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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module Bio
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#
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# = bio/appl/psort.rb - PSORT, protein sorting site prediction systems
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#
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# Copyright:: Copyright (C) 2003-2006
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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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# $Id:$
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#
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require 'bio/appl/psort/report'
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autoload :FastaFormat, 'bio/db/fasta'
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autoload :Command, 'bio/command'
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require 'cgi'
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require 'uri'
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# == A client for PSORT WWW Server
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#
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# A client for PSORT WWW Server for predicting protein subcellular
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# localization.
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#
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# PSORT family members,
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# 1. PSORT
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# 2. PSORT II
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# 3. iPSORT
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# 4. PSORT-B http://psort.org
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# 5. WoLF-PSORT
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#
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# == References
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#
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# * http://psort.hgc.jp/
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#
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class PSORT
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# a Hash for PSORT official hosts:
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# Key value (host)
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# ------- -----------------------
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# IMSUT psort.ims.u-tokyo.ac.jp
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# Okazaki psort.nibb.ac.jp
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# Peking srs.pku.edu.cn:8088
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ServerURI = {
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:IMSUT => {
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:PSORT1 => URI.parse("http://psort.hgc.jp/cgi-bin/okumura.pl"),
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:PSORT2 => URI.parse("http://psort.hgc.jp/cgi-bin/runpsort.pl") },
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:Okazaki => {
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:PSORT1 => URI.parse("http://psort.nibb.ac.jp/cgi-bin/okumura.pl"),
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:PSORT2 => URI.parse("http://psort.nibb.ac.jp/cgi-bin/runpsort.pl") },
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:Peking => {
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:PSORT1 => URI.parse("http:///src.pku.edu.cn:8088/cgi-bin/okumura.pl"),
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:PSORT2 => URI.parse("http://src.pku.edu.cn:8088/cgi-bin/runpsort.pl") },
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}
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# = Generic CGI client class
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# A generic CGI client class for Bio::PSORT::* classes.
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# The class provides an interface for CGI argument processing and output
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# report parsing.
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#
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# == Example
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#
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# class NewClient < CGIDriver
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# def initialize(host, path)
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# super(host, path)
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# end
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# end
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# private
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# def make_args(query)
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# # ...
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# end
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# def parse_report(output)
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# # ...
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# end
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#
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class CGIDriver
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# CGI query argument in Hash ({key => value, ...}).
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attr_accessor :args
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# CGI output raw text
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attr_reader :report
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# Sets remote host name and cgi path or uri.
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#
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# == Examples
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#
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# CGIDriver.new("localhost", "/cgi-bin/psort_www.pl")
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#
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# CGIDriver.new("http://localhost/cgi-bin/psort_www.pl")
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#
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# CGIDriver.new(URI.parse("http://localhost/cgi-bin/psort_www.pl"))
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#
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def initialize(host = '', path = '')
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case host.to_s
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when /^http:/
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uri = host.to_s
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else
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uri = 'http://' + host + '/' + path
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end
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@uri = URI.parse(uri)
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@args = {}
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@report = ''
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end
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# Executes a CGI ``query'' and returns aReport
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def exec(query)
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data = make_args(query)
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begin
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result = nil
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Bio::Command.start_http(@uri.host) {|http|
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result = http.post(@uri.path, data)
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}
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@report = result.body
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output = parse_report(@report)
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end
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return output
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end
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private
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# Bio::CGIDriver#make_args. An API skelton.
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def make_args(args_hash)
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# The routin should be provided in the inherited class
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end
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# Bio::CGIDriver#parse_report. An API skelton.
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def parse_report(result_body)
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# The routin should be provided in the inherited class
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end
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# Erases HTML tags
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def erase_html_tags(str)
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return str.gsub(/<\S.*?>/, '')
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end
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# Returns CGI argument text in String (key=value&) from a Hash ({key=>value}).
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def args_join(hash, delim = '&')
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tmp = []
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hash.each do |key, val|
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tmp << CGI.escape(key.to_s) + '=' + CGI.escape(val.to_s)
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end
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return tmp.join(delim) # not ';' but '&' in the psort cgi script.
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end
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end # class CGIDriver
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# = Bio::PSORT::PSORT1
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#
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# Bio::PSORT::PSORT1 is a wapper class for the original PSORT program.
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#
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# == Example
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#
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# serv = Bio::PSORT::PSORT1.imsut
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# serv.title = 'Query_title_splited_by_white space'
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# serv.exec(seq, false) # seq.class => String
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# serv.exec(seq)
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# report = serv.exec(Bio::FastaFormat.new(seq))
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# report_raw = serv.exec(Bio::FastaFormat.new(seq), false)
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#
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# == References
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#
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# 1. Nakai, K. and Kanehisa, M., A knowledge base for predicting protein
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# localization sites in eukaryotic cells, Genomics 14, 897-911 (1992).
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# [PMID:1478671]
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#
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class PSORT1
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autoload :Report, 'bio/appl/psort/report'
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# Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote)
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# connecting to the IMSUT server.
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def self.imsut
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self.new(Remote.new(ServerURI[:IMSUT][:PSORT1]))
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end
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# Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote)
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# connecting to the NIBB server.
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def self.okazaki
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self.new(Remote.new(ServerURI[:Okazaki][:PSORT1]))
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end
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# Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote)
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# connecting to the Peking server.
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def self.peking
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self.new(Remote.new(ServerURI[:Peking][:PSORT1]))
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end
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# Sets a cgi client (Bio::PSORT::PSORT1::Remote).
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#
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def initialize(driver, origin = 'yeast', title = 'MYSEQ')
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@serv = driver
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@origin = origin # Gram-positive bacterium, Gram-negative bacterium,
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# yeast, aminal, plant
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@title = title
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@sequence = ''
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end
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# An accessor of the origin argument. Default setting is "yeast".
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# Usable values:
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# 1. Gram-positive bacterium
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# 2. Gram-negative bacterium
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# 3. yeast
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# 4. animal
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# 5. plant
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attr_accessor :origin
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# An accessor of the query sequence argument.
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attr_accessor :sequence
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# An accessor of the title argument. Default setting is 'MYSEQ'.
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# The value is automatically setted if you use a query in
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# Bio::FastaFormat.
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attr_accessor :title
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# Executes the query (faa) and returns an Bio::PSORT::PSORT1::Report.
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#
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# The ``faa'' argument is acceptable a sequence both in String and in
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# Bio::FastaFormat.
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#
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# If you set the second argument is ``parsing = false'',
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# returns ourput text without any parsing.
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def exec(faa, parsing = true)
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if faa.class == Bio::FastaFormat
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@title = faa.entry_id if @title == 'MYSEQ'
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@sequence = faa.seq
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@serv.args = {'title' => @title, 'origin' => @origin}
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@serv.parsing = parsing
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return @serv.exec(sequence)
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else
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self.exec(Bio::FastaFormat.new(faa), parsing)
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end
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end
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# = Bio::PSORT::PSORT1::Remote
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# PSORT1 specific CGIDriver.
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class Remote < CGIDriver
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# Accessor for Bio::PSORT::PSORT1::Remote#origin to contein target domain.
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# Taget domains:
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# 1. Gram-positive bacterium
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# 2. Gram-negative bacterium
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# 3. yeast
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# 4. animal
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# 5. plant
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attr_accessor :origin
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# Accessor for Bio::POSRT::PSORT1#sequence to contein the query sequence.
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attr_accessor :title
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# Accessor for Bio::PSORT::PSORT1#title to contain the query title.
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attr_accessor :parsing
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# Sets remote ``host'' and cgi ``path''.
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def initialize(host, path = nil, title = 'MYSEQ', origin = 'yeast')
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@title = title
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@origin = origin
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@parsing = true
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super(host, path)
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end
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private
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# Returns parsed CGI argument.
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# An API implementation.
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def make_args(query)
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@args.update({'sequence' => query})
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return args_join(@args)
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end
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# Returns parsed output report.
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# An API implementation.
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def parse_report(str)
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str = erase_html_tags(str)
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str = Bio::PSORT::PSORT1::Report.parser(str) if @parsing
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return str
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end
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end # Class Remote
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end # class PSORT1
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# = Bio::PSORT::PSORT2
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# Bio::PSORT::PSORT2 is a wapper class for the original PSORT program.
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#
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# == Example
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#
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# serv = Bio::PSORT::PSORT2.imsut
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# serv.title = 'Query_title_splited_by_white space'
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# serv.exec(seq, false) # seq.class => String
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# serv.exec(seq)
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# report = serv.exec(Bio::FastaFormat.new(seq))
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# report_raw = serv.exec(Bio::FastaFormat.new(seq), false)
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#
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# == References
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# 1. Nakai, K. and Horton, P., PSORT: a program for detecting the sorting
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# signals of proteins and predicting their subcellular localization,
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# Trends Biochem. Sci, 24(1) 34-35 (1999).
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# [PMID:10087920]
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class PSORT2
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autoload :Report, 'bio/appl/psort/report'
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# Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote).
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#
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# PSORT official hosts:
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# key host path
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# ------- ----------------------- -------------------- ---------
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# IMSUT psort.ims.u-tokyo.ac.jp /cgi-bin/runpsort.pl (default)
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# Okazaki psort.nibb.ac.jp /cgi-bin/runpsort.pl
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# Peking srs.pku.edu.cn:8088 /cgi-bin/runpsort.pl
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def self.remote(host, path = nil)
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self.new(Remote.new(host, path))
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end
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# Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote)
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# connecting to the IMSUT server.
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def self.imsut
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self.remote(ServerURI[:IMSUT][:PSORT2])
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end
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# Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote)
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# connecting to the NIBB server.
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def self.okazaki
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self.remote(ServerURI[:Okazaki][:PSORT2])
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339
|
+
end
|
340
|
+
|
341
|
+
# Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote)
|
342
|
+
# connecting to the Peking server.
|
343
|
+
def self.peking
|
344
|
+
self.remote(ServerURI[:Peking][:PSORT2])
|
345
|
+
end
|
346
|
+
|
347
|
+
# An accessor of the origin argument.
|
348
|
+
# Default setting is ``yeast''.
|
349
|
+
attr_accessor :origin
|
350
|
+
|
351
|
+
# An accessor of the title argument. Default setting is ``QUERY''.
|
352
|
+
# The value is automatically setted if you use a query in
|
353
|
+
# Bio::FastaFormat.
|
354
|
+
attr_accessor :title
|
355
|
+
|
356
|
+
# Sets a server CGI Driver (Bio::PSORT::PSORT2::Remote).
|
357
|
+
def initialize(driver, origin = 'yeast')
|
358
|
+
@serv = driver
|
359
|
+
@origin = origin
|
360
|
+
@title = ''
|
361
|
+
end
|
362
|
+
|
363
|
+
|
364
|
+
# Executes PSORT II prediction and returns Report object
|
365
|
+
# (Bio::PSORT::PSORT2::Report) if parsing = true.
|
366
|
+
# Returns PSORT II report in text if parsing = false.
|
367
|
+
def exec(faa, parsing = true)
|
368
|
+
if faa.class == Bio::FastaFormat
|
369
|
+
@title = faa.entry_id if @title == nil
|
370
|
+
@sequence = faa.seq
|
371
|
+
@serv.args = {'origin' => @origin, 'title' => @title}
|
372
|
+
@serv.parsing = parsing
|
373
|
+
return @serv.exec(@sequence)
|
374
|
+
else
|
375
|
+
self.exec(Bio::FastaFormat.new(faa), parsing)
|
376
|
+
end
|
377
|
+
end
|
378
|
+
|
379
|
+
|
380
|
+
# = Bio::PSORT::PSORT2::Remote
|
381
|
+
# PSORT2 specific CGIDriver
|
382
|
+
class Remote < CGIDriver
|
383
|
+
|
384
|
+
# Sets remote ``host'' and cgi ``path''.
|
385
|
+
def initialize(host, path)
|
386
|
+
@origin = 'yeast'
|
387
|
+
super(host, path)
|
388
|
+
@parsing = true
|
389
|
+
end
|
390
|
+
|
391
|
+
# An accessor of the origin argument.
|
392
|
+
# Default setting is ``yeast''.
|
393
|
+
attr_accessor :origin
|
394
|
+
|
395
|
+
# An accessor of the output parsing.
|
396
|
+
# Default setting is ``true''.
|
397
|
+
attr_accessor :parsing
|
398
|
+
|
399
|
+
|
400
|
+
private
|
401
|
+
|
402
|
+
# Returns parsed CGI argument.
|
403
|
+
# An API implementation.
|
404
|
+
def make_args(query)
|
405
|
+
@args.update({'sequence' => query})
|
406
|
+
return args_join(@args)
|
407
|
+
end
|
408
|
+
|
409
|
+
|
410
|
+
# Returns parsed output report.
|
411
|
+
# An API implementation.
|
412
|
+
def parse_report(str)
|
413
|
+
str = str.gsub(/\n<hr>/i, Report::BOUNDARY)
|
414
|
+
str = erase_html_tags(str)
|
415
|
+
str = Bio::PSORT::PSORT2::Report.parser(str, self.args['title']) if @parsing
|
416
|
+
return str
|
417
|
+
end
|
418
|
+
|
419
|
+
end # class Remote
|
420
|
+
|
421
|
+
end # class PSORT2
|
422
|
+
|
423
|
+
|
424
|
+
class IPSORT
|
425
|
+
end # class IPSORT
|
426
|
+
|
427
|
+
|
428
|
+
class PSORTB
|
429
|
+
end # class PSORTB
|
430
|
+
|
431
|
+
class WoLF_PSORT
|
432
|
+
end # class PSORTB
|
433
|
+
|
434
|
+
end # class PSORT
|
435
|
+
|
436
|
+
end # module Bio
|
437
|
+
|
438
|
+
|
439
|
+
|
440
|
+
|
441
|
+
|
442
|
+
if __FILE__ == $0
|
443
|
+
|
444
|
+
begin
|
445
|
+
require 'psort/report.rb'
|
446
|
+
rescue LoadError
|
447
|
+
end
|
448
|
+
|
449
|
+
|
450
|
+
seq = ">hoge mit
|
451
|
+
MALEPIDYTT RDEDDLDENE LLMKISNAAG SSRVNDNNDD LTFVENDKII
|
452
|
+
ARYSIQTSSK QQGKASTPPV EEAEEAAPQL PSRSSAAPPP PPRRATPEKK
|
453
|
+
DVKDLKSKFE GLAASEKEEE EMENKFAPPP KKSEPTIISP KPFSKPQEPV
|
454
|
+
FKGYHVQVTA HSREIDAEYL KIVRGSDPDT TWLIISPNAK KEYEPESTGS
|
455
|
+
KKSFTPSKSP APVSKKEPVK TPSPAPAAKI PKENPWATAE YDYDAAEDNE
|
456
|
+
NIEFVDDDWW LGELEKDGSK GLFPSNYVSL LPSRNVASGA PVQKEEPEQE
|
457
|
+
SFHDFLQLFD ETKVQYGLAR RKAKQNSGNA ETKAEAPKPE VPEDEPEGEP
|
458
|
+
DDWNEPELKE RDFDQAPLKP NQSSYKPIGK IDLQKVIAEE KAKEDPRLVQ
|
459
|
+
DYKKIGNPLP GMHIEADNEE EPEENDDDWD DDEDEAAQPP ANFAAVANNL
|
460
|
+
KPTAAGSKID DDKVIKGFRN EKSPAQLWAE VSPPGSDVEK IIIIGWCPDS
|
461
|
+
APLKTRASFA PSSDIANLKN ESKLKRDSEF NSFLGTTKPP SMTESSLKND
|
462
|
+
KAEEAEQPKT EIAPSLPSRN SIPAPKQEEA PEQAPEEEIE GN
|
463
|
+
"
|
464
|
+
Seq1 = ">hgoe
|
465
|
+
LTFVENDKII NI
|
466
|
+
"
|
467
|
+
|
468
|
+
puts "\n Bio::PSORT::PSORT"
|
469
|
+
|
470
|
+
puts "\n ==> p serv = Bio::PSORT::PSORT.imsut"
|
471
|
+
p serv = Bio::PSORT::PSORT1.imsut
|
472
|
+
|
473
|
+
puts "\n ==> p serv.class "
|
474
|
+
p serv.class
|
475
|
+
|
476
|
+
puts "\n ==> p serv.title = 'Query_title_splited_by_white space'"
|
477
|
+
p serv.title = 'Query_title_splited_by_white space'
|
478
|
+
|
479
|
+
puts "\n ==> p serv.exec(seq, false) "
|
480
|
+
p serv.exec(seq, false)
|
481
|
+
|
482
|
+
puts "\n ==> p serv.exec(seq) "
|
483
|
+
p serv.exec(seq)
|
484
|
+
|
485
|
+
puts "\n ==> p report = serv.exec(Bio::FastaFormat.new(seq)) "
|
486
|
+
p report = serv.exec(Bio::FastaFormat.new(seq))
|
487
|
+
|
488
|
+
puts "\n ==> p report.class"
|
489
|
+
p report.class
|
490
|
+
|
491
|
+
|
492
|
+
puts "\n ==> p report_raw = serv.exec(Bio::FastaFormat.new(seq), false) "
|
493
|
+
p report_raw = serv.exec(Bio::FastaFormat.new(seq), false)
|
494
|
+
|
495
|
+
puts "\n ==> p report_raw.class"
|
496
|
+
p report_raw.class
|
497
|
+
|
498
|
+
|
499
|
+
puts "\n ==> p report.methods"
|
500
|
+
p report.methods
|
501
|
+
|
502
|
+
methods = ['entry_id', 'origin', 'title', 'sequence','result_info',
|
503
|
+
'reasoning', 'final_result', 'raw']
|
504
|
+
methods.each do |method|
|
505
|
+
puts "\n ==> p report.#{method}"
|
506
|
+
p eval("report.#{method}")
|
507
|
+
end
|
508
|
+
|
509
|
+
|
510
|
+
|
511
|
+
puts "\n Bio::PSORT::PSORT2"
|
512
|
+
|
513
|
+
puts "\n ==> p serv = Bio::PSORT::PSORT2.imsut"
|
514
|
+
p serv = Bio::PSORT::PSORT2.imsut
|
515
|
+
|
516
|
+
puts "\n ==> p serv.class "
|
517
|
+
p serv.class
|
518
|
+
|
519
|
+
puts "\n ==> p seq "
|
520
|
+
p seq
|
521
|
+
|
522
|
+
puts "\n ==> p serv.title = 'Query_title_splited_by_white space'"
|
523
|
+
p serv.title = 'Query_title_splited_by_white space'
|
524
|
+
|
525
|
+
puts "\n ==> p serv.exec(seq) # parsed report"
|
526
|
+
p serv.exec(seq)
|
527
|
+
|
528
|
+
puts "\n ==> p report = serv.exec(Bio::FastaFormat.new(seq)) # parsed report"
|
529
|
+
p report = serv.exec(Bio::FastaFormat.new(seq))
|
530
|
+
|
531
|
+
|
532
|
+
|
533
|
+
puts "\n ==> p serv.exec(seq, false) # report in plain text"
|
534
|
+
p serv.exec(seq, false)
|
535
|
+
|
536
|
+
puts "\n ==> p report_raw = serv.exec(Bio::FastaFormat.new(seq), false) # report in plain text"
|
537
|
+
p report_raw = serv.exec(Bio::FastaFormat.new(seq), false)
|
538
|
+
|
539
|
+
|
540
|
+
puts "\n ==> p report.methods"
|
541
|
+
p report.methods
|
542
|
+
|
543
|
+
methods = ['entry_id', 'scl', 'definition', 'seq', 'features', 'prob', 'pred', 'k', 'raw']
|
544
|
+
methods.each do |method|
|
545
|
+
puts "\n ==> p report.#{method}"
|
546
|
+
p eval("report.#{method}")
|
547
|
+
end
|
548
|
+
end
|