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 +1,130 @@
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#
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# bio/util/restriction_enzyme/double_stranded/aligned_strands.rb - Align two SingleStrand objects
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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: aligned_strands.rb,v 1.6 2007/07/16 19:28:48 k Exp $
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#
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require 'bio/util/restriction_enzyme'
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module Bio
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class RestrictionEnzyme
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class DoubleStranded
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# Align two SingleStrand objects and return a Result
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# object with +primary+ and +complement+ accessors.
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#
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class AlignedStrands
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extend CutSymbol
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extend StringFormatting
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# The object returned for alignments
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Result = Struct.new(:primary, :complement)
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# Pad and align two String objects without cut symbols.
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#
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# This will look for the sub-sequence without left and right 'n' padding
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# and re-apply 'n' padding to both strings on both sides equal to the
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# maximum previous padding on that side.
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#
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# The sub-sequences stripped of left and right 'n' padding must be of equal
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# length.
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#
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# Example:
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# AlignedStrands.align('nngattacannnnn', 'nnnnnctaatgtnn') # =>
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# <struct Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands::Result
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# primary="nnnnngattacannnnn",
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# complement="nnnnnctaatgtnnnnn">
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#
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# ---
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# *Arguments*
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# * +a+: Primary strand
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# * +b+: Complementary strand
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# *Returns*:: +Result+ object with equal padding on both strings
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def self.align(a, b)
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a = a.to_s
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b = b.to_s
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validate_input( strip_padding(a), strip_padding(b) )
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left = [left_padding(a), left_padding(b)].sort.last
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right = [right_padding(a), right_padding(b)].sort.last
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p = left + strip_padding(a) + right
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c = left + strip_padding(b) + right
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Result.new(p,c)
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end
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# Pad and align two String objects with cut symbols.
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#
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# Example:
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# AlignedStrands.with_cuts('nngattacannnnn', 'nnnnnctaatgtnn', [0, 10, 12], [0, 2, 12]) # =>
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# <struct Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands::Result
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# primary="n n n n^n g a t t a c a n n^n n^n",
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# complement="n^n n^n n c t a a t g t n^n n n n">
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#
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# Notes:
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# * To make room for the cut symbols each nucleotide is spaced out.
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# * This is meant to be able to handle multiple cuts and completely
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# unrelated cutsites on the two strands, therefore no biological
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# algorithm assumptions (shortcuts) are made.
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#
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# The sequences stripped of left and right 'n' padding must be of equal
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# length.
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#
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# ---
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# *Arguments*
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# * +a+: Primary sequence
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# * +b+: Complementary sequence
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# * +a_cuts+: Primary strand cut locations in 0-based index notation
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# * +b_cuts+: Complementary strand cut locations in 0-based index notation
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# *Returns*:: +Result+ object with equal padding on both strings and spacing between bases
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def self.align_with_cuts(a,b,a_cuts,b_cuts)
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a = a.to_s
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b = b.to_s
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validate_input( strip_padding(a), strip_padding(b) )
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+
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a_left, a_right = left_padding(a), right_padding(a)
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b_left, b_right = left_padding(b), right_padding(b)
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+
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left_diff = a_left.length - b_left.length
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right_diff = a_right.length - b_right.length
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+
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(right_diff > 0) ? (b_right += 'n' * right_diff) : (a_right += 'n' * right_diff.abs)
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+
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a_adjust = b_adjust = 0
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+
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if left_diff > 0
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b_left += 'n' * left_diff
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b_adjust = left_diff
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else
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a_left += 'n' * left_diff.abs
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a_adjust = left_diff.abs
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end
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+
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a = a_left + strip_padding(a) + a_right
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b = b_left + strip_padding(b) + b_right
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+
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a_cuts.sort.reverse.each { |c| a.insert(c+1+a_adjust, cut_symbol) }
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b_cuts.sort.reverse.each { |c| b.insert(c+1+b_adjust, cut_symbol) }
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Result.new( add_spacing(a), add_spacing(b) )
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end
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#########
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protected
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#########
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def self.validate_input(a,b)
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unless a.size == b.size
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err = "Result sequences are not the same size. Does not align sequences with differing lengths after strip_padding.\n"
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err += "#{a.size}, #{a.inspect}\n"
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err += "#{b.size}, #{b.inspect}"
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raise ArgumentError, err
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end
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end
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end # AlignedStrands
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end # DoubleStranded
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end # RestrictionEnzyme
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end # Bio
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#
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# bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb - Stores a cut location pair in 0-based index notation
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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: cut_location_pair.rb,v 1.9 2007/07/16 19:28:48 k Exp $
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#
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require 'bio/util/restriction_enzyme'
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module Bio
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class RestrictionEnzyme
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class DoubleStranded
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# Stores a single cut location pair in 0-based index notation for use with
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# DoubleStranded enzyme sequences.
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#
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class CutLocationPair < Array
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# Location of the cut on the primary strand.
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# Corresponds - or 'pairs' - to the complement cut.
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# A value of +nil+ is an explicit representation of 'no cut'.
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attr_reader :primary
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# Location of the cut on the complementary strand.
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# Corresponds - or 'pairs' - to the primary cut.
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# A value of +nil+ is an explicit representation of 'no cut'.
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attr_reader :complement
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# CutLocationPair constructor.
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#
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# Stores a single cut location pair in 0-based index notation for use with
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# DoubleStranded enzyme sequences.
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#
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# Example:
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# clp = CutLocationPair.new(3,2)
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# clp.primary # 3
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# clp.complement # 2
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#
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# ---
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# *Arguments*
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# * +pair+: May be two values represented as an Array, a Range, or a
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# combination of Integer and nil values. The first value
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# represents a cut on the primary strand, the second represents
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# a cut on the complement strand.
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# *Returns*:: nothing
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def initialize( *pair )
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a = b = nil
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if pair[0].kind_of? Array
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a,b = init_with_array( pair[0] )
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# no idea why this barfs without the second half during test/runner.rb
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# are there two Range objects running around?
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elsif pair[0].kind_of? Range or (pair[0].class.to_s == 'Range')
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#elsif pair[0].kind_of? Range
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a,b = init_with_array( [pair[0].first, pair[0].last] )
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|
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elsif pair[0].kind_of? Integer or pair[0].kind_of? NilClass
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a,b = init_with_array( [pair[0], pair[1]] )
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else
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raise ArgumentError, "#{pair[0].class} is an invalid class type to initalize CutLocationPair."
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end
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|
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super( [a,b] )
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@primary = a
|
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@complement = b
|
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return
|
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end
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+
|
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#########
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protected
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#########
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|
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def init_with_array( ary )
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validate_1(ary)
|
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a = ary.shift
|
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ary.empty? ? b = nil : b = ary.shift
|
81
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validate_2(a,b)
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[a,b]
|
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end
|
84
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+
|
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def validate_1( ary )
|
86
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unless ary.size == 1 or ary.size == 2
|
87
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raise ArgumentError, "Must be one or two elements."
|
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end
|
89
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end
|
90
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+
|
91
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def validate_2( a, b )
|
92
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if (a != nil and a < 0) or (b != nil and b < 0)
|
93
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raise ArgumentError, "0-based index notation only. Negative values are illegal."
|
94
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end
|
95
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+
|
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if a == nil and b == nil
|
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raise ArgumentError, "Neither strand has a cut. Ambiguous."
|
98
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end
|
99
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end
|
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end # CutLocationPair
|
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end # DoubleStranded
|
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end # RestrictionEnzyme
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end # Bio
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#
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# bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb - Inherits from DoubleStranded::CutLocationPair
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#
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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# License:: The Ruby License
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#
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# $Id: cut_location_pair_in_enzyme_notation.rb,v 1.7 2007/07/16 19:28:48 k Exp $
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#
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require 'bio/util/restriction_enzyme'
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|
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module Bio
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class RestrictionEnzyme
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class DoubleStranded
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# Inherits from DoubleStranded::CutLocationPair , stores the cut location pair in
|
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# enzyme notation instead of 0-based.
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#
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class CutLocationPairInEnzymeNotation < CutLocationPair
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#########
|
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protected
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24
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#########
|
25
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|
26
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def validate_2( a, b )
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27
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if (a == 0) or (b == 0)
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raise ArgumentError, "Enzyme index notation only. 0 values are illegal."
|
29
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end
|
30
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|
31
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if a == nil and b == nil
|
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raise ArgumentError, "Neither strand has a cut. Ambiguous."
|
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end
|
34
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end
|
35
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end # CutLocationPair
|
36
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end # DoubleStranded
|
37
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end # RestrictionEnzyme
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end # Bio
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@@ -0,0 +1,76 @@
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#
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2
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# bio/util/restriction_enzyme/double_stranded/cut_locations.rb - Contains an Array of CutLocationPair objects
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3
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#
|
4
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
|
5
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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6
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# License:: The Ruby License
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7
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#
|
8
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# $Id: cut_locations.rb,v 1.6 2007/07/16 19:28:48 k Exp $
|
9
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#
|
10
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+
|
11
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require 'bio/util/restriction_enzyme'
|
12
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+
|
13
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module Bio
|
14
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class RestrictionEnzyme
|
15
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class DoubleStranded
|
16
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+
|
17
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# Contains an +Array+ of CutLocationPair objects.
|
18
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#
|
19
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class CutLocations < Array
|
20
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+
|
21
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# CutLocations constructor.
|
22
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+
#
|
23
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# Contains an +Array+ of CutLocationPair objects.
|
24
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+
#
|
25
|
+
# Example:
|
26
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+
# clp1 = CutLocationPair.new(3,2)
|
27
|
+
# clp2 = CutLocationPair.new(7,9)
|
28
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+
# pairs = CutLocations.new(clp1, clp2)
|
29
|
+
#
|
30
|
+
# ---
|
31
|
+
# *Arguments*
|
32
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+
# * +args+: Any number of +CutLocationPair+ objects
|
33
|
+
# *Returns*:: nothing
|
34
|
+
def initialize(*args)
|
35
|
+
validate_args(args)
|
36
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+
super(args)
|
37
|
+
end
|
38
|
+
|
39
|
+
# Returns an +Array+ of locations of cuts on the primary strand
|
40
|
+
#
|
41
|
+
# ---
|
42
|
+
# *Arguments*
|
43
|
+
# * _none_
|
44
|
+
# *Returns*:: +Array+ of locations of cuts on the primary strand
|
45
|
+
def primary
|
46
|
+
self.collect {|a| a[0]}
|
47
|
+
end
|
48
|
+
|
49
|
+
# Returns an +Array+ of locations of cuts on the complementary strand
|
50
|
+
#
|
51
|
+
# ---
|
52
|
+
# *Arguments*
|
53
|
+
# * _none_
|
54
|
+
# *Returns*:: +Array+ of locations of cuts on the complementary strand
|
55
|
+
def complement
|
56
|
+
self.collect {|a| a[1]}
|
57
|
+
end
|
58
|
+
|
59
|
+
#########
|
60
|
+
protected
|
61
|
+
#########
|
62
|
+
|
63
|
+
def validate_args(args)
|
64
|
+
args.each do |a|
|
65
|
+
unless a.class == Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
|
66
|
+
err = "Not a CutLocationPair\n"
|
67
|
+
err += "class: #{a.class}\n"
|
68
|
+
err += "inspect: #{a.inspect}"
|
69
|
+
raise ArgumentError, err
|
70
|
+
end
|
71
|
+
end
|
72
|
+
end
|
73
|
+
end # CutLocations
|
74
|
+
end # DoubleStranded
|
75
|
+
end # RestrictionEnzyme
|
76
|
+
end # Bio
|
@@ -0,0 +1,107 @@
|
|
1
|
+
#
|
2
|
+
# bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb - Inherits from DoubleStrand::CutLocations
|
3
|
+
#
|
4
|
+
# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
|
5
|
+
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: cut_locations_in_enzyme_notation.rb,v 1.7 2007/07/16 19:28:48 k Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
require 'bio/util/restriction_enzyme'
|
12
|
+
|
13
|
+
module Bio
|
14
|
+
class RestrictionEnzyme
|
15
|
+
class DoubleStranded
|
16
|
+
|
17
|
+
# Inherits from DoubleStranded::CutLocations. Contains CutLocationPairInEnzymeNotation objects.
|
18
|
+
# Adds helper methods to convert from enzyme index notation to 0-based array index notation.
|
19
|
+
#
|
20
|
+
class CutLocationsInEnzymeNotation < CutLocations
|
21
|
+
|
22
|
+
# Returns +Array+ of locations of cuts on the primary
|
23
|
+
# strand in 0-based array index notation.
|
24
|
+
#
|
25
|
+
# ---
|
26
|
+
# *Arguments*
|
27
|
+
# * _none_
|
28
|
+
# *Returns*:: +Array+ of locations of cuts on the primary strand in 0-based array index notation.
|
29
|
+
def primary_to_array_index
|
30
|
+
helper_for_to_array_index(self.primary)
|
31
|
+
end
|
32
|
+
|
33
|
+
# Returns +Array+ of locations of cuts on the complementary
|
34
|
+
# strand in 0-based array index notation.
|
35
|
+
#
|
36
|
+
# ---
|
37
|
+
# *Arguments*
|
38
|
+
# * _none_
|
39
|
+
# *Returns*:: +Array+ of locations of cuts on the complementary strand in 0-based array index notation.
|
40
|
+
def complement_to_array_index
|
41
|
+
helper_for_to_array_index(self.complement)
|
42
|
+
end
|
43
|
+
|
44
|
+
# Returns the contents of the present CutLocationsInEnzymeNotation object as
|
45
|
+
# a CutLocations object with the contents converted from enzyme notation
|
46
|
+
# to 0-based array index notation.
|
47
|
+
#
|
48
|
+
# ---
|
49
|
+
# *Arguments*
|
50
|
+
# * _none_
|
51
|
+
# *Returns*:: +CutLocations+
|
52
|
+
def to_array_index
|
53
|
+
unless self.primary_to_array_index.size == self.complement_to_array_index.size
|
54
|
+
err = "Primary and complement strand cut locations are not available in equal numbers.\n"
|
55
|
+
err += "primary: #{self.primary_to_array_index.inspect}\n"
|
56
|
+
err += "primary.size: #{self.primary_to_array_index.size}\n"
|
57
|
+
err += "complement: #{self.complement_to_array_index.inspect}\n"
|
58
|
+
err += "complement.size: #{self.complement_to_array_index.size}"
|
59
|
+
raise IndexError, err
|
60
|
+
end
|
61
|
+
a = self.primary_to_array_index.zip(self.complement_to_array_index)
|
62
|
+
CutLocations.new( *a.collect {|cl| CutLocationPair.new(cl)} )
|
63
|
+
end
|
64
|
+
|
65
|
+
#########
|
66
|
+
protected
|
67
|
+
#########
|
68
|
+
|
69
|
+
def helper_for_to_array_index(a)
|
70
|
+
minimum = (self.primary + self.complement).flatten
|
71
|
+
minimum.delete(nil)
|
72
|
+
minimum = minimum.sort.first
|
73
|
+
|
74
|
+
return [] if minimum == nil # no elements
|
75
|
+
|
76
|
+
if minimum < 0
|
77
|
+
calc = lambda do |n|
|
78
|
+
unless n == nil
|
79
|
+
n -= 1 unless n < 0
|
80
|
+
n += minimum.abs
|
81
|
+
end
|
82
|
+
n
|
83
|
+
end
|
84
|
+
else
|
85
|
+
calc = lambda do |n|
|
86
|
+
n -= 1 unless n == nil
|
87
|
+
n
|
88
|
+
end
|
89
|
+
end
|
90
|
+
|
91
|
+
a.collect(&calc)
|
92
|
+
end
|
93
|
+
|
94
|
+
def validate_args(args)
|
95
|
+
args.each do |a|
|
96
|
+
unless a.class == Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
|
97
|
+
err = "Not a CutLocationPairInEnzymeNotation\n"
|
98
|
+
err += "class: #{a.class}\n"
|
99
|
+
err += "inspect: #{a.inspect}"
|
100
|
+
raise TypeError, err
|
101
|
+
end
|
102
|
+
end
|
103
|
+
end
|
104
|
+
end # CutLocationsInEnzymeNotation
|
105
|
+
end # DoubleStranded
|
106
|
+
end # RestrictionEnzyme
|
107
|
+
end # Bio
|