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
@@ -0,0 +1,63 @@
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#
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# test/unit/bio/appl/mafft/test_report.rb - Unit test for Bio::Alignment::MultiFastaFormat
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#
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# Copyright:: Copyright (C) 2007
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# 2005 Naohisa Goto <ng@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: test_report.rb,v 1.1 2007/07/16 12:21:39 ngoto Exp $
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#
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, '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'
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module Bio
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class TestAlignmentMultiFastaFormat < Test::Unit::TestCase
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def setup
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@na = Bio::Alignment::MultiFastaFormat.new <<__END_OF_NASEQS__
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>naseq1
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TAGATTTCGAATTTCTAGnGAACCGAACCGkACAGCCTTACATyATTCAGACCAATGTGT
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TACCAATTCGAGTATACAAGAACAGTGATAAGGTACCAAACAACGACTTCTTCCCGAACC
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>naseq2
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TAGATTTCGAATCTAGGGAATCCGATACGGACAGCCTTACATTATTCAGACCAATGTGTA
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TACCAATTCGAGAATACAAGAACGTGATAAGGTACCCAAACAACGACTTCTTCCCGAACC
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>naseq3
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TAGATTTCGAATCTAGGGAATCCGATACCGGACAGCCTTACATTATTCAGACCAATGTGT
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TACCAATTCGAGAATACAAGAACGTGATAAGGTACCCAAACAACGACTTCTTCCCGAACC
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__END_OF_NASEQS__
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@aa = Bio::Alignment::MultiFastaFormat.new <<__END_OF_AASEQS__
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>aaseq1
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MVHWTAEEKQLITGLWGKVNVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHGKKVLT
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37
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+
>aaseq2
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38
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+
MLTAEEKAAVTGFWGKVKVDEVGAEALGRLLVVYPWTQRFFEHFGDLSSADAVMNNAKVKAHGKKVLDSF
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>aaseq3
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MVHLTDAEKSAVSCLWAKVNPDEVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNPKVKAHGKKVIT
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41
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+
>aaseq4
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MVHLTDAEKAAVNGLWGKVNPDDVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNPKVKAHGKKVIN
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__END_OF_AASEQS__
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end #def setup
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def test_alignment
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assert_equal(120, @na.alignment.alignment_length)
|
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assert_equal(70, @aa.alignment.alignment_length)
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end
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def test_entries
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assert_equal(3, @na.entries.size)
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assert_equal(4, @aa.entries.size)
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end
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def test_determine_seq_method
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@na.alignment
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assert_equal(:naseq, @na.instance_eval { @seq_method })
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@aa.alignment
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assert_equal(:aaseq, @aa.instance_eval { @seq_method })
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end
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end #class TestAlignmentMultiFastaFormat
|
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end #module Bio
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#
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# test/unit/bio/appl/paml/codeml/test_rates.rb - Unit test for Bio::PAML::Codeml::Rates
|
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#
|
4
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# Copyright:: Copyright (C) 2008 Michael D. Barton <mail@michaelbarton.me.uk>
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# License:: The Ruby License
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#
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require 'pathname'
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libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 6, '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/paml/codeml/rates'
|
14
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|
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module Bio; module TestPAMLCodeml
|
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class TestCodemlRates < Test::Unit::TestCase
|
17
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|
18
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bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6)).cleanpath.to_s
|
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TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data', 'paml', 'codeml')).cleanpath.to_s
|
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def setup
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str = File.read(File.join(TEST_DATA, 'rates'))
|
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@example_rates = Bio::PAML::Codeml::Rates.new(str)
|
24
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end
|
25
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|
26
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def test_rates_first_position
|
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assert_equal('***M', @example_rates.first[:data])
|
28
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assert_equal(1, @example_rates.first[:rate])
|
29
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+
assert_equal(1, @example_rates.first[:freq])
|
30
|
+
end
|
31
|
+
|
32
|
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def test_rates_hundred_and_fiftieth_position
|
33
|
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assert('GGGG', @example_rates[149][:data])
|
34
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+
assert(0.828, @example_rates[149][:rate])
|
35
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assert(9, @example_rates[149][:freq])
|
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end
|
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|
38
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def test_rates_last_position
|
39
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assert('PHPP', @example_rates.last[:data])
|
40
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assert(1.752, @example_rates.last[:rate])
|
41
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assert(1, @example_rates.last[:freq])
|
42
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end
|
43
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end
|
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|
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end; end #module TestPAMLCodeml; module Bio
|
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#
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2
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# test/unit/bio/appl/paml/codeml/test_report.rb - Unit test for Bio::PAML::Codeml::Report
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#
|
4
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# Copyright:: Copyright (C) 2008 Michael D. Barton <mail@michaelbarton.me.uk>
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# License:: The Ruby License
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#
|
7
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|
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require 'pathname'
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libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib'))).cleanpath.to_s
|
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$:.unshift(libpath) unless $:.include?(libpath)
|
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|
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require 'test/unit'
|
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require 'bio/appl/paml/codeml/report'
|
14
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|
15
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module Bio; module TestPAMLCodeml
|
16
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class TestCodemlReport < Test::Unit::TestCase
|
17
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+
|
18
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+
bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6)).cleanpath.to_s
|
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TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data', 'paml', 'codeml')).cleanpath.to_s
|
20
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|
21
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def setup
|
22
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str = File.read(File.join(TEST_DATA, 'output.txt'))
|
23
|
+
@example_report = Bio::PAML::Codeml::Report.new(str)
|
24
|
+
end
|
25
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+
|
26
|
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def test_tree_log_likelihood
|
27
|
+
assert_equal(-1817.465211, @example_report.tree_log_likelihood)
|
28
|
+
end
|
29
|
+
|
30
|
+
def test_tree_length
|
31
|
+
assert_equal(0.77902, @example_report.tree_length)
|
32
|
+
end
|
33
|
+
|
34
|
+
def test_alpha
|
35
|
+
assert_equal(0.58871, @example_report.alpha)
|
36
|
+
end
|
37
|
+
|
38
|
+
def test_tree
|
39
|
+
tree = "(((rabbit: 0.082889, rat: 0.187866): 0.038008, human: 0.055050): 0.033639, goat-cow: 0.096992, marsupial: 0.284574);"
|
40
|
+
assert_equal(tree, @example_report.tree)
|
41
|
+
end
|
42
|
+
|
43
|
+
end
|
44
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|
45
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end; end #module TestPAMLCodeml; module Bio
|
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|
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1
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#
|
2
|
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# test/unit/bio/appl/paml/test_codeml.rb - Unit test for Bio::PAML::Codeml
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2008 Michael D. Barton <mail@michaelbarton.me.uk>
|
5
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# License:: The Ruby License
|
6
|
+
#
|
7
|
+
|
8
|
+
require 'pathname'
|
9
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+
libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
|
10
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
11
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+
|
12
|
+
require 'test/unit'
|
13
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+
require 'bio/appl/paml/codeml'
|
14
|
+
|
15
|
+
module Bio; module TestPAMLCodeml
|
16
|
+
module TestCodemlData
|
17
|
+
|
18
|
+
bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
|
19
|
+
TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data', 'paml', 'codeml')).cleanpath.to_s
|
20
|
+
|
21
|
+
def self.example_control
|
22
|
+
File.join TEST_DATA, 'control_file.txt'
|
23
|
+
end
|
24
|
+
|
25
|
+
end #module TestCodemlData
|
26
|
+
|
27
|
+
class TestCodemlInitialize < Test::Unit::TestCase
|
28
|
+
|
29
|
+
def test_new_with_one_argument
|
30
|
+
factory = Bio::PAML::Codeml.new('echo')
|
31
|
+
assert_instance_of(Bio::PAML::Codeml, factory)
|
32
|
+
assert_equal('echo', factory.instance_eval { @program })
|
33
|
+
end
|
34
|
+
|
35
|
+
def test_new_with_two_argument
|
36
|
+
factory = Bio::PAML::Codeml.new('echo', { :test => 'value' })
|
37
|
+
assert_instance_of(Bio::PAML::Codeml, factory)
|
38
|
+
assert_equal('echo', factory.instance_eval { @program })
|
39
|
+
assert_equal('value', factory.parameters[:test])
|
40
|
+
end
|
41
|
+
|
42
|
+
def test_new_with_parameters
|
43
|
+
factory = Bio::PAML::Codeml.new(nil, { :test => 'value' })
|
44
|
+
assert_instance_of(Bio::PAML::Codeml, factory)
|
45
|
+
assert_equal('codeml', factory.instance_eval { @program })
|
46
|
+
assert_equal('value', factory.parameters[:test])
|
47
|
+
end
|
48
|
+
|
49
|
+
def test_new_without_argument
|
50
|
+
factory = Bio::PAML::Codeml.new
|
51
|
+
assert_instance_of(Bio::PAML::Codeml, factory)
|
52
|
+
assert_equal('codeml', factory.instance_eval { @program })
|
53
|
+
end
|
54
|
+
|
55
|
+
end #class TestCodemlInitialize
|
56
|
+
|
57
|
+
class TestCodeml < Test::Unit::TestCase
|
58
|
+
def setup
|
59
|
+
@codeml = Bio::PAML::Codeml.new
|
60
|
+
end
|
61
|
+
|
62
|
+
def test_parameters
|
63
|
+
params = { :verbose => 1 }
|
64
|
+
@codeml.parameters = params
|
65
|
+
assert_equal(params, @codeml.parameters)
|
66
|
+
end
|
67
|
+
|
68
|
+
def test_load_parameters
|
69
|
+
str = " seqfile = test.aa \n verbose = 1 \n"
|
70
|
+
params = { :seqfile => 'test.aa', :verbose => '1' }
|
71
|
+
assert_equal(params, @codeml.load_parameters(str))
|
72
|
+
end
|
73
|
+
|
74
|
+
def test_set_default_parameters
|
75
|
+
assert_equal(Bio::PAML::Codeml::DEFAULT_PARAMETERS,
|
76
|
+
@codeml.set_default_parameters)
|
77
|
+
# modifying parameters should not affect DEFAULT_PARAMETERS
|
78
|
+
@codeml.parameters[:only_for_test] = 'this is test'
|
79
|
+
assert_not_equal(Bio::PAML::Codeml::DEFAULT_PARAMETERS,
|
80
|
+
@codeml.parameters)
|
81
|
+
end
|
82
|
+
|
83
|
+
def test_dump_parameters
|
84
|
+
params = { :seqfile => 'test.aa', :verbose => '1' }
|
85
|
+
@codeml.parameters = params
|
86
|
+
assert_equal("seqfile = test.aa\nverbose = 1\n",
|
87
|
+
@codeml.dump_parameters)
|
88
|
+
end
|
89
|
+
|
90
|
+
end #class TestCodeml
|
91
|
+
|
92
|
+
class TestCodemlControlGeneration < Test::Unit::TestCase
|
93
|
+
|
94
|
+
TEST_DATA = TestCodemlData::TEST_DATA
|
95
|
+
|
96
|
+
def generate_control_file
|
97
|
+
@tempfile_control = Tempfile.new('codeml_control')
|
98
|
+
@tempfile_control.close(false)
|
99
|
+
@tempfile_outfile = Tempfile.new('codeml_test')
|
100
|
+
@tempfile_outfile.close(false)
|
101
|
+
|
102
|
+
test_control = @tempfile_control.path
|
103
|
+
Bio::PAML::Codeml.create_control_file({
|
104
|
+
:model => 1,
|
105
|
+
:fix_kappa => 1,
|
106
|
+
:aaRatefile => File.join(TEST_DATA, 'wag.dat'),
|
107
|
+
:seqfile => File.join(TEST_DATA, 'abglobin.aa'),
|
108
|
+
:treefile => File.join(TEST_DATA, 'abglobin.trees'),
|
109
|
+
:outfile => @tempfile_outfile.path,
|
110
|
+
}, test_control)
|
111
|
+
test_control
|
112
|
+
end
|
113
|
+
private :generate_control_file
|
114
|
+
|
115
|
+
def setup
|
116
|
+
@example_control = generate_control_file
|
117
|
+
end
|
118
|
+
|
119
|
+
def teardown
|
120
|
+
@tempfile_control.close(true)
|
121
|
+
@tempfile_outfile.close(true)
|
122
|
+
end
|
123
|
+
|
124
|
+
def test_control_file_generated
|
125
|
+
assert_not_nil(File.size?(@example_control))
|
126
|
+
end
|
127
|
+
|
128
|
+
def test_expected_parameters_set_in_control_file
|
129
|
+
produced_control = File.open(@example_control) do |f|
|
130
|
+
f.inject(Hash.new) do |hash,line|
|
131
|
+
hash.store(*line.strip.split(' = '))
|
132
|
+
hash
|
133
|
+
end
|
134
|
+
end
|
135
|
+
assert_equal(File.join(TEST_DATA, 'abglobin.aa'),
|
136
|
+
produced_control['seqfile'])
|
137
|
+
assert_equal('1', produced_control['fix_kappa'])
|
138
|
+
assert_equal('1', produced_control['model'])
|
139
|
+
end
|
140
|
+
end #class TestCodemlControlGeneration
|
141
|
+
|
142
|
+
class TestControlFileUsage < Test::Unit::TestCase
|
143
|
+
|
144
|
+
def setup
|
145
|
+
@codeml = Bio::PAML::Codeml.new
|
146
|
+
@codeml.load_parameters(File.read(TestCodemlData.example_control))
|
147
|
+
end
|
148
|
+
|
149
|
+
def test_parameters_should_be_loaded_from_control
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assert_not_nil(@codeml.parameters)
|
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+
end
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+
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|
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def test_correct_parameters_should_be_loaded
|
154
|
+
assert_equal('abglobin.aa', @codeml.parameters[:seqfile])
|
155
|
+
assert_equal('1', @codeml.parameters[:fix_kappa])
|
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|
+
assert_equal('1', @codeml.parameters[:model])
|
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|
+
end
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+
|
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|
+
end #class TestControlFileUsage
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+
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|
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class TestExpectedErrorsThrown < Test::Unit::TestCase
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+
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|
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def test_error_thrown_if_seqfile_does_not_specified
|
164
|
+
codeml = Bio::PAML::Codeml.new('echo')
|
165
|
+
codeml.load_parameters(File.read(TestCodemlData.example_control))
|
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|
+
codeml.parameters[:seqfile] = nil
|
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|
+
assert_raises RuntimeError do
|
168
|
+
codeml.query_by_string()
|
169
|
+
end
|
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|
+
end
|
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|
+
|
172
|
+
end #class TestExpectedErrorsThrown
|
173
|
+
|
174
|
+
end; end #module TestPAMLCodeml; module Bio
|
@@ -0,0 +1,81 @@
|
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1
|
+
#
|
2
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+
# test/unit/bio/appl/sosui/test_report.rb - Unit test for Bio::SOSUI::Report
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
|
5
|
+
# License:: The Ruby License
|
6
|
+
#
|
7
|
+
# $Id: test_report.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
|
8
|
+
#
|
9
|
+
|
10
|
+
require 'pathname'
|
11
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+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
|
12
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
13
|
+
|
14
|
+
require 'test/unit'
|
15
|
+
require 'bio/appl/sosui/report'
|
16
|
+
|
17
|
+
|
18
|
+
module Bio
|
19
|
+
|
20
|
+
bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
|
21
|
+
test_data = Pathname.new(File.join(bioruby_root, 'test', 'data', 'SOSUI')).cleanpath.to_s
|
22
|
+
SOSUIReport = File.open(File.join(test_data, 'sample.report')).read
|
23
|
+
|
24
|
+
|
25
|
+
class TestSOSUIReportConst < Test::Unit::TestCase
|
26
|
+
|
27
|
+
def test_delimiter
|
28
|
+
assert_equal("\n>", Bio::SOSUI::Report::DELIMITER)
|
29
|
+
end
|
30
|
+
|
31
|
+
def test_rs
|
32
|
+
assert_equal("\n>", Bio::SOSUI::Report::RS)
|
33
|
+
end
|
34
|
+
|
35
|
+
end
|
36
|
+
|
37
|
+
|
38
|
+
class TestSOSUIReport < Test::Unit::TestCase
|
39
|
+
|
40
|
+
def setup
|
41
|
+
@obj = Bio::SOSUI::Report.new(SOSUIReport)
|
42
|
+
end
|
43
|
+
|
44
|
+
def test_entry_id
|
45
|
+
assert_equal('Q9HC19', @obj.entry_id)
|
46
|
+
end
|
47
|
+
|
48
|
+
def test_prediction
|
49
|
+
assert_equal('MEMBRANE PROTEIN', @obj.prediction)
|
50
|
+
end
|
51
|
+
|
52
|
+
def test_tmhs
|
53
|
+
assert_equal(Array, @obj.tmhs.class)
|
54
|
+
assert_equal(Bio::SOSUI::Report::TMH, @obj.tmhs[0].class)
|
55
|
+
end
|
56
|
+
|
57
|
+
def test_tmh
|
58
|
+
assert_equal(7, @obj.tmhs.size)
|
59
|
+
end
|
60
|
+
|
61
|
+
end # class TestSOSUIReport
|
62
|
+
|
63
|
+
class TestSOSUITMH < Test::Unit::TestCase
|
64
|
+
def setup
|
65
|
+
@obj = Bio::SOSUI::Report.new(SOSUIReport).tmhs.first
|
66
|
+
end
|
67
|
+
|
68
|
+
def test_range
|
69
|
+
assert_equal(31..53, @obj.range)
|
70
|
+
end
|
71
|
+
|
72
|
+
def test_grade
|
73
|
+
assert_equal('SECONDARY', @obj.grade)
|
74
|
+
end
|
75
|
+
|
76
|
+
def test_sequence
|
77
|
+
assert_equal('HIRMTFLRKVYSILSLQVLLTTV', @obj.sequence)
|
78
|
+
end
|
79
|
+
|
80
|
+
end # class TestSOSUITMH
|
81
|
+
end
|
@@ -0,0 +1,146 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/appl/targetp/test_report.rb - Unit test for Bio::TargetP::Report
|
3
|
+
#
|
4
|
+
# Copyright: Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
|
5
|
+
# License:: The Ruby License
|
6
|
+
#
|
7
|
+
# $Id: test_report.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
|
8
|
+
#
|
9
|
+
|
10
|
+
require 'pathname'
|
11
|
+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
|
12
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
13
|
+
|
14
|
+
require 'test/unit'
|
15
|
+
require 'bio/appl/targetp/report'
|
16
|
+
|
17
|
+
|
18
|
+
module Bio
|
19
|
+
|
20
|
+
TargetPReport_plant =<<HOGE
|
21
|
+
|
22
|
+
### ### ### T A R G E T P 1.0 prediction results ### ### ###
|
23
|
+
|
24
|
+
# Number of input sequences: 1
|
25
|
+
# Cleavage site predictions not included.
|
26
|
+
# Using PLANT networks.
|
27
|
+
|
28
|
+
# Name Length cTP mTP SP other Loc. RC
|
29
|
+
#----------------------------------------------------------------------------------
|
30
|
+
MGI_2141503 640 0.031 0.161 0.271 0.844 _ 3
|
31
|
+
#----------------------------------------------------------------------------------
|
32
|
+
# cutoff 0.00 0.00 0.00 0.00
|
33
|
+
|
34
|
+
|
35
|
+
HOGE
|
36
|
+
|
37
|
+
TargetPReport_plant_c =<<HOGE
|
38
|
+
|
39
|
+
### ### ### T A R G E T P 1.0 prediction results ### ### ###
|
40
|
+
|
41
|
+
# Number of input sequences: 1
|
42
|
+
# Cleavage site predictions included.
|
43
|
+
# Using PLANT networks.
|
44
|
+
|
45
|
+
# Name Length cTP mTP SP other Loc. RC TPlen
|
46
|
+
#----------------------------------------------------------------------------------
|
47
|
+
MGI_2141503 640 0.031 0.161 0.271 0.844 _ 3 -
|
48
|
+
#----------------------------------------------------------------------------------
|
49
|
+
# cutoff 0.00 0.00 0.00 0.00
|
50
|
+
|
51
|
+
|
52
|
+
|
53
|
+
HOGE
|
54
|
+
|
55
|
+
TargetPReport_non_plant_c =<<HOGE
|
56
|
+
|
57
|
+
### ### ### T A R G E T P 1.0 prediction results ### ### ###
|
58
|
+
|
59
|
+
# Number of input sequences: 1
|
60
|
+
# Cleavage site predictions included.
|
61
|
+
# Using NON-PLANT networks.
|
62
|
+
|
63
|
+
# Name Length mTP SP other Loc. RC TPlen
|
64
|
+
#--------------------------------------------------------------------------
|
65
|
+
MGI_96083 2187 0.292 0.053 0.746 _ 3 -
|
66
|
+
#--------------------------------------------------------------------------
|
67
|
+
# cutoff 0.00 0.00 0.00
|
68
|
+
|
69
|
+
|
70
|
+
|
71
|
+
HOGE
|
72
|
+
|
73
|
+
|
74
|
+
class TestTargetPReportConst < Test::Unit::TestCase
|
75
|
+
|
76
|
+
def test_delimiter
|
77
|
+
assert_equal("\n \n", Bio::TargetP::Report::DELIMITER)
|
78
|
+
end
|
79
|
+
|
80
|
+
def test_rs
|
81
|
+
assert_equal("\n \n", Bio::TargetP::Report::RS)
|
82
|
+
end
|
83
|
+
|
84
|
+
end # class TestTargetPReportConst
|
85
|
+
|
86
|
+
|
87
|
+
class TestTargetPReport < Test::Unit::TestCase
|
88
|
+
|
89
|
+
def setup
|
90
|
+
@obj = Bio::TargetP::Report.new(TargetPReport_plant)
|
91
|
+
end
|
92
|
+
|
93
|
+
def test_version
|
94
|
+
assert_equal('1.0', @obj.version)
|
95
|
+
end
|
96
|
+
|
97
|
+
def test_query_sequences
|
98
|
+
assert_equal(0, @obj.query_sequences)
|
99
|
+
end
|
100
|
+
|
101
|
+
def test_cleavage_site_prediction
|
102
|
+
assert_equal('not included', @obj.cleavage_site_prediction)
|
103
|
+
end
|
104
|
+
|
105
|
+
def test_networks
|
106
|
+
assert_equal('PLANT', @obj.networks)
|
107
|
+
end
|
108
|
+
|
109
|
+
def test_prediction
|
110
|
+
hash = {"Name"=>"MGI_2141503", "Loc."=>"_", "RC"=>3, "SP"=>0.271,
|
111
|
+
"other"=>0.844, "mTP"=>0.161, "cTP"=>0.031, "Length"=>640}
|
112
|
+
assert_equal(hash, @obj.pred)
|
113
|
+
assert_equal(hash, @obj.prediction)
|
114
|
+
end
|
115
|
+
|
116
|
+
def test_cutoff
|
117
|
+
hash = {"SP"=>0.0, "other"=>0.0, "mTP"=>0.0, "cTP"=>0.0}
|
118
|
+
assert_equal(hash, @obj.cutoff)
|
119
|
+
end
|
120
|
+
|
121
|
+
|
122
|
+
def test_entry_id
|
123
|
+
assert_equal('MGI_2141503', @obj.entry_id)
|
124
|
+
end
|
125
|
+
|
126
|
+
def test_name
|
127
|
+
assert_equal('MGI_2141503', @obj.name)
|
128
|
+
end
|
129
|
+
|
130
|
+
def test_query_len
|
131
|
+
assert_equal(640, @obj.query_len)
|
132
|
+
end
|
133
|
+
|
134
|
+
def test_length
|
135
|
+
assert_equal(640, @obj.length)
|
136
|
+
end
|
137
|
+
|
138
|
+
def test_loc
|
139
|
+
assert_equal('_', @obj.loc)
|
140
|
+
end
|
141
|
+
|
142
|
+
def test_rc
|
143
|
+
assert_equal(3, @obj.rc)
|
144
|
+
end
|
145
|
+
end # class TestTargetPReport
|
146
|
+
end
|