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 +1,147 @@
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#
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# test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb - Unit test for Bio::RestrictionEnzyme::SingleStrandComplement
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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/single_strand_complement'
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module Bio; module TestRestrictionEnzyme #:nodoc:
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class TestSingleStrandComplement < Test::Unit::TestCase #:nodoc:
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def setup
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@t = Bio::RestrictionEnzyme::SingleStrandComplement
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@cl = Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
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@s = Bio::Sequence::NA
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@obj_1 = @t.new(@s.new('gata'), @cl.new(-2,1,3))
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@obj_2 = @t.new('gata', -2, 1, 3)
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@obj_3 = @t.new('garraxt', [-2, 1, 7])
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@obj_4 = @t.new('nnnnnnngarraxtnn', [-2, 1, 7])
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@obj_5 = @t.new('ga^rr^axt')
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@obj_6 = @t.new('^ga^rr^axt')
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@obj_7 = @t.new('n^ngar^raxtnn^n')
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end
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def test_pattern_palindromic?
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assert_equal(true, @t.new('atgcat', 1).palindromic?)
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assert_equal(false, @t.new('atgcgta', 1).palindromic?)
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assert_equal(false, @obj_1.palindromic?)
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assert_equal(false, @obj_2.palindromic?)
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assert_equal(false, @obj_3.palindromic?)
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assert_equal(false, @obj_4.palindromic?)
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end
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def test_stripped
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assert_equal('gata', @obj_1.stripped)
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assert_equal('gata', @obj_2.stripped)
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assert_equal('garraxt', @obj_3.stripped)
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assert_equal('garraxt', @obj_4.stripped)
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end
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def test_pattern
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assert_equal('nngata', @obj_1.pattern)
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assert_equal('nngata', @obj_2.pattern)
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assert_equal('nngarraxtn', @obj_3.pattern)
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assert_equal('nngarraxtn', @obj_4.pattern)
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assert_equal('nngata', @obj_1)
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assert_equal('nngata', @obj_2)
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assert_equal('nngarraxtn', @obj_3)
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assert_equal('nngarraxtn', @obj_4)
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end
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def test_with_cut_symbols
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assert_equal('n^ng^at^a', @obj_1.with_cut_symbols)
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assert_equal('n^ng^at^a', @obj_2.with_cut_symbols)
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assert_equal('n^ng^arraxt^n', @obj_3.with_cut_symbols)
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assert_equal('n^ng^arraxt^n', @obj_4.with_cut_symbols)
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end
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def test_with_spaces
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assert_equal('n^n g^a t^a', @obj_1.with_spaces)
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assert_equal('n^n g^a t^a', @obj_2.with_spaces)
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assert_equal('n^n g^a r r a x t^n', @obj_3.with_spaces)
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assert_equal('n^n g^a r r a x t^n', @obj_4.with_spaces)
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end
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def test_cut_locations_in_enzyme_notation
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assert_equal([-2,1,3], @obj_1.cut_locations_in_enzyme_notation)
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assert_equal([-2,1,3], @obj_2.cut_locations_in_enzyme_notation)
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assert_equal([-2,1,7], @obj_3.cut_locations_in_enzyme_notation)
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assert_equal([-2,1,7], @obj_4.cut_locations_in_enzyme_notation)
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assert_equal([2,4], @obj_5.cut_locations_in_enzyme_notation)
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assert_equal([-1,2,4], @obj_6.cut_locations_in_enzyme_notation)
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assert_equal([-2,3,9], @obj_7.cut_locations_in_enzyme_notation)
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end
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90
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|
91
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def test_cut_locations
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assert_equal([0,2,4], @obj_1.cut_locations)
|
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assert_equal([0,2,4], @obj_2.cut_locations)
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assert_equal([0,2,8], @obj_3.cut_locations)
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assert_equal([0,2,8], @obj_4.cut_locations)
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assert_equal([1,3], @obj_5.cut_locations)
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assert_equal([0,2,4], @obj_6.cut_locations)
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assert_equal([0,4,10], @obj_7.cut_locations)
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end
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|
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def test_orientation
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assert_equal([3,5], @obj_1.orientation)
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assert_equal([3,5], @obj_2.orientation)
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assert_equal([3,5], @obj_3.orientation)
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assert_equal([3,5], @obj_4.orientation)
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end
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108
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|
109
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def test_creation_with_no_cuts
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@obj_8 = @t.new('garraxt')
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assert_equal([3,5], @obj_8.orientation)
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assert_equal([], @obj_8.cut_locations)
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assert_equal([], @obj_8.cut_locations_in_enzyme_notation)
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assert_equal('garraxt', @obj_8.pattern)
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end
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# NOTE
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def test_to_re
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end
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def test_argument_error
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assert_raise(ArgumentError) { @t.new('a', [0,1,2]) }
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assert_raise(ArgumentError) { @t.new('a', 0,1,2,0) }
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assert_raise(ArgumentError) { @t.new('a', [nil,1,2]) }
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assert_raise(ArgumentError) { @t.new('a', nil,1,2,nil) }
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128
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assert_raise(ArgumentError) { @t.new('a', [1,1,2]) }
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assert_raise(ArgumentError) { @t.new('a', 1,1,2,2) }
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assert_raise(ArgumentError) { @t.new(1, [1,2,3]) }
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assert_raise(ArgumentError) { @t.new('gaat^aca', [1,2,3]) }
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assert_raise(ArgumentError) { @t.new('gaat^^aca') }
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assert_raise(ArgumentError) { @t.new('z', [1,2,3]) }
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assert_raise(ArgumentError) { @t.new('g', [0,1,2]) }
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assert_raise(ArgumentError) { @t.new('g', 0,1,2,0) }
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assert_raise(ArgumentError) { @t.new('g', [0,1,1,2]) }
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assert_raise(ArgumentError) { @t.new('g', 0,1,1,2,2) }
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assert_raise(ArgumentError) { @t.new(1,2,3) }
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assert_raise(ArgumentError) { @t.new(1,2,'g') }
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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/test_string_formatting.rb - Unit test for Bio::RestrictionEnzyme::StringFormatting
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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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# License:: The Ruby License
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#
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8
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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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|
15
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require 'test/unit'
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16
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require 'bio/util/restriction_enzyme/string_formatting'
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17
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|
18
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module Bio; module TestRestrictionEnzyme #:nodoc:
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19
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|
20
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class TestStringFormatting < Test::Unit::TestCase #:nodoc:
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|
22
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include Bio::RestrictionEnzyme::StringFormatting
|
23
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|
24
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def setup
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25
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@t = String
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26
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@obj_1 = @t.new('gata')
|
27
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@obj_2 = @t.new('garraxt')
|
28
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@obj_3 = @t.new('gArraXT')
|
29
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@obj_4 = @t.new('nnnnnnngarraxtnn')
|
30
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+
end
|
31
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|
32
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def test_strip_padding
|
33
|
+
assert_equal('gata', strip_padding(@obj_1))
|
34
|
+
assert_equal('garraxt', strip_padding(@obj_2))
|
35
|
+
assert_equal('gArraXT', strip_padding(@obj_3))
|
36
|
+
assert_equal('garraxt', strip_padding(@obj_4))
|
37
|
+
end
|
38
|
+
|
39
|
+
def test_left_padding
|
40
|
+
assert_equal('', left_padding(@obj_1))
|
41
|
+
assert_equal('', left_padding(@obj_2))
|
42
|
+
assert_equal('', left_padding(@obj_3))
|
43
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+
assert_equal('nnnnnnn', left_padding(@obj_4))
|
44
|
+
end
|
45
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+
|
46
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+
def test_right_padding
|
47
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+
assert_equal('', right_padding(@obj_1))
|
48
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+
assert_equal('', right_padding(@obj_2))
|
49
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+
assert_equal('', right_padding(@obj_3))
|
50
|
+
assert_equal('nn', right_padding(@obj_4))
|
51
|
+
end
|
52
|
+
|
53
|
+
def test_add_spacing
|
54
|
+
assert_equal('n^n g^a t^a', add_spacing('n^ng^at^a') )
|
55
|
+
assert_equal('n^n g^a r r a x t^n', add_spacing('n^ng^arraxt^n') )
|
56
|
+
end
|
57
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+
|
58
|
+
end
|
59
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|
60
|
+
end; end
|
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|
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#
|
2
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# test/unit/bio/util/test_color_scheme.rb - Unit test for Bio::ColorScheme
|
3
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#
|
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
|
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#
|
8
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# $Id: test_color_scheme.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
|
9
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#
|
10
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+
|
11
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require 'pathname'
|
12
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4 , 'lib')).cleanpath.to_s
|
13
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+
$:.unshift(libpath) unless $:.include?(libpath)
|
14
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+
|
15
|
+
require 'test/unit'
|
16
|
+
require 'bio/util/color_scheme'
|
17
|
+
|
18
|
+
module Bio #:nodoc:
|
19
|
+
class TestColorScheme < Test::Unit::TestCase #:nodoc:
|
20
|
+
|
21
|
+
def test_buried
|
22
|
+
s = Bio::ColorScheme::Buried
|
23
|
+
assert_equal('00DC22', s['A'])
|
24
|
+
assert_equal('00BF3F', s[:c])
|
25
|
+
assert_equal(nil, s[nil])
|
26
|
+
assert_equal('FFFFFF', s['-'])
|
27
|
+
assert_equal('FFFFFF', s[7])
|
28
|
+
assert_equal('FFFFFF', s['junk'])
|
29
|
+
assert_equal('00CC32', s['t'])
|
30
|
+
end
|
31
|
+
|
32
|
+
end
|
33
|
+
end
|
@@ -0,0 +1,94 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/util/test_contingency_table.rb - Unit test for Bio::ContingencyTable
|
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: test_contingency_table.rb,v 1.4 2007/04/05 23:35:44 trevor Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
require 'pathname'
|
12
|
+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4 , 'lib')).cleanpath.to_s
|
13
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
14
|
+
|
15
|
+
require 'test/unit'
|
16
|
+
require 'bio/util/contingency_table'
|
17
|
+
|
18
|
+
module Bio #:nodoc:
|
19
|
+
class TestContingencyTable < Test::Unit::TestCase #:nodoc:
|
20
|
+
|
21
|
+
def lite_example(sequences, max_length, characters)
|
22
|
+
|
23
|
+
output = []
|
24
|
+
|
25
|
+
0.upto(max_length - 1) do |i|
|
26
|
+
(i+1).upto(max_length - 1) do |j|
|
27
|
+
ctable = Bio::ContingencyTable.new( characters )
|
28
|
+
sequences.each do |seq|
|
29
|
+
i_char = seq[i].chr
|
30
|
+
j_char = seq[j].chr
|
31
|
+
ctable.table[i_char][j_char] += 1
|
32
|
+
end
|
33
|
+
chi_square = ctable.chi_square
|
34
|
+
contingency_coefficient = ctable.contingency_coefficient
|
35
|
+
output << [(i+1), (j+1), chi_square, contingency_coefficient]
|
36
|
+
end
|
37
|
+
end
|
38
|
+
|
39
|
+
return output
|
40
|
+
end
|
41
|
+
|
42
|
+
|
43
|
+
def test_lite_example
|
44
|
+
ctable = Bio::ContingencyTable
|
45
|
+
allowed_letters = 'abcdefghijk'.split('')
|
46
|
+
|
47
|
+
seqs = Array.new
|
48
|
+
seqs << 'abcde'
|
49
|
+
seqs << 'abcde'
|
50
|
+
seqs << 'kacje'
|
51
|
+
seqs << 'aacae'
|
52
|
+
seqs << 'akcfa'
|
53
|
+
seqs << 'akcfe'
|
54
|
+
|
55
|
+
length_of_every_sequence = seqs[0].size # 5 letters long
|
56
|
+
|
57
|
+
results = lite_example(seqs, length_of_every_sequence, allowed_letters)
|
58
|
+
|
59
|
+
=begin
|
60
|
+
i j chi_square contingency_coefficient
|
61
|
+
1 2 2.4 0.534522483824849
|
62
|
+
1 3 0.0 0.0
|
63
|
+
1 4 6.0 0.707106781186548
|
64
|
+
1 5 0.24 0.196116135138184
|
65
|
+
2 3 0.0 0.0
|
66
|
+
2 4 12.0 0.816496580927726
|
67
|
+
2 5 2.4 0.534522483824849
|
68
|
+
3 4 0.0 0.0
|
69
|
+
3 5 0.0 0.0
|
70
|
+
4 5 2.4 0.534522483824849
|
71
|
+
=end
|
72
|
+
|
73
|
+
|
74
|
+
#assert_equal(2.4, results[0][2])
|
75
|
+
assert_equal('2.4', results[0][2].to_s)
|
76
|
+
assert_equal('0.534522483824849', results[0][3].to_s)
|
77
|
+
|
78
|
+
assert_equal('12.0', results[5][2].to_s)
|
79
|
+
assert_equal('0.816496580927726', results[5][3].to_s)
|
80
|
+
|
81
|
+
assert_equal('2.4', results[9][2].to_s)
|
82
|
+
assert_equal('0.534522483824849', results[9][3].to_s)
|
83
|
+
|
84
|
+
ctable = Bio::ContingencyTable.new
|
85
|
+
ctable.table['a']['t'] = 4
|
86
|
+
ctable.table['a']['g'] = 2
|
87
|
+
ctable.table['g']['t'] = 3
|
88
|
+
assert_equal('1.28571428571429', ctable.chi_square.to_s)
|
89
|
+
assert_equal(ctable.column_sum_all, ctable.row_sum_all)
|
90
|
+
assert_equal(ctable.column_sum_all, ctable.table_sum_all)
|
91
|
+
end
|
92
|
+
|
93
|
+
end
|
94
|
+
end
|
@@ -0,0 +1,42 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/util/restriction_enzyme.rb - Unit test for Bio::RestrictionEnzyme
|
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__), ['..'] * 4, 'lib')).cleanpath.to_s
|
13
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
14
|
+
|
15
|
+
require 'test/unit'
|
16
|
+
require 'bio/util/restriction_enzyme.rb'
|
17
|
+
|
18
|
+
module Bio; module TestRestrictionEnzyme #:nodoc:
|
19
|
+
|
20
|
+
class TestRestrictionEnzyme < Test::Unit::TestCase #:nodoc:
|
21
|
+
|
22
|
+
def setup
|
23
|
+
@t = Bio::RestrictionEnzyme
|
24
|
+
end
|
25
|
+
|
26
|
+
def test_rebase
|
27
|
+
assert_equal(@t.rebase.respond_to?(:enzymes), true)
|
28
|
+
assert_not_nil @t.rebase['AarI']
|
29
|
+
assert_nil @t.rebase['blah']
|
30
|
+
end
|
31
|
+
|
32
|
+
def test_enzyme_name
|
33
|
+
assert_equal(@t.enzyme_name?('AarI'), true)
|
34
|
+
assert_equal(@t.enzyme_name?('atgc'), false)
|
35
|
+
assert_equal(@t.enzyme_name?('aari'), true)
|
36
|
+
assert_equal(@t.enzyme_name?('EcoRI'), true)
|
37
|
+
assert_equal(@t.enzyme_name?('EcoooRI'), false)
|
38
|
+
end
|
39
|
+
|
40
|
+
end
|
41
|
+
|
42
|
+
end; end
|
@@ -0,0 +1,245 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/util/test_sirna.rb - Unit test for Bio::SiRNA.
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2005 Mitsuteru C. Nakap <n@bioruby.org>
|
5
|
+
# License:: The Ruby License
|
6
|
+
#
|
7
|
+
# $Id: test_sirna.rb,v 1.4 2007/04/05 23:35:44 trevor Exp $
|
8
|
+
#
|
9
|
+
|
10
|
+
require 'pathname'
|
11
|
+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4 , 'lib')).cleanpath.to_s
|
12
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
13
|
+
|
14
|
+
require 'test/unit'
|
15
|
+
require 'bio/util/sirna'
|
16
|
+
|
17
|
+
module Bio
|
18
|
+
|
19
|
+
RANDOM_SEQ = "ctttcggtgcggacgtaaggagtattcctgtactaactaaatggagttaccaaggtaggaccacggtaaaatcgcgagcagcctcgatacaagcgttgtgctgaagcctatcgctgacctgaaggggggcgtaagcaaggcagcggttcaccttcatcagttctgctagaaatcacctagcaccccttatcatccgcgtcaggtccattacccttcccattatgtcggactcaattgaggtgcttgtgaacttatacttgaatccaaaacgtctactgtattggcgactaaaaagcacttgtggggagtcggcttgatcagcctccattagggccaggcactgaggatcatccagttaacgtcagattcaaggtctggctcttagcactcggagttgcac"
|
20
|
+
|
21
|
+
class TestSiRNANew < Test::Unit::TestCase
|
22
|
+
def test_new
|
23
|
+
naseq = Bio::Sequence::NA.new(RANDOM_SEQ)
|
24
|
+
assert(Bio::SiRNA.new(naseq))
|
25
|
+
assert(Bio::SiRNA.new(naseq, 21))
|
26
|
+
assert(Bio::SiRNA.new(naseq, 21, 60.0))
|
27
|
+
assert(Bio::SiRNA.new(naseq, 21, 60.0, 40.0))
|
28
|
+
assert_raise(ArgumentError) { Bio::SiRNA.new(naseq, 21, 60.0, 40.0, 10.0) }
|
29
|
+
end
|
30
|
+
|
31
|
+
end
|
32
|
+
|
33
|
+
class TestSiRNA < Test::Unit::TestCase
|
34
|
+
def setup
|
35
|
+
naseq = Bio::Sequence::NA.new(RANDOM_SEQ)
|
36
|
+
@obj = Bio::SiRNA.new(naseq)
|
37
|
+
end
|
38
|
+
|
39
|
+
def test_antisense_size
|
40
|
+
assert_equal(21, @obj.antisense_size)
|
41
|
+
end
|
42
|
+
|
43
|
+
def test_max_gc_percent
|
44
|
+
assert_equal(60.0, @obj.max_gc_percent)
|
45
|
+
end
|
46
|
+
|
47
|
+
def test_min_gc_percent
|
48
|
+
assert_equal(40.0, @obj.min_gc_percent)
|
49
|
+
end
|
50
|
+
|
51
|
+
def test_uitei?
|
52
|
+
target = "aaGaa"
|
53
|
+
assert_equal(false, @obj.uitei?(target))
|
54
|
+
target = "aaAaa"
|
55
|
+
assert_equal(false, @obj.uitei?(target))
|
56
|
+
target = "G" * 9
|
57
|
+
assert_equal(false, @obj.uitei?(target))
|
58
|
+
end
|
59
|
+
|
60
|
+
def test_reynolds?
|
61
|
+
target = "G" * 9
|
62
|
+
assert_equal(false, @obj.reynolds?(target))
|
63
|
+
target = "aaaaAaaaaaaUaaAaaaaaAaa"
|
64
|
+
assert_equal(true, @obj.reynolds?(target))
|
65
|
+
end
|
66
|
+
|
67
|
+
def test_uitei
|
68
|
+
assert(@obj.uitei)
|
69
|
+
end
|
70
|
+
|
71
|
+
def test_reynolds
|
72
|
+
assert(@obj.reynolds)
|
73
|
+
end
|
74
|
+
|
75
|
+
def test_design
|
76
|
+
assert(@obj.design)
|
77
|
+
end
|
78
|
+
|
79
|
+
|
80
|
+
def test_design_uitei
|
81
|
+
assert(@obj.design('uitei'))
|
82
|
+
end
|
83
|
+
|
84
|
+
def test_design_reynolds
|
85
|
+
assert(@obj.design('reynolds'))
|
86
|
+
end
|
87
|
+
end
|
88
|
+
|
89
|
+
class TestSiRNAPairNew < Test::Unit::TestCase
|
90
|
+
def test_new
|
91
|
+
target = ""
|
92
|
+
sense = ""
|
93
|
+
antisense = ""
|
94
|
+
start = 0
|
95
|
+
stop = 1
|
96
|
+
rule = 'rule'
|
97
|
+
gc_percent = 60.0
|
98
|
+
assert_raise(ArgumentError) { Bio::SiRNA::Pair.new(target, sense, antisense, start, stop, rule) }
|
99
|
+
assert(Bio::SiRNA::Pair.new(target, sense, antisense, start, stop, rule, gc_percent))
|
100
|
+
assert_raise(ArgumentError) { Bio::SiRNA::Pair.new(target, sense, antisense, start, stop, rule, gc_percent, "") }
|
101
|
+
end
|
102
|
+
end
|
103
|
+
|
104
|
+
|
105
|
+
class TestSiRNAPair < Test::Unit::TestCase
|
106
|
+
def setup
|
107
|
+
naseq = Bio::Sequence::NA.new(RANDOM_SEQ)
|
108
|
+
@obj = Bio::SiRNA.new(naseq).design.first
|
109
|
+
end
|
110
|
+
|
111
|
+
def test_target
|
112
|
+
assert_equal("gcggacguaaggaguauuccugu", @obj.target)
|
113
|
+
end
|
114
|
+
|
115
|
+
def test_sense
|
116
|
+
assert_equal("ggacguaaggaguauuccugu", @obj.sense)
|
117
|
+
end
|
118
|
+
|
119
|
+
def test_antisense
|
120
|
+
assert_equal("aggaauacuccuuacguccgc", @obj.antisense)
|
121
|
+
end
|
122
|
+
|
123
|
+
def test_start
|
124
|
+
assert_equal(9, @obj.start)
|
125
|
+
end
|
126
|
+
|
127
|
+
def test_stop
|
128
|
+
assert_equal(32, @obj.stop)
|
129
|
+
end
|
130
|
+
|
131
|
+
def test_rule
|
132
|
+
assert_equal("uitei", @obj.rule)
|
133
|
+
end
|
134
|
+
|
135
|
+
def test_gc_percent
|
136
|
+
assert_equal(52.0, @obj.gc_percent)
|
137
|
+
end
|
138
|
+
|
139
|
+
def test_report
|
140
|
+
report =<<END
|
141
|
+
### siRNA
|
142
|
+
Start: 9
|
143
|
+
Stop: 32
|
144
|
+
Rule: uitei
|
145
|
+
GC %: 52
|
146
|
+
Target: GCGGACGUAAGGAGUAUUCCUGU
|
147
|
+
Sense: GGACGUAAGGAGUAUUCCUGU
|
148
|
+
Antisense: CGCCUGCAUUCCUCAUAAGGA
|
149
|
+
END
|
150
|
+
assert_equal(report, @obj.report)
|
151
|
+
end
|
152
|
+
end
|
153
|
+
|
154
|
+
class TestShRNANew < Test::Unit::TestCase
|
155
|
+
def test_new
|
156
|
+
pair = ""
|
157
|
+
assert(Bio::SiRNA::ShRNA.new(pair))
|
158
|
+
assert_raise(ArgumentError) { Bio::SiRNA::ShRNA.new }
|
159
|
+
assert_raise(ArgumentError) { Bio::SiRNA::ShRNA.new(pair, "") }
|
160
|
+
end
|
161
|
+
end
|
162
|
+
|
163
|
+
class TestShRNA < Test::Unit::TestCase
|
164
|
+
def setup
|
165
|
+
naseq = Bio::Sequence::NA.new(RANDOM_SEQ)
|
166
|
+
sirna = Bio::SiRNA.new(naseq)
|
167
|
+
pairs = sirna.design
|
168
|
+
@obj = Bio::SiRNA::ShRNA.new(pairs.first)
|
169
|
+
end
|
170
|
+
|
171
|
+
def test_top_strand
|
172
|
+
@obj.design
|
173
|
+
assert_equal("caccggacguaaggaguauuccugugtgtgctgtccacaggaauacuccuuacgucc", @obj.top_strand)
|
174
|
+
end
|
175
|
+
|
176
|
+
def test_top_strand_class
|
177
|
+
@obj.design
|
178
|
+
assert_equal(Bio::Sequence::NA, @obj.top_strand.class)
|
179
|
+
end
|
180
|
+
|
181
|
+
def test_top_strand_nil
|
182
|
+
assert_equal(nil, @obj.top_strand)
|
183
|
+
end
|
184
|
+
|
185
|
+
def test_bottom_strand
|
186
|
+
@obj.design
|
187
|
+
assert_equal("aaaaggacguaaggaguauuccuguggacagcacacacaggaauacuccuuacgucc", @obj.bottom_strand)
|
188
|
+
end
|
189
|
+
|
190
|
+
def test_bottom_strand_class
|
191
|
+
@obj.design
|
192
|
+
assert_equal(Bio::Sequence::NA, @obj.bottom_strand.class)
|
193
|
+
end
|
194
|
+
|
195
|
+
def test_bottom_strand_nil
|
196
|
+
assert_equal(nil, @obj.bottom_strand)
|
197
|
+
end
|
198
|
+
|
199
|
+
def test_design
|
200
|
+
assert(@obj.design)
|
201
|
+
end
|
202
|
+
|
203
|
+
def test_design_BLOCK_IT
|
204
|
+
assert_raises(NotImplementedError) { @obj.design('BLOCK-IT') }
|
205
|
+
end
|
206
|
+
|
207
|
+
def test_blocK_it
|
208
|
+
assert_equal("aaaaggacguaaggaguauuccuguggacagcacacacaggaauacuccuuacgucc", @obj.block_it)
|
209
|
+
end
|
210
|
+
|
211
|
+
def test_blocK_it_BLOCK_iT
|
212
|
+
assert_equal("aaaaggacguaaggaguauuccuguggacagcacacacaggaauacuccuuacgucc", @obj.block_it)
|
213
|
+
end
|
214
|
+
|
215
|
+
def test_blocK_it_BLOCK_IT
|
216
|
+
assert_raises(NotImplementedError) { @obj.block_it('BLOCK-IT') }
|
217
|
+
end
|
218
|
+
|
219
|
+
def test_blocK_it_piGene
|
220
|
+
assert_equal("aaaaggacguaaggaguauuccuguggacagcacacacaggaauacuccuuacgucc", @obj.block_it('piGENE'))
|
221
|
+
end
|
222
|
+
|
223
|
+
def test_blocK_it_
|
224
|
+
assert_raises(NotImplementedError) { @obj.block_it("") }
|
225
|
+
end
|
226
|
+
|
227
|
+
def test_report
|
228
|
+
report =<<END
|
229
|
+
### shRNA
|
230
|
+
Top strand shRNA (57 nt):
|
231
|
+
5'-CACCGGACGUAAGGAGUAUUCCUGUGTGTGCTGTCCACAGGAAUACUCCUUACGUCC-3'
|
232
|
+
Bottom strand shRNA (57 nt):
|
233
|
+
3'-CCUGCAUUCCUCAUAAGGACACACACGACAGGUGUCCUUAUGAGGAAUGCAGGAAAA-5'
|
234
|
+
END
|
235
|
+
#@obj.design
|
236
|
+
@obj.block_it
|
237
|
+
assert_equal(report, @obj.report)
|
238
|
+
end
|
239
|
+
|
240
|
+
def test_report_before_design
|
241
|
+
assert_raises(NoMethodError) { @obj.report }
|
242
|
+
end
|
243
|
+
end
|
244
|
+
|
245
|
+
end
|