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 +1,236 @@
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#
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# = bio/appl/blast/xmlparser.rb - BLAST XML output (-m 7) parser by XMLParser
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#
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# Copyright:: Copyright (C) 2001
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# Mitsuteru C. Nakao <n@bioruby.org>
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# Copyright:: Copyright (C) 2003
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# 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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# == Description
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#
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# A parser for blast XML report (format 7) based on the XMLParser.
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# This file is automatically loaded by bio/appl/blast/report.rb if
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# the XMLParser installed.
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#
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# BioRuby provides two implements of the paser for the blast XML format report
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# (format 7) based on the XMLParser and the REXML.
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#
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begin
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require 'xmlparser'
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rescue LoadError
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end
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module Bio
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class Blast
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class Report
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private
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def xmlparser_parse(xml)
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parser = XMLParser.new
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def parser.default; end
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begin
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tag_stack = Array.new
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hash = Hash.new
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parser.parse(xml) do |type, name, data|
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case type
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when XMLParser::START_ELEM
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tag_stack.push(name)
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hash.update(data)
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case name
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when 'Iteration'
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iteration = Iteration.new
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@iterations.push(iteration)
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when 'Hit'
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hit = Hit.new
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hit.query_id = @query_id
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hit.query_def = @query_def
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hit.query_len = @query_len
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@iterations.last.hits.push(hit)
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when 'Hsp'
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hsp = Hsp.new
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@iterations.last.hits.last.hsps.push(hsp)
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end
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when XMLParser::END_ELEM
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case name
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when /^BlastOutput/
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xmlparser_parse_program(name,hash)
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hash = Hash.new
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when /^Parameters$/
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xmlparser_parse_parameters(hash)
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hash = Hash.new
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when /^Iteration/
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xmlparser_parse_iteration(name, hash)
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hash = Hash.new
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when /^Hit/
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xmlparser_parse_hit(name, hash)
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hash = Hash.new
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when /^Hsp$/
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xmlparser_parse_hsp(hash)
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hash = Hash.new
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when /^Statistics$/
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xmlparser_parse_statistics(hash)
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hash = Hash.new
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end
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tag_stack.pop
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when XMLParser::CDATA
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if hash[tag_stack.last].nil?
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hash[tag_stack.last] = data unless data.strip.empty?
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else
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hash[tag_stack.last].concat(data) if data
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end
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when XMLParser::PI
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end
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end
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rescue XMLParserError
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line = parser.line
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column = parser.column
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print "Parse error at #{line}(#{column}) : #{$!}\n"
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end
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end
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def xmlparser_parse_program(tag, hash)
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case tag
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when 'BlastOutput_program'
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@program = hash[tag]
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when 'BlastOutput_version'
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@version = hash[tag]
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when 'BlastOutput_reference'
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@reference = hash[tag]
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when 'BlastOutput_db'
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@db = hash[tag].strip
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when 'BlastOutput_query-ID'
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@query_id = hash[tag]
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when 'BlastOutput_query-def'
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@query_def = hash[tag]
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when 'BlastOutput_query-len'
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@query_len = hash[tag].to_i
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end
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end
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# set parameter of the key as val
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def xml_set_parameter(key, val)
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#labels = {
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# 'matrix' => 'Parameters_matrix',
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# 'expect' => 'Parameters_expect',
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# 'include' => 'Parameters_include',
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# 'sc-match' => 'Parameters_sc-match',
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# 'sc-mismatch' => 'Parameters_sc-mismatch',
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# 'gap-open' => 'Parameters_gap-open',
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# 'gap-extend' => 'Parameters_gap-extend',
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# 'filter' => 'Parameters_filter',
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# 'pattern' => 'Parameters_pattern',
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# 'entrez-query' => 'Parameters_entrez-query',
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#}
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k = key.sub(/\AParameters\_/, '')
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@parameters[k] =
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case k
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when 'expect', 'include'
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val.to_f
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when /\Agap\-/, /\Asc\-/
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val.to_i
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else
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val
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end
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end
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def xmlparser_parse_parameters(hash)
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hash.each do |k, v|
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xml_set_parameter(k, v)
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end
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end
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def xmlparser_parse_iteration(tag, hash)
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case tag
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when 'Iteration_iter-num'
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@iterations.last.num = hash[tag].to_i
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when 'Iteration_message'
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@iterations.last.message = hash[tag].to_s
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# for new BLAST XML format
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when 'Iteration_query-ID'
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@iterations.last.query_id = hash[tag].to_s
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when 'Iteration_query-def'
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@iterations.last.query_def = hash[tag].to_s
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when 'Iteration_query-len'
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@iterations.last.query_len = hash[tag].to_i
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end
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end
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def xmlparser_parse_hit(tag, hash)
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hit = @iterations.last.hits.last
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case tag
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when 'Hit_num'
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hit.num = hash[tag].to_i
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when 'Hit_id'
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hit.hit_id = hash[tag].clone
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when 'Hit_def'
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hit.definition = hash[tag].clone
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when 'Hit_accession'
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hit.accession = hash[tag].clone
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when 'Hit_len'
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hit.len = hash[tag].clone.to_i
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end
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end
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def xmlparser_parse_hsp(hash)
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hsp = @iterations.last.hits.last.hsps.last
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hsp.num = hash['Hsp_num'].to_i
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hsp.bit_score = hash['Hsp_bit-score'].to_f
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hsp.score = hash['Hsp_score'].to_i
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hsp.evalue = hash['Hsp_evalue'].to_f
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hsp.query_from = hash['Hsp_query-from'].to_i
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hsp.query_to = hash['Hsp_query-to'].to_i
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hsp.hit_from = hash['Hsp_hit-from'].to_i
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hsp.hit_to = hash['Hsp_hit-to'].to_i
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hsp.pattern_from = hash['Hsp_pattern-from'].to_i
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hsp.pattern_to = hash['Hsp_pattern-to'].to_i
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hsp.query_frame = hash['Hsp_query-frame'].to_i
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hsp.hit_frame = hash['Hsp_hit-frame'].to_i
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hsp.identity = hash['Hsp_identity'].to_i
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hsp.positive = hash['Hsp_positive'].to_i
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hsp.gaps = hash['Hsp_gaps'].to_i
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hsp.align_len = hash['Hsp_align-len'].to_i
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hsp.density = hash['Hsp_density'].to_i
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hsp.qseq = hash['Hsp_qseq']
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hsp.hseq = hash['Hsp_hseq']
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hsp.midline = hash['Hsp_midline']
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end
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def xmlparser_parse_statistics(hash)
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labels = {
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'db-num' => 'Statistics_db-num',
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'db-len' => 'Statistics_db-len',
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'hsp-len' => 'Statistics_hsp-len',
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'eff-space' => 'Statistics_eff-space',
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'kappa' => 'Statistics_kappa',
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'lambda' => 'Statistics_lambda',
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'entropy' => 'Statistics_entropy'
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}
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labels.each do |k,v|
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case k
|
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when 'db-num', 'db-len', 'hsp-len'
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@iterations.last.statistics[k] = hash[v].to_i
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else
|
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@iterations.last.statistics[k] = hash[v].to_f
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end
|
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end
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end
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end # class Report
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end # class Blast
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end # module Bio
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|
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=begin
|
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|
234
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This file is automatically loaded by bio/appl/blast/report.rb
|
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|
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=end
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@@ -0,0 +1,530 @@
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#
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# = bio/appl/blat/report.rb - BLAT result parser
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#
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# Copyright:: Copyright (C) 2004, 2006, 2008 Naohisa Goto <ng@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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# BLAT result parser (psl / pslx format).
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#
|
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# == Important Notes
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#
|
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# In BLAT results, the start position of a sequnece is numbered as 0.
|
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# On the other hand, in many other homology search programs,
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# the start position of a sequence is numbered as 1.
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# To keep compatibility, the BLAT parser adds 1 to every position number.
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#
|
18
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# == References
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19
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#
|
20
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# * Kent, W.J., BLAT--the BLAST-like alignment tool,
|
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# Genome Research, 12, 656--664, 2002.
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# http://www.genome.org/cgi/content/abstract/12/4/656
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# * http://genome.ucsc.edu/goldenPath/help/blatSpec.html
|
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+
|
25
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require 'bio'
|
26
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+
|
27
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module Bio
|
28
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class Blat
|
29
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+
|
30
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# Bio::Blat::Report is a BLAT report parser class.
|
31
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# Its object may contain some Bio::Blat::Report::Hits objects.
|
32
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#
|
33
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# In BLAT results, the start position of a sequnece is numbered as 0.
|
34
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# On the other hand, in many other homology search programs,
|
35
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# the start position of a sequence is numbered as 1.
|
36
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# To keep compatibility, the BLAT parser adds 1 to every position number
|
37
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# except Bio::Blat::Report::Seqdesc and some Bio::Blat specific methods.
|
38
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#
|
39
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# Note that Bio::Blat::Report#query_def, #query_id, #query_len methods
|
40
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# simply return first hit's query_*.
|
41
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# If multiple query sequences are given, these values
|
42
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# will be incorrect.
|
43
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#
|
44
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class Report #< DB
|
45
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# Delimiter of each entry. Bio::FlatFile uses it.
|
46
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# In Bio::Blat::Report, it it nil (1 entry 1 file).
|
47
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DELIMITER = RS = nil # 1 file 1 entry
|
48
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+
|
49
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# Splitter for Bio::FlatFile
|
50
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+
FLATFILE_SPLITTER = Bio::FlatFile::Splitter::LineOriented
|
51
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+
|
52
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+
# Creates a new Bio::Blat::Report object from BLAT result text (String).
|
53
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+
# You can use Bio::FlatFile to read a file.
|
54
|
+
# Currently, results created with options -out=psl (default) or
|
55
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+
# -out=pslx are supported.
|
56
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+
def initialize(text = '')
|
57
|
+
flag = false
|
58
|
+
head = []
|
59
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+
@hits = []
|
60
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+
text.each_line do |line|
|
61
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+
if flag then
|
62
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@hits << Hit.new(line)
|
63
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+
else
|
64
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+
# for headerless data
|
65
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+
if /^\d/ =~ line then
|
66
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+
flag = true
|
67
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+
redo
|
68
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+
end
|
69
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+
line = line.chomp
|
70
|
+
if /\A\-+\s*\z/ =~ line
|
71
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+
flag = true
|
72
|
+
else
|
73
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+
head << line
|
74
|
+
end
|
75
|
+
end
|
76
|
+
end
|
77
|
+
@columns = parse_header(head) unless head.empty?
|
78
|
+
end
|
79
|
+
|
80
|
+
# Adds a header line if the header data is not yet given and
|
81
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+
# the given line is suitable for header.
|
82
|
+
# Returns self if adding header line is succeeded.
|
83
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+
# Otherwise, returns false (the line is not added).
|
84
|
+
def add_header_line(line)
|
85
|
+
return false if defined? @columns
|
86
|
+
line = line.chomp
|
87
|
+
case line
|
88
|
+
when /^\d/
|
89
|
+
@columns = (defined? @header_lines) ? parse_header(@header_lines) : []
|
90
|
+
return false
|
91
|
+
when /\A\-+\s*\z/
|
92
|
+
@columns = (defined? @header_lines) ? parse_header(@header_lines) : []
|
93
|
+
return self
|
94
|
+
else
|
95
|
+
@header_lines ||= []
|
96
|
+
@header_lines.push line
|
97
|
+
end
|
98
|
+
end
|
99
|
+
|
100
|
+
# Adds a line to the entry if the given line is regarded as
|
101
|
+
# a part of the current entry.
|
102
|
+
# If the current entry (self) is empty, or the line has the same
|
103
|
+
# query name, the line is added and returns self.
|
104
|
+
# Otherwise, returns false (the line is not added).
|
105
|
+
def add_line(line)
|
106
|
+
if /\A\s*\z/ =~ line then
|
107
|
+
return @hits.empty? ? self : false
|
108
|
+
end
|
109
|
+
hit = Hit.new(line.chomp)
|
110
|
+
if @hits.empty? or @hits.first.query.name == hit.query.name then
|
111
|
+
@hits.push hit
|
112
|
+
return self
|
113
|
+
else
|
114
|
+
return false
|
115
|
+
end
|
116
|
+
end
|
117
|
+
|
118
|
+
# hits of the result.
|
119
|
+
# Returns an Array of Bio::Blat::Report::Hit objects.
|
120
|
+
attr_reader :hits
|
121
|
+
|
122
|
+
# Returns descriptions of columns.
|
123
|
+
# Returns an Array.
|
124
|
+
# This would be a Bio::Blat specific method.
|
125
|
+
attr_reader :columns
|
126
|
+
|
127
|
+
# Parses headers.
|
128
|
+
def parse_header(ary)
|
129
|
+
while x = ary.shift
|
130
|
+
if /psLayout version (\S+)/ =~ x then
|
131
|
+
@psl_version = $1
|
132
|
+
break
|
133
|
+
elsif !(x.strip.empty?)
|
134
|
+
ary.unshift(x)
|
135
|
+
break
|
136
|
+
end
|
137
|
+
end
|
138
|
+
a0 = ary.collect { |x| x.split(/\t/) }
|
139
|
+
k = []
|
140
|
+
a0.each do |x|
|
141
|
+
x.each_index do |i|
|
142
|
+
y = x[i].strip
|
143
|
+
k[i] = k[i].to_s + (y.sub!(/\-\z/, '') ? y : y + ' ')
|
144
|
+
end
|
145
|
+
end
|
146
|
+
k.each { |x| x.strip! }
|
147
|
+
k
|
148
|
+
end
|
149
|
+
private :parse_header
|
150
|
+
|
151
|
+
# version of the psl format (String or nil).
|
152
|
+
attr_reader :psl_version
|
153
|
+
|
154
|
+
# Bio::Blat::Report::SeqDesc stores sequence information of
|
155
|
+
# query or subject of the BLAT report.
|
156
|
+
# It also includes some hit information.
|
157
|
+
class SeqDesc
|
158
|
+
# Creates a new SeqDesc object.
|
159
|
+
# It is designed to be called internally from Bio::Blat::Report class.
|
160
|
+
# Users shall not use it directly.
|
161
|
+
def initialize(gap_count, gap_bases, name, size,
|
162
|
+
st, ed, starts, seqs)
|
163
|
+
@gap_count = gap_count.to_i
|
164
|
+
@gap_bases = gap_bases.to_i
|
165
|
+
@name = name
|
166
|
+
@size = size.to_i
|
167
|
+
@start = st.to_i
|
168
|
+
@end = ed.to_i
|
169
|
+
@starts = starts.collect { |x| x.to_i }
|
170
|
+
@seqs = seqs
|
171
|
+
end
|
172
|
+
# gap count
|
173
|
+
attr_reader :gap_count
|
174
|
+
# gap bases
|
175
|
+
attr_reader :gap_bases
|
176
|
+
# name of the sequence
|
177
|
+
attr_reader :name
|
178
|
+
# length of the sequence
|
179
|
+
attr_reader :size
|
180
|
+
# start position of the first segment
|
181
|
+
attr_reader :start
|
182
|
+
# end position of the final segment
|
183
|
+
attr_reader :end
|
184
|
+
# start positions of segments.
|
185
|
+
# Returns an array of numbers.
|
186
|
+
attr_reader :starts
|
187
|
+
# sequences of segments.
|
188
|
+
# Returns an array of String.
|
189
|
+
# Returns nil if there are no sequence data.
|
190
|
+
attr_reader :seqs
|
191
|
+
end #class SeqDesc
|
192
|
+
|
193
|
+
# Sequence segment pair of BLAT result.
|
194
|
+
# Similar to Bio::Blast::Report::Hsp but lacks many methods.
|
195
|
+
class SegmentPair
|
196
|
+
# Creates a new SegmentPair object.
|
197
|
+
# It is designed to be called internally from Bio::Blat::Report class.
|
198
|
+
# Users shall not use it directly.
|
199
|
+
def initialize(query_len, target_len, strand,
|
200
|
+
blksize, qstart, tstart, qseq, tseq,
|
201
|
+
protein_flag)
|
202
|
+
@blocksize = blksize
|
203
|
+
@qseq = qseq
|
204
|
+
@hseq = hseq
|
205
|
+
@hit_strand = 'plus'
|
206
|
+
w = (protein_flag ? 3 : 1) # 3 means query=protein target=dna
|
207
|
+
case strand
|
208
|
+
when '-'
|
209
|
+
# query is minus strand
|
210
|
+
@query_strand = 'minus'
|
211
|
+
# convert positions
|
212
|
+
@query_from = query_len - qstart
|
213
|
+
@query_to = query_len - qstart - blksize + 1
|
214
|
+
# To keep compatibility, with other homology search programs,
|
215
|
+
# we add 1 to each position number.
|
216
|
+
@hit_from = tstart + 1
|
217
|
+
@hit_to = tstart + blksize * w # - 1 + 1
|
218
|
+
when '+-'
|
219
|
+
# hit is minus strand
|
220
|
+
@query_strand = 'plus'
|
221
|
+
@hit_strand = 'minus'
|
222
|
+
# To keep compatibility, with other homology search programs,
|
223
|
+
# we add 1 to each position number.
|
224
|
+
@query_from = qstart + 1
|
225
|
+
@query_to = qstart + blksize # - 1 + 1
|
226
|
+
# convert positions
|
227
|
+
@hit_from = target_len - tstart
|
228
|
+
@hit_to = target_len - tstart - blksize * w + 1
|
229
|
+
else #when '+', '++'
|
230
|
+
@query_strand = 'plus'
|
231
|
+
# To keep compatibility with other homology search programs,
|
232
|
+
# we add 1 to each position number.
|
233
|
+
@query_from = qstart + 1
|
234
|
+
@query_to = qstart + blksize # - 1 + 1
|
235
|
+
@hit_from = tstart + 1
|
236
|
+
@hit_to = tstart + blksize * w # - 1 + 1
|
237
|
+
end
|
238
|
+
end
|
239
|
+
# Returns query start position.
|
240
|
+
# CAUTION: In Blat's raw result(psl format), first position is 0.
|
241
|
+
# To keep compatibility, the parser add 1 to the position.
|
242
|
+
attr_reader :query_from
|
243
|
+
|
244
|
+
# Returns query end position.
|
245
|
+
# CAUTION: In Blat's raw result(psl format), first position is 0.
|
246
|
+
# To keep compatibility, the parser add 1 to the position.
|
247
|
+
attr_reader :query_to
|
248
|
+
|
249
|
+
# Returns query sequence.
|
250
|
+
# If sequence data is not available, returns nil.
|
251
|
+
attr_reader :qseq
|
252
|
+
|
253
|
+
# Returns strand information of the query.
|
254
|
+
# Returns 'plus' or 'minus'.
|
255
|
+
attr_reader :query_strand
|
256
|
+
|
257
|
+
# Returns target (subject, hit) start position.
|
258
|
+
# CAUTION: In Blat's raw result(psl format), first position is 0.
|
259
|
+
# To keep compatibility, the parser add 1 to the position.
|
260
|
+
attr_reader :hit_from
|
261
|
+
|
262
|
+
# Returns target (subject, hit) end position.
|
263
|
+
# CAUTION: In Blat's raw result(psl format), first position is 0.
|
264
|
+
# To keep compatibility, the parser add 1 to the position.
|
265
|
+
attr_reader :hit_to
|
266
|
+
|
267
|
+
# Returns the target (subject, hit) sequence.
|
268
|
+
# If sequence data is not available, returns nil.
|
269
|
+
attr_reader :hseq
|
270
|
+
|
271
|
+
# Returns strand information of the target (subject, hit).
|
272
|
+
# Returns 'plus' or 'minus'.
|
273
|
+
attr_reader :hit_strand
|
274
|
+
|
275
|
+
# Returns block size (length) of the segment pair.
|
276
|
+
# This would be a Bio::Blat specific method.
|
277
|
+
attr_reader :blocksize
|
278
|
+
|
279
|
+
# Returns alignment length of the segment pair.
|
280
|
+
# Returns nil if no alignment data are available.
|
281
|
+
def align_len
|
282
|
+
@qseq ? @qseq.size : nil
|
283
|
+
end
|
284
|
+
end #class SegmentPair
|
285
|
+
|
286
|
+
# Hit class for the BLAT result parser.
|
287
|
+
# Similar to Bio::Blast::Report::Hit but lacks many methods.
|
288
|
+
# Its object may contain some Bio::Blat::Report::SegmentPair objects.
|
289
|
+
class Hit
|
290
|
+
# Creates a new Hit object from a piece of BLAT result text.
|
291
|
+
# It is designed to be called internally from Bio::Blat::Report object.
|
292
|
+
# Users shall not use it directly.
|
293
|
+
def initialize(str)
|
294
|
+
@data = str.chomp.split(/\t/)
|
295
|
+
end
|
296
|
+
|
297
|
+
# Raw data of the hit.
|
298
|
+
# (Note that it doesn't add 1 to position numbers.)
|
299
|
+
attr_reader :data
|
300
|
+
|
301
|
+
# split comma-separeted text
|
302
|
+
def split_comma(str)
|
303
|
+
str.to_s.sub(/\s*\,+\s*\z/, '').split(/\s*\,\s*/)
|
304
|
+
end
|
305
|
+
private :split_comma
|
306
|
+
|
307
|
+
# Returns sequence informations of the query.
|
308
|
+
# Returns a Bio::Blat::Report::SeqDesc object.
|
309
|
+
# This would be Bio::Blat specific method.
|
310
|
+
def query
|
311
|
+
unless defined?(@query)
|
312
|
+
d = @data
|
313
|
+
@query = SeqDesc.new(d[4], d[5], d[9], d[10], d[11], d[12],
|
314
|
+
split_comma(d[19]), split_comma(d[21]))
|
315
|
+
end
|
316
|
+
@query
|
317
|
+
end
|
318
|
+
|
319
|
+
# Returns sequence informations of the target(hit).
|
320
|
+
# Returns a Bio::Blat::Report::SeqDesc object.
|
321
|
+
# This would be Bio::Blat specific method.
|
322
|
+
def target
|
323
|
+
unless defined?(@target)
|
324
|
+
d = @data
|
325
|
+
@target = SeqDesc.new(d[6], d[7], d[13], d[14], d[15], d[16],
|
326
|
+
split_comma(d[20]), split_comma(d[22]))
|
327
|
+
end
|
328
|
+
@target
|
329
|
+
end
|
330
|
+
|
331
|
+
# Match nucleotides.
|
332
|
+
def match; @data[0].to_i; end
|
333
|
+
# Mismatch nucleotides.
|
334
|
+
def mismatch; @data[1].to_i; end
|
335
|
+
|
336
|
+
# "rep. match".
|
337
|
+
# Number of bases that match but are part of repeats.
|
338
|
+
# Note that current version of BLAT always set 0.
|
339
|
+
def rep_match; @data[2].to_i; end
|
340
|
+
|
341
|
+
# "N's". Number of 'N' bases.
|
342
|
+
def n_s; @data[3].to_i; end
|
343
|
+
|
344
|
+
# Returns strand information of the hit.
|
345
|
+
# Returns '+' or '-'.
|
346
|
+
# This would be a Bio::Blat specific method.
|
347
|
+
def strand; @data[8]; end
|
348
|
+
|
349
|
+
# Number of blocks(exons, segment pairs).
|
350
|
+
def block_count; @data[17].to_i; end
|
351
|
+
|
352
|
+
# Sizes of all blocks(exons, segment pairs).
|
353
|
+
# Returns an array of numbers.
|
354
|
+
def block_sizes
|
355
|
+
unless defined?(@block_sizes) then
|
356
|
+
@block_sizes = split_comma(@data[18]).collect { |x| x.to_i }
|
357
|
+
end
|
358
|
+
@block_sizes
|
359
|
+
end
|
360
|
+
|
361
|
+
# Returns blocks(exons, segment pairs) of the hit.
|
362
|
+
# Returns an array of Bio::Blat::Report::SegmentPair objects.
|
363
|
+
def blocks
|
364
|
+
unless defined?(@blocks)
|
365
|
+
bs = block_sizes
|
366
|
+
qst = query.starts
|
367
|
+
tst = target.starts
|
368
|
+
qseqs = query.seqs
|
369
|
+
tseqs = target.seqs
|
370
|
+
pflag = self.protein?
|
371
|
+
@blocks = (0...block_count).collect do |i|
|
372
|
+
SegmentPair.new(query.size, target.size, strand, bs[i],
|
373
|
+
qst[i], tst[i], qseqs[i], tseqs[i],
|
374
|
+
pflag)
|
375
|
+
end
|
376
|
+
end
|
377
|
+
@blocks
|
378
|
+
end
|
379
|
+
alias exons blocks
|
380
|
+
|
381
|
+
#--
|
382
|
+
# Bio::BLAST::*::Report::Hit compatible methods
|
383
|
+
#++
|
384
|
+
alias hsps blocks
|
385
|
+
|
386
|
+
# Returns the length of query sequence.
|
387
|
+
def query_len; query.size; end
|
388
|
+
|
389
|
+
# Returns the name of query sequence.
|
390
|
+
def query_def; query.name; end
|
391
|
+
alias query_id query_def
|
392
|
+
|
393
|
+
# Returns the length of the target(subject) sequence.
|
394
|
+
def target_len; target.size; end
|
395
|
+
alias len target_len
|
396
|
+
|
397
|
+
# Returns the name of the target(subject) sequence.
|
398
|
+
def target_def; target.name; end
|
399
|
+
alias target_id target_def
|
400
|
+
alias definition target_def
|
401
|
+
|
402
|
+
#Iterates over each block(exon, segment pair) of the hit.
|
403
|
+
# Yields a Bio::Blat::Report::SegmentPair object.
|
404
|
+
def each(&x) #:yields: segmentpair
|
405
|
+
exons.each(&x)
|
406
|
+
end
|
407
|
+
|
408
|
+
#--
|
409
|
+
# methods described in the BLAT FAQ at the UCSC genome browser.
|
410
|
+
# (http://genome.ucsc.edu/FAQ/FAQblat#blat4)
|
411
|
+
#++
|
412
|
+
|
413
|
+
# Calculates the pslCalcMilliBad value defined in the
|
414
|
+
# BLAT FAQ (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
|
415
|
+
#
|
416
|
+
# The algorithm is taken from the BLAT FAQ
|
417
|
+
# (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
|
418
|
+
def milli_bad
|
419
|
+
w = (self.protein? ? 3 : 1)
|
420
|
+
qalen = w * (self.query.end - self.query.start)
|
421
|
+
talen = self.target.end - self.target.start
|
422
|
+
alen = (if qalen < talen then qalen; else talen; end)
|
423
|
+
return 0 if alen <= 0
|
424
|
+
d = qalen - talen
|
425
|
+
d = 0 if d < 0
|
426
|
+
total = w * (self.match + self.rep_match + self.mismatch)
|
427
|
+
return 0 if total == 0
|
428
|
+
return (1000 * (self.mismatch * w + self.query.gap_count +
|
429
|
+
(3 * Math.log(1 + d)).round) / total)
|
430
|
+
end
|
431
|
+
|
432
|
+
# Calculates the percent identity compatible with the BLAT web server
|
433
|
+
# as described in the BLAT FAQ
|
434
|
+
# (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
|
435
|
+
#
|
436
|
+
# The algorithm is taken from the BLAT FAQ
|
437
|
+
# (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
|
438
|
+
def percent_identity
|
439
|
+
100.0 - self.milli_bad * 0.1
|
440
|
+
end
|
441
|
+
|
442
|
+
# When the output data comes from the protein query, returns true.
|
443
|
+
# Otherwise (nucleotide query), returns false.
|
444
|
+
# It returns nil if this cannot be determined.
|
445
|
+
#
|
446
|
+
# The algorithm is taken from the BLAT FAQ
|
447
|
+
# (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
|
448
|
+
#
|
449
|
+
# Note: It seems that it returns true only when protein query
|
450
|
+
# with nucleotide database (blat options: -q=prot -t=dnax).
|
451
|
+
def protein?
|
452
|
+
return nil if self.block_sizes.empty?
|
453
|
+
case self.strand[1,1]
|
454
|
+
when '+'
|
455
|
+
if self.target.end == self.target.starts[-1] +
|
456
|
+
3 * self.block_sizes[-1] then
|
457
|
+
true
|
458
|
+
else
|
459
|
+
false
|
460
|
+
end
|
461
|
+
when '-'
|
462
|
+
if self.target.start == self.target.size -
|
463
|
+
self.target.starts[-1] - 3 * self.block_sizes[-1] then
|
464
|
+
true
|
465
|
+
else
|
466
|
+
false
|
467
|
+
end
|
468
|
+
else
|
469
|
+
nil
|
470
|
+
end
|
471
|
+
end
|
472
|
+
|
473
|
+
# Calculates the score compatible with the BLAT web server
|
474
|
+
# as described in the BLAT FAQ
|
475
|
+
# (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
|
476
|
+
#
|
477
|
+
# The algorithm is taken from the BLAT FAQ
|
478
|
+
# (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
|
479
|
+
def score
|
480
|
+
w = (self.protein? ? 3 : 1)
|
481
|
+
w * (self.match + (self.rep_match >> 1)) -
|
482
|
+
w * self.mismatch - self.query.gap_count - self.target.gap_count
|
483
|
+
end
|
484
|
+
end #class Hit
|
485
|
+
|
486
|
+
#--
|
487
|
+
#Bio::BLAST::*::Report compatible methods
|
488
|
+
#++
|
489
|
+
|
490
|
+
# Returns number of hits.
|
491
|
+
# Same as hits.size.
|
492
|
+
def num_hits; @hits.size; end
|
493
|
+
|
494
|
+
# Iterates over each Bio::Blat::Report::Hit object.
|
495
|
+
# Same as hits.each.
|
496
|
+
def each_hit(&x) #:yields: hit
|
497
|
+
@hits.each(&x)
|
498
|
+
end
|
499
|
+
alias each each_hit
|
500
|
+
|
501
|
+
# Returns the name of query sequence.
|
502
|
+
# CAUTION: query_* methods simply return first hit's query_*.
|
503
|
+
# If multiple query sequences are given, these values
|
504
|
+
# will be incorrect.
|
505
|
+
def query_def; (x = @hits.first) ? x.query_def : nil; end
|
506
|
+
|
507
|
+
# Returns the length of query sequence.
|
508
|
+
# CAUTION: query_* methods simply return first hit's query_*.
|
509
|
+
# If multiple query sequences are given, these values
|
510
|
+
# will be incorrect.
|
511
|
+
def query_len; (x = @hits.first) ? x.query_len : nil; end
|
512
|
+
alias query_id query_def
|
513
|
+
end #class Report
|
514
|
+
|
515
|
+
end #class Blat
|
516
|
+
end #module Bio
|
517
|
+
|
518
|
+
=begin
|
519
|
+
|
520
|
+
= Bio::Blat::Report
|
521
|
+
|
522
|
+
BLAT result parser. (psl / pslx format)
|
523
|
+
|
524
|
+
= References
|
525
|
+
|
526
|
+
* ((<URL:http://www.genome.org/cgi/content/abstract/12/4/656>))
|
527
|
+
Kent, W.J., BLAT--the BLAST-like alignment tool,
|
528
|
+
Genome Research, 12, 656--664, 2002.
|
529
|
+
|
530
|
+
=end
|