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 +1,101 @@
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#
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# test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb - Unit test for Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
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#
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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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__), ['..'] * 6, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'test/unit'
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require 'bio/sequence'
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require 'bio/util/restriction_enzyme/double_stranded/aligned_strands'
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require 'bio/util/restriction_enzyme/double_stranded'
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module Bio; module TestRestrictionEnzyme #:nodoc:
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class TestDoubleStrandedAlignedStrands < Test::Unit::TestCase #:nodoc:
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def setup
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@t = Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
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@s = Bio::Sequence::NA
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@ds = Bio::RestrictionEnzyme::DoubleStranded
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@s_1 = @s.new('gattaca')
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@s_2 = @s_1.forward_complement
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@s_3 = @s.new('tttttttnnn')
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@s_4 = @s.new('nnnaaaaaaa')
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@ds_1 = @ds.new('nnnn^ngattacann^nn^n')
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@obj_1 = @t.align(@s_1, @s_2)
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@obj_2 = @t.align(@s_1, @s_3)
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@obj_3 = @t.align(@s_1, @s_4)
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@obj_4 = @t.align(@s_3, @s_4)
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@obj_5 = @t.align(@ds_1.primary, @ds_1.complement)
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@obj_8 = @t.align_with_cuts(@ds_1.primary, @ds_1.complement, @ds_1.primary.cut_locations, @ds_1.complement.cut_locations)
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@obj_6 = @t.align_with_cuts(@s_1, @s_2, [1,2], [3,4])
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@obj_7 = @t.align_with_cuts(@s_3, @s_4, [1,2], [3,4])
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end
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def test_ds
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assert_equal('nngattacannnnn', @ds_1.primary)
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assert_equal('nnnnnctaatgtnn', @ds_1.complement)
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assert_equal( 'n^ngattacann^nn^n', @ds_1.primary.with_cut_symbols)
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assert_equal('n^nn^nnctaatgtn^n' , @ds_1.complement.with_cut_symbols)
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assert_equal([0, 10, 12], @ds_1.primary.cut_locations)
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assert_equal([0, 2, 12], @ds_1.complement.cut_locations)
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end
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def test_align
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assert_equal('gattaca', @obj_1.primary)
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assert_equal('ctaatgt', @obj_1.complement)
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assert_equal('gattacannn', @obj_2.primary)
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assert_equal('tttttttnnn', @obj_2.complement)
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assert_equal('nnngattaca', @obj_3.primary)
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assert_equal('nnnaaaaaaa', @obj_3.complement)
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assert_equal('nnntttttttnnn', @obj_4.primary)
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assert_equal('nnnaaaaaaannn', @obj_4.complement)
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assert_equal('nnnnngattacannnnn', @obj_5.primary)
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assert_equal('nnnnnctaatgtnnnnn', @obj_5.complement)
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end
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def test_align_with_cuts
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assert_equal('g a^t^t a c a', @obj_6.primary)
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assert_equal('c t a a^t^g t', @obj_6.complement)
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# Looks incorrect at first, but this is deliberate.
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# The correct cuts need to be supplied by the user.
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assert_equal('n n n t t^t^t t t t n n n', @obj_7.primary)
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assert_equal('n n n a^a^a a a a a n n n', @obj_7.complement)
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assert_equal('n n n n^n g a t t a c a n n^n n^n', @obj_8.primary)
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assert_equal('n^n n^n n c t a a t g t n^n n n n', @obj_8.complement)
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end
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|
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def test_argument_error
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assert_raise(ArgumentError) { @t.new('arg', 'agg') }
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assert_raise(ArgumentError) { @t.new(@s.new('arg'), 'agg') }
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assert_raise(ArgumentError) { @t.new('arg', @s.new('agg')) }
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assert_raise(ArgumentError) { @t.new(@s.new('argg'), @s.new('agg')) }
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end
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end
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end; end
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#
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# test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb - Unit test for Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
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#
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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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__), ['..'] * 6, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'test/unit'
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require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair'
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module Bio; module TestRestrictionEnzyme #:nodoc:
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class TestDoubleStrandedCutLocationPair < Test::Unit::TestCase #:nodoc:
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def setup
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23
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@t = Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
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@obj_1 = @t.new([3,5])
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@obj_2 = @t.new(3, 5)
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@obj_3 = @t.new((3..5))
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@obj_4 = @t.new(0..5)
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@obj_5 = @t.new(3)
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@obj_6 = @t.new(nil,3)
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@obj_7 = @t.new(3,nil)
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end
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def test_contents
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assert_equal([3,5], @obj_1)
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assert_equal([3,5], @obj_2)
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assert_equal([3,5], @obj_3)
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assert_equal([0,5], @obj_4)
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assert_equal([3,nil], @obj_5)
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assert_equal([nil,3], @obj_6)
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assert_equal([3,nil], @obj_7)
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end
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def test_primary
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assert_equal(3, @obj_1.primary)
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assert_equal(3, @obj_2.primary)
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assert_equal(3, @obj_3.primary)
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assert_equal(0, @obj_4.primary)
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assert_equal(3, @obj_5.primary)
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assert_equal(nil, @obj_6.primary)
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assert_equal(3, @obj_7.primary)
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end
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54
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def test_complement
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assert_equal(5, @obj_1.complement)
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assert_equal(5, @obj_2.complement)
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assert_equal(5, @obj_3.complement)
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assert_equal(5, @obj_4.complement)
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assert_equal(nil, @obj_5.complement)
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assert_equal(3, @obj_6.complement)
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assert_equal(nil, @obj_7.complement)
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end
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def test_argument_error
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assert_raise(ArgumentError) { @t.new([3,5,6]) }
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assert_raise(ArgumentError) { @t.new(3,-1) }
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assert_raise(ArgumentError) { @t.new(-3,1) }
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assert_raise(ArgumentError) { @t.new(nil,nil) }
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assert_raise(ArgumentError) { @t.new('3',5) }
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end
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end
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|
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end; end
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#
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# test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb - Unit test for Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
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3
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#
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4
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
|
5
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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6
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# License:: The Ruby License
|
7
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#
|
8
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# $Id:$
|
9
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#
|
10
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require 'pathname'
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12
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
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13
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$:.unshift(libpath) unless $:.include?(libpath)
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14
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|
15
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require 'test/unit'
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16
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require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation'
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17
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|
18
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module Bio; module TestRestrictionEnzyme #:nodoc:
|
19
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|
20
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class TestDoubleStrandedCutLocationPairInEnzymeNotation < Test::Unit::TestCase #:nodoc:
|
21
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|
22
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def setup
|
23
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@t = Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
|
24
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+
|
25
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@obj_1 = @t.new([3,5])
|
26
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@obj_2 = @t.new(3, 5)
|
27
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@obj_3 = @t.new((3..5))
|
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@obj_4 = @t.new(-3..5)
|
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@obj_5 = @t.new(3)
|
30
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@obj_6 = @t.new(nil,3)
|
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@obj_7 = @t.new(3,nil)
|
32
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+
end
|
33
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|
34
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def test_contents
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35
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assert_equal([3,5], @obj_1)
|
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assert_equal([3,5], @obj_2)
|
37
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assert_equal([3,5], @obj_3)
|
38
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assert_equal([-3,5], @obj_4)
|
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assert_equal([3,nil], @obj_5)
|
40
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assert_equal([nil,3], @obj_6)
|
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assert_equal([3,nil], @obj_7)
|
42
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+
end
|
43
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|
44
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def test_primary
|
45
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assert_equal(3, @obj_1.primary)
|
46
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assert_equal(3, @obj_2.primary)
|
47
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assert_equal(3, @obj_3.primary)
|
48
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assert_equal(-3, @obj_4.primary)
|
49
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assert_equal(3, @obj_5.primary)
|
50
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assert_equal(nil, @obj_6.primary)
|
51
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assert_equal(3, @obj_7.primary)
|
52
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+
end
|
53
|
+
|
54
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+
def test_complement
|
55
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assert_equal(5, @obj_1.complement)
|
56
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assert_equal(5, @obj_2.complement)
|
57
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assert_equal(5, @obj_3.complement)
|
58
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assert_equal(5, @obj_4.complement)
|
59
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assert_equal(nil, @obj_5.complement)
|
60
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assert_equal(3, @obj_6.complement)
|
61
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assert_equal(nil, @obj_7.complement)
|
62
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+
end
|
63
|
+
|
64
|
+
def test_argument_error
|
65
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+
assert_raise(ArgumentError) { @t.new([3,5,6]) }
|
66
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+
assert_raise(ArgumentError) { @t.new(0,1) }
|
67
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+
assert_raise(ArgumentError) { @t.new(0,0) }
|
68
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+
assert_raise(ArgumentError) { @t.new('3',5) }
|
69
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+
end
|
70
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+
|
71
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+
end
|
72
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|
73
|
+
end; end
|
@@ -0,0 +1,53 @@
|
|
1
|
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#
|
2
|
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# test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb - Unit test for Bio::RestrictionEnzyme::DoubleStranded::CutLocations
|
3
|
+
#
|
4
|
+
# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
|
5
|
+
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id:$
|
9
|
+
#
|
10
|
+
|
11
|
+
require 'pathname'
|
12
|
+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
|
13
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
14
|
+
|
15
|
+
require 'test/unit'
|
16
|
+
require 'bio/util/restriction_enzyme/double_stranded/cut_locations'
|
17
|
+
|
18
|
+
module Bio; module TestRestrictionEnzyme #:nodoc:
|
19
|
+
|
20
|
+
class TestDoubleStrandedCutLocations < Test::Unit::TestCase #:nodoc:
|
21
|
+
|
22
|
+
def setup
|
23
|
+
@t = Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
|
24
|
+
@tt = Bio::RestrictionEnzyme::DoubleStranded::CutLocations
|
25
|
+
|
26
|
+
|
27
|
+
@obj_1 = @t.new([3,5])
|
28
|
+
@obj_2 = @t.new(3, 5)
|
29
|
+
@obj_3 = @t.new((3..5))
|
30
|
+
@obj_4 = @t.new(3..5)
|
31
|
+
@obj_5 = @t.new(3)
|
32
|
+
@obj_6 = @t.new(nil,3)
|
33
|
+
@obj_7 = @t.new(3,nil)
|
34
|
+
|
35
|
+
@locations = @tt.new(@obj_1, @obj_2, @obj_3, @obj_4, @obj_5, @obj_6, @obj_7)
|
36
|
+
end
|
37
|
+
|
38
|
+
def test_contents
|
39
|
+
assert_equal([3,5], @locations[0])
|
40
|
+
assert_equal([3,nil], @locations[-1])
|
41
|
+
end
|
42
|
+
|
43
|
+
def test_primary
|
44
|
+
assert_equal([3, 3, 3, 3, 3, nil, 3], @locations.primary)
|
45
|
+
end
|
46
|
+
|
47
|
+
def test_complement
|
48
|
+
assert_equal([5, 5, 5, 5, nil, 3, nil], @locations.complement)
|
49
|
+
end
|
50
|
+
|
51
|
+
end
|
52
|
+
|
53
|
+
end; end
|
data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb
ADDED
@@ -0,0 +1,104 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb - Unit test for Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
|
3
|
+
#
|
4
|
+
# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
|
5
|
+
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id:$
|
9
|
+
#
|
10
|
+
|
11
|
+
require 'pathname'
|
12
|
+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
|
13
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
14
|
+
|
15
|
+
require 'test/unit'
|
16
|
+
require 'bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation'
|
17
|
+
|
18
|
+
module Bio; module TestRestrictionEnzyme #:nodoc:
|
19
|
+
|
20
|
+
class TestDoubleStrandedCutLocationsInEnzymeNotation < Test::Unit::TestCase #:nodoc:
|
21
|
+
|
22
|
+
def setup
|
23
|
+
@t = Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
|
24
|
+
@tt = Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
|
25
|
+
|
26
|
+
@obj_1 = @t.new([3,5])
|
27
|
+
@obj_2 = @t.new(3, 5)
|
28
|
+
@obj_3 = @t.new((3..5))
|
29
|
+
@obj_4 = @t.new(-3..5)
|
30
|
+
@obj_5 = @t.new(3)
|
31
|
+
@obj_6 = @t.new(nil,3)
|
32
|
+
@obj_7 = @t.new(3,nil)
|
33
|
+
@obj_8 = @t.new(-8, -7)
|
34
|
+
|
35
|
+
@locations = @tt.new(@obj_1, @obj_2, @obj_3, @obj_4, @obj_5, @obj_6, @obj_7, @obj_8)
|
36
|
+
@loc_2 = @tt.new(@t.new(-2,-2), @t.new(1,1))
|
37
|
+
@loc_3 = @tt.new(@t.new(1,2))
|
38
|
+
end
|
39
|
+
|
40
|
+
def test_contents
|
41
|
+
assert_equal([3,5], @locations[0])
|
42
|
+
assert_equal([3,nil], @locations[-2])
|
43
|
+
end
|
44
|
+
|
45
|
+
def test_primary
|
46
|
+
assert_equal([3, 3, 3, -3, 3, nil, 3, -8], @locations.primary)
|
47
|
+
end
|
48
|
+
|
49
|
+
def test_complement
|
50
|
+
assert_equal([5, 5, 5, 5, nil, 3, nil, -7], @locations.complement)
|
51
|
+
end
|
52
|
+
|
53
|
+
def test_primary_to_array_index
|
54
|
+
assert_equal([10, 10, 10, 5, 10, nil, 10, 0], @locations.primary_to_array_index)
|
55
|
+
assert_equal([0,2], @loc_2.primary_to_array_index)
|
56
|
+
assert_equal([0], @loc_3.primary_to_array_index)
|
57
|
+
end
|
58
|
+
|
59
|
+
def test_primary_to_array_index_class
|
60
|
+
assert_equal(Array, @locations.primary_to_array_index.class)
|
61
|
+
assert_equal(Array, @loc_2.primary_to_array_index.class)
|
62
|
+
end
|
63
|
+
|
64
|
+
def test_complement_to_array_index
|
65
|
+
assert_equal([12, 12, 12, 12, nil, 10, nil, 1], @locations.complement_to_array_index)
|
66
|
+
assert_equal([0,2], @loc_2.complement_to_array_index)
|
67
|
+
assert_equal([1], @loc_3.complement_to_array_index)
|
68
|
+
end
|
69
|
+
|
70
|
+
def test_complement_to_array_index_class
|
71
|
+
assert_equal(Array, @locations.complement_to_array_index.class)
|
72
|
+
assert_equal(Array, @loc_2.complement_to_array_index.class)
|
73
|
+
end
|
74
|
+
|
75
|
+
def test_to_array_index
|
76
|
+
assert_equal(
|
77
|
+
[
|
78
|
+
[10, 12],
|
79
|
+
[10, 12],
|
80
|
+
[10, 12],
|
81
|
+
[5, 12],
|
82
|
+
[10, nil],
|
83
|
+
[nil, 10],
|
84
|
+
[10, nil],
|
85
|
+
[0, 1]
|
86
|
+
], @locations.to_array_index)
|
87
|
+
|
88
|
+
assert_equal(
|
89
|
+
[
|
90
|
+
[0, 0],
|
91
|
+
[2, 2],
|
92
|
+
], @loc_2.to_array_index)
|
93
|
+
|
94
|
+
assert_equal([[0,1]], @loc_3.to_array_index)
|
95
|
+
end
|
96
|
+
|
97
|
+
def test_to_array_index_class
|
98
|
+
assert_equal(Bio::RestrictionEnzyme::DoubleStranded::CutLocations, @locations.to_array_index.class)
|
99
|
+
assert_equal(Bio::RestrictionEnzyme::DoubleStranded::CutLocations, @loc_2.to_array_index.class)
|
100
|
+
end
|
101
|
+
|
102
|
+
end
|
103
|
+
|
104
|
+
end; end
|
data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb
ADDED
@@ -0,0 +1,83 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb - Unit test for Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
|
3
|
+
#
|
4
|
+
# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
|
5
|
+
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id:$
|
9
|
+
#
|
10
|
+
|
11
|
+
require 'pathname'
|
12
|
+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
|
13
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
14
|
+
|
15
|
+
require 'test/unit'
|
16
|
+
require 'bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation'
|
17
|
+
|
18
|
+
module Bio; module TestRestrictionEnzyme #:nodoc:
|
19
|
+
|
20
|
+
class TestSingleStrandCutLocationsInEnzymeNotation < Test::Unit::TestCase #:nodoc:
|
21
|
+
|
22
|
+
def setup
|
23
|
+
@t = Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
|
24
|
+
@obj_1 = @t.new([-2,1,3])
|
25
|
+
@obj_2 = @t.new(-2,1,3)
|
26
|
+
@obj_3 = @t.new(7,1,3)
|
27
|
+
|
28
|
+
@obj_4 = @t.new(-7,-8,-2,1,3)
|
29
|
+
end
|
30
|
+
|
31
|
+
def test_max
|
32
|
+
assert_equal(3, @obj_1.max)
|
33
|
+
assert_equal(3, @obj_2.max)
|
34
|
+
assert_equal(7, @obj_3.max)
|
35
|
+
end
|
36
|
+
|
37
|
+
def test_min
|
38
|
+
assert_equal(-2, @obj_1.min)
|
39
|
+
assert_equal(-2, @obj_2.min)
|
40
|
+
assert_equal(1, @obj_3.min)
|
41
|
+
end
|
42
|
+
|
43
|
+
def test_to_array_index
|
44
|
+
assert_equal([0,2,4], @obj_1.to_array_index)
|
45
|
+
assert_equal([0,2,4], @obj_2.to_array_index)
|
46
|
+
assert_equal([0,2,6], @obj_3.to_array_index)
|
47
|
+
|
48
|
+
assert_equal([0, 1, 6, 8, 10], @obj_4.to_array_index)
|
49
|
+
end
|
50
|
+
|
51
|
+
def test_initialize_with_pattern
|
52
|
+
@obj_5 = @t.new('n^ng^arraxt^n')
|
53
|
+
@obj_6 = @t.new('g^arraxt^n')
|
54
|
+
@obj_7 = @t.new('nnn^nn^nga^rraxt^nn')
|
55
|
+
@obj_8 = @t.new('^g^arraxt^n')
|
56
|
+
|
57
|
+
assert_equal([-2,1,7], @obj_5)
|
58
|
+
assert_equal([0,2,8], @obj_5.to_array_index)
|
59
|
+
|
60
|
+
assert_equal([1,7], @obj_6)
|
61
|
+
assert_equal([0,6], @obj_6.to_array_index)
|
62
|
+
|
63
|
+
assert_equal([-4, -2, 2, 7], @obj_7)
|
64
|
+
assert_equal([0, 2, 5, 10], @obj_7.to_array_index)
|
65
|
+
|
66
|
+
assert_equal([-1,1,7], @obj_8)
|
67
|
+
assert_equal([0,1,7], @obj_8.to_array_index)
|
68
|
+
end
|
69
|
+
|
70
|
+
def test_argument_error
|
71
|
+
assert_raise(ArgumentError) { @t.new([0,1,2]) }
|
72
|
+
assert_raise(ArgumentError) { @t.new(0,1,2,0) }
|
73
|
+
|
74
|
+
assert_raise(ArgumentError) { @t.new([nil,1,2]) }
|
75
|
+
assert_raise(ArgumentError) { @t.new(nil,1,2,nil) }
|
76
|
+
|
77
|
+
assert_raise(ArgumentError) { @t.new([1,1,2]) }
|
78
|
+
assert_raise(ArgumentError) { @t.new(1,1,2,2) }
|
79
|
+
end
|
80
|
+
|
81
|
+
end
|
82
|
+
|
83
|
+
end; end
|