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
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#
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# = bio/db/kegg/taxonomy.rb - KEGG taxonomy parser class
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#
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# Copyright:: Copyright (C) 2007 Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: taxonomy.rb,v 1.2 2007/07/09 10:29:16 k Exp $
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#
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module Bio
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class KEGG
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# == Description
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#
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# Parse the KEGG 'taxonomy' file which describes taxonomic classification
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# of organisms.
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#
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# == References
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#
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# The KEGG 'taxonomy' file is available at
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#
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# * ftp://ftp.genome.jp/pub/kegg/genes/taxonomy
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#
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class Taxonomy
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def initialize(filename, orgs = [])
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# Stores the taxonomic tree as a linked list (implemented in Hash), so
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# every node need to have unique name (key) to work correctly
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@tree = Hash.new
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# Also stores the taxonomic tree as a list of arrays (full path)
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@path = Array.new
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# Also stores all leaf nodes (organism codes) of every intermediate nodes
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@leaves = Hash.new
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# tentative name for the root node (use accessor to change)
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@root = 'Genes'
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hier = Array.new
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level = 0
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label = nil
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File.open(filename).each do |line|
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next if line.strip.empty?
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# line for taxonomic hierarchy (indent according to the number of # marks)
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if line[/^#/]
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level = line[/^#+/].length
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label = line[/[A-z].*/]
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hier[level] = sanitize(label)
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# line for organims name (unify different strains of a species)
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else
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tax, org, name, desc = line.chomp.split("\t")
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if orgs.nil? or orgs.empty? or orgs.include?(org)
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species, strain, = name.split('_')
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# (0) Grouping of the strains of the same species.
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# If the name of species is the same as the previous line,
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# add the species to the same species group.
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# ex. Gamma/enterobacteria has a large number of organisms,
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# so sub grouping of strains is needed for E.coli strains etc.
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#
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# However, if the species name is already used, need to avoid
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# collision of species name as the current implementation stores
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# the tree as a Hash, which may cause the infinite loop.
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#
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# (1) If species name == the intermediate node of other lineage
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# Add '_sp' to the species name to avoid the conflict (1-1), and if
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# 'species_sp' is already taken, use 'species_strain' instead (1-2).
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# ex. Bacteria/Proteobacteria/Beta/T.denitrificans/tbd
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# Bacteria/Proteobacteria/Epsilon/T.denitrificans_ATCC33889/tdn
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# -> Bacteria/Proteobacteria/Beta/T.denitrificans/tbd
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# Bacteria/Proteobacteria/Epsilon/T.denitrificans_sp/tdn
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#
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# (2) If species name == the intermediate node of the same lineage
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# Add '_sp' to the species name to avoid the conflict.
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# ex. Bacteria/Cyanobacgteria/Cyanobacteria_CYA/cya
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# Bacteria/Cyanobacgteria/Cyanobacteria_CYB/cya
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# Bacteria/Proteobacteria/Magnetococcus/Magnetococcus_MC1/mgm
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# -> Bacteria/Cyanobacgteria/Cyanobacteria_sp/cya
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# Bacteria/Cyanobacgteria/Cyanobacteria_sp/cya
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# Bacteria/Proteobacteria/Magnetococcus/Magnetococcus_sp/mgm
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sp_group = "#{species}_sp"
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if @tree[species]
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if hier[level+1] == species
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# case (0)
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else
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# case (1-1)
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species = sp_group
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# case (1-2)
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if @tree[sp_group] and hier[level+1] != species
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species = name
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end
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end
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else
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if hier[level] == species
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# case (2)
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species = sp_group
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end
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end
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# 'hier' is an array of the taxonomic tree + species and strain name.
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# ex. [nil, Eukaryotes, Fungi, Ascomycetes, Saccharomycetes] +
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# [S_cerevisiae, sce]
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hier[level+1] = species # sanitize(species)
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hier[level+2] = org
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ary = hier[1, level+2]
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warn ary.inspect if $DEBUG
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add_to_tree(ary)
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add_to_leaves(ary)
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add_to_path(ary)
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end
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end
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end
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return tree
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end
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attr_reader :tree
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attr_reader :path
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attr_reader :leaves
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attr_accessor :root
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def organisms(group)
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@leaves[group]
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end
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# Add a new path [node, subnode, subsubnode, ..., leaf] under the root node
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# and every intermediate nodes stores their child nodes as a Hash.
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def add_to_tree(ary)
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parent = @root
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ary.each do |node|
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@tree[parent] ||= Hash.new
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@tree[parent][node] = nil
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parent = node
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end
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end
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# Add a new path [node, subnode, subsubnode, ..., leaf] under the root node
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# and stores leaf nodes to the every intermediate nodes as an Array.
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def add_to_leaves(ary)
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leaf = ary.last
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ary.each do |node|
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@leaves[node] ||= Array.new
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@leaves[node] << leaf
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end
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end
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# Add a new path [node, subnode, subsubnode, ..., leaf] under the root node
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# and stores the path itself in an Array.
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def add_to_path(ary)
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@path << ary
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end
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# Compaction of intermediate nodes of the resulted taxonomic tree.
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# - If child node has only one child node (grandchild), make the child of
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# grandchild as a grandchild.
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# ex.
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# Plants / Monocotyledons / grass family / osa
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# --> Plants / Monocotyledons / osa
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#
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def compact(node = root)
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# if the node has children
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if subnodes = @tree[node]
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# obtain grandchildren for each child
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subnodes.keys.each do |subnode|
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if subsubnodes = @tree[subnode]
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# if the number of grandchild node is 1
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if subsubnodes.keys.size == 1
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# obtain the name of the grandchild node
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subsubnode = subsubnodes.keys.first
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# obtain the child of the grandchlid node
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if subsubsubnodes = @tree[subsubnode]
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# make the child of grandchild node as a chlid of child node
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@tree[subnode] = subsubsubnodes
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# delete grandchild node
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@tree[subnode].delete(subsubnode)
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warn "--- compact: #{subsubnode} is replaced by #{subsubsubnodes}" if $DEBUG
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# retry until new grandchild also needed to be compacted.
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retry
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end
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end
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end
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# repeat recurseively
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compact(subnode)
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end
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end
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end
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# Reduction of the leaf node of the resulted taxonomic tree.
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# - If the parent node have only one leaf node, replace parent node
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# with the leaf node.
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# ex.
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# Plants / Monocotyledons / osa
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# --> Plants / osa
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#
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def reduce(node = root)
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# if the node has children
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if subnodes = @tree[node]
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# obtain grandchildren for each child
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subnodes.keys.each do |subnode|
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if subsubnodes = @tree[subnode]
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# if the number of grandchild node is 1
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if subsubnodes.keys.size == 1
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# obtain the name of the grandchild node
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subsubnode = subsubnodes.keys.first
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# if the grandchild node is a leaf node
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unless @tree[subsubnode]
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# make the grandchild node as a child node
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@tree[node].update(subsubnodes)
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# delete child node
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@tree[node].delete(subnode)
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warn "--- reduce: #{subnode} is replaced by #{subsubnode}" if $DEBUG
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end
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end
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end
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# repeat recursively
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reduce(subnode)
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end
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end
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end
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# Traverse the taxonomic tree by the depth first search method
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# under the given (root or intermediate) node.
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def dfs(parent, &block)
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if children = @tree[parent]
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yield parent, children
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children.keys.each do |child|
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dfs(child, &block)
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end
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end
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end
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# Similar to the dfs method but also passes the current level of the nest
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# to the iterator.
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def dfs_with_level(parent, &block)
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@level ||= 0
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if children = @tree[parent]
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yield parent, children, @level
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@level += 1
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children.keys.each do |child|
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dfs_with_level(child, &block)
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end
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@level -= 1
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end
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end
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# Convert the taxonomic tree structure to a simple ascii art.
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def to_s
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result = "#{@root}\n"
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@tree[@root].keys.each do |node|
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result += ascii_tree(node, " ")
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end
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return result
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end
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private
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# Helper method for the to_s method.
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def ascii_tree(node, indent)
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result = "#{indent}+- #{node}\n"
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indent += " "
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@tree[node].keys.each do |child|
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if @tree[child]
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result += ascii_tree(child, indent)
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else
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result += "#{indent}+- #{child}\n"
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end
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end
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return result
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end
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def sanitize(str)
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str.gsub(/[^A-z0-9]/, '_')
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end
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end # Taxonomy
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end # KEGG
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end # Bio
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if __FILE__ == $0
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# Usage:
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# % wget ftp://ftp.genome.jp/pub/kegg/genes/taxonomy
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# % ruby taxonomy.rb taxonomy | less -S
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taxonomy = ARGV.shift
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org_list = ARGV.shift || nil
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if org_list
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orgs = File.readlines(org_list).map{|x| x.strip}
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else
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orgs = nil
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end
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tree = Bio::KEGG::Taxonomy.new(taxonomy, orgs)
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puts ">>> tree - original"
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puts tree
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puts ">>> tree - after compact"
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tree.compact
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puts tree
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puts ">>> tree - after reduce"
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tree.reduce
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puts tree
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puts ">>> path - sorted"
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tree.path.sort.each do |path|
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puts path.join("/")
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end
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puts ">>> group : orgs"
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tree.dfs(tree.root) do |parent, children|
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if orgs = tree.organisms(parent)
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puts "#{parent.ljust(30)} (#{orgs.size})\t#{orgs.join(', ')}"
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end
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end
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puts ">>> group : subgroups"
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tree.dfs_with_level(tree.root) do |parent, children, level|
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subgroups = children.keys.sort
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indent = " " * level
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label = "#{indent} #{level} #{parent}"
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puts "#{label.ljust(35)}\t#{subgroups.join(', ')}"
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end
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end
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@@ -0,0 +1,209 @@
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#
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# bio/db/lasergene.rb - Interface for DNAStar Lasergene sequence file format
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#
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
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# Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu)
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# License:: The Ruby License
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#
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# $Id: lasergene.rb,v 1.3 2007/04/05 23:35:40 trevor Exp $
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module Bio #:nodoc:
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#
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# bio/db/lasergene.rb - Interface for DNAStar Lasergene sequence file format
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#
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
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# Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu)
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# License:: The Ruby License
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#
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# = Description
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#
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# Bio::Lasergene reads DNAStar Lasergene formatted sequence files, or +.seq+
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# files. It only expects to find one sequence per file.
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#
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# = Usage
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#
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# require 'bio'
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# filename = 'MyFile.seq'
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# lseq = Bio::Lasergene.new( IO.readlines(filename) )
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# lseq.entry_id # => "Contig 1"
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# lseq.seq # => ATGACGTATCCAAAGAGGCGTTACC
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#
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# = Comments
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#
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# I'm only aware of the following three kinds of Lasergene file formats. Feel
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# free to send me other examples that may not currently be accounted for.
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#
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# File format 1:
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#
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# ## begin ##
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# "Contig 1" (1,934)
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# Contig Length: 934 bases
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# Average Length/Sequence: 467 bases
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# Total Sequence Length: 1869 bases
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# Top Strand: 2 sequences
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# Bottom Strand: 2 sequences
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# Total: 4 sequences
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# ^^
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# ATGACGTATCCAAAGAGGCGTTACCGGAGAAGAAGACACCGCCCCCGCAGTCCTCTTGGCCAGATCCTCCGCCGCCGCCCCTGGCTCGTCCACCCCCGCCACAGTTACCGCTGGAGAAGGAAAAATGGCATCTTCAWCACCCGCCTATCCCGCAYCTTCGGAWRTACTATCAAGCGAACCACAGTCAGAACGCCCTCCTGGGCGGTGGACATGATGAGATTCAATATTAATGACTTTCTTCCCCCAGGAGGGGGCTCAAACCCCCGCTCTGTGCCCTTTGAATACTACAGAATAAGAAAGGTTAAGGTTGAATTCTGGCCCTGCTCCCCGATCACCCAGGGTGACAGGGGAATGGGCTCCAGTGCTGWTATTCTAGMTGATRRCTTKGTAACAAAGRCCACAGCCCTCACCTATGACCCCTATGTAAACTTCTCCTCCCGCCATACCATAACCCAGCCCTTCTCCTACCRCTCCCGYTACTTTACCCCCAAACCTGTCCTWGATKCCACTATKGATKACTKCCAACCAAACAACAAAAGAAACCAGCTGTGGSTGAGACTACAWACTGCTGGAAATGTAGACCWCGTAGGCCTSGGCACTGCGTKCGAAAACAGTATATACGACCAGGAATACAATATCCGTGTMACCATGTATGTACAATTCAGAGAATTTAATCTTAAAGACCCCCCRCTTMACCCKTAATGAATAATAAMAACCATTACGAAGTGATAAAAWAGWCTCAGTAATTTATTYCATATGGAAATTCWSGGCATGGGGGGGAAAGGGTGACGAACKKGCCCCCTTCCTCCSTSGMYTKTTCYGTAGCATTCYTCCAMAAYACCWAGGCAGYAMTCCTCCSATCAAGAGcYTSYACAGCTGGGACAGCAGTTGAGGAGGACCATTCAAAGGGGGTCGGATTGCTGGTAATCAGA
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# ## end ##
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#
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#
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# File format 2:
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#
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# ## begin ##
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# ^^: 350,935
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# Contig 1 (1,935)
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# Contig Length: 935 bases
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# Average Length/Sequence: 580 bases
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# Total Sequence Length: 2323 bases
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# Top Strand: 2 sequences
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# Bottom Strand: 2 sequences
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# Total: 4 sequences
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# ^^
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# ATGTCGGGGAAATGCTTGACCGCGGGCTACTGCTCATCATTGCTTTCTTTGTGGTATATCGTGCCGTTCTGTTTTGCTGTGCTCGTCAACGCCAGCGGCGACAGCAGCTCTCATTTTCAGTCGATTTATAACTTGACGTTATGTGAGCTGAATGGCACGAACTGGCTGGCAGACAACTTTAACTGGGCTGTGGAGACTTTTGTCATCTTCCCCGTGTTGACTCACATTGTTTCCTATGGTGCACTCACTACCAGTCATTTTCTTGACACAGTTGGTCTAGTTACTGTGTCTACCGCCGGGTTTTATCACGGGCGGTACGTCTTGAGTAGCATCTACGCGGTCTGTGCTCTGGCTGCGTTGATTTGCTTCGCCATCAGGTTTGCGAAGAACTGCATGTCCTGGCGCTACTCTTGCACTAGATACACCAACTTCCTCCTGGACACCAAGGGCAGACTCTATCGTTGGCGGTCGCCTGTCATCATAGAGAAAGGGGGTAAGGTTGAGGTCGAAGGTCATCTGATCGATCTCAAAAGAGTTGTGCTTGATGGCTCTGTGGCGACACCTTTAACCAGAGTTTCAGCGGAACAATGGGGTCGTCCCTAGACGACTTTTGCCATGATAGTACAGCCCCACAGAAGGTGCTCTTGGCGTTTTCCATCACCTACACGCCAGTGATGATATATGCCCTAAAGGTAAGCCGCGGCCGACTTTTGGGGCTTCTGCACCTTTTGATTTTTTTGAACTGTGCCTTTACTTTCGGGTACATGACATTCGTGCACTTTCGGAGCACGAACAAGGTCGCGCTCACTATGGGAGCAGTAGTCGCACTCCTTTGGGGGGTGTACTCAGCCATAGAAACCTGGAAATTCATCACCTCCAGATGCCGTTGTGCTTGCTAGGCCGCAAGTACATTCTGGCCCCTGCCCACCACGTTG
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# ## end ##
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#
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# File format 3 (non-standard Lasergene header):
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#
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# ## begin ##
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# LOCUS PRU87392 15411 bp RNA linear VRL 17-NOV-2000
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# DEFINITION Porcine reproductive and respiratory syndrome virus strain VR-2332,
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# complete genome.
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# ACCESSION U87392 AF030244 U00153
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# VERSION U87392.3 GI:11192298
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# [...cut...]
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# 3'UTR 15261..15411
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# polyA_site 15409
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# ORIGIN
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# ^^
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# atgacgtataggtgttggctctatgccttggcatttgtattgtcaggagctgtgaccattggcacagcccaaaacttgctgcacagaaacacccttctgtgatagcctccttcaggggagcttagggtttgtccctagcaccttgcttccggagttgcactgctttacggtctctccacccctttaaccatgtctgggatacttgatcggtgcacgtgtacccccaatgccagggtgtttatggcggagggccaagtctactgcacacgatgcctcagtgcacggtctctccttcccctgaacctccaagtttctgagctcggggtgctaggcctattctacaggcccgaagagccactccggtggacgttgccacgtgcattccccactgttgagtgctcccccgccggggcctgctggctttctgcaatctttccaatcgcacgaatgaccagtggaaacctgaacttccaacaaagaatggtacgggtcgcagctgagctttacagagccggccagctcacccctgcagtcttgaaggctctacaagtttatgaacggggttgccgctggtaccccattgttggacctgtccctggagtggccgttttcgccaattccctacatgtgagtgataaacctttcccgggagcaactcacgtgttgaccaacctgccgctcccgcagagacccaagcctgaagacttttgcccctttgagtgtgctatggctactgtctatgacattggtcatgacgccgtcatgtatgtggccgaaaggaaagtctcctgggcccctcgtggcggggatgaagtgaaatttgaagctgtccccggggagttgaagttgattgcgaaccggctccgcacctccttcccgccccaccacacagtggacatgtctaagttcgccttcacagcccctgggtgtggtgtttctatgcgggtcgaacgccaacacggctgccttcccgctgacactgtccctgaaggcaactgctggtggagcttgtttgacttgcttccactggaagttcagaacaaagaaattcgccatgctaaccaatttggctaccagaccaagcatggtgtctctggcaagtacctacagcggaggctgca[...cut...]
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# ## end ##
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#
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class Lasergene
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# Entire header before the sequence
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attr_reader :comments
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# Sequence
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# Bio::Sequence::NA or Bio::Sequence::AA object
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attr_reader :sequence
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# Name of sequence
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# * Parsed from standard Lasergene header
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attr_reader :name
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# Contig length, length of present sequence
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# * Parsed from standard Lasergene header
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attr_reader :contig_length
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# Average length per sequence
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# * Parsed from standard Lasergene header
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attr_reader :average_length
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# Length of parent sequence
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# * Parsed from standard Lasergene header
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attr_reader :total_length
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# Number of top strand sequences
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# * Parsed from standard Lasergene header
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attr_reader :top_strand_sequences
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# Number of bottom strand sequences
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# * Parsed from standard Lasergene header
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attr_reader :bottom_strand_sequences
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# Number of sequences
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# * Parsed from standard Lasergene header
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attr_reader :total_sequences
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DELIMITER_1 = '^\^\^:' # Match '^^:' at the beginning of a line
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DELIMITER_2 = '^\^\^' # Match '^^' at the beginning of a line
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def initialize(lines)
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process(lines)
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end
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# Is the comment header recognized as standard Lasergene format?
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#
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# ---
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# *Arguments*
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# * _none_
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# *Returns*:: +true+ _or_ +false+
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def standard_comment?
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@standard_comment
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end
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# Sequence
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#
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# Bio::Sequence::NA or Bio::Sequence::AA object
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def seq
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@sequence
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end
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# Name of sequence
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# * Parsed from standard Lasergene header
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def entry_id
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@name
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end
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#########
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protected
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#########
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def process(lines)
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delimiter_1_indices = []
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delimiter_2_indices = []
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# If the data from the file is passed as one big String instead of
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# broken into an Array, convert lines to an Array
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if lines.kind_of? String
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lines = lines.tr("\r", '').split("\n")
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end
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lines.each_with_index do |line, index|
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if line.match DELIMITER_1
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delimiter_1_indices << index
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elsif line.match DELIMITER_2
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delimiter_2_indices << index
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end
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end
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raise InputError, "More than one delimiter of type '#{DELIMITER_1}'" if delimiter_1_indices.size > 1
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raise InputError, "More than one delimiter of type '#{DELIMITER_2}'" if delimiter_2_indices.size > 1
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raise InputError, "No comment to data separator of type '#{DELIMITER_2}'" if delimiter_2_indices.size < 1
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if !delimiter_1_indices.empty?
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# toss out DELIMETER_1 and anything preceding it
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@comments = lines[ (delimiter_1_indices[0] + 1) .. (delimiter_2_indices[0] - 1) ]
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else
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@comments = lines[ 0 .. (delimiter_2_indices[0] - 1) ]
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end
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@standard_comment = false
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if @comments[0] =~ %r{(.+)\s+\(\d+,\d+\)} # if we have a standard Lasergene comment
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@standard_comment = true
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@name = $1
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comments.each do |comment|
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if comment.match('Contig Length:\s+(\d+)')
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@contig_length = $1.to_i
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elsif comment.match('Average Length/Sequence:\s+(\d+)')
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@average_length = $1.to_i
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elsif comment.match('Total Sequence Length:\s+(\d+)')
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@total_length = $1.to_i
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elsif comment.match('Top Strand:\s+(\d+)')
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@top_strand_sequences = $1.to_i
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elsif comment.match('Bottom Strand:\s+(\d+)')
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@bottom_strand_sequences = $1.to_i
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elsif comment.match('Total:\s+(\d+)')
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@total_sequences = $1.to_i
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end
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end
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end
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@comments = @comments.join('')
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@sequence = Bio::Sequence.auto( lines[ (delimiter_2_indices[0] + 1) .. -1 ].join('') )
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end
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end # Lasergene
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end # Bio
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