wwood-bioruby 1.2.11
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- data/README.rdoc +205 -0
- data/README_DEV.rdoc +285 -0
- data/VERSION.yml +4 -0
- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +293 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/lib/bio.rb +306 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +505 -0
- data/lib/bio/appl/blast/ddbj.rb +142 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/genomenet.rb +263 -0
- data/lib/bio/appl/blast/ncbioptions.rb +220 -0
- data/lib/bio/appl/blast/remote.rb +105 -0
- data/lib/bio/appl/blast/report.rb +767 -0
- data/lib/bio/appl/blast/rexml.rb +144 -0
- data/lib/bio/appl/blast/rpsblast.rb +277 -0
- data/lib/bio/appl/blast/wublast.rb +635 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blat/report.rb +530 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta.rb +235 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/gcg/msf.rb +212 -0
- data/lib/bio/appl/gcg/seq.rb +195 -0
- data/lib/bio/appl/genscan/report.rb +552 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/hmmer/report.rb +683 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/paml/baseml.rb +95 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/codeml.rb +242 -0
- data/lib/bio/appl/paml/codeml/rates.rb +67 -0
- data/lib/bio/appl/paml/codeml/report.rb +67 -0
- data/lib/bio/appl/paml/common.rb +348 -0
- data/lib/bio/appl/paml/common_report.rb +38 -0
- data/lib/bio/appl/paml/yn00.rb +103 -0
- data/lib/bio/appl/paml/yn00/report.rb +32 -0
- data/lib/bio/appl/phylip/alignment.rb +133 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/psort/report.rb +542 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +124 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sosui/report.rb +151 -0
- data/lib/bio/appl/spidey/report.rb +593 -0
- data/lib/bio/appl/targetp/report.rb +267 -0
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +231 -0
- data/lib/bio/command.rb +593 -0
- data/lib/bio/compat/features.rb +157 -0
- data/lib/bio/compat/references.rb +128 -0
- data/lib/bio/data/aa.rb +353 -0
- data/lib/bio/data/codontable.rb +722 -0
- data/lib/bio/data/na.rb +223 -0
- data/lib/bio/db.rb +329 -0
- data/lib/bio/db/aaindex.rb +357 -0
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +67 -0
- data/lib/bio/db/biosql/sequence.rb +508 -0
- data/lib/bio/db/embl/common.rb +352 -0
- data/lib/bio/db/embl/embl.rb +500 -0
- data/lib/bio/db/embl/embl_to_biosequence.rb +85 -0
- data/lib/bio/db/embl/format_embl.rb +190 -0
- data/lib/bio/db/embl/sptr.rb +1283 -0
- data/lib/bio/db/embl/swissprot.rb +42 -0
- data/lib/bio/db/embl/trembl.rb +41 -0
- data/lib/bio/db/embl/uniprot.rb +42 -0
- data/lib/bio/db/fantom.rb +597 -0
- data/lib/bio/db/fasta.rb +410 -0
- data/lib/bio/db/fasta/defline.rb +532 -0
- data/lib/bio/db/fasta/fasta_to_biosequence.rb +63 -0
- data/lib/bio/db/fasta/format_fasta.rb +97 -0
- data/lib/bio/db/genbank/common.rb +307 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/format_genbank.rb +187 -0
- data/lib/bio/db/genbank/genbank.rb +250 -0
- data/lib/bio/db/genbank/genbank_to_biosequence.rb +86 -0
- data/lib/bio/db/genbank/genpept.rb +60 -0
- data/lib/bio/db/genbank/refseq.rb +18 -0
- data/lib/bio/db/gff.rb +1846 -0
- data/lib/bio/db/go.rb +481 -0
- data/lib/bio/db/kegg/brite.rb +41 -0
- data/lib/bio/db/kegg/compound.rb +131 -0
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +148 -0
- data/lib/bio/db/kegg/expression.rb +155 -0
- data/lib/bio/db/kegg/genes.rb +263 -0
- data/lib/bio/db/kegg/genome.rb +241 -0
- data/lib/bio/db/kegg/glycan.rb +166 -0
- data/lib/bio/db/kegg/keggtab.rb +357 -0
- data/lib/bio/db/kegg/kgml.rb +256 -0
- data/lib/bio/db/kegg/orthology.rb +136 -0
- data/lib/bio/db/kegg/reaction.rb +82 -0
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +107 -0
- data/lib/bio/db/medline.rb +326 -0
- data/lib/bio/db/nbrf.rb +191 -0
- data/lib/bio/db/newick.rb +658 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +29 -0
- data/lib/bio/db/pdb/atom.rb +77 -0
- data/lib/bio/db/pdb/chain.rb +210 -0
- data/lib/bio/db/pdb/chemicalcomponent.rb +224 -0
- data/lib/bio/db/pdb/model.rb +148 -0
- data/lib/bio/db/pdb/pdb.rb +1911 -0
- data/lib/bio/db/pdb/residue.rb +176 -0
- data/lib/bio/db/pdb/utils.rb +399 -0
- data/lib/bio/db/prosite.rb +597 -0
- data/lib/bio/db/rebase.rb +456 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/db/url.rb +42 -0
- data/lib/bio/feature.rb +139 -0
- data/lib/bio/io/biosql/biodatabase.rb +64 -0
- data/lib/bio/io/biosql/bioentry.rb +29 -0
- data/lib/bio/io/biosql/bioentry_dbxref.rb +11 -0
- data/lib/bio/io/biosql/bioentry_path.rb +12 -0
- data/lib/bio/io/biosql/bioentry_qualifier_value.rb +10 -0
- data/lib/bio/io/biosql/bioentry_reference.rb +10 -0
- data/lib/bio/io/biosql/bioentry_relationship.rb +10 -0
- data/lib/bio/io/biosql/biosequence.rb +11 -0
- data/lib/bio/io/biosql/comment.rb +7 -0
- data/lib/bio/io/biosql/config/database.yml +20 -0
- data/lib/bio/io/biosql/dbxref.rb +13 -0
- data/lib/bio/io/biosql/dbxref_qualifier_value.rb +12 -0
- data/lib/bio/io/biosql/location.rb +32 -0
- data/lib/bio/io/biosql/location_qualifier_value.rb +11 -0
- data/lib/bio/io/biosql/ontology.rb +10 -0
- data/lib/bio/io/biosql/reference.rb +9 -0
- data/lib/bio/io/biosql/seqfeature.rb +32 -0
- data/lib/bio/io/biosql/seqfeature_dbxref.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_path.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_qualifier_value.rb +20 -0
- data/lib/bio/io/biosql/seqfeature_relationship.rb +11 -0
- data/lib/bio/io/biosql/taxon.rb +12 -0
- data/lib/bio/io/biosql/taxon_name.rb +9 -0
- data/lib/bio/io/biosql/term.rb +27 -0
- data/lib/bio/io/biosql/term_dbxref.rb +11 -0
- data/lib/bio/io/biosql/term_path.rb +12 -0
- data/lib/bio/io/biosql/term_relationship.rb +13 -0
- data/lib/bio/io/biosql/term_relationship_term.rb +11 -0
- data/lib/bio/io/biosql/term_synonym.rb +10 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +638 -0
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +163 -0
- data/lib/bio/io/fetch.rb +195 -0
- data/lib/bio/io/flatfile.rb +482 -0
- data/lib/bio/io/flatfile/autodetection.rb +545 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/buffer.rb +237 -0
- data/lib/bio/io/flatfile/index.rb +1381 -0
- data/lib/bio/io/flatfile/indexer.rb +805 -0
- data/lib/bio/io/flatfile/splitter.rb +297 -0
- data/lib/bio/io/higet.rb +73 -0
- data/lib/bio/io/hinv.rb +442 -0
- data/lib/bio/io/keggapi.rb +805 -0
- data/lib/bio/io/ncbirest.rb +733 -0
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +307 -0
- data/lib/bio/io/registry.rb +292 -0
- data/lib/bio/io/soapwsdl.rb +119 -0
- data/lib/bio/io/sql.rb +186 -0
- data/lib/bio/location.rb +867 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +960 -0
- data/lib/bio/reference.rb +602 -0
- data/lib/bio/sequence.rb +456 -0
- data/lib/bio/sequence/aa.rb +152 -0
- data/lib/bio/sequence/adapter.rb +108 -0
- data/lib/bio/sequence/common.rb +310 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/dblink.rb +54 -0
- data/lib/bio/sequence/format.rb +358 -0
- data/lib/bio/sequence/format_raw.rb +23 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +491 -0
- data/lib/bio/shell.rb +44 -0
- data/lib/bio/shell/core.rb +578 -0
- data/lib/bio/shell/demo.rb +146 -0
- data/lib/bio/shell/interface.rb +218 -0
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +71 -0
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +218 -0
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +105 -0
- data/lib/bio/shell/plugin/flatfile.rb +101 -0
- data/lib/bio/shell/plugin/keggapi.rb +181 -0
- data/lib/bio/shell/plugin/midi.rb +430 -0
- data/lib/bio/shell/plugin/obda.rb +45 -0
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +247 -0
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +102 -0
- data/lib/bio/tree.rb +852 -0
- data/lib/bio/util/color_scheme.rb +191 -0
- data/lib/bio/util/color_scheme/buried.rb +59 -0
- data/lib/bio/util/color_scheme/helix.rb +59 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +64 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +31 -0
- data/lib/bio/util/color_scheme/strand.rb +59 -0
- data/lib/bio/util/color_scheme/taylor.rb +50 -0
- data/lib/bio/util/color_scheme/turn.rb +59 -0
- data/lib/bio/util/color_scheme/zappo.rb +50 -0
- data/lib/bio/util/contingency_table.rb +370 -0
- data/lib/bio/util/restriction_enzyme.rb +228 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
- data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +200 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/aaindex/DAYM780301 +30 -0
- data/test/data/aaindex/PRAM900102 +20 -0
- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
- data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
- data/test/data/blast/2.2.15.blastp.m7 +876 -0
- data/test/data/blast/b0002.faa +15 -0
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- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/blast/blastp-multi.m7 +188 -0
- data/test/data/command/echoarg2.bat +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/embl/AB090716.embl.rel89 +63 -0
- data/test/data/fasta/example1.txt +75 -0
- data/test/data/fasta/example2.txt +21 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/paml/codeml/control_file.txt +30 -0
- data/test/data/paml/codeml/output.txt +78 -0
- data/test/data/paml/codeml/rates +217 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/rpsblast/misc.rpsblast +193 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/functional/bio/appl/test_pts1.rb +115 -0
- data/test/functional/bio/io/test_ensembl.rb +229 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -0
- data/test/functional/bio/sequence/test_output_embl.rb +51 -0
- data/test/functional/bio/test_command.rb +301 -0
- data/test/runner.rb +14 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_ncbioptions.rb +112 -0
- data/test/unit/bio/appl/blast/test_report.rb +1135 -0
- data/test/unit/bio/appl/blast/test_rpsblast.rb +398 -0
- data/test/unit/bio/appl/genscan/test_report.rb +182 -0
- data/test/unit/bio/appl/hmmer/test_report.rb +342 -0
- data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
- data/test/unit/bio/appl/mafft/test_report.rb +63 -0
- data/test/unit/bio/appl/paml/codeml/test_rates.rb +45 -0
- data/test/unit/bio/appl/paml/codeml/test_report.rb +45 -0
- data/test/unit/bio/appl/paml/test_codeml.rb +174 -0
- data/test/unit/bio/appl/sosui/test_report.rb +81 -0
- data/test/unit/bio/appl/targetp/test_report.rb +146 -0
- data/test/unit/bio/appl/test_blast.rb +277 -0
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_psort.rb +57 -0
- data/test/unit/bio/appl/test_pts1.rb +77 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +126 -0
- data/test/unit/bio/data/test_aa.rb +90 -0
- data/test/unit/bio/data/test_codontable.rb +107 -0
- data/test/unit/bio/data/test_na.rb +80 -0
- data/test/unit/bio/db/embl/test_common.rb +117 -0
- data/test/unit/bio/db/embl/test_embl.rb +214 -0
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +203 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1812 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +31 -0
- data/test/unit/bio/db/kegg/test_genes.rb +45 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +152 -0
- data/test/unit/bio/db/test_aaindex.rb +197 -0
- data/test/unit/bio/db/test_fasta.rb +250 -0
- data/test/unit/bio/db/test_gff.rb +1190 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_medline.rb +127 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +364 -0
- data/test/unit/bio/db/test_prosite.rb +1437 -0
- data/test/unit/bio/db/test_rebase.rb +101 -0
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/db/test_url.rb +36 -0
- data/test/unit/bio/io/flatfile/test_autodetection.rb +375 -0
- data/test/unit/bio/io/flatfile/test_buffer.rb +251 -0
- data/test/unit/bio/io/flatfile/test_splitter.rb +369 -0
- data/test/unit/bio/io/test_ddbjxml.rb +80 -0
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +42 -0
- data/test/unit/bio/io/test_flatfile.rb +505 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +115 -0
- data/test/unit/bio/sequence/test_common.rb +373 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -0
- data/test/unit/bio/sequence/test_dblink.rb +58 -0
- data/test/unit/bio/sequence/test_na.rb +330 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +185 -0
- data/test/unit/bio/test_alignment.rb +1025 -0
- data/test/unit/bio/test_command.rb +349 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +144 -0
- data/test/unit/bio/test_location.rb +599 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +499 -0
- data/test/unit/bio/test_reference.rb +252 -0
- data/test/unit/bio/test_sequence.rb +329 -0
- data/test/unit/bio/test_shell.rb +18 -0
- data/test/unit/bio/test_tree.rb +593 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +101 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
- data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
- data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
- data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
- data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
- data/test/unit/bio/util/test_color_scheme.rb +33 -0
- data/test/unit/bio/util/test_contingency_table.rb +94 -0
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +245 -0
- metadata +543 -0
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#
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# test/unit/bio/util/restriction_enzyme/test_analysis.rb - Unit test for Bio::RestrictionEnzyme::Analysis
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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__), ['..'] * 5, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'test/unit'
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require 'bio/util/restriction_enzyme/analysis'
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require 'bio/sequence'
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module Bio; module TestRestrictionEnzyme #:nodoc:
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class TestAnalysis < Test::Unit::TestCase #:nodoc:
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def setup
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@enz = Bio::RestrictionEnzyme
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@t = Bio::RestrictionEnzyme::Analysis
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@obj_1 = @t.cut('cagagag', 'ag^ag')
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@obj_2 = @t.cut('agagag', 'ag^ag')
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@obj_3 = @t.cut('cagagagt', 'ag^ag')
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e1 = @enz.new('atgcatgc', [3,3])
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@obj_4 = @t.cut('atgcatgcatgc', e1)
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@obj_4bd = @t.cut('atgcatgcatgccc', e1, 'cc^c') # mix of always cut and sometimes cut
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e2 = @enz.new('atgcatgc', [3,5])
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@obj_5 = @t.cut('atgcatgcatgc', e2)
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e3 = @enz.new('anna', [1,1], [3,3])
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e4 = @enz.new('gg', [1,1])
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@obj_6 = @t.cut('agga', e3, e4)
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@obj_7 = @t.cut('gaccaggaaaaagaccaggaaagcctggaaaagttaac', 'EcoRII')
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@obj_7b = @t.cut('gaccaggaaaaagaccaggaaagcctggaaaagttaaccc', 'EcoRII', 'HincII', 'cc^c')
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@obj_7bd = @t.cut_without_permutations('gaccaggaaaaagaccaggaaagcctggaaaagttaaccc', 'EcoRII', 'HincII', 'cc^c')
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@obj_8 = @t.cut('gaccaggaaaaagaccaggaaagcctggaaaagttaac', 'EcoRII', 'HincII')
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@obj_9 = @t.cut('aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa', 'EcoRII')
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@obj_9 = @t.cut('aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa', 'EcoRII', 'HincII')
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@obj_1d = @t.cut_without_permutations('cagagag', 'ag^ag')
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@obj_2d = @t.cut_without_permutations('agagag', 'ag^ag')
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@obj_3d = @t.cut_without_permutations('cagagagt', 'ag^ag')
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e1 = @enz.new('atgcatgc', [3,3])
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@obj_4d = @t.cut_without_permutations('atgcatgcatgc', e1)
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e2 = @enz.new('atgcatgc', [3,5])
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@obj_5d = @t.cut_without_permutations('atgcatgcatgc', e2)
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e3 = @enz.new('anna', [1,1], [3,3])
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e4 = @enz.new('gg', [1,1])
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@obj_6d = @t.cut_without_permutations('agga', e3, e4)
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@obj_7d = @t.cut_without_permutations('gaccaggaaaaagaccaggaaagcctggaaaagttaac', 'EcoRII')
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@obj_8d = @t.cut_without_permutations('gaccaggaaaaagaccaggaaagcctggaaaagttaac', 'EcoRII', 'HincII')
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@obj_98 = @t.cut('', 'EcoRII', 'HincII')
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@obj_99 = @t.cut_without_permutations('', 'EcoRII', 'HincII')
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@obj_vr1 = @t.cut('gaccaggaaaaagaccaggaaagcctggaaaagttaac', 'EcoRII', {:view_ranges => true})
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@obj_vr2 = @t.cut('cagagag', {:view_ranges => true}, 'ag^ag')
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end
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def test_cut
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assert_equal(["ag", "cag"], @obj_1.primary)
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assert_equal(["gtc", "tc"], @obj_1.complement)
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assert_equal(2, @obj_1.size)
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assert_equal(Bio::RestrictionEnzyme::Fragments, @obj_1.class)
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assert_equal(Bio::RestrictionEnzyme::Fragment, @obj_1[0].class)
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assert_equal(["ag"], @obj_2.primary)
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assert_equal(["ag", "agt", "cag"], @obj_3.primary)
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assert_equal(["atg", "atgcatg", "catg", "catgc"], @obj_4.primary)
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=begin
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A T G^C A T G C
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A T G C A T G C A T G C
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A T G^C A T G^C A T G C
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A T G C A T G^C A T G C
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=end
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assert_equal(["atg", "atgcatg", "catgc", "catgcatgc"], @obj_5.primary)
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assert_equal(["a", "ag", "g", "ga"], @obj_6.primary)
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assert_equal(["ccaggaaaaaga", "ccaggaaag", "cctggaaaagttaac", "ga"], @obj_7.primary)
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assert_equal(["aac", "ccaggaaaaaga", "ccaggaaag", "cctggaaaagtt", "ga"], @obj_8.primary)
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=begin
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e1 = @enz.new('atgcatgc', [3,3])
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@obj_4bd = @t.cut('atgcatgcatgccc', e1, 'cc^c') # mix of sometimes cut and always cut
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[#<struct Bio::RestrictionEnzyme::Analysis::UniqueFragment
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primary="atgcatg",
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complement="tacgtac">,
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#<struct Bio::RestrictionEnzyme::Analysis::UniqueFragment
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primary="catgcc",
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complement="gtacg ">,
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#<struct Bio::RestrictionEnzyme::Analysis::UniqueFragment
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primary=" c",
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complement="gg">,
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#<struct Bio::RestrictionEnzyme::Analysis::UniqueFragment
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primary="atg",
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complement="tac">,
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#<struct Bio::RestrictionEnzyme::Analysis::UniqueFragment
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primary="catg",
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complement="gtac">]
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=end
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assert_equal(["atg", "atgcatg", "c", "catg", "catgcc"], @obj_4bd.primary)
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assert_equal(["gg", "gtac", "gtacg", "tac", "tacgtac"], @obj_4bd.complement)
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end
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def test_cut_without_permutations
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assert_equal(["ag", "cag"], @obj_1d.primary)
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assert_equal(["ag"], @obj_2d.primary)
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assert_equal(["ag", "agt", "cag"], @obj_3d.primary)
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assert_equal(["atg", "catg", "catgc"], @obj_4d.primary)
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assert_equal(["atg", "catg", "catgc"], @obj_5d.primary)
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assert_equal(["a", "g"], @obj_6d.primary)
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assert_equal(["ccaggaaaaaga", "ccaggaaag", "cctggaaaagttaac", "ga"], @obj_7d.primary)
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assert_equal(["aac", "ccaggaaaaaga", "ccaggaaag", "cctggaaaagtt", "ga"], @obj_8d.primary)
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end
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def test_cut_from_bio_sequence_na
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assert_equal(["ag", "cag"], Bio::Sequence::NA.new('cagagag').cut_with_enzyme('ag^ag').primary )
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assert_equal(["ag", "cag"], Bio::Sequence::NA.new('cagagag').cut_with_enzymes('ag^ag').primary )
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assert_equal(["ag", "cag"], Bio::Sequence::NA.new('cagagag').cut_with_enzymes('ag^ag', 'EcoRII').primary )
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# Note how EcoRII needs extra padding on the beginning and ending of the
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# sequence 'ccagg' to make the match since the cut must occur between
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# two nucleotides and can not occur on the very end of the sequence.
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#
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# EcoRII:
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# :blunt: "0"
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# :c2: "5"
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# :c4: "0"
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# :c1: "-1"
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# :pattern: CCWGG
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# :len: "5"
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# :name: EcoRII
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# :c3: "0"
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# :ncuts: "2"
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#
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# -1 1 2 3 4 5
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# 5' - n^c c w g g n - 3'
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# 3' - n g g w c c^n - 5'
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#
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# (w == [at])
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assert_equal(["ag", "agccagg", "cag"], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('ag^ag', 'EcoRII').primary )
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assert_equal(["ag", "agccagg", "cag"], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('ag^ag').primary )
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assert_equal(:no_cuts_found, Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('EcoRII') )
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assert_equal(["ag", "ag", "cag", "ccaggt"], Bio::Sequence::NA.new('cagagagccaggt').cut_with_enzymes('ag^ag', 'EcoRII').primary )
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assert_equal(["ag", "agccaggt", "cag"], Bio::Sequence::NA.new('cagagagccaggt').cut_with_enzymes('ag^ag').primary )
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assert_equal(["cagagag", "ccaggt"], Bio::Sequence::NA.new('cagagagccaggt').cut_with_enzymes('EcoRII').primary )
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assert_equal(["a", "gtctctcggtcc"], Bio::Sequence::NA.new('cagagagccaggt').cut_with_enzymes('EcoRII').complement )
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end
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def test_view_ranges
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assert_equal(["ccaggaaaaaga", "ccaggaaag", "cctggaaaagttaac", "ga"], @obj_vr1.primary)
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assert_equal(["ctggtcc", "tttcggacc", "ttttcaattg", "tttttctggtcc"], @obj_vr1.complement)
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a0 = @obj_vr1[0]
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assert_equal('ga ', a0.primary)
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assert_equal('ctggtcc', a0.complement)
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assert_equal(0, a0.p_left)
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assert_equal(1, a0.p_right)
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assert_equal(0, a0.c_left)
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assert_equal(6, a0.c_right)
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a1 = @obj_vr1[1]
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assert_equal('ccaggaaaaaga ', a1.primary)
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assert_equal(' tttttctggtcc', a1.complement)
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assert_equal(2, a1.p_left)
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assert_equal(13, a1.p_right)
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assert_equal(7, a1.c_left)
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assert_equal(18, a1.c_right)
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a2 = @obj_vr1[2]
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assert_equal('ccaggaaag ', a2.primary)
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assert_equal(' tttcggacc', a2.complement)
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assert_equal(14, a2.p_left)
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assert_equal(22, a2.p_right)
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assert_equal(19, a2.c_left)
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assert_equal(27, a2.c_right)
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a3 = @obj_vr1[3]
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assert_equal('cctggaaaagttaac', a3.primary)
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assert_equal(' ttttcaattg', a3.complement)
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assert_equal(23, a3.p_left)
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assert_equal(37, a3.p_right)
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assert_equal(28, a3.c_left)
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assert_equal(37, a3.c_right)
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a4 = @obj_vr1[4]
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assert_equal(nil, a4)
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assert_equal(["ag", "ag", "cag"], @obj_vr2.primary)
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assert_equal(["gtc", "tc", "tc"], @obj_vr2.complement)
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a0 = @obj_vr2[0]
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assert_equal('cag', a0.primary)
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assert_equal('gtc', a0.complement)
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assert_equal(0, a0.p_left)
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assert_equal(2, a0.p_right)
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assert_equal(0, a0.c_left)
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assert_equal(2, a0.c_right)
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a1 = @obj_vr2[1]
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assert_equal('ag', a1.primary)
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assert_equal('tc', a1.complement)
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assert_equal(3, a1.p_left)
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assert_equal(4, a1.p_right)
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assert_equal(3, a1.c_left)
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assert_equal(4, a1.c_right)
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a2 = @obj_vr2[2]
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assert_equal('ag', a2.primary)
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assert_equal('tc', a2.complement)
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assert_equal(5, a2.p_left)
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assert_equal(6, a2.p_right)
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assert_equal(5, a2.c_left)
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assert_equal(6, a2.c_right)
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a3 = @obj_vr2[3]
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assert_equal(nil, a3)
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end
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end
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end; end
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@@ -0,0 +1,44 @@
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#
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2
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# test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb - Unit test for Bio::RestrictionEnzyme::CutSymbol
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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>
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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
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7
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#
|
8
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# $Id:$
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9
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#
|
10
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+
|
11
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require 'pathname'
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12
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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|
15
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require 'test/unit'
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16
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require 'bio/util/restriction_enzyme/cut_symbol'
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17
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|
18
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module Bio; module TestRestrictionEnzyme #:nodoc:
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+
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class TestCutSymbol < Test::Unit::TestCase #:nodoc:
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include Bio::RestrictionEnzyme::CutSymbol
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def setup
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end
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def test_methods
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assert_equal('^', cut_symbol)
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assert_equal('|', set_cut_symbol('|'))
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assert_equal('|', cut_symbol)
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assert_equal('\\|', escaped_cut_symbol)
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assert_equal(/\|/, re_cut_symbol)
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assert_equal('^', set_cut_symbol('^'))
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assert_equal(3, "abc^de" =~ re_cut_symbol)
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assert_equal(nil, "abc^de" =~ re_cut_symbol_adjacent)
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assert_equal(3, "abc^^de" =~ re_cut_symbol_adjacent)
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assert_equal(4, "a^bc^^de" =~ re_cut_symbol_adjacent)
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assert_equal(nil, "a^bc^de" =~ re_cut_symbol_adjacent)
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end
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+
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end
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end; end
|
@@ -0,0 +1,115 @@
|
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1
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#
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# test/unit/bio/util/restriction_enzyme/test_double_stranded.rb - Unit test for Bio::RestrictionEnzyme::DoubleStranded
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#
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4
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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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11
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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+
require 'test/unit'
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require 'bio/util/restriction_enzyme/double_stranded'
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require 'bio/sequence'
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module Bio; module TestRestrictionEnzyme #:nodoc:
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class TestDoubleStranded < Test::Unit::TestCase #:nodoc:
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|
23
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def setup
|
24
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@t = Bio::RestrictionEnzyme::DoubleStranded
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@cl = Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
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@s = String
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27
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@obj_1 = @t.new(@s.new('gata'), [1,2])
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@obj_2 = @t.new('gata', [1,2])
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@obj_3 = @t.new('garraxt', [1,2])
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@obj_4 = @t.new('nnnnnnngarraxtnn', [1,2])
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33
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+
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34
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@obj_5 = @t.new('garraxt', @cl.new(3,2), @cl.new(-2,-1), @cl.new(9,11))
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@obj_6 = @t.new('garraxt', @cl.new(3,2))
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36
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+
@obj_7 = @t.new('garraxt', @cl.new(3,2), @cl.new(9,11))
|
37
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+
|
38
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+
# @obj_8 = @t.new('garraxt', 3..2, 9..11)
|
39
|
+
@obj_9 = @t.new('garraxt', [3,2], [9,11])
|
40
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+
|
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@obj_10 = @t.new('garraxt', [3,2], [9,11])
|
42
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+
|
43
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@obj_11 = @t.new('n^ngar^raxtnn^n')
|
44
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+
@obj_12 = @t.new('nnnn^ngar^raxtnn^nnnn')
|
45
|
+
|
46
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+
@obj_13 = @t.new(Bio::RestrictionEnzyme.rebase['EcoRII'])
|
47
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@obj_14 = @t.new('EcoRII')
|
48
|
+
@obj_15 = @t.new('ecorii')
|
49
|
+
end
|
50
|
+
|
51
|
+
def test_primary
|
52
|
+
assert_equal('nngarraxtnnn', @obj_5.primary)
|
53
|
+
end
|
54
|
+
|
55
|
+
def test_primary_with_cut_symbols
|
56
|
+
assert_equal('n^ngar^raxtnn^n', @obj_5.primary.with_cut_symbols)
|
57
|
+
assert_equal('gar^raxt', @obj_6.primary.with_cut_symbols)
|
58
|
+
assert_equal('gar^raxtnn^n', @obj_7.primary.with_cut_symbols)
|
59
|
+
|
60
|
+
# assert_equal('gar^raxtnn^n', @obj_8.primary.with_cut_symbols)
|
61
|
+
assert_equal('gar^raxtnn^n', @obj_9.primary.with_cut_symbols)
|
62
|
+
|
63
|
+
assert_equal('gar^raxtnn^n', @obj_10.primary.with_cut_symbols)
|
64
|
+
|
65
|
+
assert_equal('n^ngar^raxtnn^n', @obj_11.primary.with_cut_symbols)
|
66
|
+
assert_equal('n^ngar^raxtnn^n', @obj_12.primary.with_cut_symbols)
|
67
|
+
|
68
|
+
assert_equal('n^ccwgg', @obj_13.primary.with_cut_symbols)
|
69
|
+
assert_equal('n^ccwgg', @obj_14.primary.with_cut_symbols)
|
70
|
+
assert_equal('n^ccwgg', @obj_15.primary.with_cut_symbols)
|
71
|
+
end
|
72
|
+
|
73
|
+
def test_complement_with_cut_symbols
|
74
|
+
assert_equal('n^ct^yytxannnn^n', @obj_5.complement.with_cut_symbols)
|
75
|
+
assert_equal('ct^yytxa', @obj_6.complement.with_cut_symbols)
|
76
|
+
assert_equal('ct^yytxannnn^n', @obj_7.complement.with_cut_symbols)
|
77
|
+
|
78
|
+
# assert_equal('ct^yytxannnn^n', @obj_8.complement.with_cut_symbols)
|
79
|
+
assert_equal('ct^yytxannnn^n', @obj_9.complement.with_cut_symbols)
|
80
|
+
|
81
|
+
assert_equal('ct^yytxannnn^n', @obj_10.complement.with_cut_symbols)
|
82
|
+
|
83
|
+
assert_equal('n^nnctyy^txan^n', @obj_11.complement.with_cut_symbols)
|
84
|
+
assert_equal('n^nnctyy^txan^n', @obj_12.complement.with_cut_symbols)
|
85
|
+
|
86
|
+
assert_equal('ggwcc^n', @obj_13.complement.with_cut_symbols)
|
87
|
+
assert_equal('ggwcc^n', @obj_14.complement.with_cut_symbols)
|
88
|
+
assert_equal('ggwcc^n', @obj_15.complement.with_cut_symbols)
|
89
|
+
end
|
90
|
+
|
91
|
+
def test_complement
|
92
|
+
assert_equal('nctyytxannnnn', @obj_5.complement)
|
93
|
+
end
|
94
|
+
|
95
|
+
def test_cut_locations
|
96
|
+
assert_equal([[4, 3], [0, 1], [10, 12]], @obj_5.cut_locations)
|
97
|
+
end
|
98
|
+
|
99
|
+
def test_cut_locations_in_enzyme_notation
|
100
|
+
assert_equal([[3, 2], [-2, -1], [9, 11]], @obj_5.cut_locations_in_enzyme_notation)
|
101
|
+
end
|
102
|
+
|
103
|
+
def test_argument_error
|
104
|
+
assert_raise(ArgumentError) { @t.new('garraxt', [3,2,9,11]) }
|
105
|
+
assert_raise(ArgumentError) { @t.new(Bio::RestrictionEnzyme.rebase['ecorii'] )}
|
106
|
+
assert_raise(ArgumentError) { @t.new(Bio::RestrictionEnzyme.rebase['EzzRII']) }
|
107
|
+
end
|
108
|
+
|
109
|
+
# NOTE
|
110
|
+
def test_to_re
|
111
|
+
end
|
112
|
+
|
113
|
+
end
|
114
|
+
|
115
|
+
end; end
|
@@ -0,0 +1,147 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/util/restriction_enzyme/test_single_strand.rb - Unit test for Bio::RestrictionEnzyme::SingleStrand
|
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__), ['..'] * 5, 'lib')).cleanpath.to_s
|
13
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
14
|
+
|
15
|
+
require 'test/unit'
|
16
|
+
require 'bio/util/restriction_enzyme/single_strand'
|
17
|
+
|
18
|
+
module Bio; module TestRestrictionEnzyme #:nodoc:
|
19
|
+
|
20
|
+
class TestSingleStrand < Test::Unit::TestCase #:nodoc:
|
21
|
+
|
22
|
+
def setup
|
23
|
+
@t = Bio::RestrictionEnzyme::SingleStrand
|
24
|
+
@cl = Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
|
25
|
+
@s = Bio::Sequence::NA
|
26
|
+
|
27
|
+
@obj_1 = @t.new(@s.new('gata'), @cl.new(-2,1,3))
|
28
|
+
@obj_2 = @t.new('gata', -2, 1, 3)
|
29
|
+
@obj_3 = @t.new('garraxt', [-2, 1, 7])
|
30
|
+
@obj_4 = @t.new('nnnnnnngarraxtnn', [-2, 1, 7])
|
31
|
+
|
32
|
+
@obj_5 = @t.new('ga^rr^axt')
|
33
|
+
@obj_6 = @t.new('^ga^rr^axt')
|
34
|
+
@obj_7 = @t.new('n^ngar^raxtnn^n')
|
35
|
+
end
|
36
|
+
|
37
|
+
def test_pattern_palindromic?
|
38
|
+
assert_equal(true, @t.new('atgcat', 1).palindromic?)
|
39
|
+
assert_equal(false, @t.new('atgcgta', 1).palindromic?)
|
40
|
+
|
41
|
+
assert_equal(false, @obj_1.palindromic?)
|
42
|
+
assert_equal(false, @obj_2.palindromic?)
|
43
|
+
assert_equal(false, @obj_3.palindromic?)
|
44
|
+
assert_equal(false, @obj_4.palindromic?)
|
45
|
+
end
|
46
|
+
|
47
|
+
def test_stripped
|
48
|
+
assert_equal('gata', @obj_1.stripped)
|
49
|
+
assert_equal('gata', @obj_2.stripped)
|
50
|
+
assert_equal('garraxt', @obj_3.stripped)
|
51
|
+
assert_equal('garraxt', @obj_4.stripped)
|
52
|
+
end
|
53
|
+
|
54
|
+
def test_pattern
|
55
|
+
assert_equal('nngata', @obj_1.pattern)
|
56
|
+
assert_equal('nngata', @obj_2.pattern)
|
57
|
+
assert_equal('nngarraxtn', @obj_3.pattern)
|
58
|
+
assert_equal('nngarraxtn', @obj_4.pattern)
|
59
|
+
|
60
|
+
assert_equal('nngata', @obj_1)
|
61
|
+
assert_equal('nngata', @obj_2)
|
62
|
+
assert_equal('nngarraxtn', @obj_3)
|
63
|
+
assert_equal('nngarraxtn', @obj_4)
|
64
|
+
end
|
65
|
+
|
66
|
+
def test_with_cut_symbols
|
67
|
+
assert_equal('n^ng^at^a', @obj_1.with_cut_symbols)
|
68
|
+
assert_equal('n^ng^at^a', @obj_2.with_cut_symbols)
|
69
|
+
assert_equal('n^ng^arraxt^n', @obj_3.with_cut_symbols)
|
70
|
+
assert_equal('n^ng^arraxt^n', @obj_4.with_cut_symbols)
|
71
|
+
end
|
72
|
+
|
73
|
+
def test_with_spaces
|
74
|
+
assert_equal('n^n g^a t^a', @obj_1.with_spaces)
|
75
|
+
assert_equal('n^n g^a t^a', @obj_2.with_spaces)
|
76
|
+
assert_equal('n^n g^a r r a x t^n', @obj_3.with_spaces)
|
77
|
+
assert_equal('n^n g^a r r a x t^n', @obj_4.with_spaces)
|
78
|
+
end
|
79
|
+
|
80
|
+
def test_cut_locations_in_enzyme_notation
|
81
|
+
assert_equal([-2,1,3], @obj_1.cut_locations_in_enzyme_notation)
|
82
|
+
assert_equal([-2,1,3], @obj_2.cut_locations_in_enzyme_notation)
|
83
|
+
assert_equal([-2,1,7], @obj_3.cut_locations_in_enzyme_notation)
|
84
|
+
assert_equal([-2,1,7], @obj_4.cut_locations_in_enzyme_notation)
|
85
|
+
|
86
|
+
assert_equal([2,4], @obj_5.cut_locations_in_enzyme_notation)
|
87
|
+
assert_equal([-1,2,4], @obj_6.cut_locations_in_enzyme_notation)
|
88
|
+
assert_equal([-2,3,9], @obj_7.cut_locations_in_enzyme_notation)
|
89
|
+
end
|
90
|
+
|
91
|
+
def test_cut_locations
|
92
|
+
assert_equal([0,2,4], @obj_1.cut_locations)
|
93
|
+
assert_equal([0,2,4], @obj_2.cut_locations)
|
94
|
+
assert_equal([0,2,8], @obj_3.cut_locations)
|
95
|
+
assert_equal([0,2,8], @obj_4.cut_locations)
|
96
|
+
|
97
|
+
assert_equal([1,3], @obj_5.cut_locations)
|
98
|
+
assert_equal([0,2,4], @obj_6.cut_locations)
|
99
|
+
assert_equal([0,4,10], @obj_7.cut_locations)
|
100
|
+
end
|
101
|
+
|
102
|
+
def test_orientation
|
103
|
+
assert_equal([5,3], @obj_1.orientation)
|
104
|
+
assert_equal([5,3], @obj_2.orientation)
|
105
|
+
assert_equal([5,3], @obj_3.orientation)
|
106
|
+
assert_equal([5,3], @obj_4.orientation)
|
107
|
+
end
|
108
|
+
|
109
|
+
def test_creation_with_no_cuts
|
110
|
+
@obj_8 = @t.new('garraxt')
|
111
|
+
assert_equal([5,3], @obj_8.orientation)
|
112
|
+
assert_equal([], @obj_8.cut_locations)
|
113
|
+
assert_equal([], @obj_8.cut_locations_in_enzyme_notation)
|
114
|
+
assert_equal('garraxt', @obj_8.pattern)
|
115
|
+
end
|
116
|
+
|
117
|
+
# NOTE
|
118
|
+
def test_to_re
|
119
|
+
end
|
120
|
+
|
121
|
+
def test_argument_error
|
122
|
+
assert_raise(ArgumentError) { @t.new('a', [0,1,2]) }
|
123
|
+
assert_raise(ArgumentError) { @t.new('a', 0,1,2,0) }
|
124
|
+
|
125
|
+
assert_raise(ArgumentError) { @t.new('a', [nil,1,2]) }
|
126
|
+
assert_raise(ArgumentError) { @t.new('a', nil,1,2,nil) }
|
127
|
+
|
128
|
+
assert_raise(ArgumentError) { @t.new('a', [1,1,2]) }
|
129
|
+
assert_raise(ArgumentError) { @t.new('a', 1,1,2,2) }
|
130
|
+
|
131
|
+
assert_raise(ArgumentError) { @t.new(1, [1,2,3]) }
|
132
|
+
assert_raise(ArgumentError) { @t.new('gaat^aca', [1,2,3]) }
|
133
|
+
assert_raise(ArgumentError) { @t.new('gaat^^aca') }
|
134
|
+
assert_raise(ArgumentError) { @t.new('z', [1,2,3]) }
|
135
|
+
|
136
|
+
assert_raise(ArgumentError) { @t.new('g', [0,1,2]) }
|
137
|
+
assert_raise(ArgumentError) { @t.new('g', 0,1,2,0) }
|
138
|
+
assert_raise(ArgumentError) { @t.new('g', [0,1,1,2]) }
|
139
|
+
assert_raise(ArgumentError) { @t.new('g', 0,1,1,2,2) }
|
140
|
+
assert_raise(ArgumentError) { @t.new(1,2,3) }
|
141
|
+
assert_raise(ArgumentError) { @t.new(1,2,'g') }
|
142
|
+
end
|
143
|
+
|
144
|
+
|
145
|
+
end
|
146
|
+
|
147
|
+
end; end
|