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 +1,32 @@
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#
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# test/unit/bio/io/test_soapwsdl.rb - Unit test for SOAP/WSDL
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#
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# Copytight:: 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.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/io/soapwsdl'
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module Bio
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class TestSOAPWSDL < Test::Unit::TestCase
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def setup
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@obj = Bio::SOAPWSDL
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end
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def test_methods
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methods = ['list_methods','wsdl', 'wsdl=', 'log', 'log=']
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assert_equal(methods.sort, (@obj.instance_methods - Object.methods).sort.collect { |x| x.to_s })
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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/sequence/test_aa.rb - Unit test for Bio::Sequencce::AA
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#
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# Copyright:: Copyright (C) 2006
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# Mitsuteru C. Nakao <n@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: test_aa.rb,v 1.5 2007/12/03 06:19:12 nakao Exp $
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#
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require 'pathname'
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libpath = Pathname.new(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/sequence'
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require 'bio/sequence/aa'
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module Bio
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class TestSequenceAANew < Test::Unit::TestCase
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def test_new
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str = "RRLEHTFVFL RNFSLMLLRY"
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assert(Bio::Sequence::AA.new(str))
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end
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def test_new_t
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str = "RRLEHTFVFLRNFSLMLLRY"
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str_t = "RRLEHTFVFL\tRNFSLMLLRY"
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assert_equal(str, Bio::Sequence::AA.new(str_t))
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end
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def test_new_n
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str = "RRLEHTFVFLRNFSLMLLRY"
|
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str_n = "RRLEHTFVFL\nRNFSLMLLRY"
|
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assert_equal(str, Bio::Sequence::AA.new(str_n))
|
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|
+
end
|
40
|
+
|
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|
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def test_new_r
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str = "RRLEHTFVFLRNFSLMLLRY"
|
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str_r = "RRLEHTFVFL\n\rRNFSLMLLRY"
|
44
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assert_equal(str, Bio::Sequence::AA.new(str_r))
|
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|
+
end
|
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+
|
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end
|
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|
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|
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class TestSequenceAA < Test::Unit::TestCase
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|
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def setup
|
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str = "RRLEHTFVFLRNFSLMLLRY"
|
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@obj = Bio::Sequence::AA.new(str)
|
55
|
+
end
|
56
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+
|
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|
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def test_to_s
|
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str = "RRLEHTFVFLRNFSLMLLRY"
|
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assert_equal(str, @obj.to_s)
|
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|
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end
|
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|
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def test_molecular_weight
|
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assert_in_delta(2612.105, @obj.molecular_weight, 1e-4)
|
64
|
+
end
|
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|
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|
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def test_to_re
|
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re = /RRLEHTFVFLRNFSLMLLRY/
|
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assert_equal(re, @obj.to_re)
|
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@obj[1, 1] = 'B'
|
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re = /R[DNB]LEHTFVFLRNFSLMLLRY/
|
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assert_equal(re, @obj.to_re)
|
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end
|
73
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|
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def test_codes
|
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ary = ["Arg", "Arg", "Leu", "Glu", "His", "Thr", "Phe", "Val",
|
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"Phe", "Leu", "Arg", "Asn", "Phe", "Ser", "Leu", "Met",
|
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"Leu", "Leu", "Arg", "Tyr"]
|
78
|
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assert_equal(ary, @obj.codes)
|
79
|
+
end
|
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|
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def test_names
|
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ary = ["arginine", "arginine", "leucine", "glutamic acid",
|
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"histidine", "threonine", "phenylalanine", "valine",
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"phenylalanine", "leucine", "arginine", "asparagine",
|
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"phenylalanine", "serine", "leucine", "methionine",
|
86
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"leucine", "leucine", "arginine", "tyrosine"]
|
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assert_equal(ary, @obj.names)
|
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end
|
89
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|
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def test_ph_counts
|
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# str = "RRLEHTFVFLRNFSLMLLRY"
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assert_equal 1, @obj.acidic_count
|
93
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assert_equal 5, @obj.basic_count
|
94
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+
end
|
95
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|
96
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def test_empty_ph_counts
|
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@empty = Bio::Sequence::AA.new('')
|
98
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assert_equal 0, @empty.acidic_count
|
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assert_equal 0, @empty.basic_count
|
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end
|
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|
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end
|
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|
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|
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require 'bio/sequence/aa'
|
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|
108
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class TestSequenceAACompat < Test::Unit::TestCase
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109
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def test_aa_self_randomize
|
110
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composition = Bio::Sequence::AA.new("WWDTGAK").composition
|
111
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assert(Bio::Sequence::AA.randomize(composition))
|
112
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+
end
|
113
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+
end
|
114
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+
|
115
|
+
end
|
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#
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# test/unit/bio/sequence/test_common.rb - Unit test for Bio::Sequencce::Common
|
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#
|
4
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# Copyright:: Copyright (C) 2006-2008
|
5
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# Mitsuteru C. Nakao <n@bioruby.org>,
|
6
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# Naohisa Goto <ng@bioruby.org>
|
7
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# License:: The Ruby License
|
8
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#
|
9
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# $Id:$
|
10
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#
|
11
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+
|
12
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require 'pathname'
|
13
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
|
14
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$:.unshift(libpath) unless $:.include?(libpath)
|
15
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|
16
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require 'test/unit'
|
17
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require 'bio/sequence'
|
18
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require 'bio/sequence/common'
|
19
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+
|
20
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module Bio; module TestSequenceCommon
|
21
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+
|
22
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+
class TSequence < String
|
23
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+
include Bio::Sequence::Common
|
24
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+
end
|
25
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+
|
26
|
+
class TestSequenceCommon < Test::Unit::TestCase
|
27
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+
|
28
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def setup
|
29
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@obj = TSequence.new('atgcatgcatgcatgcaaaa')
|
30
|
+
end
|
31
|
+
|
32
|
+
def test_to_s
|
33
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+
assert_equal('atgcatgcatgcatgcaaaa', @obj.to_s)
|
34
|
+
end
|
35
|
+
|
36
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def test_to_str
|
37
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assert_equal('atgcatgcatgcatgcaaaa', @obj.to_str)
|
38
|
+
end
|
39
|
+
|
40
|
+
def test_seq
|
41
|
+
str = "atgcatgcatgcatgcaaaa"
|
42
|
+
assert_equal(str, @obj.seq)
|
43
|
+
end
|
44
|
+
|
45
|
+
# <<(*arg)
|
46
|
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def test_push
|
47
|
+
str = "atgcatgcatgcatgcaaaaA"
|
48
|
+
assert_equal(str, @obj << "A")
|
49
|
+
end
|
50
|
+
|
51
|
+
# concat(*arg)
|
52
|
+
def test_concat
|
53
|
+
str = "atgcatgcatgcatgcaaaaA"
|
54
|
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assert_equal(str, @obj.concat("A"))
|
55
|
+
end
|
56
|
+
|
57
|
+
# +(*arg)
|
58
|
+
def test_sum
|
59
|
+
str = "atgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaa"
|
60
|
+
assert_equal(str, @obj + @obj)
|
61
|
+
end
|
62
|
+
|
63
|
+
# window_search(window_size, step_size = 1)
|
64
|
+
def test_window_search
|
65
|
+
@obj.window_search(4) do |subseq|
|
66
|
+
assert_equal(20, @obj.size)
|
67
|
+
end
|
68
|
+
end
|
69
|
+
|
70
|
+
#total(hash)
|
71
|
+
def test_total
|
72
|
+
hash = {'a' => 1, 'c' => 2, 'g' => 4, 't' => 3}
|
73
|
+
assert_equal(44.0, @obj.total(hash))
|
74
|
+
end
|
75
|
+
|
76
|
+
def test_composition
|
77
|
+
composition = {"a"=>8, "c"=>4, "g"=>4, "t"=>4}
|
78
|
+
assert_equal(composition, @obj.composition)
|
79
|
+
end
|
80
|
+
|
81
|
+
def test_splicing
|
82
|
+
#(position)
|
83
|
+
assert_equal("atgcatgc", @obj.splicing("join(1..4, 13..16)"))
|
84
|
+
end
|
85
|
+
end
|
86
|
+
|
87
|
+
|
88
|
+
class TestSequenceCommonNormalize < Test::Unit::TestCase
|
89
|
+
def test_no_normalize
|
90
|
+
str = "atgcatgcatgcatgcaaaA"
|
91
|
+
obj = TSequence.new(str)
|
92
|
+
assert_equal("atgcatgcatgcatgcaaaA", obj)
|
93
|
+
end
|
94
|
+
|
95
|
+
def test_normalize_A
|
96
|
+
str = "atgcatgcatgcatgcaaaA"
|
97
|
+
seq = TSequence.new(str)
|
98
|
+
assert_equal("atgcatgcatgcatgcaaaA", seq)
|
99
|
+
obj = seq.normalize!
|
100
|
+
assert_equal("atgcatgcatgcatgcaaaA", obj)
|
101
|
+
end
|
102
|
+
|
103
|
+
def test_normalize_a
|
104
|
+
str = "atgcatgcatgcatgcaaa"
|
105
|
+
seq = TSequence.new(str)
|
106
|
+
assert_equal("atgcatgcatgcatgcaaa", seq)
|
107
|
+
obj = seq.normalize!
|
108
|
+
assert_equal("atgcatgcatgcatgcaaa", obj)
|
109
|
+
end
|
110
|
+
end
|
111
|
+
|
112
|
+
|
113
|
+
class TestSequenceCommonRandomize < Test::Unit::TestCase
|
114
|
+
|
115
|
+
def setup
|
116
|
+
@str = "attcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatgaaagatgttatc"
|
117
|
+
@seq = TSequence.new(@str)
|
118
|
+
@orig = TSequence.new(@str)
|
119
|
+
end
|
120
|
+
|
121
|
+
# test for Bio::Sequence::Common#randomize(hash = nil)
|
122
|
+
def test_randomize
|
123
|
+
rseqs = (0..2).collect { |i| @seq.randomize }
|
124
|
+
|
125
|
+
# not breaking given seq?
|
126
|
+
assert_equal(@orig, @seq)
|
127
|
+
|
128
|
+
# same length?
|
129
|
+
rseqs.each do |rseq|
|
130
|
+
assert_equal(@orig.length, rseq.length)
|
131
|
+
end
|
132
|
+
|
133
|
+
# same composition?
|
134
|
+
[ 'a', 'c', 'g', 't', 'n' ].each do |chr|
|
135
|
+
count = @orig.count(chr)
|
136
|
+
rseqs.each do |rseq|
|
137
|
+
assert_equal(count, rseq.count(chr))
|
138
|
+
end
|
139
|
+
end
|
140
|
+
|
141
|
+
# randomized? (very simple check)
|
142
|
+
assert(rseqs[0] != rseqs[1])
|
143
|
+
assert(rseqs[0] != rseqs[2])
|
144
|
+
assert(rseqs[1] != rseqs[2])
|
145
|
+
end
|
146
|
+
|
147
|
+
# testing Bio::Sequence::Common#randomize() { |x| ... }
|
148
|
+
def test_randomize_with_block
|
149
|
+
composition = Hash.new(0)
|
150
|
+
[ 'a', 'c', 'g', 't' ].each do |chr|
|
151
|
+
composition[chr] = @seq.count(chr)
|
152
|
+
end
|
153
|
+
|
154
|
+
rseqs = (0..2).collect do |i|
|
155
|
+
newcomposition = Hash.new(0)
|
156
|
+
newseq = ''
|
157
|
+
ret = @seq.randomize do |c|
|
158
|
+
assert_kind_of(TSequence, c)
|
159
|
+
newcomposition[c] += 1
|
160
|
+
newseq.concat c
|
161
|
+
end
|
162
|
+
# same length?
|
163
|
+
assert_equal(@orig.length, newseq.length)
|
164
|
+
# same composition?
|
165
|
+
assert_equal(composition, newcomposition)
|
166
|
+
# returned value is empty sequence?
|
167
|
+
assert_equal(TSequence.new(''), ret)
|
168
|
+
# not breaking given seq?
|
169
|
+
assert_equal(@orig, @seq)
|
170
|
+
newseq
|
171
|
+
end
|
172
|
+
|
173
|
+
# randomized? (very simple check)
|
174
|
+
assert(rseqs[0] != rseqs[1])
|
175
|
+
assert(rseqs[0] != rseqs[2])
|
176
|
+
assert(rseqs[1] != rseqs[2])
|
177
|
+
end
|
178
|
+
|
179
|
+
# testing Bio::Sequence::Common#randomize(hash)
|
180
|
+
def test_randomize_with_hash
|
181
|
+
hash = { 'a' => 20, 'c' => 19, 'g' => 18, 't' => 17 }
|
182
|
+
hash.default = 0
|
183
|
+
len = 0
|
184
|
+
hash.each_value { |v| len += v }
|
185
|
+
|
186
|
+
rseqs = (0..2).collect do |i|
|
187
|
+
rseq = @seq.randomize(hash)
|
188
|
+
# same length?
|
189
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+
assert_equal(len, rseq.length)
|
190
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+
# same composition?
|
191
|
+
[ 'a', 'c', 'g', 't', 'n' ].each do |chr|
|
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|
+
assert_equal(hash[chr], rseq.count(chr))
|
193
|
+
end
|
194
|
+
# returned value is instance of TSequence?
|
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|
+
assert_instance_of(TSequence, rseq)
|
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+
# not breaking given seq?
|
197
|
+
assert_equal(@orig, @seq)
|
198
|
+
rseq
|
199
|
+
end
|
200
|
+
|
201
|
+
# randomized? (very simple check)
|
202
|
+
assert(rseqs[0] != rseqs[1])
|
203
|
+
assert(rseqs[0] != rseqs[2])
|
204
|
+
assert(rseqs[1] != rseqs[2])
|
205
|
+
end
|
206
|
+
|
207
|
+
# testing Bio::Sequence::Common#randomize(hash) { |x| ... }
|
208
|
+
def test_randomize_with_hash_block
|
209
|
+
hash = { 'a' => 20, 'c' => 19, 'g' => 18, 't' => 17 }
|
210
|
+
hash.default = 0
|
211
|
+
len = 0
|
212
|
+
hash.each_value { |v| len += v }
|
213
|
+
|
214
|
+
rseqs = (0..2).collect do |i|
|
215
|
+
newcomposition = Hash.new(0)
|
216
|
+
newseq = ''
|
217
|
+
ret = @seq.randomize(hash) do |c|
|
218
|
+
#assert_kind_of(TSequence, c)
|
219
|
+
assert_kind_of(String, c)
|
220
|
+
newcomposition[c] += 1
|
221
|
+
newseq.concat c
|
222
|
+
end
|
223
|
+
# same length?
|
224
|
+
assert_equal(len, newseq.length)
|
225
|
+
# same composition?
|
226
|
+
assert_equal(hash, newcomposition)
|
227
|
+
# returned value is empty TSequence?
|
228
|
+
assert_equal(TSequence.new(''), ret)
|
229
|
+
# not breaking given seq?
|
230
|
+
assert_equal(@orig, @seq)
|
231
|
+
newseq
|
232
|
+
end
|
233
|
+
|
234
|
+
# randomized? (very simple check)
|
235
|
+
assert(rseqs[0] != rseqs[1])
|
236
|
+
assert(rseqs[0] != rseqs[2])
|
237
|
+
assert(rseqs[1] != rseqs[2])
|
238
|
+
end
|
239
|
+
|
240
|
+
def chi2(hist, f, k)
|
241
|
+
chi2 = 0
|
242
|
+
(0...k).each do |i|
|
243
|
+
chi2 += ((hist[i] - f) ** 2).quo(f)
|
244
|
+
end
|
245
|
+
chi2
|
246
|
+
end
|
247
|
+
private :chi2
|
248
|
+
|
249
|
+
# chi-square test for distribution of chi2 values from
|
250
|
+
# distribution of index('a')
|
251
|
+
def randomize_equiprobability
|
252
|
+
# Reference: http://www.geocities.jp/m_hiroi/light/pystat04.html
|
253
|
+
seq = TSequence.new('ccccgggtta') # length must be 10
|
254
|
+
k = 10
|
255
|
+
hist = Array.new(k, 0)
|
256
|
+
iter = 200
|
257
|
+
# F for index('a')
|
258
|
+
f = iter.quo(seq.length).to_f
|
259
|
+
|
260
|
+
# chi2 distribution, degree of freedom 9
|
261
|
+
# Reference: http://www.geocities.jp/m_hiroi/light/pystat04.html
|
262
|
+
# Reference: http://keisan.casio.jp/has10/SpecExec.cgi
|
263
|
+
# P = 0.9, 0.8, 0.7, ... 0.1, 0
|
264
|
+
chi2_table = [ 14.684, 12.242, 10.656, 9.414, 8.343,
|
265
|
+
7.357, 6.393, 5.380, 4.168, 0.000 ]
|
266
|
+
|
267
|
+
chi2_hist = Array.new(k, 0)
|
268
|
+
chi2_iter = 200
|
269
|
+
chi2_iter.times do
|
270
|
+
hist.fill(0)
|
271
|
+
iter.times { hist[yield(seq).index('a')] += 1 }
|
272
|
+
chi2 = chi2(hist, f, k)
|
273
|
+
idx = (0...(chi2_table.size)).find { |i| chi2 >= chi2_table[i] }
|
274
|
+
chi2_hist[idx] += 1
|
275
|
+
end
|
276
|
+
|
277
|
+
chi2_f = chi2_iter.quo(k).to_f
|
278
|
+
chi2_chi2 = chi2(chi2_hist, chi2_f, k)
|
279
|
+
#$stderr.puts chi2_chi2
|
280
|
+
|
281
|
+
## chi-square test, freedom 9, significance level 5%
|
282
|
+
#assert_operator(16.919, :>, chi2_chi2, "test of chi2 < 16.919 failed (#{chi2_chi2})")
|
283
|
+
# chi-square test, freedom 9, significance level 1%
|
284
|
+
assert_operator(21.666, :>, chi2_chi2, "test of chi2 < 21.666 failed (#{chi2_chi2})")
|
285
|
+
end
|
286
|
+
private :randomize_equiprobability
|
287
|
+
|
288
|
+
def test_randomize_equiprobability
|
289
|
+
randomize_equiprobability { |seq| seq.randomize }
|
290
|
+
end
|
291
|
+
|
292
|
+
def test_randomize_with_hash_equiprobability
|
293
|
+
hash = { 'c' => 4, 'g' => 3, 't' => 2, 'a' => 1 }
|
294
|
+
randomize_equiprobability { |seq| seq.randomize(hash) }
|
295
|
+
end
|
296
|
+
|
297
|
+
## disabled because it takes too long time.
|
298
|
+
#def test_randomize_with_block_equiprobability
|
299
|
+
# randomize_equiprobability do |seq|
|
300
|
+
# newseq = ''
|
301
|
+
# seq.randomize do |c|
|
302
|
+
# newseq.concat c
|
303
|
+
# end
|
304
|
+
# newseq
|
305
|
+
# end
|
306
|
+
#end
|
307
|
+
|
308
|
+
## disabled because it takes too long time.
|
309
|
+
#def test_randomize_with_hash_block_equiprobability
|
310
|
+
# hash = { 'c' => 4, 'g' => 3, 't' => 2, 'a' => 1 }
|
311
|
+
# randomize_equiprobability do |seq|
|
312
|
+
# newseq = ''
|
313
|
+
# seq.randomize(hash) do |c|
|
314
|
+
# newseq.concat c
|
315
|
+
# end
|
316
|
+
# newseq
|
317
|
+
# end
|
318
|
+
#end
|
319
|
+
|
320
|
+
end
|
321
|
+
|
322
|
+
|
323
|
+
class TestSequenceCommonSubseq < Test::Unit::TestCase
|
324
|
+
#def subseq(s = 1, e = self.length)
|
325
|
+
|
326
|
+
def test_to_s_returns_self_as_string
|
327
|
+
s = "abcefghijklmnop"
|
328
|
+
sequence = TSequence.new(s)
|
329
|
+
assert_equal(s, sequence.to_s, "wrong value")
|
330
|
+
assert_instance_of(String, sequence.to_s, "not a String")
|
331
|
+
end
|
332
|
+
|
333
|
+
def test_subseq_returns_RuntimeError_blank_sequence_default_end
|
334
|
+
sequence = TSequence.new("")
|
335
|
+
assert_raise(RuntimeError) { sequence.subseq(5) }
|
336
|
+
end
|
337
|
+
|
338
|
+
def test_subseq_returns_RuntimeError_start_less_than_one
|
339
|
+
sequence = TSequence.new("blahblah")
|
340
|
+
assert_raise(RuntimeError) { sequence.subseq(0) }
|
341
|
+
end
|
342
|
+
|
343
|
+
def test_subseq_returns_subsequence
|
344
|
+
sequence = TSequence.new("hahasubhehe")
|
345
|
+
assert_equal("sub", sequence.subseq(5,7))
|
346
|
+
end
|
347
|
+
|
348
|
+
end
|
349
|
+
|
350
|
+
|
351
|
+
# Test Sequence#window_wearch
|
352
|
+
class TestSequenceCommonWindowSearch < Test::Unit::TestCase
|
353
|
+
|
354
|
+
def test_window_search_with_width_3_default_step_no_residual
|
355
|
+
sequence = TSequence.new("agtca")
|
356
|
+
windows = []
|
357
|
+
returned_value = sequence.window_search(3) { |window| windows << window }
|
358
|
+
assert_equal(["agt", "gtc", "tca"], windows, "windows wrong")
|
359
|
+
assert_equal("", returned_value, "returned value wrong")
|
360
|
+
end
|
361
|
+
|
362
|
+
# added
|
363
|
+
def test_window_search_with_width_3_step_two_with_residual
|
364
|
+
sequence = TSequence.new("agtcat")
|
365
|
+
windows = []
|
366
|
+
returned_value = sequence.window_search(3, 2) { |window| windows << window }
|
367
|
+
assert_equal(["agt", "tca"], windows, "windows wrong")
|
368
|
+
assert_equal("t", returned_value, "returned value wrong")
|
369
|
+
end
|
370
|
+
|
371
|
+
end
|
372
|
+
|
373
|
+
end; end #module Bio; module TestSequenceCommon
|