wwood-bioruby 1.2.11
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- data/README.rdoc +205 -0
- data/README_DEV.rdoc +285 -0
- data/VERSION.yml +4 -0
- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +293 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/lib/bio.rb +306 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +505 -0
- data/lib/bio/appl/blast/ddbj.rb +142 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/genomenet.rb +263 -0
- data/lib/bio/appl/blast/ncbioptions.rb +220 -0
- data/lib/bio/appl/blast/remote.rb +105 -0
- data/lib/bio/appl/blast/report.rb +767 -0
- data/lib/bio/appl/blast/rexml.rb +144 -0
- data/lib/bio/appl/blast/rpsblast.rb +277 -0
- data/lib/bio/appl/blast/wublast.rb +635 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blat/report.rb +530 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta.rb +235 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/gcg/msf.rb +212 -0
- data/lib/bio/appl/gcg/seq.rb +195 -0
- data/lib/bio/appl/genscan/report.rb +552 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/hmmer/report.rb +683 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/paml/baseml.rb +95 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/codeml.rb +242 -0
- data/lib/bio/appl/paml/codeml/rates.rb +67 -0
- data/lib/bio/appl/paml/codeml/report.rb +67 -0
- data/lib/bio/appl/paml/common.rb +348 -0
- data/lib/bio/appl/paml/common_report.rb +38 -0
- data/lib/bio/appl/paml/yn00.rb +103 -0
- data/lib/bio/appl/paml/yn00/report.rb +32 -0
- data/lib/bio/appl/phylip/alignment.rb +133 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/psort/report.rb +542 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +124 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sosui/report.rb +151 -0
- data/lib/bio/appl/spidey/report.rb +593 -0
- data/lib/bio/appl/targetp/report.rb +267 -0
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +231 -0
- data/lib/bio/command.rb +593 -0
- data/lib/bio/compat/features.rb +157 -0
- data/lib/bio/compat/references.rb +128 -0
- data/lib/bio/data/aa.rb +353 -0
- data/lib/bio/data/codontable.rb +722 -0
- data/lib/bio/data/na.rb +223 -0
- data/lib/bio/db.rb +329 -0
- data/lib/bio/db/aaindex.rb +357 -0
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +67 -0
- data/lib/bio/db/biosql/sequence.rb +508 -0
- data/lib/bio/db/embl/common.rb +352 -0
- data/lib/bio/db/embl/embl.rb +500 -0
- data/lib/bio/db/embl/embl_to_biosequence.rb +85 -0
- data/lib/bio/db/embl/format_embl.rb +190 -0
- data/lib/bio/db/embl/sptr.rb +1283 -0
- data/lib/bio/db/embl/swissprot.rb +42 -0
- data/lib/bio/db/embl/trembl.rb +41 -0
- data/lib/bio/db/embl/uniprot.rb +42 -0
- data/lib/bio/db/fantom.rb +597 -0
- data/lib/bio/db/fasta.rb +410 -0
- data/lib/bio/db/fasta/defline.rb +532 -0
- data/lib/bio/db/fasta/fasta_to_biosequence.rb +63 -0
- data/lib/bio/db/fasta/format_fasta.rb +97 -0
- data/lib/bio/db/genbank/common.rb +307 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/format_genbank.rb +187 -0
- data/lib/bio/db/genbank/genbank.rb +250 -0
- data/lib/bio/db/genbank/genbank_to_biosequence.rb +86 -0
- data/lib/bio/db/genbank/genpept.rb +60 -0
- data/lib/bio/db/genbank/refseq.rb +18 -0
- data/lib/bio/db/gff.rb +1846 -0
- data/lib/bio/db/go.rb +481 -0
- data/lib/bio/db/kegg/brite.rb +41 -0
- data/lib/bio/db/kegg/compound.rb +131 -0
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +148 -0
- data/lib/bio/db/kegg/expression.rb +155 -0
- data/lib/bio/db/kegg/genes.rb +263 -0
- data/lib/bio/db/kegg/genome.rb +241 -0
- data/lib/bio/db/kegg/glycan.rb +166 -0
- data/lib/bio/db/kegg/keggtab.rb +357 -0
- data/lib/bio/db/kegg/kgml.rb +256 -0
- data/lib/bio/db/kegg/orthology.rb +136 -0
- data/lib/bio/db/kegg/reaction.rb +82 -0
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +107 -0
- data/lib/bio/db/medline.rb +326 -0
- data/lib/bio/db/nbrf.rb +191 -0
- data/lib/bio/db/newick.rb +658 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +29 -0
- data/lib/bio/db/pdb/atom.rb +77 -0
- data/lib/bio/db/pdb/chain.rb +210 -0
- data/lib/bio/db/pdb/chemicalcomponent.rb +224 -0
- data/lib/bio/db/pdb/model.rb +148 -0
- data/lib/bio/db/pdb/pdb.rb +1911 -0
- data/lib/bio/db/pdb/residue.rb +176 -0
- data/lib/bio/db/pdb/utils.rb +399 -0
- data/lib/bio/db/prosite.rb +597 -0
- data/lib/bio/db/rebase.rb +456 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/db/url.rb +42 -0
- data/lib/bio/feature.rb +139 -0
- data/lib/bio/io/biosql/biodatabase.rb +64 -0
- data/lib/bio/io/biosql/bioentry.rb +29 -0
- data/lib/bio/io/biosql/bioentry_dbxref.rb +11 -0
- data/lib/bio/io/biosql/bioentry_path.rb +12 -0
- data/lib/bio/io/biosql/bioentry_qualifier_value.rb +10 -0
- data/lib/bio/io/biosql/bioentry_reference.rb +10 -0
- data/lib/bio/io/biosql/bioentry_relationship.rb +10 -0
- data/lib/bio/io/biosql/biosequence.rb +11 -0
- data/lib/bio/io/biosql/comment.rb +7 -0
- data/lib/bio/io/biosql/config/database.yml +20 -0
- data/lib/bio/io/biosql/dbxref.rb +13 -0
- data/lib/bio/io/biosql/dbxref_qualifier_value.rb +12 -0
- data/lib/bio/io/biosql/location.rb +32 -0
- data/lib/bio/io/biosql/location_qualifier_value.rb +11 -0
- data/lib/bio/io/biosql/ontology.rb +10 -0
- data/lib/bio/io/biosql/reference.rb +9 -0
- data/lib/bio/io/biosql/seqfeature.rb +32 -0
- data/lib/bio/io/biosql/seqfeature_dbxref.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_path.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_qualifier_value.rb +20 -0
- data/lib/bio/io/biosql/seqfeature_relationship.rb +11 -0
- data/lib/bio/io/biosql/taxon.rb +12 -0
- data/lib/bio/io/biosql/taxon_name.rb +9 -0
- data/lib/bio/io/biosql/term.rb +27 -0
- data/lib/bio/io/biosql/term_dbxref.rb +11 -0
- data/lib/bio/io/biosql/term_path.rb +12 -0
- data/lib/bio/io/biosql/term_relationship.rb +13 -0
- data/lib/bio/io/biosql/term_relationship_term.rb +11 -0
- data/lib/bio/io/biosql/term_synonym.rb +10 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +638 -0
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +163 -0
- data/lib/bio/io/fetch.rb +195 -0
- data/lib/bio/io/flatfile.rb +482 -0
- data/lib/bio/io/flatfile/autodetection.rb +545 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/buffer.rb +237 -0
- data/lib/bio/io/flatfile/index.rb +1381 -0
- data/lib/bio/io/flatfile/indexer.rb +805 -0
- data/lib/bio/io/flatfile/splitter.rb +297 -0
- data/lib/bio/io/higet.rb +73 -0
- data/lib/bio/io/hinv.rb +442 -0
- data/lib/bio/io/keggapi.rb +805 -0
- data/lib/bio/io/ncbirest.rb +733 -0
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +307 -0
- data/lib/bio/io/registry.rb +292 -0
- data/lib/bio/io/soapwsdl.rb +119 -0
- data/lib/bio/io/sql.rb +186 -0
- data/lib/bio/location.rb +867 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +960 -0
- data/lib/bio/reference.rb +602 -0
- data/lib/bio/sequence.rb +456 -0
- data/lib/bio/sequence/aa.rb +152 -0
- data/lib/bio/sequence/adapter.rb +108 -0
- data/lib/bio/sequence/common.rb +310 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/dblink.rb +54 -0
- data/lib/bio/sequence/format.rb +358 -0
- data/lib/bio/sequence/format_raw.rb +23 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +491 -0
- data/lib/bio/shell.rb +44 -0
- data/lib/bio/shell/core.rb +578 -0
- data/lib/bio/shell/demo.rb +146 -0
- data/lib/bio/shell/interface.rb +218 -0
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +71 -0
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +218 -0
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +105 -0
- data/lib/bio/shell/plugin/flatfile.rb +101 -0
- data/lib/bio/shell/plugin/keggapi.rb +181 -0
- data/lib/bio/shell/plugin/midi.rb +430 -0
- data/lib/bio/shell/plugin/obda.rb +45 -0
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +247 -0
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +102 -0
- data/lib/bio/tree.rb +852 -0
- data/lib/bio/util/color_scheme.rb +191 -0
- data/lib/bio/util/color_scheme/buried.rb +59 -0
- data/lib/bio/util/color_scheme/helix.rb +59 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +64 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +31 -0
- data/lib/bio/util/color_scheme/strand.rb +59 -0
- data/lib/bio/util/color_scheme/taylor.rb +50 -0
- data/lib/bio/util/color_scheme/turn.rb +59 -0
- data/lib/bio/util/color_scheme/zappo.rb +50 -0
- data/lib/bio/util/contingency_table.rb +370 -0
- data/lib/bio/util/restriction_enzyme.rb +228 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
- data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +200 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/aaindex/DAYM780301 +30 -0
- data/test/data/aaindex/PRAM900102 +20 -0
- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
- data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
- data/test/data/blast/2.2.15.blastp.m7 +876 -0
- data/test/data/blast/b0002.faa +15 -0
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- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/blast/blastp-multi.m7 +188 -0
- data/test/data/command/echoarg2.bat +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/embl/AB090716.embl.rel89 +63 -0
- data/test/data/fasta/example1.txt +75 -0
- data/test/data/fasta/example2.txt +21 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/paml/codeml/control_file.txt +30 -0
- data/test/data/paml/codeml/output.txt +78 -0
- data/test/data/paml/codeml/rates +217 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/rpsblast/misc.rpsblast +193 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/functional/bio/appl/test_pts1.rb +115 -0
- data/test/functional/bio/io/test_ensembl.rb +229 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -0
- data/test/functional/bio/sequence/test_output_embl.rb +51 -0
- data/test/functional/bio/test_command.rb +301 -0
- data/test/runner.rb +14 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_ncbioptions.rb +112 -0
- data/test/unit/bio/appl/blast/test_report.rb +1135 -0
- data/test/unit/bio/appl/blast/test_rpsblast.rb +398 -0
- data/test/unit/bio/appl/genscan/test_report.rb +182 -0
- data/test/unit/bio/appl/hmmer/test_report.rb +342 -0
- data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
- data/test/unit/bio/appl/mafft/test_report.rb +63 -0
- data/test/unit/bio/appl/paml/codeml/test_rates.rb +45 -0
- data/test/unit/bio/appl/paml/codeml/test_report.rb +45 -0
- data/test/unit/bio/appl/paml/test_codeml.rb +174 -0
- data/test/unit/bio/appl/sosui/test_report.rb +81 -0
- data/test/unit/bio/appl/targetp/test_report.rb +146 -0
- data/test/unit/bio/appl/test_blast.rb +277 -0
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_psort.rb +57 -0
- data/test/unit/bio/appl/test_pts1.rb +77 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +126 -0
- data/test/unit/bio/data/test_aa.rb +90 -0
- data/test/unit/bio/data/test_codontable.rb +107 -0
- data/test/unit/bio/data/test_na.rb +80 -0
- data/test/unit/bio/db/embl/test_common.rb +117 -0
- data/test/unit/bio/db/embl/test_embl.rb +214 -0
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +203 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1812 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +31 -0
- data/test/unit/bio/db/kegg/test_genes.rb +45 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +152 -0
- data/test/unit/bio/db/test_aaindex.rb +197 -0
- data/test/unit/bio/db/test_fasta.rb +250 -0
- data/test/unit/bio/db/test_gff.rb +1190 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_medline.rb +127 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +364 -0
- data/test/unit/bio/db/test_prosite.rb +1437 -0
- data/test/unit/bio/db/test_rebase.rb +101 -0
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/db/test_url.rb +36 -0
- data/test/unit/bio/io/flatfile/test_autodetection.rb +375 -0
- data/test/unit/bio/io/flatfile/test_buffer.rb +251 -0
- data/test/unit/bio/io/flatfile/test_splitter.rb +369 -0
- data/test/unit/bio/io/test_ddbjxml.rb +80 -0
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +42 -0
- data/test/unit/bio/io/test_flatfile.rb +505 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +115 -0
- data/test/unit/bio/sequence/test_common.rb +373 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -0
- data/test/unit/bio/sequence/test_dblink.rb +58 -0
- data/test/unit/bio/sequence/test_na.rb +330 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +185 -0
- data/test/unit/bio/test_alignment.rb +1025 -0
- data/test/unit/bio/test_command.rb +349 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +144 -0
- data/test/unit/bio/test_location.rb +599 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +499 -0
- data/test/unit/bio/test_reference.rb +252 -0
- data/test/unit/bio/test_sequence.rb +329 -0
- data/test/unit/bio/test_shell.rb +18 -0
- data/test/unit/bio/test_tree.rb +593 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +101 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
- data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
- data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
- data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
- data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
- data/test/unit/bio/util/test_color_scheme.rb +33 -0
- data/test/unit/bio/util/test_contingency_table.rb +94 -0
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +245 -0
- metadata +543 -0
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#
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# test/unit/bio/appl/test_blast.rb - Unit test for Bio::Blast
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#
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# Copyright:: Copyright (C) 2005 Mitsuteru 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 'pathname'
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libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib'))).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'test/unit'
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require 'bio/appl/blast'
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module Bio
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class TestBlastData
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bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4)).cleanpath.to_s
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TestDataBlast = Pathname.new(File.join(bioruby_root, 'test', 'data', 'blast')).cleanpath.to_s
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def self.input
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File.open(File.join(TestDataBlast, 'b0002.faa')).read
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end
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def self.output(format = '7')
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case format
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when '0'
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File.open(File.join(TestDataBlast, 'b0002.faa.m0')).read
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when '7'
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File.open(File.join(TestDataBlast, 'b0002.faa.m7')).read
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when '8'
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File.open(File.join(TestDataBlast, 'b0002.faa.m8')).read
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end
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end
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end
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class TestBlast < Test::Unit::TestCase
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def setup
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@program = 'blastp'
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@db = 'test'
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@option = []
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@server = 'localhost'
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@blast = Bio::Blast.new(@program, @db, @option, @server)
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end
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def test_new
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blast = Bio::Blast.new(@program, @db)
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assert_equal(@program, blast.program)
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assert_equal(@db, blast.db)
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assert(blast.options)
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assert_equal('local', blast.server)
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assert_equal('blastall', blast.blastall)
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end
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def test_new_opt_string
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blast = Bio::Blast.new(@program, @db, '-m 7 -F F')
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assert_equal(['-m', '7', '-F', 'F'], blast.options)
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end
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def test_program
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assert_equal(@program, @blast.program)
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end
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def test_db
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assert_equal(@db, @blast.db)
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end
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def test_options
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assert_equal([], @blast.options)
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end
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def test_option
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assert_equal('', @blast.option)
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end
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def test_option_set
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@blast.option = '-m 7 -p T'
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assert_equal('-m 7 -p T', @blast.option)
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end
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def test_option_set_m0
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@blast.option = '-m 0'
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assert_equal('-m 0', @blast.option)
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end
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def test_server
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assert_equal(@server, @blast.server)
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end
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def test_blastll
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assert_equal('blastall', @blast.blastall)
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end
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def test_matrix
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assert_equal(nil, @blast.matrix)
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end
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def test_filter
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assert_equal(nil, @blast.filter)
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end
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def test_parser
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assert_equal(nil, @blast.instance_eval { @parser })
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end
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def test_output
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assert_equal('', @blast.output)
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end
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def test_format
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assert(@blast.format)
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end
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def test_self_local
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assert(Bio::Blast.local(@program, @db, @option))
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end
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def test_self_local
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assert(Bio::Blast.remote(@program, @db, @option))
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end
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def test_query
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# to be tested in test/functional/bio/test_blast.rb
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end
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def test_blast_reports_xml
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ret = Bio::Blast.reports_xml(TestBlastData.output)
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assert_instance_of(Array, ret)
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count = 0
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ret.each do |report|
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count += 1
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assert_instance_of(Bio::Blast::Report, report)
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end
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assert_equal(1, count)
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end
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def test_blast_reports_xml_with_block
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count = 0
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Bio::Blast.reports_xml(TestBlastData.output) do |report|
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count += 1
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assert_instance_of(Bio::Blast::Report, report)
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end
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assert_equal(1, count)
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end
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def test_blast_reports_format0
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ret = Bio::Blast.reports(TestBlastData.output('0'))
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assert_instance_of(Array, ret)
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count = 0
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ret.each do |report|
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count += 1
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assert_instance_of(Bio::Blast::Default::Report, report)
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end
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assert_equal(1, count)
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end
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def test_blast_reports_format7
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ret = Bio::Blast.reports(TestBlastData.output('7'))
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assert_instance_of(Array, ret)
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count = 0
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ret.each do |report|
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count += 1
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assert_instance_of(Bio::Blast::Report, report)
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end
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assert_equal(1, count)
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end
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def test_blast_reports_format8
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ret = Bio::Blast.reports(TestBlastData.output('8'))
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assert_instance_of(Array, ret)
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count = 0
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ret.each do |report|
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count += 1
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assert_kind_of(Bio::Blast::Report, report)
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end
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assert_equal(1, count)
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end
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def test_blast_reports_format0_with_block
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count = 0
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Bio::Blast.reports(TestBlastData.output('0')) do |report|
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count += 1
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assert_instance_of(Bio::Blast::Default::Report, report)
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end
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assert_equal(1, count)
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end
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def test_blast_reports_format7_with_block
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count = 0
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Bio::Blast.reports(TestBlastData.output('7')) do |report|
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count += 1
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assert_instance_of(Bio::Blast::Report, report)
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end
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assert_equal(1, count)
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end
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def test_blast_reports_format8_with_block
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count = 0
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Bio::Blast.reports(TestBlastData.output('8')) do |report|
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count += 1
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assert_kind_of(Bio::Blast::Report, report)
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end
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assert_equal(1, count)
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end
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def test_blast_reports_format7_with_parser
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ret = Bio::Blast.reports(TestBlastData.output('7'), :rexml)
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assert_instance_of(Array, ret)
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count = 0
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ret.each do |report|
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count += 1
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assert_instance_of(Bio::Blast::Report, report)
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end
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assert_equal(1, count)
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end
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def test_blast_reports_format8_with_parser
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ret = Bio::Blast.reports(TestBlastData.output('8'), :tab)
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assert_instance_of(Array, ret)
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count = 0
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ret.each do |report|
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count += 1
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assert_kind_of(Bio::Blast::Report, report)
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end
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assert_equal(1, count)
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end
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def test_blast_reports_format7_with_parser_with_block
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count = 0
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Bio::Blast.reports(TestBlastData.output('7'), :rexml) do |report|
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count += 1
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assert_instance_of(Bio::Blast::Report, report)
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end
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assert_equal(1, count)
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end
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def test_blast_reports_format8_with_parser_with_block
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count = 0
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Bio::Blast.reports(TestBlastData.output('8'), :tab) do |report|
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count += 1
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assert_kind_of(Bio::Blast::Report, report)
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end
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assert_equal(1, count)
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end
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def test_make_command_line
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@blast = Bio::Blast.new(@program, @db, '-m 7 -F F')
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assert_equal(["blastall", "-p", "blastp", "-d", "test", "-m", "7", "-F", "F"],
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@blast.instance_eval { make_command_line })
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end
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def test_make_command_line_2
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@blast = Bio::Blast.new(@program, @db, '-m 0 -F F')
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assert_equal(["blastall", "-p", "blastp", "-d", "test", "-m", "0", "-F", "F"],
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@blast.instance_eval { make_command_line })
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end
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def test_parse_result
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assert(@blast.instance_eval { parse_result(TestBlastData.output) })
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end
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def test_exec_local
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# to be tested in test/functional/bio/test_blast.rb
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end
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def test_exec_genomenet
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# to be tested in test/functional/bio/test_blast.rb
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end
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def test_exec_ncbi
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# to be tested in test/functional/bio/test_blast.rb
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end
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end
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end
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#
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# test/unit/bio/appl/test_fasta.rb - Unit test for Bio::Fasta
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#
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# Copyright:: Copyright (C) 2006
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5
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# Mitsuteru C. Nakao <n@bioruby.org>
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6
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# License:: The Ruby License
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7
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#
|
8
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# $Id:$
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9
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#
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10
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|
11
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require 'pathname'
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libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib'))).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'test/unit'
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require 'bio/appl/fasta'
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18
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module Bio
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20
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|
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class TestFastaInitialize < Test::Unit::TestCase
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def test_new_1
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23
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program = 'string'
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db = 'string'
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25
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option = ['-e', '0.001']
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26
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server = 'local'
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27
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assert_raise(ArgumentError) { Bio::Fasta.new() }
|
28
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assert_raise(ArgumentError) { Bio::Fasta.new(program) }
|
29
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+
assert(Bio::Fasta.new(program, db))
|
30
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assert(Bio::Fasta.new(program, db, option))
|
31
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assert(Bio::Fasta.new(program, db, option, server))
|
32
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assert_raise(ArgumentError) { Bio::Fasta.new(program, db, option, server, nil) }
|
33
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+
end
|
34
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|
35
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def test_option_backward_compatibility
|
36
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fasta = Bio::Fasta.new('program', 'db', "-e 10")
|
37
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+
assert_equal([ '-Q', '-H', '-m','10', '-e', '10'], fasta.options)
|
38
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+
end
|
39
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+
|
40
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def test_option
|
41
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+
fasta = Bio::Fasta.new('program', 'db', ["-e", "10"])
|
42
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+
assert_equal([ '-Q', '-H', '-m','10', '-e', '10'], fasta.options)
|
43
|
+
end
|
44
|
+
end
|
45
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+
|
46
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+
|
47
|
+
class TestFasta < Test::Unit::TestCase
|
48
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+
|
49
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def setup
|
50
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+
program = 'ssearch'
|
51
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+
db = 'nr'
|
52
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+
option = ['-e', '10']
|
53
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+
@obj = Bio::Fasta.new(program, db, option)
|
54
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+
end
|
55
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+
|
56
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+
def test_program
|
57
|
+
assert_equal('ssearch', @obj.program)
|
58
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+
@obj.program = 'lalign'
|
59
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+
assert_equal('lalign', @obj.program)
|
60
|
+
end
|
61
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+
|
62
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+
def test_db
|
63
|
+
assert_equal('nr', @obj.db)
|
64
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+
@obj.db = 'refseq'
|
65
|
+
assert_equal('refseq', @obj.db)
|
66
|
+
end
|
67
|
+
|
68
|
+
def test_options
|
69
|
+
assert_equal(["-Q", "-H", "-m", "10", "-e", "10"], @obj.options)
|
70
|
+
@obj.options = ['-Q', '-H', '-m', '8']
|
71
|
+
assert_equal(['-Q', '-H', '-m', '8'], @obj.options)
|
72
|
+
end
|
73
|
+
|
74
|
+
def test_server
|
75
|
+
assert_equal('local', @obj.server)
|
76
|
+
@obj.server = 'genomenet'
|
77
|
+
assert_equal('genomenet', @obj.server)
|
78
|
+
end
|
79
|
+
|
80
|
+
def test_ktup
|
81
|
+
assert_equal(nil, @obj.ktup)
|
82
|
+
@obj.ktup = 6
|
83
|
+
assert_equal(6, @obj.ktup)
|
84
|
+
end
|
85
|
+
def test_matrix
|
86
|
+
assert_equal(nil, @obj.matrix)
|
87
|
+
@obj.matrix = 'PAM120'
|
88
|
+
assert_equal('PAM120', @obj.matrix)
|
89
|
+
end
|
90
|
+
|
91
|
+
def test_output
|
92
|
+
assert_equal('', @obj.output)
|
93
|
+
# assert_raise(NoMethodError) { @obj.output = "" }
|
94
|
+
end
|
95
|
+
|
96
|
+
def test_option
|
97
|
+
option = ['-M'].join(' ')
|
98
|
+
assert(@obj.option = option)
|
99
|
+
assert_equal(option, @obj.option)
|
100
|
+
end
|
101
|
+
|
102
|
+
def test_format
|
103
|
+
assert_equal(10, @obj.format)
|
104
|
+
end
|
105
|
+
|
106
|
+
def test_format_arg_str
|
107
|
+
assert(@obj.format = '1')
|
108
|
+
assert_equal(1, @obj.format)
|
109
|
+
end
|
110
|
+
|
111
|
+
def test_format_arg_integer
|
112
|
+
assert(@obj.format = 2)
|
113
|
+
assert_equal(2, @obj.format)
|
114
|
+
end
|
115
|
+
end
|
116
|
+
|
117
|
+
class TestFastaQuery < Test::Unit::TestCase
|
118
|
+
def test_self_parser
|
119
|
+
end
|
120
|
+
def test_self_local
|
121
|
+
# test/functional/bio/test_fasta.rb
|
122
|
+
end
|
123
|
+
def test_self_remote
|
124
|
+
# test/functional/bio/test_fasta.rb
|
125
|
+
end
|
126
|
+
def test_query
|
127
|
+
end
|
128
|
+
end
|
129
|
+
|
130
|
+
end
|
@@ -0,0 +1,57 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/appl/test_psort.rb - Unit test for Bio::WoLF_PSORT
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2008
|
5
|
+
# Ben J Woodcroft <donttrustben somewhere near gmail.com>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
|
9
|
+
require 'pathname'
|
10
|
+
libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib'))).cleanpath.to_s
|
11
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
12
|
+
|
13
|
+
require 'test/unit'
|
14
|
+
require 'bio/appl/psort'
|
15
|
+
|
16
|
+
class WoLFPsortTest < Test::Unit::TestCase
|
17
|
+
def test_parse_summary_line_nil
|
18
|
+
assert_nil Bio::PSORT::WoLF_PSORT::Report.parse_from_summary('plant', "# k used for kNN is: 14\n")
|
19
|
+
end
|
20
|
+
|
21
|
+
def test_parse_summary_one_line
|
22
|
+
assert_equal Bio::PSORT::WoLF_PSORT::Report.new('gcn5a', 'plant', {'nucl' => 12, 'cyto' => 1, 'plas' => 1, 'cyto_plas' => 1}),
|
23
|
+
Bio::PSORT::WoLF_PSORT::Report.parse_from_summary('plant', "gcn5a nucl 12, cyto 1, plas 1, cyto_plas 1")
|
24
|
+
end
|
25
|
+
|
26
|
+
def test_parse_summary_one_line_fungi
|
27
|
+
assert_equal Bio::PSORT::WoLF_PSORT::Report.new('gcn5a', 'plant', {'cyto' => 17, 'nucl' => 9, 'cyto_pero' => 9}),
|
28
|
+
Bio::PSORT::WoLF_PSORT::Report.parse_from_summary('plant', "gcn5a cyto 17, nucl 9, cyto_pero 9")
|
29
|
+
end
|
30
|
+
|
31
|
+
def test_amino_acid_sequence_prediction
|
32
|
+
# catalase pero 8, nucl 2, mito 1.5, cyto_nucl 1.5, mito_plas 1.5
|
33
|
+
assert_equal Bio::PSORT::WoLF_PSORT::Report.new('wolf', 'plant', {'pero' => 8.0, 'nucl' => 2.0, 'mito' => 1.5, 'mito_plas' => 1.5, 'cyto_nucl' => 1.5}),
|
34
|
+
Bio::PSORT::WoLF_PSORT.exec_local_from_sequence(
|
35
|
+
'MTQVPPVTFQQYGPVITTSAGNPVDDNQNSVTAGPYGPAILSNFHLIDKLAHFDRERIPE
|
36
|
+
RVVHAKGGGAFGYFEVTHDITRFCKAKLFEKIGKRTPVFARFSTVAGESGSADTRRDPRG
|
37
|
+
FALKFYTEEGNWDMVGNNTPIFFVRDAIKFPDFIHTQKRHPQTHLHDPNMVWDFFSLVPE
|
38
|
+
SVHQVTFLYTDRGTPDGFRHMNGYGSHTFKFINKDNEAFYVKWHFKTNQGIKNLNRQRAK
|
39
|
+
ELESEDPDYAVRDLFNAIAKREFPSWTFCIQVMPLKDAETYKWNVFDVTKVWPHGDYPLI
|
40
|
+
PVGRLVLDRNPENYFQDVEQAAFAPAHMVPGIEPSEDRMLQGRMFSYIDTHRHRLGANYH
|
41
|
+
QIPVNRPWNARGGDYSVRDGPMCVDGNKGSQLNYEPNSVDGFPKEDRNAAVSGTTTVSGT
|
42
|
+
VACHPQEHPNSDFEQPGNFYRTVLSEPEREALIGNIAEHLRQARRDIQERQVKIFYKCDP
|
43
|
+
EYGERVARAIGLPTAACYPAKM*'.gsub(/\s/,''),
|
44
|
+
'plant'
|
45
|
+
)
|
46
|
+
end
|
47
|
+
|
48
|
+
def test_too_small_amino_acid_sequence_prediction
|
49
|
+
# known problem - too short for WoLF_PSORT?
|
50
|
+
assert_nil Bio::PSORT::WoLF_PSORT.exec_local_from_sequence('MRTLKTEVEKGFLSTMFVQELATPKG', 'animal')
|
51
|
+
end
|
52
|
+
|
53
|
+
def test_highest_predicted_localization
|
54
|
+
assert_equal 'cyto', Bio::PSORT::WoLF_PSORT::Report.new('gcn5a', 'plant', {'cyto' => 17, 'nucl' => 9, 'cyto_pero' => 9}).highest_predicted_localization
|
55
|
+
assert_equal 'cyto_pero', Bio::PSORT::WoLF_PSORT::Report.new('gcn5a', 'plant', {'cyto' => 17, 'nucl' => 9, 'cyto_pero' => 90}).highest_predicted_localization
|
56
|
+
end
|
57
|
+
end
|