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 +1,599 @@
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#
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# test/unit/bio/test_location.rb - Unit test for Bio::Location and Bio::Locations
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#
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# Copyright:: Copyright (C) 2004 Moses Hohman <mmhohman@northwestern.edu>
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# 2008 Naohisa Goto <ng@bioruby.org>
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# License:: The Ruby License
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#
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# $Id:$
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#
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'test/unit'
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require 'bio/location'
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module Bio
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class TestLocations < Test::Unit::TestCase
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def test_should_not_modify_argument
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assert_nothing_raised {
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Locations.new(' 123..456 '.freeze)
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}
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end
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def test_normal
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loc = Locations.new('123..456')
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assert_equal([123, 456], loc.span)
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assert_equal(123..456, loc.range)
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assert_equal(1, loc[0].strand)
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end
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def test_hat
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loc = Locations.new('754^755')
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assert_equal([754, 755], loc.span, "span wrong")
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assert_equal(754..755, loc.range, "range wrong")
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assert_equal(1, loc[0].strand, "strand wrong")
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assert_equal(true, loc[0].carat, "carat wrong")
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end
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def test_complement
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loc = Locations.new('complement(53^54)')
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assert_equal([53, 54], loc.span, "span wrong")
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assert_equal(53..54, loc.range, "range wrong")
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assert_equal(-1, loc[0].strand, "strand wrong")
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assert_equal(true, loc[0].carat, "carat wrong")
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end
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def test_replace_single_base
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loc = Locations.new('replace(4792^4793,"a")')
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assert_equal("a", loc[0].sequence)
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end
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end
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class TestLocationsRoundTrip < Test::Unit::TestCase
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class TestLoc
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def initialize(*arg)
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@xref_id = nil
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@lt = nil
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@from = nil
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@gt = nil
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@to = nil
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@carat = nil
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@sequence = nil
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@strand = 1
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arg.each do |x|
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case x
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when :complement
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@strand = -1
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when '<'
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@lt = true
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when '>'
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@gt = true
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when '..'
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# do nothing
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when '^'
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@carat = true
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when Integer
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@from ||= x
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@to = x
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when Hash
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@sequence ||= x[:sequence]
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else
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@xref_id ||= x
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end
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end
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end
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def to_location
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loc = Bio::Location.new
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loc.from = @from
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loc.to = @to
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loc.gt = @gt
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loc.lt = @lt
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loc.strand = @strand
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loc.xref_id = @xref_id
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loc.sequence = @sequence
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loc.carat = @carat
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loc
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end
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end #class TestLoc
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TestData =
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[
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# (C) n^m
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#
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# * [AB015179] 754^755
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[ 'AB015179', '754^755',
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nil,
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TestLoc.new(754, '^', 755)
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],
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# * [AF179299] complement(53^54)
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# (see below)
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# * [CELXOL1ES] replace(4480^4481,"")
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# (see below)
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# * [ECOUW87] replace(4792^4793,"a")
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# (see below)
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# * [APLPCII] replace(1905^1906,"acaaagacaccgccctacgcc")
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# (see below)
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# (n.m) and one-of() are not supported.
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# (D) (n.m)
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#
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# * [HACSODA] 157..(800.806)
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# * [HALSODB] (67.68)..(699.703)
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# * [AP001918] (45934.45974)..46135
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# * [BACSPOJ] <180..(731.761)
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# * [BBU17998] (88.89)..>1122
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# * [ECHTGA] complement((1700.1708)..(1715.1721))
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# * [ECPAP17] complement(<22..(255.275))
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# * [LPATOVGNS] complement((64.74)..1525)
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# * [PIP404CG] join((8298.8300)..10206,1..855)
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# * [BOVMHDQBY4] join(M30006.1:(392.467)..575,M30005.1:415..681,M30004.1:129..410,M30004.1:907..1017,521..534)
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# * [HUMMIC2A] replace((651.655)..(651.655),"")
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# * [HUMSOD102] order(L44135.1:(454.445)..>538,<1..181)
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#
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# (n.m) and one-of() are not supported.
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# (E) one-of
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#
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# * [ECU17136] one-of(898,900)..983
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# * [CELCYT1A] one-of(5971..6308,5971..6309)
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# * [DMU17742] 8050..one-of(10731,10758,10905,11242)
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# * [PFU27807] one-of(623,627,632)..one-of(628,633,637)
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# * [BTBAINH1] one-of(845,953,963,1078,1104)..1354
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# * [ATU39449] join(one-of(969..1094,970..1094,995..1094,1018..1094),1518..1587,1726..2119,2220..2833,2945..3215)
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#
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# (F) join, order, group
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#
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# * [AB037374S2] join(AB037374.1:1..177,1..807)
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[ 'AB037374S2', 'join(AB037374.1:1..177,1..807)',
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nil,
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TestLoc.new('AB037374.1', 1, 177),
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TestLoc.new(1, 807)
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],
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# * [AP000001] join(complement(1..61),complement(AP000007.1:252907..253505))
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# (see below)
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# * [ASNOS11] join(AF130124.1:<2563..2964,AF130125.1:21..157,AF130126.1:12..174,AF130127.1:21..112,AF130128.1:21..162,AF130128.1:281..595,AF130128.1:661..842,AF130128.1:916..1030,AF130129.1:21..115,AF130130.1:21..165,AF130131.1:21..125,AF130132.1:21..428,AF130132.1:492..746,AF130133.1:21..168,AF130133.1:232..401,AF130133.1:475..906,AF130133.1:970..1107,AF130133.1:1176..1367,21..>128)
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[ 'ASNOS11', 'join(AF130124.1:<2563..2964,AF130125.1:21..157,AF130126.1:12..174,AF130127.1:21..112,AF130128.1:21..162,AF130128.1:281..595,AF130128.1:661..842,AF130128.1:916..1030,AF130129.1:21..115,AF130130.1:21..165,AF130131.1:21..125,AF130132.1:21..428,AF130132.1:492..746,AF130133.1:21..168,AF130133.1:232..401,AF130133.1:475..906,AF130133.1:970..1107,AF130133.1:1176..1367,21..>128)',
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nil,
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TestLoc.new('AF130124.1', '<', 2563, 2964),
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TestLoc.new('AF130125.1', 21, 157),
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TestLoc.new('AF130126.1', 12, 174),
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TestLoc.new('AF130127.1', 21, 112),
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TestLoc.new('AF130128.1', 21, 162),
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TestLoc.new('AF130128.1', 281, 595),
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TestLoc.new('AF130128.1', 661, 842),
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TestLoc.new('AF130128.1', 916, 1030),
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TestLoc.new('AF130129.1', 21, 115),
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TestLoc.new('AF130130.1', 21, 165),
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TestLoc.new('AF130131.1', 21, 125),
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TestLoc.new('AF130132.1', 21, 428),
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TestLoc.new('AF130132.1', 492, 746),
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TestLoc.new('AF130133.1', 21, 168),
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TestLoc.new('AF130133.1', 232, 401),
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TestLoc.new('AF130133.1', 475, 906),
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TestLoc.new('AF130133.1', 970, 1107),
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TestLoc.new('AF130133.1', 1176, 1367),
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TestLoc.new(21, '>', 128)
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],
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# * [AARPOB2] order(AF194507.1:<1..510,1..>871)
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# (see below)
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# * [AF006691] order(912..1918,20410..21416)
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[ 'AF006691', 'order(912..1918,20410..21416)',
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:order,
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TestLoc.new(912,1918),
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TestLoc.new(20410,21416)
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],
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# * [AF024666] complement(order(13965..14892,18919..19224))
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# (Note that in older version of GenBank, the order of
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# "order" and "complement" was different.)
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# * [AF024666] order(complement(18919..19224),complement(13965..14892))
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[ 'AF024666', 'complement(order(13965..14892,18919..19224))',
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:complement_order,
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TestLoc.new(13965, 14892),
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TestLoc.new(18919, 19224)
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],
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# * [AF264948] order(27066..27076,27089..27099,27283..27314,27330..27352)
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[ 'AF264948',
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'order(27066..27076,27089..27099,27283..27314,27330..27352)',
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:order,
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TestLoc.new(27066, 27076),
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TestLoc.new(27089, 27099),
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TestLoc.new(27283, 27314),
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TestLoc.new(27330, 27352)
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],
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# * [D63363] order(3..26,complement(964..987))
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# (see below)
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# * [ECOCURLI2] order(complement(1009..>1260),complement(AF081827.1:<1..177))
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[ 'ECOCURLI2',
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'order(complement(1009..>1260),complement(AF081827.1:<1..177))',
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:order,
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TestLoc.new(:complement, 1009, '>', 1260),
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TestLoc.new(:complement, 'AF081827.1', '<', 1, 177)
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],
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# * [S72388S2] order(join(S72388.1:757..911,S72388.1:609..1542),1..>139)
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# (not supported)
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# * [HEYRRE07] order(complement(1..38),complement(M82666.1:1..140),complement(M82665.1:1..176),complement(M82664.1:1..215),complement(M82663.1:1..185),complement(M82662.1:1..49),complement(M82661.1:1..133))
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[ 'HEYRRE07',
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'order(complement(1..38),complement(M82666.1:1..140),complement(M82665.1:1..176),complement(M82664.1:1..215),complement(M82663.1:1..185),complement(M82662.1:1..49),complement(M82661.1:1..133))',
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:order,
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TestLoc.new(:complement, 1, 38),
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TestLoc.new(:complement, 'M82666.1', 1, 140),
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TestLoc.new(:complement, 'M82665.1', 1, 176),
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TestLoc.new(:complement, 'M82664.1', 1, 215),
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TestLoc.new(:complement, 'M82663.1', 1, 185),
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TestLoc.new(:complement, 'M82662.1', 1, 49),
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TestLoc.new(:complement, 'M82661.1', 1, 133)
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],
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# * [COL11A1G34] order(AF101079.1:558..1307,AF101080.1:1..749,AF101081.1:1..898,AF101082.1:1..486,AF101083.1:1..942,AF101084.1:1..1734,AF101085.1:1..2385,AF101086.1:1..1813,AF101087.1:1..2287,AF101088.1:1..1073,AF101089.1:1..989,AF101090.1:1..5017,AF101091.1:1..3401,AF101092.1:1..1225,AF101093.1:1..1072,AF101094.1:1..989,AF101095.1:1..1669,AF101096.1:1..918,AF101097.1:1..1114,AF101098.1:1..1074,AF101099.1:1..1709,AF101100.1:1..986,AF101101.1:1..1934,AF101102.1:1..1699,AF101103.1:1..940,AF101104.1:1..2330,AF101105.1:1..4467,AF101106.1:1..1876,AF101107.1:1..2465,AF101108.1:1..1150,AF101109.1:1..1170,AF101110.1:1..1158,AF101111.1:1..1193,1..611)
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[ 'COL11A1G34',
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|
+
'order(AF101079.1:558..1307,AF101080.1:1..749,AF101081.1:1..898,AF101082.1:1..486,AF101083.1:1..942,AF101084.1:1..1734,AF101085.1:1..2385,AF101086.1:1..1813,AF101087.1:1..2287,AF101088.1:1..1073,AF101089.1:1..989,AF101090.1:1..5017,AF101091.1:1..3401,AF101092.1:1..1225,AF101093.1:1..1072,AF101094.1:1..989,AF101095.1:1..1669,AF101096.1:1..918,AF101097.1:1..1114,AF101098.1:1..1074,AF101099.1:1..1709,AF101100.1:1..986,AF101101.1:1..1934,AF101102.1:1..1699,AF101103.1:1..940,AF101104.1:1..2330,AF101105.1:1..4467,AF101106.1:1..1876,AF101107.1:1..2465,AF101108.1:1..1150,AF101109.1:1..1170,AF101110.1:1..1158,AF101111.1:1..1193,1..611)',
|
249
|
+
:order,
|
250
|
+
TestLoc.new('AF101079.1', 558, 1307),
|
251
|
+
TestLoc.new('AF101080.1', 1, 749),
|
252
|
+
TestLoc.new('AF101081.1', 1, 898),
|
253
|
+
TestLoc.new('AF101082.1', 1, 486),
|
254
|
+
TestLoc.new('AF101083.1', 1, 942),
|
255
|
+
TestLoc.new('AF101084.1', 1, 1734),
|
256
|
+
TestLoc.new('AF101085.1', 1, 2385),
|
257
|
+
TestLoc.new('AF101086.1', 1, 1813),
|
258
|
+
TestLoc.new('AF101087.1', 1, 2287),
|
259
|
+
TestLoc.new('AF101088.1', 1, 1073),
|
260
|
+
TestLoc.new('AF101089.1', 1, 989),
|
261
|
+
TestLoc.new('AF101090.1', 1, 5017),
|
262
|
+
TestLoc.new('AF101091.1', 1, 3401),
|
263
|
+
TestLoc.new('AF101092.1', 1, 1225),
|
264
|
+
TestLoc.new('AF101093.1', 1, 1072),
|
265
|
+
TestLoc.new('AF101094.1', 1, 989),
|
266
|
+
TestLoc.new('AF101095.1', 1, 1669),
|
267
|
+
TestLoc.new('AF101096.1', 1, 918),
|
268
|
+
TestLoc.new('AF101097.1', 1, 1114),
|
269
|
+
TestLoc.new('AF101098.1', 1, 1074),
|
270
|
+
TestLoc.new('AF101099.1', 1, 1709),
|
271
|
+
TestLoc.new('AF101100.1', 1, 986),
|
272
|
+
TestLoc.new('AF101101.1', 1, 1934),
|
273
|
+
TestLoc.new('AF101102.1', 1, 1699),
|
274
|
+
TestLoc.new('AF101103.1', 1, 940),
|
275
|
+
TestLoc.new('AF101104.1', 1, 2330),
|
276
|
+
TestLoc.new('AF101105.1', 1, 4467),
|
277
|
+
TestLoc.new('AF101106.1', 1, 1876),
|
278
|
+
TestLoc.new('AF101107.1', 1, 2465),
|
279
|
+
TestLoc.new('AF101108.1', 1, 1150),
|
280
|
+
TestLoc.new('AF101109.1', 1, 1170),
|
281
|
+
TestLoc.new('AF101110.1', 1, 1158),
|
282
|
+
TestLoc.new('AF101111.1', 1, 1193),
|
283
|
+
TestLoc.new(1, 611)
|
284
|
+
],
|
285
|
+
|
286
|
+
# group() are found in the COMMENT field only (in GenBank 122.0)
|
287
|
+
#
|
288
|
+
# gbpat2.seq: FT repeat_region group(598..606,611..619)
|
289
|
+
# gbpat2.seq: FT repeat_region group(8..16,1457..1464).
|
290
|
+
# gbpat2.seq: FT variation group(t1,t2)
|
291
|
+
# gbpat2.seq: FT variation group(t1,t3)
|
292
|
+
# gbpat2.seq: FT variation group(t1,t2,t3)
|
293
|
+
# gbpat2.seq: FT repeat_region group(11..202,203..394)
|
294
|
+
# gbpri9.seq:COMMENT Residues reported = 'group(1..2145);'.
|
295
|
+
#
|
296
|
+
|
297
|
+
# (G) ID:location
|
298
|
+
# * [AARPOB2] order(AF194507.1:<1..510,1..>871)
|
299
|
+
[ 'AARPOB2', 'order(AF194507.1:<1..510,1..>871)',
|
300
|
+
:order,
|
301
|
+
TestLoc.new('AF194507.1', '<', 1, 510),
|
302
|
+
TestLoc.new(1, '>', 871)
|
303
|
+
],
|
304
|
+
# * [AF178221S4] join(AF178221.1:<1..60,AF178222.1:1..63,AF178223.1:1..42,1..>90)
|
305
|
+
[ 'AF178221S4',
|
306
|
+
'join(AF178221.1:<1..60,AF178222.1:1..63,AF178223.1:1..42,1..>90)',
|
307
|
+
nil,
|
308
|
+
TestLoc.new('AF178221.1', '<', 1, 60),
|
309
|
+
TestLoc.new('AF178222.1', 1, 63),
|
310
|
+
TestLoc.new('AF178223.1', 1, 42),
|
311
|
+
TestLoc.new( 1, '>', 90)
|
312
|
+
],
|
313
|
+
# * [BOVMHDQBY4] join(M30006.1:(392.467)..575,M30005.1:415..681,M30004.1:129..410,M30004.1:907..1017,521..534)
|
314
|
+
# not supported
|
315
|
+
|
316
|
+
# * [HUMSOD102] order(L44135.1:(454.445)..>538,<1..181)
|
317
|
+
# not supported
|
318
|
+
|
319
|
+
# * [SL16SRRN1] order(<1..>267,X67092.1:<1..>249,X67093.1:<1..>233)
|
320
|
+
[ 'SL16SRRN1',
|
321
|
+
'order(<1..>267,X67092.1:<1..>249,X67093.1:<1..>233)',
|
322
|
+
:order,
|
323
|
+
TestLoc.new( '<', 1, '>', 267),
|
324
|
+
TestLoc.new('X67092.1', '<', 1, '>', 249),
|
325
|
+
TestLoc.new('X67093.1', '<', 1, '>', 233)
|
326
|
+
],
|
327
|
+
|
328
|
+
# (I) <, >
|
329
|
+
# * [A5U48871] <1..>318
|
330
|
+
[ 'A5U48871', '<1..>318',
|
331
|
+
nil,
|
332
|
+
TestLoc.new('<', 1, '>', 318)
|
333
|
+
],
|
334
|
+
|
335
|
+
# * [AA23SRRNP] <1..388
|
336
|
+
[ 'AA23SRRNP', '<1..388',
|
337
|
+
nil,
|
338
|
+
TestLoc.new('<', 1, 388)
|
339
|
+
],
|
340
|
+
|
341
|
+
# * [AA23SRRNP] 503..>1010
|
342
|
+
[ 'AA23SRRNP', '503..>1010',
|
343
|
+
nil,
|
344
|
+
TestLoc.new(503, '>', 1010)
|
345
|
+
],
|
346
|
+
|
347
|
+
# * [AAM5961] complement(<1..229)
|
348
|
+
[ 'AAM5961', 'complement(<1..229)',
|
349
|
+
nil,
|
350
|
+
TestLoc.new(:complement, '<', 1, 229)
|
351
|
+
],
|
352
|
+
|
353
|
+
# * [AAM5961] complement(5231..>5598)
|
354
|
+
[ 'AAM5961', 'complement(5231..>5598)',
|
355
|
+
nil,
|
356
|
+
TestLoc.new(:complement, 5231, '>', 5598)
|
357
|
+
],
|
358
|
+
|
359
|
+
# * [AF043934] join(<1,60..99,161..241,302..370,436..594,676..887,993..1141,1209..1329,1387..1559,1626..1646,1708..>1843)
|
360
|
+
[ 'AF043934', 'join(<1,60..99,161..241,302..370,436..594,676..887,993..1141,1209..1329,1387..1559,1626..1646,1708..>1843)',
|
361
|
+
nil,
|
362
|
+
TestLoc.new('<', 1),
|
363
|
+
TestLoc.new(60, 99),
|
364
|
+
TestLoc.new(161,241),
|
365
|
+
TestLoc.new(302,370),
|
366
|
+
TestLoc.new(436,594),
|
367
|
+
TestLoc.new(676,887),
|
368
|
+
TestLoc.new(993,1141),
|
369
|
+
TestLoc.new(1209,1329),
|
370
|
+
TestLoc.new(1387,1559),
|
371
|
+
TestLoc.new(1626,1646),
|
372
|
+
TestLoc.new(1708, '>', 1843)
|
373
|
+
],
|
374
|
+
|
375
|
+
# * [BACSPOJ] <180..(731.761)
|
376
|
+
# not supported
|
377
|
+
|
378
|
+
# * [BBU17998] (88.89)..>1122
|
379
|
+
# not supported
|
380
|
+
|
381
|
+
# * [AARPOB2] order(AF194507.1:<1..510,1..>871)
|
382
|
+
# (see above)
|
383
|
+
|
384
|
+
# * [SL16SRRN1] order(<1..>267,X67092.1:<1..>249,X67093.1:<1..>233)
|
385
|
+
# (see above)
|
386
|
+
|
387
|
+
# (J) complement
|
388
|
+
# * [AF179299] complement(53^54)
|
389
|
+
[ 'AF179299', 'complement(53^54)',
|
390
|
+
nil,
|
391
|
+
TestLoc.new(:complement, 53, '^', 54)
|
392
|
+
],
|
393
|
+
|
394
|
+
# * [AP000001] join(complement(1..61),complement(AP000007.1:252907..253505))
|
395
|
+
[ 'AP000001',
|
396
|
+
'join(complement(1..61),complement(AP000007.1:252907..253505))',
|
397
|
+
nil,
|
398
|
+
TestLoc.new(:complement, 1, 61),
|
399
|
+
TestLoc.new(:complement, 'AP000007.1', 252907, 253505)
|
400
|
+
],
|
401
|
+
|
402
|
+
# * [AF209868S2] order(complement(1..>308),complement(AF209868.1:75..336))
|
403
|
+
[ 'AF209868S2',
|
404
|
+
'order(complement(1..>308),complement(AF209868.1:75..336))',
|
405
|
+
:order,
|
406
|
+
TestLoc.new(:complement, 1, '>', 308),
|
407
|
+
TestLoc.new(:complement, 'AF209868.1', 75, 336)
|
408
|
+
],
|
409
|
+
|
410
|
+
# * [CPPLCG] complement(<1..(1093.1098))
|
411
|
+
# not supported
|
412
|
+
|
413
|
+
# * [D63363] order(3..26,complement(964..987))
|
414
|
+
[ 'D63363]', 'order(3..26,complement(964..987))',
|
415
|
+
:order,
|
416
|
+
TestLoc.new(3,26),
|
417
|
+
TestLoc.new(:complement, 964, 987)
|
418
|
+
],
|
419
|
+
|
420
|
+
# * [ECHTGA] complement((1700.1708)..(1715.1721))
|
421
|
+
# not supported
|
422
|
+
|
423
|
+
# * [ECOUXW] complement(order(1636..1641,1658..1663))
|
424
|
+
# (Note that in older version of GenBank, the order of
|
425
|
+
# "order" and "complement" was different.)
|
426
|
+
# * [ECOUXW] order(complement(1658..1663),complement(1636..1641))
|
427
|
+
#
|
428
|
+
[ 'ECOUXW', 'complement(order(1636..1641,1658..1663))',
|
429
|
+
:complement_order,
|
430
|
+
TestLoc.new(:complement, 1636, 1641),
|
431
|
+
TestLoc.new(:complement, 1658, 1663)
|
432
|
+
],
|
433
|
+
|
434
|
+
# * [LPATOVGNS] complement((64.74)..1525)
|
435
|
+
# not supported
|
436
|
+
|
437
|
+
# * [AF129075] complement(join(71606..71829,75327..75446,76039..76203,76282..76353,76914..77029,77114..77201,77276..77342,78138..78316,79755..79892,81501..81562,81676..81856,82341..82490,84208..84287,85032..85122,88316..88403))
|
438
|
+
[ 'AF129075',
|
439
|
+
'complement(join(71606..71829,75327..75446,76039..76203,76282..76353,76914..77029,77114..77201,77276..77342,78138..78316,79755..79892,81501..81562,81676..81856,82341..82490,84208..84287,85032..85122,88316..88403))',
|
440
|
+
:complement_join,
|
441
|
+
TestLoc.new(71606,71829),
|
442
|
+
TestLoc.new(75327,75446),
|
443
|
+
TestLoc.new(76039,76203),
|
444
|
+
TestLoc.new(76282,76353),
|
445
|
+
TestLoc.new(76914,77029),
|
446
|
+
TestLoc.new(77114,77201),
|
447
|
+
TestLoc.new(77276,77342),
|
448
|
+
TestLoc.new(78138,78316),
|
449
|
+
TestLoc.new(79755,79892),
|
450
|
+
TestLoc.new(81501,81562),
|
451
|
+
TestLoc.new(81676,81856),
|
452
|
+
TestLoc.new(82341,82490),
|
453
|
+
TestLoc.new(84208,84287),
|
454
|
+
TestLoc.new(85032,85122),
|
455
|
+
TestLoc.new(88316,88403)
|
456
|
+
],
|
457
|
+
|
458
|
+
# * [ZFDYST2] join(AF137145.1:<1..18,complement(<1..99))
|
459
|
+
[ 'ZFDYST2', 'join(AF137145.1:<1..18,complement(<1..99))',
|
460
|
+
nil,
|
461
|
+
TestLoc.new('AF137145.1', '<', 1, 18),
|
462
|
+
TestLoc.new(:complement, '<', 1, 99)
|
463
|
+
],
|
464
|
+
|
465
|
+
# (K) replace
|
466
|
+
# * [CSU27710] replace(64,"A")
|
467
|
+
[ 'CSU27710', 'replace(64,"a")',
|
468
|
+
nil,
|
469
|
+
TestLoc.new(64, :sequence => "a")
|
470
|
+
],
|
471
|
+
|
472
|
+
# * [CELXOL1ES] replace(5256,"t")
|
473
|
+
[ 'CELXOL1ES', 'replace(5256,"t")',
|
474
|
+
nil,
|
475
|
+
TestLoc.new(5256,:sequence => "t")
|
476
|
+
],
|
477
|
+
|
478
|
+
# * [ANICPC] replace(1..468,"")
|
479
|
+
[ 'ANICPC', 'replace(1..468,"")',
|
480
|
+
nil,
|
481
|
+
TestLoc.new(1, 468, :sequence => "")
|
482
|
+
],
|
483
|
+
|
484
|
+
# * [CSU27710] replace(67..68,"GC")
|
485
|
+
[ 'CSU27710', 'replace(67..68,"gc")',
|
486
|
+
nil,
|
487
|
+
TestLoc.new(67, 68, :sequence => "gc")
|
488
|
+
],
|
489
|
+
|
490
|
+
# * [CELXOL1ES] replace(4480^4481,"") <= ? only one case in GenBank 122.0
|
491
|
+
[ 'CELXOL1ES', 'replace(4480^4481,"")',
|
492
|
+
nil,
|
493
|
+
TestLoc.new(4480, '^', 4481, :sequence => "")
|
494
|
+
],
|
495
|
+
|
496
|
+
# * [ECOUW87] replace(4792^4793,"a")
|
497
|
+
[ 'ECOUW87', 'replace(4792^4793,"a")',
|
498
|
+
nil,
|
499
|
+
TestLoc.new(4792, '^', 4793, :sequence => "a")
|
500
|
+
],
|
501
|
+
|
502
|
+
# * [CEU34893] replace(1..22,"ggttttaacccagttactcaag")
|
503
|
+
[ 'CEU34893', 'replace(1..22,"ggttttaacccagttactcaag")',
|
504
|
+
nil,
|
505
|
+
TestLoc.new(1, 22, :sequence => "ggttttaacccagttactcaag")
|
506
|
+
],
|
507
|
+
|
508
|
+
# * [APLPCII] replace(1905^1906,"acaaagacaccgccctacgcc")
|
509
|
+
[ 'APLPCII', 'replace(1905^1906,"acaaagacaccgccctacgcc")',
|
510
|
+
nil,
|
511
|
+
TestLoc.new(1905, '^', 1906, :sequence => "acaaagacaccgccctacgcc")
|
512
|
+
],
|
513
|
+
|
514
|
+
# * [MBDR3S1] replace(1400..>9281,"")
|
515
|
+
[ 'MBDR3S1', 'replace(1400..>9281,"")',
|
516
|
+
nil,
|
517
|
+
TestLoc.new(1400, '>', 9281, :sequence => "")
|
518
|
+
],
|
519
|
+
|
520
|
+
# * [HUMMHDPB1F] replace(complement(36..37),"ttc")
|
521
|
+
[ 'HUMMHDPB1F', 'replace(complement(36..37),"ttc")',
|
522
|
+
nil,
|
523
|
+
TestLoc.new(:complement, 36, 37, :sequence => "ttc")
|
524
|
+
],
|
525
|
+
|
526
|
+
# * [HUMMIC2A] replace((651.655)..(651.655),"")
|
527
|
+
# not supported
|
528
|
+
|
529
|
+
# * [LEIMDRPGP] replace(1..1554,"L01572")
|
530
|
+
# not supported
|
531
|
+
|
532
|
+
# * [TRBND3] replace(376..395,"atttgtgtgtggtaatta")
|
533
|
+
[ 'TRBND3', 'replace(376..395,"atttgtgtgtggtaatta")',
|
534
|
+
nil,
|
535
|
+
TestLoc.new(376, 395, :sequence => "atttgtgtgtggtaatta")
|
536
|
+
],
|
537
|
+
|
538
|
+
# * [TRBND3] replace(376..395,"atttgtgtgggtaatttta")
|
539
|
+
# * [TRBND3] replace(376..395,"attttgttgttgttttgttttgaatta")
|
540
|
+
# * [TRBND3] replace(376..395,"atgtgtggtgaatta")
|
541
|
+
# * [TRBND3] replace(376..395,"atgtgtgtggtaatta")
|
542
|
+
# * [TRBND3] replace(376..395,"gatttgttgtggtaatttta")
|
543
|
+
# (see above)
|
544
|
+
|
545
|
+
# * [MSU09460] replace(193,"t")
|
546
|
+
[ 'MSU09460', 'replace(193,"t")',
|
547
|
+
nil,
|
548
|
+
TestLoc.new(193, :sequence => "t")
|
549
|
+
],
|
550
|
+
|
551
|
+
# * [HUMMAGE12X] replace(3002..3003, "GC")
|
552
|
+
[ 'HUMMAGE12X', 'replace(3002..3003,"gc")',
|
553
|
+
nil,
|
554
|
+
TestLoc.new(3002, 3003, :sequence => "gc")
|
555
|
+
],
|
556
|
+
|
557
|
+
# * [ADR40FIB] replace(510..520, "taatcctaccg")
|
558
|
+
[ 'ADR40FIB', 'replace(510..520,"taatcctaccg")',
|
559
|
+
nil,
|
560
|
+
TestLoc.new(510, 520, :sequence => "taatcctaccg")
|
561
|
+
],
|
562
|
+
|
563
|
+
# * [RATDYIIAAB] replace(1306..1443,"aagaacatccacggagtcagaactgggctcttcacgccggatttggcgttcgaggccattgtgaaaaagcaggcaatgcaccagcaagctcagttcctacccctgcgtggacctggttatccaggagctaatcagtacagttaggtggtcaagctgaaagagccctgtctgaaa")
|
564
|
+
[ 'RATDYIIAAB', 'replace(1306..1443,"aagaacatccacggagtcagaactgggctcttcacgccggatttggcgttcgaggccattgtgaaaaagcaggcaatgcaccagcaagctcagttcctacccctgcgtggacctggttatccaggagctaatcagtacagttaggtggtcaagctgaaagagccctgtctgaaa")',
|
565
|
+
nil,
|
566
|
+
TestLoc.new(1306, 1443, :sequence => "aagaacatccacggagtcagaactgggctcttcacgccggatttggcgttcgaggccattgtgaaaaagcaggcaatgcaccagcaagctcagttcctacccctgcgtggacctggttatccaggagctaatcagtacagttaggtggtcaagctgaaagagccctgtctgaaa")
|
567
|
+
]
|
568
|
+
] #TestData=
|
569
|
+
|
570
|
+
def test_locations_to_s
|
571
|
+
TestData.each do |a|
|
572
|
+
label = a[0]
|
573
|
+
str = a[1]
|
574
|
+
op = a[2]
|
575
|
+
locs = a[3..-1]
|
576
|
+
locs.collect! { |x| x.to_location }
|
577
|
+
case op
|
578
|
+
when :complement_join, :complement_order
|
579
|
+
locs.reverse!
|
580
|
+
locs.each { |loc| loc.strand = -1 }
|
581
|
+
op = op.to_s.sub(/complement_/, '').intern
|
582
|
+
end
|
583
|
+
locations = Bio::Locations.new(locs)
|
584
|
+
locations.operator = op if op
|
585
|
+
assert_equal(str, locations.to_s, "to_s: wrong for #{label}")
|
586
|
+
end
|
587
|
+
end
|
588
|
+
|
589
|
+
def test_locations_roundtrip
|
590
|
+
TestData.each do |a|
|
591
|
+
label = a[0]
|
592
|
+
str = a[1]
|
593
|
+
locations = Bio::Locations.new(str)
|
594
|
+
assert_equal(str, locations.to_s, "round trip: wrong for #{label}")
|
595
|
+
end
|
596
|
+
end
|
597
|
+
|
598
|
+
end
|
599
|
+
end
|