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/io/flatfile/autodetection.rb - file format auto-detection
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#
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# Copyright (C) 2001-2006 Naohisa Goto <ng@bioruby.org>
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#
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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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#
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# See documents for Bio::FlatFile::AutoDetect and Bio::FlatFile.
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#
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require 'tsort'
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require 'bio/io/flatfile'
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module Bio
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class FlatFile
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# AutoDetect automatically determines database class of given data.
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class AutoDetect
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include TSort
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# Array to store autodetection rules.
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# This is defined only for inspect.
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class RulesArray < Array
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# visualize contents
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def inspect
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"[#{self.collect { |e| e.name.inspect }.join(' ')}]"
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end
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end #class RulesArray
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# Template of a single rule of autodetection
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class RuleTemplate
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# Creates a new element.
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def self.[](*arg)
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self.new(*arg)
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end
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# Creates a new element.
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def initialize
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@higher_priority_elements = RulesArray.new
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@lower_priority_elements = RulesArray.new
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@name = nil
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end
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# self is prior to the _elem_.
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def is_prior_to(elem)
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return nil if self == elem
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elem.higher_priority_elements << self
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self.lower_priority_elements << elem
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true
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end
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# higher priority elements
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attr_reader :higher_priority_elements
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# lower priority elements
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attr_reader :lower_priority_elements
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# database classes
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attr_reader :dbclasses
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# unique name of the element
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attr_accessor :name
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# If given text (and/or meta information) is known, returns
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# the database class.
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# Otherwise, returns nil or false.
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#
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# _text_ will be a String.
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# _meta_ will be a Hash.
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# _meta_ may contain following keys.
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# :path => pathname, filename or uri.
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def guess(text, meta)
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nil
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end
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private
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# Gets constant from constant name given as a string.
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def str2const(str)
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const = Object
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str.split(/\:\:/).each do |x|
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const = const.const_get(x)
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end
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const
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end
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# Gets database class from given object.
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# Current implementation is:
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# if _obj_ is kind of String, regarded as a constant.
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# Otherwise, returns _obj_ as is.
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def get_dbclass(obj)
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obj.kind_of?(String) ? str2const(obj) : obj
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end
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end #class Rule_Template
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# RuleDebug is a class for debugging autodetect classes/methods
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class RuleDebug < RuleTemplate
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# Creates a new instance.
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def initialize(name)
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super()
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@name = name
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end
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# prints information to the $stderr.
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def guess(text, meta)
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$stderr.puts @name
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$stderr.puts text.inspect
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$stderr.puts meta.inspect
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nil
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end
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end #class RuleDebug
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# Special element that is always top or bottom priority.
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class RuleSpecial < RuleTemplate
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def initialize(name)
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#super()
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@name = name
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end
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# modification of @name is inhibited.
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def name=(x)
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raise 'cannot modify name'
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end
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# always returns void array
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def higher_priority_elements
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[]
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end
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# always returns void array
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def lower_priority_elements
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[]
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end
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end #class RuleSpecial
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# Special element that is always top priority.
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TopRule = RuleSpecial.new('top')
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# Special element that is always bottom priority.
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BottomRule = RuleSpecial.new('bottom')
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# A autodetection rule to use a regular expression
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class RuleRegexp < RuleTemplate
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# Creates a new instance.
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def initialize(dbclass, re)
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super()
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@re = re
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@name = dbclass.to_s
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@dbclass = nil
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@dbclass_lazy = dbclass
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end
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# database class (lazy evaluation)
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def dbclass
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unless @dbclass
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@dbclass = get_dbclass(@dbclass_lazy)
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end
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@dbclass
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end
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private :dbclass
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# returns database classes
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def dbclasses
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[ dbclass ]
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end
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# If given text matches the regexp, returns the database class.
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# Otherwise, returns nil or false.
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# _meta_ is ignored.
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def guess(text, meta)
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@re =~ text ? dbclass : nil
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end
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end #class RuleRegexp
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# A autodetection rule to use more than two regular expressions.
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# If given string matches one of the regular expressions,
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# returns the database class.
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class RuleRegexp2 < RuleRegexp
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# Creates a new instance.
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def initialize(dbclass, *regexps)
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super(dbclass, nil)
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@regexps = regexps
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end
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# If given text matches one of the regexp, returns the database class.
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# Otherwise, returns nil or false.
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# _meta_ is ignored.
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def guess(text, meta)
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@regexps.each do |re|
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return dbclass if re =~ text
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end
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nil
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end
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end #class RuleRegexp
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# A autodetection rule that passes data to the proc object.
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class RuleProc < RuleTemplate
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# Creates a new instance.
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def initialize(*dbclasses, &proc)
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super()
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@proc = proc
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@dbclasses = nil
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@dbclasses_lazy = dbclasses
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@name = dbclasses.collect { |x| x.to_s }.join('|')
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end
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# database classes (lazy evaluation)
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def dbclasses
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unless @dbclasses
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@dbclasses = @dbclasses_lazy.collect { |x| get_dbclass(x) }
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end
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@dbclasses
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end
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# If given text (and/or meta information) is known, returns
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# the database class.
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# Otherwise, returns nil or false.
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#
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# Refer RuleTemplate#guess for _meta_.
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def guess(text, meta)
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@proc.call(text)
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end
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end #class RuleProc
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# Creates a new Autodetect object
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def initialize
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# stores autodetection rules.
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@rules = Hash.new
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# stores elements (cache)
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@elements = nil
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self.add(TopRule)
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self.add(BottomRule)
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end
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# Adds a new element.
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# Returns _elem_.
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def add(elem)
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raise 'element name conflicts' if @rules[elem.name]
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@elements = nil
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@rules[elem.name] = elem
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elem
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end
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# (required by TSort.)
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# For all elements, yields each element.
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def tsort_each_node(&x)
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@rules.each_value(&x)
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end
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# (required by TSort.)
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# For a given element, yields each child
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# (= lower priority elements) of the element.
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def tsort_each_child(elem)
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if elem == TopRule then
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@rules.each_value do |e|
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yield e unless e == TopRule or
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e.lower_priority_elements.index(TopRule)
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end
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elsif elem == BottomRule then
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@rules.each_value do |e|
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yield e if e.higher_priority_elements.index(BottomRule)
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end
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else
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elem.lower_priority_elements.each do |e|
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yield e if e != BottomRule
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end
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unless elem.higher_priority_elements.index(BottomRule)
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yield BottomRule
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end
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end
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end
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# Returns current elements as an array
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# whose order fulfills all elements' priorities.
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def elements
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unless @elements
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ary = tsort
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ary.reverse!
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@elements = ary
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end
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@elements
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end
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# rebuilds the object and clears internal cache.
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def rehash
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@rules.rehash
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@elements = nil
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end
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# visualizes the object (mainly for debug)
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def inspect
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"<#{self.class.to_s} " +
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self.elements.collect { |e| e.name.inspect }.join(' ') +
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">"
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end
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# Iterates over each element.
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def each_rule(&x) #:yields: elem
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elements.each(&x)
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end
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# Autodetect from the text.
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# Returns a database class if succeeded.
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# Returns nil if failed.
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def autodetect(text, meta = {})
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r = nil
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elements.each do |e|
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#$stderr.puts e.name
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r = e.guess(text, meta)
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break if r
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end
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r
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end
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# autodetect from the FlatFile object.
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# Returns a database class if succeeded.
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# Returns nil if failed.
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def autodetect_flatfile(ff, lines = 31)
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meta = {}
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stream = ff.instance_eval { @stream }
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begin
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path = stream.path
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rescue NameError
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end
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if path then
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meta[:path] = path
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# call autodetect onece with meta and without any read action
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if r = self.autodetect(stream.prefetch_buffer, meta)
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return r
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end
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end
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# reading stream
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1.upto(lines) do |x|
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break unless line = stream.prefetch_gets
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if line.strip.size > 0 then
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if r = self.autodetect(stream.prefetch_buffer, meta)
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return r
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end
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end
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end
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return nil
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end
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# default autodetect object for class method
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@default = nil
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# returns the default autodetect object
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def self.default
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unless @default then
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@default = self.make_default
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end
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@default
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end
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# sets the default autodetect object.
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def self.default=(ad)
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@default = ad
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end
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# make a new autodetect object
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def self.[](*arg)
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a = self.new
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arg.each { |e| a.add(e) }
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a
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end
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# make a default of default autodetect object
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def self.make_default
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a = self[
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genbank = RuleRegexp[ 'Bio::GenBank',
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/^LOCUS .+ bp .*[a-z]*[DR]?NA/ ],
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genpept = RuleRegexp[ 'Bio::GenPept',
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373
|
+
/^LOCUS .+ aa .+/ ],
|
374
|
+
medline = RuleRegexp[ 'Bio::MEDLINE',
|
375
|
+
/^PMID\- [0-9]+$/ ],
|
376
|
+
embl = RuleRegexp[ 'Bio::EMBL',
|
377
|
+
/^ID .+\; .*(DNA|RNA|XXX)\;/ ],
|
378
|
+
sptr = RuleRegexp2[ 'Bio::SPTR',
|
379
|
+
/^ID .+\; *PRT\;/,
|
380
|
+
/^ID [-A-Za-z0-9_\.]+ .+\; *[0-9]+ *AA\./ ],
|
381
|
+
prosite = RuleRegexp[ 'Bio::PROSITE',
|
382
|
+
/^ID [-A-Za-z0-9_\.]+\; (PATTERN|RULE|MATRIX)\.$/ ],
|
383
|
+
transfac = RuleRegexp[ 'Bio::TRANSFAC',
|
384
|
+
/^AC [-A-Za-z0-9_\.]+$/ ],
|
385
|
+
|
386
|
+
aaindex = RuleProc.new('Bio::AAindex1', 'Bio::AAindex2') do |text|
|
387
|
+
if /^H [-A-Z0-9_\.]+$/ =~ text then
|
388
|
+
if text =~ /^M [rc]/ then
|
389
|
+
Bio::AAindex2
|
390
|
+
elsif text =~ /^I A\/L/ then
|
391
|
+
Bio::AAindex1
|
392
|
+
else
|
393
|
+
false #fail to determine
|
394
|
+
end
|
395
|
+
else
|
396
|
+
nil
|
397
|
+
end
|
398
|
+
end,
|
399
|
+
|
400
|
+
litdb = RuleRegexp[ 'Bio::LITDB',
|
401
|
+
/^CODE [0-9]+$/ ],
|
402
|
+
brite = RuleRegexp[ 'Bio::KEGG::BRITE',
|
403
|
+
/^Entry [A-Z0-9]+/ ],
|
404
|
+
orthology = RuleRegexp[ 'Bio::KEGG::ORTHOLOGY',
|
405
|
+
/^ENTRY .+ KO\s*/ ],
|
406
|
+
drug = RuleRegexp[ 'Bio::KEGG::DRUG',
|
407
|
+
/^ENTRY .+ Drug\s*/ ],
|
408
|
+
glycan = RuleRegexp[ 'Bio::KEGG::GLYCAN',
|
409
|
+
/^ENTRY .+ Glycan\s*/ ],
|
410
|
+
enzyme = RuleRegexp2[ 'Bio::KEGG::ENZYME',
|
411
|
+
/^ENTRY EC [0-9\.]+$/,
|
412
|
+
/^ENTRY .+ Enzyme\s*/
|
413
|
+
],
|
414
|
+
compound = RuleRegexp2[ 'Bio::KEGG::COMPOUND',
|
415
|
+
/^ENTRY C[A-Za-z0-9\._]+$/,
|
416
|
+
/^ENTRY .+ Compound\s*/
|
417
|
+
],
|
418
|
+
reaction = RuleRegexp2[ 'Bio::KEGG::REACTION',
|
419
|
+
/^ENTRY R[A-Za-z0-9\._]+$/,
|
420
|
+
/^ENTRY .+ Reaction\s*/
|
421
|
+
],
|
422
|
+
genes = RuleRegexp[ 'Bio::KEGG::GENES',
|
423
|
+
/^ENTRY .+ (CDS|gene|.*RNA|Contig) / ],
|
424
|
+
genome = RuleRegexp[ 'Bio::KEGG::GENOME',
|
425
|
+
/^ENTRY [a-z]+$/ ],
|
426
|
+
|
427
|
+
fantom = RuleProc.new('Bio::FANTOM::MaXML::Cluster',
|
428
|
+
'Bio::FANTOM::MaXML::Sequence') do |text|
|
429
|
+
if /\<\!DOCTYPE\s+maxml\-(sequences|clusters)\s+SYSTEM/ =~ text
|
430
|
+
case $1
|
431
|
+
when 'clusters'
|
432
|
+
Bio::FANTOM::MaXML::Cluster
|
433
|
+
when 'sequences'
|
434
|
+
Bio::FANTOM::MaXML::Sequence
|
435
|
+
else
|
436
|
+
nil #unknown
|
437
|
+
end
|
438
|
+
else
|
439
|
+
nil
|
440
|
+
end
|
441
|
+
end,
|
442
|
+
|
443
|
+
pdb = RuleRegexp[ 'Bio::PDB',
|
444
|
+
/^HEADER .{40}\d\d\-[A-Z]{3}\-\d\d [0-9A-Z]{4}/ ],
|
445
|
+
het = RuleRegexp[ 'Bio::PDB::ChemicalComponent',
|
446
|
+
/^RESIDUE +.+ +\d+\s*$/ ],
|
447
|
+
|
448
|
+
clustal = RuleRegexp2[ 'Bio::ClustalW::Report',
|
449
|
+
/^CLUSTAL .*\(.*\).*sequence +alignment/,
|
450
|
+
/^CLUSTAL FORMAT for T-COFFEE/ ],
|
451
|
+
|
452
|
+
gcg_msf = RuleRegexp[ 'Bio::GCG::Msf',
|
453
|
+
/^!!(N|A)A_MULTIPLE_ALIGNMENT .+/ ],
|
454
|
+
|
455
|
+
gcg_seq = RuleRegexp[ 'Bio::GCG::Seq',
|
456
|
+
/^!!(N|A)A_SEQUENCE .+/ ],
|
457
|
+
|
458
|
+
blastxml = RuleRegexp[ 'Bio::Blast::Report',
|
459
|
+
/\<\!DOCTYPE BlastOutput PUBLIC / ],
|
460
|
+
wublast = RuleRegexp[ 'Bio::Blast::WU::Report',
|
461
|
+
/^BLAST.? +[\-\.\w]+\-WashU +\[[\-\.\w ]+\]/ ],
|
462
|
+
wutblast = RuleRegexp[ 'Bio::Blast::WU::Report_TBlast',
|
463
|
+
/^TBLAST.? +[\-\.\w]+\-WashU +\[[\-\.\w ]+\]/ ],
|
464
|
+
blast = RuleRegexp[ 'Bio::Blast::Default::Report',
|
465
|
+
/^BLAST.? +[\-\.\w]+ +\[[\-\.\w ]+\]/ ],
|
466
|
+
tblast = RuleRegexp[ 'Bio::Blast::Default::Report_TBlast',
|
467
|
+
/^TBLAST.? +[\-\.\w]+ +\[[\-\.\w ]+\]/ ],
|
468
|
+
rpsblast = RuleRegexp[ 'Bio::Blast::RPSBlast::Report',
|
469
|
+
/^RPS\-BLAST.? +[\-\.\w]+ +\[[\-\.\w ]+\]/ ],
|
470
|
+
|
471
|
+
blat = RuleRegexp[ 'Bio::Blat::Report',
|
472
|
+
/^psLayout version \d+/ ],
|
473
|
+
spidey = RuleRegexp[ 'Bio::Spidey::Report',
|
474
|
+
/^\-\-SPIDEY version .+\-\-$/ ],
|
475
|
+
hmmer = RuleRegexp[ 'Bio::HMMER::Report',
|
476
|
+
/^HMMER +\d+\./ ],
|
477
|
+
sim4 = RuleRegexp[ 'Bio::Sim4::Report',
|
478
|
+
/^seq1 \= .*\, \d+ bp(\r|\r?\n)seq2 \= .*\, \d+ bp(\r|\r?\n)/ ],
|
479
|
+
|
480
|
+
fastaformat = RuleProc.new('Bio::FastaFormat',
|
481
|
+
'Bio::NBRF',
|
482
|
+
'Bio::FastaNumericFormat') do |text|
|
483
|
+
if /^>.+$/ =~ text
|
484
|
+
case text
|
485
|
+
when /^>([PF]1|[DR][LC]|N[13]|XX)\;.+/
|
486
|
+
Bio::NBRF
|
487
|
+
when /^>.+$\s+(^\#.*$\s*)*^\s*\d*\s*[-a-zA-Z_\.\[\]\(\)\*\+\$]+/
|
488
|
+
Bio::FastaFormat
|
489
|
+
when /^>.+$\s+^\s*\d+(\s+\d+)*\s*$/
|
490
|
+
Bio::FastaNumericFormat
|
491
|
+
else
|
492
|
+
false
|
493
|
+
end
|
494
|
+
else
|
495
|
+
nil
|
496
|
+
end
|
497
|
+
end
|
498
|
+
]
|
499
|
+
|
500
|
+
# dependencies
|
501
|
+
# NCBI
|
502
|
+
genbank.is_prior_to genpept
|
503
|
+
# EMBL/UniProt
|
504
|
+
embl.is_prior_to sptr
|
505
|
+
sptr.is_prior_to prosite
|
506
|
+
prosite.is_prior_to transfac
|
507
|
+
# KEGG
|
508
|
+
#aaindex.is_prior_to litdb
|
509
|
+
#litdb.is_prior_to brite
|
510
|
+
brite.is_prior_to orthology
|
511
|
+
orthology.is_prior_to drug
|
512
|
+
drug.is_prior_to glycan
|
513
|
+
glycan.is_prior_to enzyme
|
514
|
+
enzyme.is_prior_to compound
|
515
|
+
compound.is_prior_to reaction
|
516
|
+
reaction.is_prior_to genes
|
517
|
+
genes.is_prior_to genome
|
518
|
+
# PDB
|
519
|
+
pdb.is_prior_to het
|
520
|
+
# BLAST
|
521
|
+
wublast.is_prior_to wutblast
|
522
|
+
wutblast.is_prior_to blast
|
523
|
+
blast.is_prior_to tblast
|
524
|
+
# FastaFormat
|
525
|
+
BottomRule.is_prior_to(fastaformat)
|
526
|
+
|
527
|
+
# for debug
|
528
|
+
#debug_first = RuleDebug.new('debug_first')
|
529
|
+
#a.add(debug_first)
|
530
|
+
#debug_first.is_prior_to(TopRule)
|
531
|
+
|
532
|
+
## for debug
|
533
|
+
#debug_last = RuleDebug.new('debug_last')
|
534
|
+
#a.add(debug_last)
|
535
|
+
#BottomRule.is_prior_to(debug_last)
|
536
|
+
#fastaformat.is_prior_to(debug_last)
|
537
|
+
|
538
|
+
a.rehash
|
539
|
+
return a
|
540
|
+
end
|
541
|
+
|
542
|
+
end #class AutoDetect
|
543
|
+
end #class FlatFile
|
544
|
+
end #module Bio
|
545
|
+
|