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 +1,144 @@
|
|
1
|
+
#
|
2
|
+
# = bio/appl/blast/rexml.rb - BLAST XML output (-m 7) parser by REXML
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2002, 2003 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
|
+
begin
|
15
|
+
require 'rexml/document'
|
16
|
+
rescue LoadError
|
17
|
+
end
|
18
|
+
|
19
|
+
module Bio
|
20
|
+
class Blast
|
21
|
+
class Report
|
22
|
+
|
23
|
+
private
|
24
|
+
|
25
|
+
def rexml_parse(xml)
|
26
|
+
dom = REXML::Document.new(xml)
|
27
|
+
rexml_parse_program(dom)
|
28
|
+
dom.elements.each("*//Iteration") do |e|
|
29
|
+
@iterations.push(rexml_parse_iteration(e))
|
30
|
+
end
|
31
|
+
end
|
32
|
+
|
33
|
+
def rexml_parse_program(dom)
|
34
|
+
hash = {}
|
35
|
+
dom.root.each_element_with_text do |e|
|
36
|
+
name, text = e.name, e.text
|
37
|
+
case name
|
38
|
+
when 'BlastOutput_param'
|
39
|
+
e.elements["Parameters"].each_element_with_text do |p|
|
40
|
+
xml_set_parameter(p.name, p.text)
|
41
|
+
end
|
42
|
+
else
|
43
|
+
hash[name] = text if text.strip.size > 0
|
44
|
+
end
|
45
|
+
end
|
46
|
+
@program = hash['BlastOutput_program']
|
47
|
+
@version = hash['BlastOutput_version']
|
48
|
+
@reference = hash['BlastOutput_reference']
|
49
|
+
@db = hash['BlastOutput_db']
|
50
|
+
@query_id = hash['BlastOutput_query-ID']
|
51
|
+
@query_def = hash['BlastOutput_query-def']
|
52
|
+
@query_len = hash['BlastOutput_query-len'].to_i
|
53
|
+
end
|
54
|
+
|
55
|
+
def rexml_parse_iteration(e)
|
56
|
+
iteration = Iteration.new
|
57
|
+
e.elements.each do |i|
|
58
|
+
case i.name
|
59
|
+
when 'Iteration_iter-num'
|
60
|
+
iteration.num = i.text.to_i
|
61
|
+
when 'Iteration_hits'
|
62
|
+
i.elements.each("Hit") do |h|
|
63
|
+
iteration.hits.push(rexml_parse_hit(h))
|
64
|
+
end
|
65
|
+
when 'Iteration_message'
|
66
|
+
iteration.message = i.text
|
67
|
+
when 'Iteration_stat'
|
68
|
+
i.elements["Statistics"].each_element_with_text do |s|
|
69
|
+
k = s.name.sub(/Statistics_/, '')
|
70
|
+
v = s.text =~ /\D/ ? s.text.to_f : s.text.to_i
|
71
|
+
iteration.statistics[k] = v
|
72
|
+
end
|
73
|
+
|
74
|
+
# for new BLAST XML format
|
75
|
+
when 'Iteration_query-ID'
|
76
|
+
iteration.query_id = i.text
|
77
|
+
when 'Iteration_query-def'
|
78
|
+
iteration.query_def = i.text
|
79
|
+
when 'Iteration_query-len'
|
80
|
+
iteration.query_len = i.text.to_i
|
81
|
+
end
|
82
|
+
end #case i.name
|
83
|
+
|
84
|
+
return iteration
|
85
|
+
end
|
86
|
+
|
87
|
+
def rexml_parse_hit(e)
|
88
|
+
hit = Hit.new
|
89
|
+
hash = {}
|
90
|
+
hit.query_id = @query_id
|
91
|
+
hit.query_def = @query_def
|
92
|
+
hit.query_len = @query_len
|
93
|
+
e.elements.each do |h|
|
94
|
+
case h.name
|
95
|
+
when 'Hit_hsps'
|
96
|
+
h.elements.each("Hsp") do |s|
|
97
|
+
hit.hsps.push(rexml_parse_hsp(s))
|
98
|
+
end
|
99
|
+
else
|
100
|
+
hash[h.name] = h.text
|
101
|
+
end
|
102
|
+
end
|
103
|
+
hit.num = hash['Hit_num'].to_i
|
104
|
+
hit.hit_id = hash['Hit_id']
|
105
|
+
hit.len = hash['Hit_len'].to_i
|
106
|
+
hit.definition = hash['Hit_def']
|
107
|
+
hit.accession = hash['Hit_accession']
|
108
|
+
return hit
|
109
|
+
end
|
110
|
+
|
111
|
+
def rexml_parse_hsp(e)
|
112
|
+
hsp = Hsp.new
|
113
|
+
hash = {}
|
114
|
+
e.each_element_with_text do |h|
|
115
|
+
hash[h.name] = h.text
|
116
|
+
end
|
117
|
+
hsp.num = hash['Hsp_num'].to_i
|
118
|
+
hsp.bit_score = hash['Hsp_bit-score'].to_f
|
119
|
+
hsp.score = hash['Hsp_score'].to_i
|
120
|
+
hsp.evalue = hash['Hsp_evalue'].to_f
|
121
|
+
hsp.query_from = hash['Hsp_query-from'].to_i
|
122
|
+
hsp.query_to = hash['Hsp_query-to'].to_i
|
123
|
+
hsp.hit_from = hash['Hsp_hit-from'].to_i
|
124
|
+
hsp.hit_to = hash['Hsp_hit-to'].to_i
|
125
|
+
hsp.pattern_from = hash['Hsp_pattern-from'].to_i
|
126
|
+
hsp.pattern_to = hash['Hsp_pattern-to'].to_i
|
127
|
+
hsp.query_frame = hash['Hsp_query-frame'].to_i
|
128
|
+
hsp.hit_frame = hash['Hsp_hit-frame'].to_i
|
129
|
+
hsp.identity = hash['Hsp_identity'].to_i
|
130
|
+
hsp.positive = hash['Hsp_positive'].to_i
|
131
|
+
hsp.gaps = hash['Hsp_gaps'].to_i
|
132
|
+
hsp.align_len = hash['Hsp_align-len'].to_i
|
133
|
+
hsp.density = hash['Hsp_density'].to_i
|
134
|
+
hsp.qseq = hash['Hsp_qseq']
|
135
|
+
hsp.hseq = hash['Hsp_hseq']
|
136
|
+
hsp.midline = hash['Hsp_midline']
|
137
|
+
return hsp
|
138
|
+
end
|
139
|
+
|
140
|
+
end
|
141
|
+
end
|
142
|
+
end
|
143
|
+
|
144
|
+
|
@@ -0,0 +1,277 @@
|
|
1
|
+
#
|
2
|
+
# = bio/appl/blast/rpsblast.rb - NCBI RPS Blast default output 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
|
+
# NCBI RPS Blast (Reversed Position Specific Blast) default
|
12
|
+
# (-m 0 option) output parser class, Bio::Blast::RPSBlast::Report
|
13
|
+
# and related classes/modules.
|
14
|
+
#
|
15
|
+
# == References
|
16
|
+
#
|
17
|
+
# * Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
|
18
|
+
# Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
|
19
|
+
# "Gapped BLAST and PSI-BLAST: a new generation of protein database search
|
20
|
+
# programs", Nucleic Acids Res. 25:3389-3402.
|
21
|
+
# * ftp://ftp.ncbi.nih.gov/blast/documents/rpsblast.html
|
22
|
+
# * http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml
|
23
|
+
#
|
24
|
+
|
25
|
+
require 'bio/appl/blast/format0'
|
26
|
+
require 'bio/io/flatfile'
|
27
|
+
|
28
|
+
module Bio
|
29
|
+
class Blast
|
30
|
+
|
31
|
+
# NCBI RPS Blast (Reversed Position Specific Blast) namespace.
|
32
|
+
# Currently, this module is existing only for separating namespace.
|
33
|
+
# To parse RPSBlast results, see Bio::Blast::RPSBlast::Report documents.
|
34
|
+
module RPSBlast
|
35
|
+
|
36
|
+
# Flatfile splitter for RPS-BLAST reports.
|
37
|
+
# It is internally used when reading RPS-BLAST report.
|
38
|
+
# Normally, users do not need to use it directly.
|
39
|
+
#
|
40
|
+
# Note for Windows: RPS-BLAST results generated in Microsoft Windows
|
41
|
+
# may not be parsed correctly due to the line feed code problem.
|
42
|
+
# For a workaroud, convert line feed codes from Windows(DOS) to UNIX.
|
43
|
+
#
|
44
|
+
class RPSBlastSplitter < Bio::FlatFile::Splitter::Template
|
45
|
+
|
46
|
+
# Separator used to distinguish start of each report
|
47
|
+
ReportHead = /\A\n*(RPS\-BLAST|Query\=)/
|
48
|
+
|
49
|
+
# Delimiter used for IO#gets
|
50
|
+
Delimiter = "\n\n"
|
51
|
+
|
52
|
+
# creates a new splitter object
|
53
|
+
def initialize(klass, bstream)
|
54
|
+
super(klass, bstream)
|
55
|
+
@entry_head = nil
|
56
|
+
end
|
57
|
+
|
58
|
+
# Skips leader of the entry.
|
59
|
+
# In this class, only skips space characters.
|
60
|
+
def skip_leader
|
61
|
+
stream.skip_spaces
|
62
|
+
return nil
|
63
|
+
end
|
64
|
+
|
65
|
+
# Rewinds the stream
|
66
|
+
def rewind
|
67
|
+
@entry_head = nil
|
68
|
+
super
|
69
|
+
end
|
70
|
+
|
71
|
+
# gets an entry
|
72
|
+
def get_entry
|
73
|
+
p0 = stream_pos()
|
74
|
+
pieces = []
|
75
|
+
flag_head = false # reached to start of header
|
76
|
+
flag_body = false # reached to start of body (Query=...)
|
77
|
+
while x = stream.gets(Delimiter)
|
78
|
+
if ReportHead =~ x then
|
79
|
+
case $1
|
80
|
+
when 'RPS-BLAST'
|
81
|
+
if pieces.empty? then
|
82
|
+
@entry_head = nil
|
83
|
+
flag_head = true
|
84
|
+
else
|
85
|
+
stream.ungets(x)
|
86
|
+
break
|
87
|
+
end
|
88
|
+
when 'Query='
|
89
|
+
if flag_body then
|
90
|
+
stream.ungets(x)
|
91
|
+
break
|
92
|
+
else
|
93
|
+
@entry_head = pieces.join('') if flag_head
|
94
|
+
flag_body = true
|
95
|
+
end
|
96
|
+
else
|
97
|
+
raise 'Bug: should not reach here'
|
98
|
+
end
|
99
|
+
end #if ReportHead...
|
100
|
+
pieces.push x
|
101
|
+
end #while
|
102
|
+
p1 = stream_pos()
|
103
|
+
|
104
|
+
self.entry_start_pos = p0
|
105
|
+
self.entry =
|
106
|
+
if pieces.empty? then
|
107
|
+
nil
|
108
|
+
elsif !flag_head and @entry_head then
|
109
|
+
@entry_head + pieces.join('')
|
110
|
+
else
|
111
|
+
pieces.join('')
|
112
|
+
end
|
113
|
+
self.entry_ended_pos = p1
|
114
|
+
return self.entry
|
115
|
+
end
|
116
|
+
end #class RPSBlastSplitter
|
117
|
+
|
118
|
+
# NCBI RPS Blast (Reversed Position Specific Blast)
|
119
|
+
# default output parser.
|
120
|
+
#
|
121
|
+
# It supports defalut (-m 0 option) output of the "rpsblast" command.
|
122
|
+
#
|
123
|
+
# Because this class inherits Bio::Blast::Default::Report,
|
124
|
+
# almost all methods are eqaul to Bio::Blast::Default::Report.
|
125
|
+
# Only DELIMITER (and RS) and few methods are different.
|
126
|
+
#
|
127
|
+
# By using Bio::FlatFile, (for example, Bio::FlatFile.open),
|
128
|
+
# rpsblast result generated from multiple query sequences is
|
129
|
+
# automatically splitted into multiple
|
130
|
+
# Bio::BLast::RPSBlast::Report objects corresponding to
|
131
|
+
# query sequences.
|
132
|
+
#
|
133
|
+
# Note for multi-fasta results WITH using Bio::FlatFile:
|
134
|
+
# Each splitted result is concatenated with header of the
|
135
|
+
# result which describes RPS-BLAST version and database
|
136
|
+
# information, if possible.
|
137
|
+
#
|
138
|
+
# Note for multi-fasta results WITHOUT using Bio::FlatFile:
|
139
|
+
# When parsing an output of rpsblast command running with
|
140
|
+
# multi-fasta sequences WITHOUT using Bio::FlatFile,
|
141
|
+
# each query's result is stored as an "iteration" of PSI-Blast.
|
142
|
+
# This behavior may be changed in the future.
|
143
|
+
#
|
144
|
+
# Note for nucleotide results: This class is not tested with
|
145
|
+
# nucleotide query and/or nucleotide databases.
|
146
|
+
#
|
147
|
+
class Report < Bio::Blast::Default::Report
|
148
|
+
# Delimter of each entry for RPS-BLAST.
|
149
|
+
DELIMITER = RS = "\nRPS-BLAST"
|
150
|
+
|
151
|
+
# (Integer) excess read size included in DELIMITER.
|
152
|
+
DELIMITER_OVERRUN = 9 # "RPS-BLAST"
|
153
|
+
|
154
|
+
# splitter for Bio::FlatFile support
|
155
|
+
FLATFILE_SPLITTER = RPSBlastSplitter
|
156
|
+
|
157
|
+
# Creates a new Report object from a string.
|
158
|
+
#
|
159
|
+
# Using Bio::FlatFile.open (or some other methods)
|
160
|
+
# is recommended instead of using this method directly.
|
161
|
+
# Refer Bio::Blast::RPSBlast::Report document for more information.
|
162
|
+
#
|
163
|
+
# Note for multi-fasta results WITHOUT using Bio::FlatFile:
|
164
|
+
# When parsing an output of rpsblast command running with
|
165
|
+
# multi-fasta sequences WITHOUT using Bio::FlatFile,
|
166
|
+
# each query's result is stored as an "iteration" of PSI-Blast.
|
167
|
+
# This behavior may be changed in the future.
|
168
|
+
#
|
169
|
+
# Note for nucleotide results: This class is not tested with
|
170
|
+
# nucleotide query and/or nucleotide databases.
|
171
|
+
#
|
172
|
+
def initialize(str)
|
173
|
+
str = str.sub(/\A\s+/, '')
|
174
|
+
# remove trailing entries for sure
|
175
|
+
str.sub!(/\n(RPS\-BLAST.*)/m, "\n")
|
176
|
+
@entry_overrun = $1
|
177
|
+
@entry = str
|
178
|
+
data = str.split(/(?:^[ \t]*\n)+/)
|
179
|
+
|
180
|
+
if data[0] and /\AQuery\=/ !~ data[0] then
|
181
|
+
format0_split_headers(data)
|
182
|
+
end
|
183
|
+
@iterations = format0_split_search(data)
|
184
|
+
format0_split_stat_params(data)
|
185
|
+
end
|
186
|
+
|
187
|
+
# Returns definition of the query.
|
188
|
+
# For a result of multi-fasta input, the first query's definition
|
189
|
+
# is returned (The same as <tt>iterations.first.query_def</tt>).
|
190
|
+
def query_def
|
191
|
+
iterations.first.query_def
|
192
|
+
end
|
193
|
+
|
194
|
+
# Returns length of the query.
|
195
|
+
# For a result of multi-fasta input, the first query's length
|
196
|
+
# is returned (The same as <tt>iterations.first.query_len</tt>).
|
197
|
+
def query_len
|
198
|
+
iterations.first.query_len
|
199
|
+
end
|
200
|
+
|
201
|
+
private
|
202
|
+
|
203
|
+
# Splits headers into the first line, reference, query line and
|
204
|
+
# database line.
|
205
|
+
def format0_split_headers(data)
|
206
|
+
@f0header = data.shift
|
207
|
+
@f0references = []
|
208
|
+
while data[0] and /\ADatabase\:/ !~ data[0]
|
209
|
+
@f0references.push data.shift
|
210
|
+
end
|
211
|
+
@f0database = data.shift
|
212
|
+
# In special case, a void line is inserted after database name.
|
213
|
+
if /\A +[\d\,]+ +sequences\; +[\d\,]+ total +letters\s*\z/ =~ data[0] then
|
214
|
+
@f0database.concat "\n"
|
215
|
+
@f0database.concat data.shift
|
216
|
+
end
|
217
|
+
end
|
218
|
+
|
219
|
+
# Splits the search results.
|
220
|
+
def format0_split_search(data)
|
221
|
+
iterations = []
|
222
|
+
dummystr = 'Searching..................................................done'
|
223
|
+
if r = data[0] and /^Searching/ =~ r then
|
224
|
+
dummystr = data.shift
|
225
|
+
end
|
226
|
+
while r = data[0] and /^Query\=/ =~ r
|
227
|
+
iterations << Iteration.new(data, dummystr)
|
228
|
+
end
|
229
|
+
iterations
|
230
|
+
end
|
231
|
+
|
232
|
+
# Iteration class for RPS-Blast.
|
233
|
+
# Though RPS-Blast does not iterate like PSI-BLAST,
|
234
|
+
# it aims to store a result of single query sequence.
|
235
|
+
#
|
236
|
+
# Normally, the instance of the class is generated
|
237
|
+
# by Bio::Blast::RPSBlast::Report object.
|
238
|
+
#
|
239
|
+
class Iteration < Bio::Blast::Default::Report::Iteration
|
240
|
+
# Creates a new Iteration object.
|
241
|
+
# It is designed to be called only internally from
|
242
|
+
# the Bio::Blast::RPSBlast::Report class.
|
243
|
+
# Users shall not use the method directly.
|
244
|
+
def initialize(data, dummystr)
|
245
|
+
if /\AQuery\=/ =~ data[0] then
|
246
|
+
sc = StringScanner.new(data.shift)
|
247
|
+
sc.skip(/\s*/)
|
248
|
+
if sc.skip_until(/Query\= */) then
|
249
|
+
q = []
|
250
|
+
begin
|
251
|
+
q << sc.scan(/.*/)
|
252
|
+
sc.skip(/\s*^ ?/)
|
253
|
+
end until !sc.rest or r = sc.skip(/ *\( *([\,\d]+) *letters *\)\s*\z/)
|
254
|
+
@query_len = sc[1].delete(',').to_i if r
|
255
|
+
@query_def = q.join(' ')
|
256
|
+
end
|
257
|
+
end
|
258
|
+
data.unshift(dummystr)
|
259
|
+
|
260
|
+
super(data)
|
261
|
+
end
|
262
|
+
|
263
|
+
# definition of the query
|
264
|
+
attr_reader :query_def
|
265
|
+
|
266
|
+
# length of the query sequence
|
267
|
+
attr_reader :query_len
|
268
|
+
|
269
|
+
end #class Iteration
|
270
|
+
|
271
|
+
end #class Report
|
272
|
+
|
273
|
+
end #module RPSBlast
|
274
|
+
|
275
|
+
end #module Blast
|
276
|
+
end #module Bio
|
277
|
+
|
@@ -0,0 +1,635 @@
|
|
1
|
+
#
|
2
|
+
# = bio/appl/blast/wublast.rb - WU-BLAST default output parser
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2003, 2008 Naohisa GOTO <ng@bioruby.org>
|
5
|
+
# License:: The Ruby License
|
6
|
+
#
|
7
|
+
# $Id:$
|
8
|
+
#
|
9
|
+
# == Description
|
10
|
+
#
|
11
|
+
# WU-BLAST default output parser.
|
12
|
+
#
|
13
|
+
# The parser is still incomplete and may contain many bugs,
|
14
|
+
# because I didn't have WU-BLAST license.
|
15
|
+
# It was tested under web-based WU-BLAST results and
|
16
|
+
# obsolete version downloaded from http://blast.wustl.edu/ .
|
17
|
+
#
|
18
|
+
# == References
|
19
|
+
#
|
20
|
+
# * http://blast.wustl.edu/
|
21
|
+
# * http://www.ebi.ac.uk/blast2/
|
22
|
+
#
|
23
|
+
|
24
|
+
require 'bio/appl/blast/format0'
|
25
|
+
|
26
|
+
module Bio
|
27
|
+
class Blast
|
28
|
+
module WU #:nodoc:
|
29
|
+
|
30
|
+
# Bio::Blast::WU::Report parses WU-BLAST default output
|
31
|
+
# and stores information in the data.
|
32
|
+
# It may contain a Bio::Blast::WU::Report::Iteration object.
|
33
|
+
# Because it inherits Bio::Blast::Default::Report,
|
34
|
+
# please also refer Bio::Blast::Default::Report.
|
35
|
+
class Report < Default::Report
|
36
|
+
|
37
|
+
# Returns parameters (???)
|
38
|
+
def parameters
|
39
|
+
parse_parameters
|
40
|
+
@parameters
|
41
|
+
end
|
42
|
+
|
43
|
+
# Returns parameter matrix (???)
|
44
|
+
def parameter_matrix
|
45
|
+
parse_parameters
|
46
|
+
@parameter_matrix
|
47
|
+
end
|
48
|
+
|
49
|
+
# Returns e-value threshold specified when BLAST was executed.
|
50
|
+
def expect; parse_parameters; @parameters['E']; end
|
51
|
+
|
52
|
+
# Returns warning messages.
|
53
|
+
def warnings
|
54
|
+
unless defined?(@warnings)
|
55
|
+
@warnings = @f0warnings
|
56
|
+
iterations.each { |x| @warnings.concat(x.warnings) }
|
57
|
+
end
|
58
|
+
@warnings
|
59
|
+
end
|
60
|
+
|
61
|
+
# Returns notice messages.
|
62
|
+
def notice
|
63
|
+
unless defined?(@notice)
|
64
|
+
@notice = @f0notice.to_s.gsub(/\s+/, ' ').strip
|
65
|
+
end #unless
|
66
|
+
@notice
|
67
|
+
end
|
68
|
+
|
69
|
+
# (WU-BLAST) Returns record number of the query.
|
70
|
+
# It may only be available for reports with multiple queries.
|
71
|
+
# Returns an Integer or nil.
|
72
|
+
def query_record_number
|
73
|
+
format0_parse_query
|
74
|
+
@query_record_number
|
75
|
+
end
|
76
|
+
|
77
|
+
# (WU-BLAST) Returns exit code for the execution.
|
78
|
+
# Returns an Integer or nil.
|
79
|
+
def exit_code
|
80
|
+
if defined? @exit_code then
|
81
|
+
@exit_code
|
82
|
+
else
|
83
|
+
nil
|
84
|
+
end
|
85
|
+
end
|
86
|
+
|
87
|
+
# (WU-BLAST) Returns fatal error information.
|
88
|
+
# Returns nil or an array containing String.
|
89
|
+
def fatal_errors
|
90
|
+
if defined? @fatal_errors then
|
91
|
+
@fatal_errors
|
92
|
+
else
|
93
|
+
nil
|
94
|
+
end
|
95
|
+
end
|
96
|
+
|
97
|
+
# Returns the name (filename or title) of the database.
|
98
|
+
def db
|
99
|
+
unless defined?(@db)
|
100
|
+
if /Database *\: *(.*)/m =~ @f0database then
|
101
|
+
a = $1.split(/^/)
|
102
|
+
if a.size > 1 and /\ASearching\..+ done\s*\z/ =~ a[-1] then
|
103
|
+
a.pop
|
104
|
+
end
|
105
|
+
if a.size > 1 and /\A +[\d\,]+ +sequences\; +[\d\,]+ total +letters\.?\s*\z/ =~ a[-1] then
|
106
|
+
a.pop
|
107
|
+
end
|
108
|
+
@db = a.collect { |x| x.sub(/\s+\z/, '') }.join(' ')
|
109
|
+
end
|
110
|
+
end #unless
|
111
|
+
@db
|
112
|
+
end
|
113
|
+
|
114
|
+
private
|
115
|
+
# Parses the query lines (begins with "Query = ").
|
116
|
+
def format0_parse_query
|
117
|
+
unless defined?(@query_def)
|
118
|
+
sc = StringScanner.new(@f0query)
|
119
|
+
sc.skip(/\s*/)
|
120
|
+
if sc.skip_until(/Query\= */) then
|
121
|
+
q = []
|
122
|
+
begin
|
123
|
+
q << sc.scan(/.*/)
|
124
|
+
sc.skip(/\s*^ ?/)
|
125
|
+
end until !sc.rest or r = sc.skip(/ *\( *([\,\d]+) *letters *(\; *record *([\,\d]+) *)?\)\s*\z/)
|
126
|
+
@query_len = sc[1].delete(',').to_i if r
|
127
|
+
@query_record_number = sc[3].delete(',').to_i if r and sc[2]
|
128
|
+
@query_def = q.join(' ')
|
129
|
+
end
|
130
|
+
end
|
131
|
+
end
|
132
|
+
|
133
|
+
# Splits headers.
|
134
|
+
def format0_split_headers(data)
|
135
|
+
@f0header = data.shift
|
136
|
+
@f0references = []
|
137
|
+
while r = data.first
|
138
|
+
case r
|
139
|
+
when /^Reference\: /
|
140
|
+
@f0references.push data.shift
|
141
|
+
when /^Copyright /
|
142
|
+
@f0copyright = data.shift
|
143
|
+
when /^Notice\: /
|
144
|
+
@f0notice = data.shift
|
145
|
+
when /^Query\= /
|
146
|
+
break
|
147
|
+
else
|
148
|
+
break
|
149
|
+
end
|
150
|
+
end
|
151
|
+
@f0query = data.shift
|
152
|
+
@f0warnings ||= []
|
153
|
+
while r = data.first and r =~ /^WARNING\: /
|
154
|
+
@f0warnings << data.shift
|
155
|
+
end
|
156
|
+
return if r = data.first and /\AParameters\:/ =~ r
|
157
|
+
if r = data.first and !(/^Database\: / =~ r)
|
158
|
+
@f0translate_info = data.shift
|
159
|
+
end
|
160
|
+
@f0database = data.shift
|
161
|
+
end
|
162
|
+
|
163
|
+
# Splits search data.
|
164
|
+
def format0_split_search(data)
|
165
|
+
@f0warnings ||= []
|
166
|
+
while r = data.first and r =~ /^WARNING\: /
|
167
|
+
@f0warnings << data.shift
|
168
|
+
end
|
169
|
+
[ Iteration.new(data) ]
|
170
|
+
end
|
171
|
+
|
172
|
+
# Splits statistics parameters.
|
173
|
+
def format0_split_stat_params(data)
|
174
|
+
@f0warnings ||= []
|
175
|
+
while r = data.first and r =~ /^WARNING\: /
|
176
|
+
@f0warnings << data.shift
|
177
|
+
end
|
178
|
+
@f0wu_params = []
|
179
|
+
@f0wu_stats = []
|
180
|
+
ary = @f0wu_params
|
181
|
+
while r = data.shift
|
182
|
+
case r
|
183
|
+
when /\AStatistics\:/
|
184
|
+
ary = @f0wu_stats
|
185
|
+
when /\AEXIT CODE *(\d+)\s*$/
|
186
|
+
@exit_code = $1.to_i
|
187
|
+
r = nil
|
188
|
+
when /\AFATAL\: /
|
189
|
+
@fatal_errors ||= []
|
190
|
+
@fatal_errors.push r
|
191
|
+
r = nil
|
192
|
+
when /\AWARNING\: /
|
193
|
+
@f0warnings ||= []
|
194
|
+
@f0warnings << r
|
195
|
+
r = nil
|
196
|
+
end
|
197
|
+
ary << r if r
|
198
|
+
end
|
199
|
+
@f0dbstat = F0dbstat.new(@f0wu_stats)
|
200
|
+
itr = @iterations[0]
|
201
|
+
x = @f0dbstat
|
202
|
+
itr.instance_eval { @f0dbstat = x } if itr
|
203
|
+
end
|
204
|
+
|
205
|
+
# Splits parameters.
|
206
|
+
def parse_parameters
|
207
|
+
unless defined?(@parse_parameters)
|
208
|
+
@parameters = {}
|
209
|
+
@parameter_matrix = []
|
210
|
+
@f0wu_params.each do |x|
|
211
|
+
if /^ Query/ =~ x then
|
212
|
+
@parameter_matrix << x
|
213
|
+
else
|
214
|
+
x.split(/^/).each do |y|
|
215
|
+
if /\A\s*(.+)\s*\=\s*(.*)\s*/ =~ y then
|
216
|
+
@parameters[$1] = $2
|
217
|
+
elsif /\AParameters\:/ =~ y then
|
218
|
+
; #ignore this
|
219
|
+
elsif /\A\s*(.+)\s*$/ =~ y then
|
220
|
+
@parameters[$1] = true
|
221
|
+
end
|
222
|
+
end
|
223
|
+
end
|
224
|
+
end
|
225
|
+
if ev = @parameters['E'] then
|
226
|
+
ev = '1' + ev if ev[0] == ?e
|
227
|
+
@parameters['E'] = ev.to_f
|
228
|
+
end
|
229
|
+
@parse_parameters = true
|
230
|
+
end
|
231
|
+
end
|
232
|
+
|
233
|
+
# Stores database statistics.
|
234
|
+
# Internal use only. Users must not use the class.
|
235
|
+
class F0dbstat < Default::Report::F0dbstat #:nodoc:
|
236
|
+
def initialize(ary)
|
237
|
+
@f0stat = ary
|
238
|
+
@hash = {}
|
239
|
+
end
|
240
|
+
|
241
|
+
#--
|
242
|
+
#undef :f0params
|
243
|
+
#undef :matrix, :gap_open, :gap_extend,
|
244
|
+
# :eff_space, :expect, :sc_match, :sc_mismatch,
|
245
|
+
# :num_hits
|
246
|
+
#++
|
247
|
+
|
248
|
+
# Parses database statistics.
|
249
|
+
def parse_dbstat
|
250
|
+
unless defined?(@parse_dbstat)
|
251
|
+
parse_colon_separated_params(@hash, @f0stat)
|
252
|
+
@database = @hash['Database']
|
253
|
+
@posted_date = @hash['Posted']
|
254
|
+
if val = @hash['# of letters in database'] then
|
255
|
+
@db_len = val.tr(',', '').to_i
|
256
|
+
end
|
257
|
+
if val = @hash['# of sequences in database'] then
|
258
|
+
@db_num = val.tr(',', '').to_i
|
259
|
+
end
|
260
|
+
@parse_dbstat = true
|
261
|
+
end #unless
|
262
|
+
end #def
|
263
|
+
private :parse_dbstat
|
264
|
+
|
265
|
+
end #class F0dbstat
|
266
|
+
|
267
|
+
#--
|
268
|
+
#class Frame
|
269
|
+
#end #class FrameParams
|
270
|
+
#++
|
271
|
+
|
272
|
+
# Iteration class for WU-BLAST report.
|
273
|
+
# Though WU-BLAST does not iterate like PSI-BLAST,
|
274
|
+
# Bio::Blast::WU::Report::Iteration aims to keep compatibility
|
275
|
+
# with Bio::Blast::Default::Report::* classes.
|
276
|
+
# It may contain some Bio::Blast::WU::Report::Hit objects.
|
277
|
+
# Because it inherits Bio::Blast::Default::Report::Iteration,
|
278
|
+
# please also refer Bio::Blast::Default::Report::Iteration.
|
279
|
+
class Iteration < Default::Report::Iteration
|
280
|
+
# Creates a new Iteration object.
|
281
|
+
# It is designed to be called only internally from
|
282
|
+
# the Bio::Blast::WU::Report class.
|
283
|
+
# Users shall not use the method directly.
|
284
|
+
def initialize(data)
|
285
|
+
@f0stat = []
|
286
|
+
@f0dbstat = Default::Report::AlwaysNil.instance
|
287
|
+
@f0hitlist = []
|
288
|
+
@hits = []
|
289
|
+
@num = 1
|
290
|
+
@f0message = []
|
291
|
+
@f0warnings = []
|
292
|
+
return unless r = data.first
|
293
|
+
return if /\AParameters\:$/ =~ r
|
294
|
+
@f0hitlist << data.shift
|
295
|
+
return unless r = data.shift
|
296
|
+
unless /\*{3} +NONE +\*{3}/ =~ r then
|
297
|
+
@f0hitlist << r
|
298
|
+
while r = data.first and /^WARNING\: / =~ r
|
299
|
+
@f0warnings << data.shift
|
300
|
+
end
|
301
|
+
while r = data.first and /^\>/ =~ r
|
302
|
+
@hits << Hit.new(data)
|
303
|
+
end
|
304
|
+
end #unless
|
305
|
+
end
|
306
|
+
|
307
|
+
# Returns warning messages.
|
308
|
+
def warnings
|
309
|
+
@f0warnings
|
310
|
+
end
|
311
|
+
|
312
|
+
private
|
313
|
+
# Parses hit list.
|
314
|
+
def parse_hitlist
|
315
|
+
unless defined?(@parse_hitlist)
|
316
|
+
r = @f0hitlist.shift.to_s
|
317
|
+
if /Reading/ =~ r and /Frame/ =~ r then
|
318
|
+
flag_tblast = true
|
319
|
+
spnum = 5
|
320
|
+
else
|
321
|
+
flag_tblast = nil
|
322
|
+
spnum = 4
|
323
|
+
end
|
324
|
+
i = 0
|
325
|
+
@f0hitlist.each do |x|
|
326
|
+
b = x.split(/^/)
|
327
|
+
b.collect! { |y| y.empty? ? nil : y }
|
328
|
+
b.compact!
|
329
|
+
b.each do |y|
|
330
|
+
y.strip!
|
331
|
+
y.reverse!
|
332
|
+
z = y.split(/\s+/, spnum)
|
333
|
+
z.each { |y| y.reverse! }
|
334
|
+
dfl = z.pop
|
335
|
+
h = @hits[i]
|
336
|
+
unless h then
|
337
|
+
h = Hit.new([ dfl.to_s.sub(/\.+\z/, '') ])
|
338
|
+
@hits[i] = h
|
339
|
+
end
|
340
|
+
z.pop if flag_tblast #ignore Reading Frame
|
341
|
+
scr = z.pop
|
342
|
+
scr = (scr ? scr.to_i : nil)
|
343
|
+
pval = z.pop.to_s
|
344
|
+
pval = '1' + pval if pval[0] == ?e
|
345
|
+
pval = (pval.empty? ? (1.0/0.0) : pval.to_f)
|
346
|
+
nnum = z.pop.to_i
|
347
|
+
h.instance_eval {
|
348
|
+
@score = scr
|
349
|
+
@pvalue = pval
|
350
|
+
@n_number = nnum
|
351
|
+
}
|
352
|
+
i += 1
|
353
|
+
end
|
354
|
+
end #each
|
355
|
+
@parse_hitlist = true
|
356
|
+
end #unless
|
357
|
+
end
|
358
|
+
end #class Iteration
|
359
|
+
|
360
|
+
# Bio::Blast::WU::Report::Hit contains information about a hit.
|
361
|
+
# It may contain some Bio::Blast::WU::Report::HSP objects.
|
362
|
+
#
|
363
|
+
# Because it inherits Bio::Blast::Default::Report::Hit,
|
364
|
+
# please also refer Bio::Blast::Default::Report::Hit.
|
365
|
+
class Hit < Default::Report::Hit
|
366
|
+
# Creates a new Hit object.
|
367
|
+
# It is designed to be called only internally from the
|
368
|
+
# Bio::Blast::WU::Report::Iteration class.
|
369
|
+
# Users should not call the method directly.
|
370
|
+
def initialize(data)
|
371
|
+
@f0hitname = data.shift
|
372
|
+
@hsps = []
|
373
|
+
while r = data.first
|
374
|
+
if r =~ /^\s*(?:Plus|Minus) +Strand +HSPs\:/ then
|
375
|
+
data.shift
|
376
|
+
r = data.first
|
377
|
+
end
|
378
|
+
if /\A\s+Score/ =~ r then
|
379
|
+
@hsps << HSP.new(data)
|
380
|
+
else
|
381
|
+
break
|
382
|
+
end
|
383
|
+
end
|
384
|
+
@again = false
|
385
|
+
end
|
386
|
+
|
387
|
+
# Returns score.
|
388
|
+
def score
|
389
|
+
@score
|
390
|
+
end
|
391
|
+
# p-value
|
392
|
+
attr_reader :pvalue
|
393
|
+
# n-number (???)
|
394
|
+
attr_reader :n_number
|
395
|
+
end #class Hit
|
396
|
+
|
397
|
+
# Bio::Blast::WU::Report::HSP holds information about the hsp
|
398
|
+
# (high-scoring segment pair).
|
399
|
+
#
|
400
|
+
# Because it inherits Bio::Blast::Default::Report::HSP,
|
401
|
+
# please also refer Bio::Blast::Default::Report::HSP.
|
402
|
+
class HSP < Default::Report::HSP
|
403
|
+
# p-value
|
404
|
+
attr_reader :pvalue if false #dummy
|
405
|
+
method_after_parse_score :pvalue
|
406
|
+
# p_sum_n (???)
|
407
|
+
attr_reader :p_sum_n if false #dummy
|
408
|
+
method_after_parse_score :p_sum_n
|
409
|
+
end #class HSP
|
410
|
+
|
411
|
+
end #class Report
|
412
|
+
|
413
|
+
# WU-BLAST default output parser for TBLAST.
|
414
|
+
# All methods are equal to Bio::Blast::WU::Report.
|
415
|
+
# Only DELIMITER (and RS) is different.
|
416
|
+
class Report_TBlast < Report
|
417
|
+
# Delimter of each entry for TBLAST. Bio::FlatFile uses it.
|
418
|
+
DELIMITER = RS = "\nTBLAST"
|
419
|
+
|
420
|
+
# (Integer) excess read size included in DELIMITER.
|
421
|
+
DELIMITER_OVERRUN = 6 # "TBLAST"
|
422
|
+
end #class Report_TBlast
|
423
|
+
|
424
|
+
end #module WU
|
425
|
+
end #class Blast
|
426
|
+
end #module Bio
|
427
|
+
|
428
|
+
######################################################################
|
429
|
+
|
430
|
+
if __FILE__ == $0
|
431
|
+
|
432
|
+
Bio::FlatFile.open(Bio::Blast::WU::Report, ARGF) do |ff|
|
433
|
+
ff.each do |rep|
|
434
|
+
|
435
|
+
print "# === Bio::Blast::WU::Report\n"
|
436
|
+
puts
|
437
|
+
print " rep.program #=> "; p rep.program
|
438
|
+
print " rep.version #=> "; p rep.version
|
439
|
+
print " rep.reference #=> "; p rep.reference
|
440
|
+
print " rep.notice #=> "; p rep.notice
|
441
|
+
print " rep.db #=> "; p rep.db
|
442
|
+
#print " rep.query_id #=> "; p rep.query_id
|
443
|
+
print " rep.query_def #=> "; p rep.query_def
|
444
|
+
print " rep.query_len #=> "; p rep.query_len
|
445
|
+
#puts
|
446
|
+
print " rep.version_number #=> "; p rep.version_number
|
447
|
+
print " rep.version_date #=> "; p rep.version_date
|
448
|
+
puts
|
449
|
+
|
450
|
+
print "# === Parameters\n"
|
451
|
+
#puts
|
452
|
+
print " rep.parameters #=> "; p rep.parameters
|
453
|
+
puts
|
454
|
+
#@#print " rep.matrix #=> "; p rep.matrix
|
455
|
+
print " rep.expect #=> "; p rep.expect
|
456
|
+
#print " rep.inclusion #=> "; p rep.inclusion
|
457
|
+
#@#print " rep.sc_match #=> "; p rep.sc_match
|
458
|
+
#@#print " rep.sc_mismatch #=> "; p rep.sc_mismatch
|
459
|
+
#@#print " rep.gap_open #=> "; p rep.gap_open
|
460
|
+
#@#print " rep.gap_extend #=> "; p rep.gap_extend
|
461
|
+
#print " rep.filter #=> "; p rep.filter
|
462
|
+
#@#print " rep.pattern #=> "; p rep.pattern
|
463
|
+
#print " rep.entrez_query #=> "; p rep.entrez_query
|
464
|
+
#puts
|
465
|
+
#@#print " rep.pattern_positions #=> "; p rep.pattern_positions
|
466
|
+
puts
|
467
|
+
|
468
|
+
print "# === Statistics (last iteration's)\n"
|
469
|
+
#puts
|
470
|
+
#print " rep.statistics #=> "; p rep.statistics
|
471
|
+
puts
|
472
|
+
print " rep.db_num #=> "; p rep.db_num
|
473
|
+
print " rep.db_len #=> "; p rep.db_len
|
474
|
+
#print " rep.hsp_len #=> "; p rep.hsp_len
|
475
|
+
#@#print " rep.eff_space #=> "; p rep.eff_space
|
476
|
+
#@#print " rep.kappa #=> "; p rep.kappa
|
477
|
+
#@#print " rep.lambda #=> "; p rep.lambda
|
478
|
+
#@#print " rep.entropy #=> "; p rep.entropy
|
479
|
+
puts
|
480
|
+
#@#print " rep.num_hits #=> "; p rep.num_hits
|
481
|
+
#@#print " rep.gapped_kappa #=> "; p rep.gapped_kappa
|
482
|
+
#@#print " rep.gapped_lambda #=> "; p rep.gapped_lambda
|
483
|
+
#@#print " rep.gapped_entropy #=> "; p rep.gapped_entropy
|
484
|
+
#@#print " rep.posted_date #=> "; p rep.posted_date
|
485
|
+
puts
|
486
|
+
|
487
|
+
#@#print "# === Message (last iteration's)\n"
|
488
|
+
#@#puts
|
489
|
+
#@#print " rep.message #=> "; p rep.message
|
490
|
+
#puts
|
491
|
+
#@#print " rep.converged? #=> "; p rep.converged?
|
492
|
+
#puts
|
493
|
+
|
494
|
+
print "# === Warning messages\n"
|
495
|
+
print " rep.warnings #=> "; p rep.warnings
|
496
|
+
|
497
|
+
print "# === Iterations\n"
|
498
|
+
puts
|
499
|
+
print " rep.itrerations.each do |itr|\n"
|
500
|
+
puts
|
501
|
+
|
502
|
+
rep.iterations.each do |itr|
|
503
|
+
|
504
|
+
print "# --- Bio::Blast::WU::Report::Iteration\n"
|
505
|
+
puts
|
506
|
+
|
507
|
+
print " itr.num #=> "; p itr.num
|
508
|
+
#print " itr.statistics #=> "; p itr.statistics
|
509
|
+
puts
|
510
|
+
print " itr.warnings #=> "; p itr.warnings
|
511
|
+
print " itr.message #=> "; p itr.message
|
512
|
+
print " itr.hits.size #=> "; p itr.hits.size
|
513
|
+
#puts
|
514
|
+
#@#print " itr.hits_newly_found.size #=> "; p itr.hits_newly_found.size;
|
515
|
+
#@#print " itr.hits_found_again.size #=> "; p itr.hits_found_again.size;
|
516
|
+
if itr.hits_for_pattern then
|
517
|
+
itr.hits_for_pattern.each_with_index do |hp, hpi|
|
518
|
+
print " itr.hits_for_pattern[#{hpi}].size #=> "; p hp.size;
|
519
|
+
end
|
520
|
+
end
|
521
|
+
print " itr.converged? #=> "; p itr.converged?
|
522
|
+
puts
|
523
|
+
|
524
|
+
print " itr.hits.each do |hit|\n"
|
525
|
+
puts
|
526
|
+
|
527
|
+
itr.hits.each_with_index do |hit, i|
|
528
|
+
|
529
|
+
print "# --- Bio::Blast::WU::Report::Hit"
|
530
|
+
print " ([#{i}])\n"
|
531
|
+
puts
|
532
|
+
|
533
|
+
#print " hit.num #=> "; p hit.num
|
534
|
+
#print " hit.hit_id #=> "; p hit.hit_id
|
535
|
+
print " hit.len #=> "; p hit.len
|
536
|
+
print " hit.definition #=> "; p hit.definition
|
537
|
+
#print " hit.accession #=> "; p hit.accession
|
538
|
+
#puts
|
539
|
+
print " hit.found_again? #=> "; p hit.found_again?
|
540
|
+
#puts
|
541
|
+
print " hit.score #=> "; p hit.score
|
542
|
+
print " hit.pvalue #=> "; p hit.pvalue
|
543
|
+
print " hit.n_number #=> "; p hit.n_number
|
544
|
+
|
545
|
+
print " --- compatible/shortcut ---\n"
|
546
|
+
#print " hit.query_id #=> "; p hit.query_id
|
547
|
+
#print " hit.query_def #=> "; p hit.query_def
|
548
|
+
#print " hit.query_len #=> "; p hit.query_len
|
549
|
+
#print " hit.target_id #=> "; p hit.target_id
|
550
|
+
print " hit.target_def #=> "; p hit.target_def
|
551
|
+
print " hit.target_len #=> "; p hit.target_len
|
552
|
+
|
553
|
+
print " --- first HSP's values (shortcut) ---\n"
|
554
|
+
print " hit.evalue #=> "; p hit.evalue
|
555
|
+
print " hit.bit_score #=> "; p hit.bit_score
|
556
|
+
print " hit.identity #=> "; p hit.identity
|
557
|
+
#print " hit.overlap #=> "; p hit.overlap
|
558
|
+
|
559
|
+
print " hit.query_seq #=> "; p hit.query_seq
|
560
|
+
print " hit.midline #=> "; p hit.midline
|
561
|
+
print " hit.target_seq #=> "; p hit.target_seq
|
562
|
+
|
563
|
+
print " hit.query_start #=> "; p hit.query_start
|
564
|
+
print " hit.query_end #=> "; p hit.query_end
|
565
|
+
print " hit.target_start #=> "; p hit.target_start
|
566
|
+
print " hit.target_end #=> "; p hit.target_end
|
567
|
+
print " hit.lap_at #=> "; p hit.lap_at
|
568
|
+
print " --- first HSP's vaules (shortcut) ---\n"
|
569
|
+
print " --- compatible/shortcut ---\n"
|
570
|
+
|
571
|
+
puts
|
572
|
+
print " hit.hsps.size #=> "; p hit.hsps.size
|
573
|
+
if hit.hsps.size == 0 then
|
574
|
+
puts " (HSP not found: please see blastall's -b and -v options)"
|
575
|
+
puts
|
576
|
+
else
|
577
|
+
|
578
|
+
puts
|
579
|
+
print " hit.hsps.each do |hsp|\n"
|
580
|
+
puts
|
581
|
+
|
582
|
+
hit.hsps.each_with_index do |hsp, j|
|
583
|
+
|
584
|
+
print "# --- Bio::Blast::WU::Report::Hsp"
|
585
|
+
print " ([#{j}])\n"
|
586
|
+
puts
|
587
|
+
#print " hsp.num #=> "; p hsp.num
|
588
|
+
print " hsp.bit_score #=> "; p hsp.bit_score
|
589
|
+
print " hsp.score #=> "; p hsp.score
|
590
|
+
print " hsp.evalue #=> "; p hsp.evalue
|
591
|
+
print " hsp.identity #=> "; p hsp.identity
|
592
|
+
print " hsp.gaps #=> "; p hsp.gaps
|
593
|
+
print " hsp.positive #=> "; p hsp.positive
|
594
|
+
print " hsp.align_len #=> "; p hsp.align_len
|
595
|
+
#print " hsp.density #=> "; p hsp.density
|
596
|
+
puts
|
597
|
+
print " hsp.pvalue #=> "; p hsp.pvalue
|
598
|
+
print " hsp.p_sum_n #=> "; p hsp.p_sum_n
|
599
|
+
puts
|
600
|
+
|
601
|
+
print " hsp.query_frame #=> "; p hsp.query_frame
|
602
|
+
print " hsp.query_from #=> "; p hsp.query_from
|
603
|
+
print " hsp.query_to #=> "; p hsp.query_to
|
604
|
+
|
605
|
+
print " hsp.hit_frame #=> "; p hsp.hit_frame
|
606
|
+
print " hsp.hit_from #=> "; p hsp.hit_from
|
607
|
+
print " hsp.hit_to #=> "; p hsp.hit_to
|
608
|
+
|
609
|
+
#print " hsp.pattern_from#=> "; p hsp.pattern_from
|
610
|
+
#print " hsp.pattern_to #=> "; p hsp.pattern_to
|
611
|
+
|
612
|
+
print " hsp.qseq #=> "; p hsp.qseq
|
613
|
+
print " hsp.midline #=> "; p hsp.midline
|
614
|
+
print " hsp.hseq #=> "; p hsp.hseq
|
615
|
+
puts
|
616
|
+
print " hsp.percent_identity #=> "; p hsp.percent_identity
|
617
|
+
#print " hsp.mismatch_count #=> "; p hsp.mismatch_count
|
618
|
+
#
|
619
|
+
print " hsp.query_strand #=> "; p hsp.query_strand
|
620
|
+
print " hsp.hit_strand #=> "; p hsp.hit_strand
|
621
|
+
print " hsp.percent_positive #=> "; p hsp.percent_positive
|
622
|
+
print " hsp.percent_gaps #=> "; p hsp.percent_gaps
|
623
|
+
puts
|
624
|
+
|
625
|
+
end #each
|
626
|
+
end #if hit.hsps.size == 0
|
627
|
+
end
|
628
|
+
end
|
629
|
+
end #ff.each
|
630
|
+
end #FlatFile.open
|
631
|
+
|
632
|
+
end #if __FILE__ == $0
|
633
|
+
|
634
|
+
######################################################################
|
635
|
+
|