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 +1,252 @@
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#
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# = test/bio/tc_pathway.rb - Unit test for Bio::Pathway
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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_reference.rb,v 1.3.2.2 2008/06/17 12:24:41 ngoto Exp $
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#
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), [".."] * 3, "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/reference'
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require 'bio/compat/references'
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module Bio
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class TestReference < Test::Unit::TestCase
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def setup
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hash = {'authors' => [ "Hoge, J.P.", "Fuga, F.B." ], 'title' => "Title of the study.",
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'journal' => "Theor. J. Hoge", 'volume' => 12, 'issue' => 3, 'pages' => "123-145",
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'year' => 2001, 'pubmed' => 12345678, 'medline' => 98765432, 'abstract' => "Hoge fuga. hoge fuga.",
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'url' => "http://example.com", 'mesh' => ['Hoge'], 'affiliations' => ['Tokyo']}
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@obj = Bio::Reference.new(hash)
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end
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def test_authors
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ary = [ "Hoge, J.P.", "Fuga, F.B." ]
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assert_equal(ary, @obj.authors)
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end
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def test_journal
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str = 'Theor. J. Hoge'
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assert_equal(str, @obj.journal)
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end
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def test_volume
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str = 12
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assert_equal(str, @obj.volume)
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end
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def test_issue
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str = 3
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assert_equal(str, @obj.issue)
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end
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def test_pages
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str = '123-145'
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assert_equal(str, @obj.pages)
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end
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def test_year
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str = 2001
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assert_equal(str, @obj.year)
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end
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def test_pubmed
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str = 12345678
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assert_equal(str, @obj.pubmed)
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end
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def test_abstract
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str = 'Hoge fuga. hoge fuga.'
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assert_equal(str, @obj.abstract)
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end
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def test_url
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str = 'http://example.com'
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assert_equal(str, @obj.url)
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end
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def test_mesh
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str = ['Hoge']
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assert_equal(str, @obj.mesh)
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end
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def test_affiliations
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str = ['Tokyo']
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assert_equal(str, @obj.affiliations)
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end
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def test_format_general
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str = 'Hoge, J.P., Fuga, F.B. (2001). "Title of the study." Theor. J. Hoge 12:123-145.'
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assert_equal(str, @obj.format)
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assert_equal(str, @obj.format('general'))
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assert_equal(str, @obj.general)
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end
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def test_format_endnote
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str = "%0 Journal Article\n%A Hoge, J.P.\n%A Fuga, F.B.\n%D 2001\n%T Title of the study.\n%J Theor. J. Hoge\n%V 12\n%N 3\n%P 123-145\n%M 12345678\n%U http://example.com\n%X Hoge fuga. hoge fuga.\n%K Hoge\n%+ Tokyo"
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assert_equal(str, @obj.format('endnote'))
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assert_equal(str, @obj.endnote)
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end
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def test_format_bibitem
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str = "\\bibitem{PMID:12345678}\nHoge, J.P., Fuga, F.B.\nTitle of the study.,\n{\\em Theor. J. Hoge}, 12(3):123--145, 2001."
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assert_equal(str, @obj.format('bibitem'))
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assert_equal(str, @obj.bibitem)
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end
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def test_format_bibtex
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str =<<__END__
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@article{PMID:12345678,
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author = {Hoge, J.P. and Fuga, F.B.},
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title = {Title of the study.},
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journal = {Theor. J. Hoge},
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year = {2001},
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volume = {12},
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number = {3},
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pages = {123--145},
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url = {http://example.com},
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}
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__END__
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assert_equal(str, @obj.format('bibtex'))
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assert_equal(str, @obj.bibtex)
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end
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def test_format_bibtex_with_arguments
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str =<<__END__
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@inproceedings{YourArticle,
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author = {Hoge, J.P. and Fuga, F.B.},
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title = {Title of the study.},
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year = {2001},
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volume = {12},
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number = {3},
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pages = {123--145},
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booktitle = {Theor. J. Hoge},
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month = {December},
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}
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__END__
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assert_equal(str, @obj.format('bibtex', 'inproceedings', 'YourArticle',
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{ 'journal' => false,
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'url' => false,
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'booktitle' => @obj.journal,
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'month' => 'December'}))
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assert_equal(str, @obj.bibtex('inproceedings', 'YourArticle',
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{ 'journal' => false,
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'url' => false,
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'booktitle' => @obj.journal,
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'month' => 'December'}))
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end
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def test_format_rd
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str = "== Title of the study.\n\n* Hoge, J.P. and Fuga, F.B.\n\n* Theor. J. Hoge 2001 12:123-145 [PMID:12345678]\n\nHoge fuga. hoge fuga."
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assert_equal(str, @obj.format('rd'))
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assert_equal(str, @obj.rd)
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end
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def test_format_nature
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str = 'Hoge, J.P. & Fuga, F.B. Title of the study. Theor. J. Hoge 12, 123-145 (2001).'
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assert_equal(str, @obj.format('Nature'))
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assert_equal(str, @obj.format('nature'))
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assert_equal(str, @obj.nature)
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end
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def test_format_science
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str = 'J.P. Hoge, F.B. Fuga, Theor. J. Hoge 12 123 (2001).'
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assert_equal(str, @obj.format('Science'))
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assert_equal(str, @obj.format('science'))
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assert_equal(str, @obj.science)
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end
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def test_format_genome_biol
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str = 'Hoge JP, Fuga FB: Title of the study. Theor J Hoge 2001, 12:123-145.'
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assert_equal(str, @obj.format('genome biol'))
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assert_equal(str, @obj.genome_biol)
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end
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def test_format_genome_res
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str = "Hoge, J.P. and Fuga, F.B. 2001.\n Title of the study. Theor. J. Hoge 12: 123-145."
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assert_equal(str, @obj.format('genome res'))
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assert_equal(str, @obj.genome_res)
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end
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def test_format_nar
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str = 'Hoge, J.P. and Fuga, F.B. (2001) Title of the study. Theor. J. Hoge, 12, 123-145.'
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assert_equal(str, @obj.format('nar'))
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assert_equal(str, @obj.nar)
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end
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def test_format_current
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str = 'Hoge JP, Fuga FB: Title of the study. Theor J Hoge 2001, 12:123-145.'
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assert_equal(str, @obj.format('current biology'))
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end
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def test_format_trends
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str = 'Hoge, J.P. and Fuga, F.B. (2001) Title of the study. Theor. J. Hoge 12, 123-145'
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assert_equal(str, @obj.trends)
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end
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def test_format_cell
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str = 'Hoge, J.P. and Fuga, F.B. (2001). Title of the study. Theor. J. Hoge 12, 123-145.'
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assert_equal(str, @obj.format('cell'))
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end
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end
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class NullStderr
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def initialize
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@log = []
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end
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def write(*arg)
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#p arg
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@log.push([ :write, *arg ])
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nil
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end
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def method_missing(*arg)
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#p arg
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@log.push arg
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nil
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end
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end
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class TestReferences < Test::Unit::TestCase
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def setup
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# To suppress warning messages, $stderr is replaced by dummy object.
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@stderr_orig = $stderr
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$stderr = NullStderr.new
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|
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hash = {}
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ary = [Bio::Reference.new(hash),
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Bio::Reference.new(hash)]
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@obj = Bio::References.new(ary)
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end
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def teardown
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# bring back $stderr
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$stderr = @stderr_orig
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end
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def test_append
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hash = {}
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ref = Bio::Reference.new(hash)
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assert(@obj.append(ref))
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end
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def test_each
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@obj.each do |ref|
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assert(ref)
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end
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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/test_sequence.rb - Unit test for Bio::Sequencce
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#
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4
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# Copyright:: Copyright (C) 2004
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5
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# Moses Hohman <mmhohman@northwestern.edu>
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6
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# 2006 Mitsuteru C. Nakao <n@bioruby.org>
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# License:: The Ruby License
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8
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#
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# $Id: test_sequence.rb,v 1.9 2007/04/05 23:35:42 trevor Exp $
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10
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#
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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__), ['..'] * 3, 'lib')).cleanpath.to_s
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14
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$:.unshift(libpath) unless $:.include?(libpath)
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15
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|
16
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require 'test/unit'
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17
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require 'bio/sequence'
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|
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module Bio
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class TestSequence < Test::Unit::TestCase
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21
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22
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def setup
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23
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@na = Sequence::NA.new('atgcatgcatgcatgcaaaa')
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24
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@rna = Sequence::NA.new('augcaugcaugcaugcaaaa')
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@aa = Sequence::AA.new('ACDEFGHIKLMNPQRSTVWYU')
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26
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end
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27
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|
28
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|
29
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# "main" method tests translated into unit tests
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30
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|
31
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# Test Sequence::NA.new
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32
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|
33
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def test_DNA_new_blank_sequence
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34
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sequence = Sequence::NA.new('')
|
35
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assert_equal(0, sequence.size)
|
36
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+
end
|
37
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+
|
38
|
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def test_DNA_new_sequence_downcases_symbols
|
39
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+
string = 'atgcatgcATGCATGCAAAA'
|
40
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sequence = Sequence::NA.new(string)
|
41
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+
assert_equal(string.downcase, sequence.to_s)
|
42
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+
end
|
43
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+
|
44
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def test_RNA_new_sequence
|
45
|
+
string = 'augcaugcaugcaugcaaaa'
|
46
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+
sequence = Sequence::NA.new(string)
|
47
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+
assert_equal(string, sequence.to_s)
|
48
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+
end
|
49
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+
|
50
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+
# added
|
51
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|
52
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def test_DNA_new_sequence_removes_whitespace
|
53
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+
sequence = Sequence::NA.new("a g\tc\nt\ra")
|
54
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assert_equal("agcta", sequence)
|
55
|
+
end
|
56
|
+
|
57
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+
# Test Sequence::AA.new
|
58
|
+
|
59
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def test_AA_new_blank_sequence
|
60
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sequence = Sequence::AA.new('')
|
61
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assert_equal(0, sequence.size)
|
62
|
+
end
|
63
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+
|
64
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+
def test_AA_new_sequence_all_legal_symbols
|
65
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+
string = 'ACDEFGHIKLMNPQRSTVWYU'
|
66
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+
sequence = Sequence::AA.new(string)
|
67
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+
assert_equal(string, sequence.to_s)
|
68
|
+
end
|
69
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+
|
70
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+
# added
|
71
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+
|
72
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+
def test_AA_new_sequence_upcases_symbols
|
73
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+
string = 'upcase'
|
74
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+
sequence = Sequence::AA.new(string)
|
75
|
+
assert_equal(string.upcase, sequence.to_s)
|
76
|
+
end
|
77
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+
|
78
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+
def test_AA_new_sequence_removes_whitespace
|
79
|
+
sequence = Sequence::AA.new("S T\tR\nI\rP")
|
80
|
+
assert_equal("STRIP", sequence)
|
81
|
+
end
|
82
|
+
|
83
|
+
# test element indexing
|
84
|
+
|
85
|
+
def test_element_reference_operator_with_two_arguments
|
86
|
+
sequence = Sequence::NA.new("atggggggtc")
|
87
|
+
assert_equal("gggggg", sequence[2,6])
|
88
|
+
end
|
89
|
+
|
90
|
+
# added
|
91
|
+
def test_element_reference_operator_with_one_argument
|
92
|
+
sequence = Sequence::NA.new("atggggggtc")
|
93
|
+
assert_equal(?t, sequence[1])
|
94
|
+
end
|
95
|
+
|
96
|
+
|
97
|
+
# Test Sequence#total
|
98
|
+
|
99
|
+
def test_total
|
100
|
+
sequence = Sequence::NA.new("catccagtccctggt")
|
101
|
+
assert_equal(2346, sequence.total({'a'=>1000, 'g'=>100, 't'=>10, 'c'=>1}))
|
102
|
+
end
|
103
|
+
|
104
|
+
# Test Sequence#composition
|
105
|
+
|
106
|
+
def test_dna_composition
|
107
|
+
sequence = Sequence::NA.new("aggtttcccc")
|
108
|
+
expected = {'a'=>1,'g'=>2,'t'=>3,'c'=>4}
|
109
|
+
expected.default = 0
|
110
|
+
assert_equal(expected, sequence.composition)
|
111
|
+
end
|
112
|
+
|
113
|
+
def test_rna_composition
|
114
|
+
sequence = Sequence::NA.new("agguuucccc")
|
115
|
+
expected = {'a'=>1,'g'=>2,'u'=>3,'c'=>4}
|
116
|
+
expected.default = 0
|
117
|
+
assert_equal(expected, sequence.composition)
|
118
|
+
end
|
119
|
+
|
120
|
+
# I don't get splicing
|
121
|
+
|
122
|
+
# Test Sequence::NA#complement
|
123
|
+
|
124
|
+
def test_dna_sequence_complement
|
125
|
+
assert_equal('ttttgcatgcatgcatgcat', @na.complement)
|
126
|
+
end
|
127
|
+
|
128
|
+
def test_rna_sequence_complement
|
129
|
+
assert_equal('uuuugcaugcaugcaugcau', @rna.complement)
|
130
|
+
end
|
131
|
+
|
132
|
+
def test_ambiguous_dna_sequence_complement
|
133
|
+
assert_equal("nwsbvhdkmyrcgta", Sequence::NA.new('tacgyrkmhdbvswn').complement)
|
134
|
+
end
|
135
|
+
|
136
|
+
def test_ambiguous_rna_sequence_complement
|
137
|
+
assert_equal("nwsbvhdkmyrcgua", Sequence::NA.new('uacgyrkmhdbvswn').complement)
|
138
|
+
end
|
139
|
+
|
140
|
+
# Test Sequence::NA#translate
|
141
|
+
|
142
|
+
def test_dna_sequence_translate
|
143
|
+
assert_equal("MHACMQ", @na.translate)
|
144
|
+
end
|
145
|
+
|
146
|
+
def test_rna_sequence_translate
|
147
|
+
assert_equal("MHACMQ", @rna.translate)
|
148
|
+
end
|
149
|
+
|
150
|
+
# Test Sequence::NA#gc_percent
|
151
|
+
|
152
|
+
def test_dna_gc_percent
|
153
|
+
assert_equal(40, @na.gc_percent)
|
154
|
+
end
|
155
|
+
|
156
|
+
def test_rna_gc_percent
|
157
|
+
assert_equal(40, @rna.gc_percent)
|
158
|
+
end
|
159
|
+
|
160
|
+
# Test Sequence::NA#illegal_bases
|
161
|
+
|
162
|
+
def test_valid_dna_sequence_illegal_bases
|
163
|
+
assert_equal([], @na.illegal_bases)
|
164
|
+
end
|
165
|
+
|
166
|
+
def test_invalid_nucleic_acid_illegal_bases
|
167
|
+
string = 'tacgyrkmhdbvswn'
|
168
|
+
expected = []
|
169
|
+
string[4..-1].each_byte { |val| expected << val.chr }
|
170
|
+
assert_equal(expected.sort, Sequence::NA.new(string).illegal_bases)
|
171
|
+
end
|
172
|
+
|
173
|
+
def test_invalid_nucleic_acid_illegal_bases_more
|
174
|
+
string = ('abcdefghijklmnopqrstuvwxyz-!%#$@')
|
175
|
+
expected = []
|
176
|
+
'bdefhijklmnopqrsvwxyz-!%#$@'.each_byte { |val| expected << val.chr }
|
177
|
+
assert_equal(expected.sort, Sequence::NA.new(string).illegal_bases)
|
178
|
+
end
|
179
|
+
|
180
|
+
# Test Sequence::NA#molecular_weight
|
181
|
+
|
182
|
+
def test_dna_molecular_weight
|
183
|
+
assert_in_delta(6174.3974, @na.molecular_weight, 1e-5)
|
184
|
+
end
|
185
|
+
|
186
|
+
def test_rna_molecular_weight
|
187
|
+
assert_in_delta(6438.2774, @rna.molecular_weight, 1e-5)
|
188
|
+
end
|
189
|
+
|
190
|
+
# Test Sequence::NA#to_re
|
191
|
+
|
192
|
+
def test_dna_to_re
|
193
|
+
assert_equal(/atgc[agr][tcy][acm][tgk][atgrwkd][atcwmyh][agcmrsv][tgcyskb][gcw][atw][atgcyrwskmbdhvn]/, Sequence::NA.new('atgcrymkdhvbswn').to_re)
|
194
|
+
end
|
195
|
+
|
196
|
+
def test_rna_to_re
|
197
|
+
assert_equal(/augc[agr][ucy][acm][ugk][augrwkd][aucwmyh][agcmrsv][ugcyskb][gcw][auw][augcyrwskmbdhvn]/, Sequence::NA.new('augcrymkdhvbswn').to_re)
|
198
|
+
end
|
199
|
+
|
200
|
+
# Test Sequence::NA#names
|
201
|
+
|
202
|
+
def test_nucleic_acid_names
|
203
|
+
# It is a Bio::NucleicAcid feature.
|
204
|
+
# assert_equal(["adenine", "cytosine", "guanine", "thymine", "uracil"], Sequence::NA.new('acgtu').names)
|
205
|
+
assert(Sequence::NA.new('acgtu').names)
|
206
|
+
end
|
207
|
+
|
208
|
+
# Test Sequence::NA#pikachu
|
209
|
+
|
210
|
+
def test_dna_pikachu
|
211
|
+
assert_equal("pika", Sequence::NA.new('atgc').pikachu)
|
212
|
+
end
|
213
|
+
|
214
|
+
def test_rna_pikachu
|
215
|
+
assert_equal("pika", Sequence::NA.new('augc').pikachu)
|
216
|
+
end
|
217
|
+
|
218
|
+
# Test Sequence::NA#randomize
|
219
|
+
|
220
|
+
def test_randomize_dna_retains_composition
|
221
|
+
assert_equal(@na.composition, @na.randomize.composition)
|
222
|
+
end
|
223
|
+
|
224
|
+
# this test has a neglibly small chance of failure
|
225
|
+
def test_two_consecutive_dna_randomizations_not_equal
|
226
|
+
assert_not_equal(@na.randomize, @na.randomize)
|
227
|
+
end
|
228
|
+
|
229
|
+
def test_randomize_dna_can_be_chained
|
230
|
+
assert_equal(@na.composition, @na.randomize.randomize.composition)
|
231
|
+
end
|
232
|
+
|
233
|
+
def test_randomize_dna_with_block
|
234
|
+
appended = ""
|
235
|
+
@na.randomize {|x| appended << x}
|
236
|
+
assert_equal(@na.composition, Sequence::NA.new(appended).composition)
|
237
|
+
end
|
238
|
+
|
239
|
+
# Test Sequence::NA.randomize(counts)
|
240
|
+
|
241
|
+
def test_NA_randomize_with_counts
|
242
|
+
counts = {'a'=>10,'c'=>20,'g'=>30,'u'=>40}
|
243
|
+
counts.default = 0
|
244
|
+
assert_equal(counts, Sequence::NA.randomize(counts).composition)
|
245
|
+
end
|
246
|
+
|
247
|
+
def test_NA_randomize_with_counts_and_block
|
248
|
+
appended = ""
|
249
|
+
counts = {'a'=>10,'c'=>20,'g'=>30,'u'=>40}
|
250
|
+
counts.default = 0
|
251
|
+
Sequence::NA.randomize(counts) {|x| appended << x}
|
252
|
+
assert_equal(counts, Sequence::NA.new(appended).composition)
|
253
|
+
end
|
254
|
+
|
255
|
+
# Test Sequence::AA#codes
|
256
|
+
|
257
|
+
def test_amino_acid_codes
|
258
|
+
assert_equal(["Ala", "Cys", "Asp", "Glu", "Phe", "Gly", "His", "Ile", "Lys",
|
259
|
+
"Leu", "Met", "Asn", "Pro", "Gln", "Arg", "Ser", "Thr", "Val", "Trp",
|
260
|
+
"Tyr", "Sec"], @aa.codes)
|
261
|
+
end
|
262
|
+
|
263
|
+
# Test Sequence::AA#names
|
264
|
+
|
265
|
+
def test_amino_acid_names
|
266
|
+
assert_equal(["alanine", "cysteine", "aspartic acid", "glutamic acid", "phenylalanine",
|
267
|
+
"glycine", "histidine", "isoleucine", "lysine", "leucine", "methionine",
|
268
|
+
"asparagine", "proline", "glutamine", "arginine", "serine", "threonine",
|
269
|
+
"valine", "tryptophan", "tyrosine", "selenocysteine"], @aa.names)
|
270
|
+
end
|
271
|
+
|
272
|
+
# Test Sequence::AA#molecular_weight
|
273
|
+
|
274
|
+
def test_amino_acid_molecular_weight
|
275
|
+
assert_in_delta(2395.725, @aa.subseq(1,20).molecular_weight, 0.0001)
|
276
|
+
end
|
277
|
+
|
278
|
+
#Test Sequence::AA#randomize
|
279
|
+
|
280
|
+
def test_amino_acid_randomize_has_same_composition
|
281
|
+
aaseq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA'
|
282
|
+
s = Sequence::AA.new(aaseq)
|
283
|
+
assert_equal(s.composition, s.randomize.composition)
|
284
|
+
end
|
285
|
+
|
286
|
+
# this test has a neglibly small chance of failure
|
287
|
+
def test_consecutive_amino_acid_randomizes_are_not_equal
|
288
|
+
aaseq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA'
|
289
|
+
s = Sequence::AA.new(aaseq)
|
290
|
+
assert_not_equal(s.randomize, s.randomize)
|
291
|
+
end
|
292
|
+
|
293
|
+
def test_amino_acid_randomize_can_be_chained
|
294
|
+
aaseq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA'
|
295
|
+
s = Sequence::AA.new(aaseq)
|
296
|
+
assert_equal(s.randomize.composition, s.randomize.randomize.composition)
|
297
|
+
end
|
298
|
+
end
|
299
|
+
|
300
|
+
|
301
|
+
class TestNATranslate < Test::Unit::TestCase
|
302
|
+
def setup
|
303
|
+
@obj = Bio::Sequence::NA.new("AAA")
|
304
|
+
end
|
305
|
+
|
306
|
+
def test_translate
|
307
|
+
assert_equal("K", @obj.translate)
|
308
|
+
end
|
309
|
+
def test_translate_1
|
310
|
+
assert_equal("K", @obj.translate(1))
|
311
|
+
end
|
312
|
+
def test_translate_2
|
313
|
+
assert_equal("", @obj.translate(2))
|
314
|
+
end
|
315
|
+
def test_translate_3
|
316
|
+
assert_equal("", @obj.translate(3))
|
317
|
+
end
|
318
|
+
def test_translate_4
|
319
|
+
assert_equal("F", @obj.translate(4))
|
320
|
+
end
|
321
|
+
def test_translate_5
|
322
|
+
assert_equal("", @obj.translate(5))
|
323
|
+
end
|
324
|
+
def test_translate_5
|
325
|
+
assert_equal("", @obj.translate(6))
|
326
|
+
end
|
327
|
+
end
|
328
|
+
|
329
|
+
end
|