\"POST\" name\=\"clust_check\"\>.*\n/, '')
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txt.gsub!(/\<input[^\>]+value\=\"[^\"]*\"[^\>]*\>/i, '')
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txt.gsub!(/\<(a|form|select|input|option|img)\s+[^\>]+\>/i, '')
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txt.gsub!(/\<\/(a|form|select|input|option|img)\>/i, '')
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@output = txt.gsub(/\<\;/, '<')
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report = parse_result(@output.dup)
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else
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raise 'cannot understand response'
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end
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end
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return report
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end
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end # Fasta
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end # Bio
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if __FILE__ == $0
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begin
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require 'pp'
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alias p pp
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rescue
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end
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# serv = Bio::Fasta.local('fasta34', 'hoge.nuc')
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# serv = Bio::Fasta.local('fasta34', 'hoge.pep')
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# serv = Bio::Fasta.local('ssearch34', 'hoge.pep')
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# This may take 3 minutes or so.
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serv = Bio::Fasta.remote('fasta', 'genes')
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p serv.query(ARGF.read)
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end
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@@ -0,0 +1,325 @@
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#
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# = bio/appl/fasta/format10.rb - FASTA output (-m 10) parser
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#
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# Copyright:: Copyright (C) 2002 Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: format10.rb,v 1.7 2007/04/06 12:04:05 k Exp $
|
8
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#
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9
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|
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require 'bio/appl/fasta'
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module Bio
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class Fasta
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# Summarized results of the fasta execution results.
|
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class Report
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|
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def initialize(data)
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# header lines - brief list of the hits
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if data.sub!(/.*\nThe best scores are/m, '')
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data.sub!(/(.*)\n\n>>>/m, '')
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@list = "The best scores are" + $1
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else
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data.sub!(/.*\n!!\s+/m, '')
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data.sub!(/.*/) { |x| @list = x; '' }
|
26
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end
|
27
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|
28
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# body lines - fasta execution result
|
29
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program, *hits = data.split(/\n>>/)
|
30
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# trailing lines - log messages of the execution
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32
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@log = hits.pop
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33
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@log.sub!(/.*<\n/m, '')
|
34
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@log.strip!
|
35
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|
36
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# parse results
|
37
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@program = Program.new(program)
|
38
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@hits = []
|
39
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+
|
40
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hits.each do |x|
|
41
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@hits.push(Hit.new(x))
|
42
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end
|
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end
|
44
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|
45
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# Returns the 'The best scores are' lines as a String.
|
46
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attr_reader :list
|
47
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+
|
48
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# Returns the trailing lines including library size, execution date,
|
49
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# fasta function used, and fasta versions as a String.
|
50
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attr_reader :log
|
51
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|
52
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# Returns a Bio::Fasta::Report::Program object.
|
53
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attr_reader :program
|
54
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|
55
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# Returns an Array of Bio::Fasta::Report::Hit objects.
|
56
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attr_reader :hits
|
57
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|
58
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# Iterates on each Bio::Fasta::Report::Hit object.
|
59
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def each
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60
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@hits.each do |x|
|
61
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yield x
|
62
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+
end
|
63
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+
end
|
64
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+
|
65
|
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# Returns an Array of Bio::Fasta::Report::Hit objects having
|
66
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+
# better evalue than 'evalue_max'.
|
67
|
+
def threshold(evalue_max = 0.1)
|
68
|
+
list = []
|
69
|
+
@hits.each do |x|
|
70
|
+
list.push(x) if x.evalue < evalue_max
|
71
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+
end
|
72
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return list
|
73
|
+
end
|
74
|
+
|
75
|
+
# Returns an Array of Bio::Fasta::Report::Hit objects having
|
76
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+
# longer overlap length than 'length_min'.
|
77
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+
def lap_over(length_min = 0)
|
78
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+
list = []
|
79
|
+
@hits.each do |x|
|
80
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+
list.push(x) if x.overlap > length_min
|
81
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+
end
|
82
|
+
return list
|
83
|
+
end
|
84
|
+
|
85
|
+
# Log of the fasta execution environments.
|
86
|
+
class Program
|
87
|
+
def initialize(data)
|
88
|
+
@definition, *program = data.split(/\n/)
|
89
|
+
@program = {}
|
90
|
+
|
91
|
+
pat = /;\s+([^:]+):\s+(.*)/
|
92
|
+
|
93
|
+
program.each do |x|
|
94
|
+
if pat.match(x)
|
95
|
+
@program[$1] = $2
|
96
|
+
end
|
97
|
+
end
|
98
|
+
end
|
99
|
+
|
100
|
+
# Returns a String containing query and library filenames.
|
101
|
+
attr_reader :definition
|
102
|
+
|
103
|
+
# Accessor for a Hash containing 'mp_name', 'mp_ver', 'mp_argv',
|
104
|
+
# 'pg_name', 'pg_ver, 'pg_matrix', 'pg_gap-pen', 'pg_ktup',
|
105
|
+
# 'pg_optcut', 'pg_cgap', 'mp_extrap', 'mp_stats', and 'mp_KS' values.
|
106
|
+
attr_reader :program
|
107
|
+
end
|
108
|
+
|
109
|
+
|
110
|
+
class Hit
|
111
|
+
def initialize(data)
|
112
|
+
score, query, target = data.split(/\n>/)
|
113
|
+
|
114
|
+
@definition, *score = score.split(/\n/)
|
115
|
+
@score = {}
|
116
|
+
|
117
|
+
pat = /;\s+([^:]+):\s+(.*)/
|
118
|
+
|
119
|
+
score.each do |x|
|
120
|
+
if pat.match(x)
|
121
|
+
@score[$1] = $2
|
122
|
+
end
|
123
|
+
end
|
124
|
+
|
125
|
+
@query = Query.new(query)
|
126
|
+
@target = Target.new(target)
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127
|
+
end
|
128
|
+
attr_reader :definition, :score, :query, :target
|
129
|
+
|
130
|
+
# E-value score
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131
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+
def evalue
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132
|
+
if @score['fa_expect']
|
133
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+
@score['fa_expect'].to_f
|
134
|
+
elsif @score['sw_expect']
|
135
|
+
@score['sw_expect'].to_f
|
136
|
+
elsif @score['fx_expect']
|
137
|
+
@score['fx_expect'].to_f
|
138
|
+
elsif @score['tx_expect']
|
139
|
+
@score['tx_expect'].to_f
|
140
|
+
end
|
141
|
+
end
|
142
|
+
|
143
|
+
# Bit score
|
144
|
+
def bit_score
|
145
|
+
if @score['fa_bits']
|
146
|
+
@score['fa_bits'].to_f
|
147
|
+
elsif @score['sw_bits']
|
148
|
+
@score['sw_bits'].to_f
|
149
|
+
elsif @score['fx_bits']
|
150
|
+
@score['fx_bits'].to_f
|
151
|
+
elsif @score['tx_bits']
|
152
|
+
@score['tx_bits'].to_f
|
153
|
+
end
|
154
|
+
end
|
155
|
+
|
156
|
+
def direction
|
157
|
+
@score['fa_frame'] || @score['sw_frame'] || @score['fx_frame'] || @score['tx_frame']
|
158
|
+
end
|
159
|
+
|
160
|
+
# Smith-Waterman score
|
161
|
+
def sw
|
162
|
+
@score['sw_score'].to_i
|
163
|
+
end
|
164
|
+
|
165
|
+
# percent identity
|
166
|
+
def identity
|
167
|
+
@score['sw_ident'].to_f
|
168
|
+
end
|
169
|
+
|
170
|
+
# overlap length
|
171
|
+
def overlap
|
172
|
+
@score['sw_overlap'].to_i
|
173
|
+
end
|
174
|
+
|
175
|
+
# Shortcuts for the methods of Bio::Fasta::Report::Hit::Query
|
176
|
+
|
177
|
+
def query_id
|
178
|
+
@query.entry_id
|
179
|
+
end
|
180
|
+
|
181
|
+
def target_id
|
182
|
+
@target.entry_id
|
183
|
+
end
|
184
|
+
|
185
|
+
def query_def
|
186
|
+
@query.definition
|
187
|
+
end
|
188
|
+
|
189
|
+
def target_def
|
190
|
+
@target.definition
|
191
|
+
end
|
192
|
+
|
193
|
+
def query_len
|
194
|
+
@query.length
|
195
|
+
end
|
196
|
+
|
197
|
+
# Shortcuts for the methods of Bio::Fasta::Report::Hit::Target
|
198
|
+
|
199
|
+
def target_len
|
200
|
+
@target.length
|
201
|
+
end
|
202
|
+
|
203
|
+
def query_seq
|
204
|
+
@query.sequence
|
205
|
+
end
|
206
|
+
|
207
|
+
def target_seq
|
208
|
+
@target.sequence
|
209
|
+
end
|
210
|
+
|
211
|
+
def query_type
|
212
|
+
@query.moltype
|
213
|
+
end
|
214
|
+
|
215
|
+
def target_type
|
216
|
+
@target.moltype
|
217
|
+
end
|
218
|
+
|
219
|
+
# Information on matching region
|
220
|
+
|
221
|
+
def query_start
|
222
|
+
@query.start
|
223
|
+
end
|
224
|
+
|
225
|
+
def query_end
|
226
|
+
@query.stop
|
227
|
+
end
|
228
|
+
|
229
|
+
def target_start
|
230
|
+
@target.start
|
231
|
+
end
|
232
|
+
|
233
|
+
def target_end
|
234
|
+
@target.stop
|
235
|
+
end
|
236
|
+
|
237
|
+
def lap_at
|
238
|
+
[ query_start, query_end, target_start, target_end ]
|
239
|
+
end
|
240
|
+
|
241
|
+
|
242
|
+
class Query
|
243
|
+
def initialize(data)
|
244
|
+
@definition, *data = data.split(/\n/)
|
245
|
+
@data = {}
|
246
|
+
@sequence = ''
|
247
|
+
|
248
|
+
pat = /;\s+([^:]+):\s+(.*)/
|
249
|
+
|
250
|
+
data.each do |x|
|
251
|
+
if pat.match(x)
|
252
|
+
@data[$1] = $2
|
253
|
+
else
|
254
|
+
@sequence += x
|
255
|
+
end
|
256
|
+
end
|
257
|
+
end
|
258
|
+
|
259
|
+
# Returns the definition of the entry as a String.
|
260
|
+
# You can access this value by Report::Hit#query_def method.
|
261
|
+
attr_reader :definition
|
262
|
+
|
263
|
+
# Returns a Hash containing 'sq_len', 'sq_offset', 'sq_type',
|
264
|
+
# 'al_start', 'al_stop', and 'al_display_start' values.
|
265
|
+
# You can access most of these values by Report::Hit#query_* methods.
|
266
|
+
attr_reader :data
|
267
|
+
|
268
|
+
# Returns the sequence (with gaps) as a String.
|
269
|
+
# You can access this value by the Report::Hit#query_seq method.
|
270
|
+
attr_reader :sequence
|
271
|
+
|
272
|
+
# Returns the first word in the definition as a String.
|
273
|
+
# You can get this value by Report::Hit#query_id method.
|
274
|
+
def entry_id
|
275
|
+
@definition[/\S+/]
|
276
|
+
end
|
277
|
+
|
278
|
+
# Returns the sequence length.
|
279
|
+
# You can access this value by the Report::Hit#query_len method.
|
280
|
+
def length
|
281
|
+
@data['sq_len'].to_i
|
282
|
+
end
|
283
|
+
|
284
|
+
# Returns 'p' for protein sequence, 'D' for nucleotide sequence.
|
285
|
+
def moltype
|
286
|
+
@data['sq_type']
|
287
|
+
end
|
288
|
+
|
289
|
+
# Returns alignment start position. You can also access this value
|
290
|
+
# by Report::Hit#query_start method for shortcut.
|
291
|
+
def start
|
292
|
+
@data['al_start'].to_i
|
293
|
+
end
|
294
|
+
|
295
|
+
# Returns alignment end position. You can access this value
|
296
|
+
# by Report::Hit#query_end method for shortcut.
|
297
|
+
def stop
|
298
|
+
@data['al_stop'].to_i
|
299
|
+
end
|
300
|
+
|
301
|
+
end
|
302
|
+
|
303
|
+
# Same as Bio::Fasta::Report::Hit::Query but for Target.
|
304
|
+
class Target < Query; end
|
305
|
+
end
|
306
|
+
|
307
|
+
end # Report
|
308
|
+
|
309
|
+
end # Fasta
|
310
|
+
end # Bio
|
311
|
+
|
312
|
+
|
313
|
+
if __FILE__ == $0
|
314
|
+
begin
|
315
|
+
require 'pp'
|
316
|
+
alias p pp
|
317
|
+
rescue
|
318
|
+
end
|
319
|
+
|
320
|
+
rep = Bio::Fasta::Report.new(ARGF.read)
|
321
|
+
p rep
|
322
|
+
|
323
|
+
end
|
324
|
+
|
325
|
+
|