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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# = bio/appl/psort/report.rb - PSORT systems report classes
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#
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# Copyright:: Copyright (C) 2003
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# Mitsuteru C. Nakao <n@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: report.rb,v 1.15 2007/04/05 23:35:40 trevor Exp $
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#
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# == A Report classes for PSORT Systems
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#
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require 'bio/appl/psort'
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module Bio
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autoload :Sequence, 'bio/sequence'
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class PSORT
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class PSORT1
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# = Bio::PSORT::PSORT1::Report
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# Parser class for PSORT1 output report.
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#
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# == Example
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class Report
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# Returns aBio::PSORT::PSORT1::Report.
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def self.parser(output_report)
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self.default_parser(output_report)
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end
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# Returns aBio::PSORT::PSORT1::Report.
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def self.default_parser(output_report)
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rpt = self.new
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rpt.raw = output_report
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query_info = output_report.scan(/^Query Information\n\n(.+?)\n\n/m)[0][0].split(/\n/)
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result_info = output_report.scan(/^Result Information\n\n(.+?)\n\n\*/m)[0][0]
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step1 = output_report.scan(/^\*\*\* Reasoning Step: 1\n\n(.+?)\n\n/m)[0][0]
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step2 = output_report.scan(/^\*\*\* Reasoning Step: 2\n\n(.+?)\n\n/m)[0][0]
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final_result = output_report.scan(/\n\n----- Final Results -----\n\n(.+?)\n\n\n/m)[0][0]
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rpt.entry_id = query_info[2].scan(/^>(\S+) */).to_s
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rpt.origin = query_info[0].scan(/ORIGIN (\w+)/).to_s
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rpt.sequence = Bio::Sequence::AA.new(query_info[3..query_info.size].to_s)
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# rpt.reasoning
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rpt.final_result = final_result.split(/\n/).map {|x|
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x = x.strip.split(/---/).map {|y| y.strip }
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{ 'prediction' => x[0],
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'certainty' => x[1].scan(/Certainty= (\d\.\d{3})/).to_s,
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'comment' => x[1].scan(/\((\w+)\)/).to_s
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}
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}
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return rpt
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end
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attr_accessor :entry_id
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attr_accessor :origin
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attr_accessor :title
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attr_accessor :sequence
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attr_accessor :result_info
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attr_accessor :reasoning
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attr_accessor :final_result
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attr_accessor :raw
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# Constructs aBio::PSORT::PSORT1::Report object.
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def initialize(entry_id = '', origin = '', title = '', sequence = '',
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result_info = '', reasoning = {}, final_result = [])
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@entry_id = entry_id
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@origin = origin
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@title = title
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@sequence = sequence
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@result_info = result_info
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@reasoning = reasoning
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@final_result = final_result
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@raw = ''
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end
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end # class Report
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end # class PSORT1
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class PSORT2
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# Subcellular localization name codes used by PSORT2
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SclNames = {
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'csk' => 'cytoskeletal',
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'cyt' => 'cytoplasmic',
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'nuc' => 'nuclear',
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'mit' => 'mitochondrial',
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'ves' => 'vesicles of secretory system',
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'end' => 'endoplasmic reticulum',
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'gol' => 'Golgi',
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'vac' => 'vacuolar',
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'pla' => 'plasma membrane',
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'pox' => 'peroxisomal',
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'exc' => 'extracellular, including cell wall',
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'---' => 'other'
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}
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# Feature name codes
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Features = [
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'psg', # PSG: PSG score
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'gvh', # GvH: GvH score
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'alm', # ALOM: $xmax
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'tms', # ALOM: $count
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'top', # MTOP: Charge difference: $mtopscr
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'mit', # MITDISC: Score: $score
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'mip', # Gavel: motif at $isite
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'nuc', # NUCDISC: NLS Score: $score
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'erl', # KDEL: ($seg|none)
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'erm', # ER Membrane Retention Signals: ($cseg|none) $scr
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'pox', # SKL: ($pat|none) $scr
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'px2', # PTS2: (found|none) ($#match < 0) ? 0 : ($#match+1);
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'vac', # VAC: (found|none) ($#match < 0) ? 0 : ($#match+1);
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'rnp', # RNA-binding motif: (found|none) ($#match < 0) ? 0 : ($#match+1);
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'act', # Actinin-type actin-binding motif: (found|none) $hit
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'caa', # Prenylation motif: (2|1|0) CaaX,CXC,CC,nil
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'yqr', # memYQRL: (found|none) $scr
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'tyr', # Tyrosines in the tail: (none|\S+[,])
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# 10 * scalar(@ylist) / ($end - $start + 1);
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'leu', # Dileucine motif in the tail: (none|found) $scr
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'gpi', # >>> Seem to be GPI anchored
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'myr', # NMYR: (none|\w) $scr
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'dna', # checking 63 PROSITE DNA binding motifs: $hit
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'rib', # checking 71 PROSITE ribosomal protein motifs: $hit
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'bac', # checking 33 PROSITE prokaryotic DNA binding motifs: $hit
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'm1a', # $mtype eq '1a'
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'm1b', # $mtype eq '1b'
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'm2', # $mtype eq '2 '
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'mNt', # $mtype eq 'Nt'
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'm3a', # $mtype eq '3a'
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'm3b', # $mtype eq '3b'
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'm_', # $mtype eq '__' tms == 0
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'ncn', # NNCN: ($NetOutput[1] > $NetOutput[0]) ? $output : (-$output);
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'lps', # COIL: $count
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'len' # $leng
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]
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# Feature name codes (long version).
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FeaturesLong = {
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'psg' => 'PSG',
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'gvh' => 'GvH',
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'tms' => 'ALOM',
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'alm' => 'ALOM',
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'top' => 'MTOP',
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'mit' => 'MITDISC',
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'mip' => 'Gavel',
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'nuc' => 'NUCDISC',
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'erl' => 'KDEL',
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'erm' => 'ER Membrane Retention Signals',
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'pox' => 'SKL',
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'px2' => 'PTS2',
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'vac' => 'VAC',
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'rnp' => 'RNA-binding motif',
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'act' => 'Actinin-type actin-binding motif',
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'caa' => 'Prenylation motif',
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'yqr' => 'memYQRL',
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'tyr' => 'Tyrosines in the tail',
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'leu' => 'Dileucine motif in the tail',
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'gpi' => '>>> Seems to be GPI anchored',
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'myr' => 'NMYR',
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'dna' => 'checking 63 PROSITE DNA binding motifs',
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'rib' => 'checking 71 PROSITE ribosomal protein motifs',
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'bac' => 'ochecking 33 PROSITE prokaryotic DNA binding motifs:',
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'm1a' => '',
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'm1b' => '',
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'm2' => '',
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'mNt' => '',
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'm3a' => '',
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'm3b' => '',
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'm_' => '',
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'ncn' => 'NNCN',
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'lps' => 'COIL',
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'len' => 'AA' # length of input sequence
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}
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# = Bio::PSORT::PSORT2::Report
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# Report parser classe for PSORT II(PSORT2).
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# == Example
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class Report
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# Report boundary string.
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BOUNDARY = '-' * 75
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# Report delimiter.
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RS = DELIMITER = "\)\n\n#{BOUNDARY}"
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# entry_id of query sequence.
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attr_accessor :entry_id
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# Given subcellular localization (three letters code).
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attr_accessor :scl
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# Definition of query sequence.
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attr_accessor :definition
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# Sequence of query sequence.
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attr_accessor :seq
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# k parameter of k-nearest neighbors classifier.
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attr_accessor :k
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# Feature vector used the kNN prediction.
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attr_accessor :features
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# Probability vector of kNN prediction.
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attr_accessor :prob
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# Predicted subcellular localization (three letters code).
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attr_accessor :pred
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# Raw text of output report.
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attr_accessor :raw
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# Constructs aBio::PSORT::PSORT2::Report object.
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def initialize(raw = '', entry_id = nil, scl = nil, definition = nil,
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seq = nil, k = nil, features = {}, prob = {}, pred = nil)
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@entry_id = entry_id
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@scl = scl
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@definition = definition
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@seq = seq
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@features = features
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@prob = prob
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@pred = pred
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@k = k
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@raw = raw
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end
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# Parses output report with output format detection automatically.
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def self.parser(str, entry_id)
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case str
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when /^ psg:/ # default report
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self.default_parser(str, entry_id)
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when /^PSG:/ # -v report
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self.v_parser(str, entry_id)
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when /: too short length /
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self.too_short_parser(str, entry_id)
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when /PSORT II server/
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tmp = self.new(ent, entry_id)
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else
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raise ArgumentError, "invalid format\n[#{str}]"
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end
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end
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# Parser for ``too short length'' report.
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#
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# $id: too short length ($leng), skipped\n";
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def self.too_short_parser(ent, entry_id = nil)
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report = self.new(ent)
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report.entry_id = entry_id
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if ent =~ /^(.+)?: too short length/
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report.entry_id = $1 unless report.entry_id
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report.scl = '---'
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end
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report
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end
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# Parser for the default report format.
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# ``psort report'' output.
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def self.default_parser(ent, entry_id = nil)
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report = self.new(ent, entry_id)
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ent = ent.split(/\n\n/).map {|e| e.chomp }
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report.set_header_line(ent[0])
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# feature matrix
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ent[1].gsub(/\n/,' ').strip.split(/ /).map {|fe|
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pair = fe.split(/: /)
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report.features[pair[0].strip] = pair[1].strip.to_f
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}
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report.prob = self.set_kNN_prob(ent[2])
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report.set_prediction(ent[3])
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return report
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end
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# Returns header information.
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def set_header_line(str)
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str.sub!(/^-+\n/,'')
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tmp = str.split(/\t| /)
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@entry_id = tmp.shift.sub(/^-+/,'').strip unless @entry_id
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case tmp.join(' ').chomp
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when /\(\d+ aa\) (.+)$/
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@definition = $1
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else
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@definition = tmp.join(' ').chomp
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end
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scl = @definition.split(' ')[0]
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@scl = scl if SclNames.keys.index(scl)
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end
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# Returns @prob value.
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def self.set_kNN_prob(str)
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prob = Hash.new
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Bio::PSORT::PSORT2::SclNames.keys.each {|a|
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prob.update( {a => 0.0} )
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}
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str.gsub(/\t/,'').split(/\n/).each {|a|
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val,scl = a.strip.split(/ %: /)
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key = Bio::PSORT::PSORT2::SclNames.index(scl)
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prob[key] = val.to_f
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}
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return prob
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end
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# Returns @prob and @k values.
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def set_prediction(str)
|
324
|
+
case str
|
325
|
+
when /prediction for (\S+?) is (\w{3}) \(k=(\d+)\)/
|
326
|
+
@entry_id ||= $1 unless @entry_id
|
327
|
+
@pred = $2
|
328
|
+
@k = $3
|
329
|
+
else
|
330
|
+
raise ArgumentError,
|
331
|
+
"Invalid format at(#{self.entry_id}):\n[#{str}]\n"
|
332
|
+
end
|
333
|
+
end
|
334
|
+
|
335
|
+
|
336
|
+
# Parser for the verbose output report format.
|
337
|
+
# ``psort -v report'' and WWW server output.
|
338
|
+
def self.v_parser(ent, entry_id = nil)
|
339
|
+
report = Bio::PSORT::PSORT2::Report.new(ent, entry_id)
|
340
|
+
|
341
|
+
ent = ent.split(/\n\n/).map {|e| e.chomp }
|
342
|
+
ent.each_with_index {|e, i|
|
343
|
+
unless /^(\w|-|\>|\t)/ =~ e
|
344
|
+
j = self.__send__(:search_j, i, ent)
|
345
|
+
ent[i - j] += e
|
346
|
+
ent[i] = nil
|
347
|
+
end
|
348
|
+
if /^none/ =~ e # psort output bug
|
349
|
+
j = self.__send__(:search_j, i, ent)
|
350
|
+
ent[i - j] += e
|
351
|
+
ent[i] = nil
|
352
|
+
end
|
353
|
+
}
|
354
|
+
ent.compact!
|
355
|
+
|
356
|
+
if /^ PSORT II server/ =~ ent[0] # for WWW version
|
357
|
+
ent.shift
|
358
|
+
delline = ''
|
359
|
+
ent.each {|e| delline = e if /^Results of Subprograms/ =~ e }
|
360
|
+
i = ent.index(delline)
|
361
|
+
ent.delete(delline)
|
362
|
+
ent.delete_at(i - 1)
|
363
|
+
end
|
364
|
+
|
365
|
+
report.set_header_line(ent.shift)
|
366
|
+
report.seq = Bio::Sequence::AA.new(ent.shift)
|
367
|
+
|
368
|
+
fent, pent = self.divent(ent)
|
369
|
+
report.set_features(fent)
|
370
|
+
report.prob = self.set_kNN_prob(pent[0].strip)
|
371
|
+
report.set_prediction(pent[1].strip)
|
372
|
+
|
373
|
+
return report
|
374
|
+
end
|
375
|
+
|
376
|
+
|
377
|
+
#
|
378
|
+
def self.search_j(i, ent)
|
379
|
+
j = 1
|
380
|
+
1.upto(ent.size) {|x|
|
381
|
+
if ent[i - x]
|
382
|
+
j = x
|
383
|
+
break
|
384
|
+
end
|
385
|
+
}
|
386
|
+
return j
|
387
|
+
end
|
388
|
+
private_class_method :search_j
|
389
|
+
|
390
|
+
|
391
|
+
# Divides entry body
|
392
|
+
def self.divent(entry)
|
393
|
+
boundary = entry.index(BOUNDARY)
|
394
|
+
return entry[0..(boundary - 1)], entry[(boundary + 2)..(entry.length)]
|
395
|
+
end
|
396
|
+
|
397
|
+
# Sets @features values.
|
398
|
+
def set_features(features_ary)
|
399
|
+
features_ary.each {|fent|
|
400
|
+
key = fent.split(/\:( |\n)/)[0].strip
|
401
|
+
self.features[key] = fent # unless /^\>/ =~ key
|
402
|
+
}
|
403
|
+
self.features['AA'] = self.seq.length
|
404
|
+
end
|
405
|
+
|
406
|
+
end # class Report
|
407
|
+
|
408
|
+
end # class PSORT2
|
409
|
+
|
410
|
+
|
411
|
+
class WoLF_PSORT
|
412
|
+
# taken from http://wolfpsort.org/aboutWoLF_PSORT.html.en
|
413
|
+
LOCATIONS = [
|
414
|
+
'chlo',
|
415
|
+
'cyto',
|
416
|
+
'cysk',
|
417
|
+
'E.R.',
|
418
|
+
'extr',
|
419
|
+
'golg',
|
420
|
+
'lyso',
|
421
|
+
'mito',
|
422
|
+
'nucl',
|
423
|
+
'pero',
|
424
|
+
'plas',
|
425
|
+
'vacu'
|
426
|
+
]
|
427
|
+
ORGANISM_TYPES = [
|
428
|
+
'animal',
|
429
|
+
'plant',
|
430
|
+
'fungi'
|
431
|
+
]
|
432
|
+
|
433
|
+
class Report
|
434
|
+
# Name of the sequence that has been analyzed, according
|
435
|
+
# to WoLF_PSORT output
|
436
|
+
attr_accessor :name
|
437
|
+
|
438
|
+
# plant, fungal or animal as a string
|
439
|
+
attr_accessor :organism_type
|
440
|
+
|
441
|
+
# A hash of scores output, for example {'cyto' => 12}
|
442
|
+
# keys of the hash are strings representing localisations
|
443
|
+
# values of the hash are float output scores
|
444
|
+
attr_accessor :score_hash
|
445
|
+
|
446
|
+
def initialize(name=nil, organism_type=nil, score_hash={})
|
447
|
+
@name = name
|
448
|
+
@organism_type = organism_type
|
449
|
+
@score_hash = score_hash
|
450
|
+
end
|
451
|
+
|
452
|
+
# Given an output line from a the runWolfPsortSummary script,
|
453
|
+
# return a report with all the included information in it
|
454
|
+
def self.parse_from_summary(organism_type, line)
|
455
|
+
line.strip!
|
456
|
+
return nil if line.match(/^\#/) #ignore the first comment line
|
457
|
+
|
458
|
+
rep = self.new
|
459
|
+
rep.organism_type = organism_type
|
460
|
+
|
461
|
+
line.split(', ').each_with_index do |fraction, index|
|
462
|
+
splits = fraction.split(' ')
|
463
|
+
if index == 0
|
464
|
+
raise ArgumentError, "invalid format\n[#{line}]" if splits.length != 3
|
465
|
+
rep.name = splits[0]
|
466
|
+
rep.score_hash[splits[1]] = splits[2].to_f
|
467
|
+
else
|
468
|
+
raise ArgumentError, "invalid format\n[#{line}]" if splits.length != 2
|
469
|
+
rep.score_hash[splits[0]] = splits[1].to_f
|
470
|
+
end
|
471
|
+
end
|
472
|
+
|
473
|
+
return rep
|
474
|
+
end
|
475
|
+
|
476
|
+
# Equivalence to another WoLF_PSORT report. Written mainly
|
477
|
+
# with testing in mind
|
478
|
+
def ==(another)
|
479
|
+
[:organism_type, :name, :score_hash].each do |attr|
|
480
|
+
return false if self.send(attr) != another.send(attr)
|
481
|
+
end
|
482
|
+
return true
|
483
|
+
end
|
484
|
+
|
485
|
+
# Return the string of the highest predicted localisation
|
486
|
+
# recorded in the score hash
|
487
|
+
def highest_predicted_localization
|
488
|
+
@score_hash.max{ |a,b|
|
489
|
+
a[1] <=> b[1]
|
490
|
+
}[0]
|
491
|
+
end
|
492
|
+
end # class Report
|
493
|
+
end # class WoLF_PSORT
|
494
|
+
|
495
|
+
end # class PSORT
|
496
|
+
|
497
|
+
end # module Bio
|
498
|
+
|
499
|
+
|
500
|
+
|
501
|
+
|
502
|
+
|
503
|
+
# testing code
|
504
|
+
|
505
|
+
if __FILE__ == $0
|
506
|
+
|
507
|
+
|
508
|
+
while entry = $<.gets(Bio::PSORT::PSORT2::Report::DELIMITER)
|
509
|
+
|
510
|
+
puts "\n ==> a = Bio::PSORT::PSORT2::Report.parser(entry)"
|
511
|
+
a = Bio::PSORT::PSORT2::Report.parser(entry)
|
512
|
+
|
513
|
+
puts "\n ==> a.entry_id "
|
514
|
+
p a.entry_id
|
515
|
+
puts "\n ==> a.scl "
|
516
|
+
p a.scl
|
517
|
+
puts "\n ==> a.pred "
|
518
|
+
p a.pred
|
519
|
+
puts "\n ==> a.prob "
|
520
|
+
p a.prob
|
521
|
+
p a.prob.keys.sort.map {|k| k.rjust(4)}.inspect.gsub('"','')
|
522
|
+
p a.prob.keys.sort.map {|k| a.prob[k].to_s.rjust(4) }.inspect.gsub('"','')
|
523
|
+
|
524
|
+
puts "\n ==> a.k "
|
525
|
+
p a.k
|
526
|
+
puts "\n ==> a.definition"
|
527
|
+
p a.definition
|
528
|
+
puts "\n ==> a.seq"
|
529
|
+
p a.seq
|
530
|
+
|
531
|
+
puts "\n ==> a.features.keys.sort "
|
532
|
+
p a.features.keys.sort
|
533
|
+
|
534
|
+
a.features.keys.sort.each do |key|
|
535
|
+
puts "\n ==> a.features['#{key}'] "
|
536
|
+
puts a.features[key]
|
537
|
+
end
|
538
|
+
|
539
|
+
|
540
|
+
end
|
541
|
+
|
542
|
+
end
|