wwood-bioruby 1.2.11
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- data/README.rdoc +205 -0
- data/README_DEV.rdoc +285 -0
- data/VERSION.yml +4 -0
- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +293 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/lib/bio.rb +306 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +505 -0
- data/lib/bio/appl/blast/ddbj.rb +142 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/genomenet.rb +263 -0
- data/lib/bio/appl/blast/ncbioptions.rb +220 -0
- data/lib/bio/appl/blast/remote.rb +105 -0
- data/lib/bio/appl/blast/report.rb +767 -0
- data/lib/bio/appl/blast/rexml.rb +144 -0
- data/lib/bio/appl/blast/rpsblast.rb +277 -0
- data/lib/bio/appl/blast/wublast.rb +635 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blat/report.rb +530 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta.rb +235 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/gcg/msf.rb +212 -0
- data/lib/bio/appl/gcg/seq.rb +195 -0
- data/lib/bio/appl/genscan/report.rb +552 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/hmmer/report.rb +683 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/paml/baseml.rb +95 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/codeml.rb +242 -0
- data/lib/bio/appl/paml/codeml/rates.rb +67 -0
- data/lib/bio/appl/paml/codeml/report.rb +67 -0
- data/lib/bio/appl/paml/common.rb +348 -0
- data/lib/bio/appl/paml/common_report.rb +38 -0
- data/lib/bio/appl/paml/yn00.rb +103 -0
- data/lib/bio/appl/paml/yn00/report.rb +32 -0
- data/lib/bio/appl/phylip/alignment.rb +133 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/psort/report.rb +542 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +124 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sosui/report.rb +151 -0
- data/lib/bio/appl/spidey/report.rb +593 -0
- data/lib/bio/appl/targetp/report.rb +267 -0
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +231 -0
- data/lib/bio/command.rb +593 -0
- data/lib/bio/compat/features.rb +157 -0
- data/lib/bio/compat/references.rb +128 -0
- data/lib/bio/data/aa.rb +353 -0
- data/lib/bio/data/codontable.rb +722 -0
- data/lib/bio/data/na.rb +223 -0
- data/lib/bio/db.rb +329 -0
- data/lib/bio/db/aaindex.rb +357 -0
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +67 -0
- data/lib/bio/db/biosql/sequence.rb +508 -0
- data/lib/bio/db/embl/common.rb +352 -0
- data/lib/bio/db/embl/embl.rb +500 -0
- data/lib/bio/db/embl/embl_to_biosequence.rb +85 -0
- data/lib/bio/db/embl/format_embl.rb +190 -0
- data/lib/bio/db/embl/sptr.rb +1283 -0
- data/lib/bio/db/embl/swissprot.rb +42 -0
- data/lib/bio/db/embl/trembl.rb +41 -0
- data/lib/bio/db/embl/uniprot.rb +42 -0
- data/lib/bio/db/fantom.rb +597 -0
- data/lib/bio/db/fasta.rb +410 -0
- data/lib/bio/db/fasta/defline.rb +532 -0
- data/lib/bio/db/fasta/fasta_to_biosequence.rb +63 -0
- data/lib/bio/db/fasta/format_fasta.rb +97 -0
- data/lib/bio/db/genbank/common.rb +307 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/format_genbank.rb +187 -0
- data/lib/bio/db/genbank/genbank.rb +250 -0
- data/lib/bio/db/genbank/genbank_to_biosequence.rb +86 -0
- data/lib/bio/db/genbank/genpept.rb +60 -0
- data/lib/bio/db/genbank/refseq.rb +18 -0
- data/lib/bio/db/gff.rb +1846 -0
- data/lib/bio/db/go.rb +481 -0
- data/lib/bio/db/kegg/brite.rb +41 -0
- data/lib/bio/db/kegg/compound.rb +131 -0
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +148 -0
- data/lib/bio/db/kegg/expression.rb +155 -0
- data/lib/bio/db/kegg/genes.rb +263 -0
- data/lib/bio/db/kegg/genome.rb +241 -0
- data/lib/bio/db/kegg/glycan.rb +166 -0
- data/lib/bio/db/kegg/keggtab.rb +357 -0
- data/lib/bio/db/kegg/kgml.rb +256 -0
- data/lib/bio/db/kegg/orthology.rb +136 -0
- data/lib/bio/db/kegg/reaction.rb +82 -0
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +107 -0
- data/lib/bio/db/medline.rb +326 -0
- data/lib/bio/db/nbrf.rb +191 -0
- data/lib/bio/db/newick.rb +658 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +29 -0
- data/lib/bio/db/pdb/atom.rb +77 -0
- data/lib/bio/db/pdb/chain.rb +210 -0
- data/lib/bio/db/pdb/chemicalcomponent.rb +224 -0
- data/lib/bio/db/pdb/model.rb +148 -0
- data/lib/bio/db/pdb/pdb.rb +1911 -0
- data/lib/bio/db/pdb/residue.rb +176 -0
- data/lib/bio/db/pdb/utils.rb +399 -0
- data/lib/bio/db/prosite.rb +597 -0
- data/lib/bio/db/rebase.rb +456 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/db/url.rb +42 -0
- data/lib/bio/feature.rb +139 -0
- data/lib/bio/io/biosql/biodatabase.rb +64 -0
- data/lib/bio/io/biosql/bioentry.rb +29 -0
- data/lib/bio/io/biosql/bioentry_dbxref.rb +11 -0
- data/lib/bio/io/biosql/bioentry_path.rb +12 -0
- data/lib/bio/io/biosql/bioentry_qualifier_value.rb +10 -0
- data/lib/bio/io/biosql/bioentry_reference.rb +10 -0
- data/lib/bio/io/biosql/bioentry_relationship.rb +10 -0
- data/lib/bio/io/biosql/biosequence.rb +11 -0
- data/lib/bio/io/biosql/comment.rb +7 -0
- data/lib/bio/io/biosql/config/database.yml +20 -0
- data/lib/bio/io/biosql/dbxref.rb +13 -0
- data/lib/bio/io/biosql/dbxref_qualifier_value.rb +12 -0
- data/lib/bio/io/biosql/location.rb +32 -0
- data/lib/bio/io/biosql/location_qualifier_value.rb +11 -0
- data/lib/bio/io/biosql/ontology.rb +10 -0
- data/lib/bio/io/biosql/reference.rb +9 -0
- data/lib/bio/io/biosql/seqfeature.rb +32 -0
- data/lib/bio/io/biosql/seqfeature_dbxref.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_path.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_qualifier_value.rb +20 -0
- data/lib/bio/io/biosql/seqfeature_relationship.rb +11 -0
- data/lib/bio/io/biosql/taxon.rb +12 -0
- data/lib/bio/io/biosql/taxon_name.rb +9 -0
- data/lib/bio/io/biosql/term.rb +27 -0
- data/lib/bio/io/biosql/term_dbxref.rb +11 -0
- data/lib/bio/io/biosql/term_path.rb +12 -0
- data/lib/bio/io/biosql/term_relationship.rb +13 -0
- data/lib/bio/io/biosql/term_relationship_term.rb +11 -0
- data/lib/bio/io/biosql/term_synonym.rb +10 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +638 -0
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +163 -0
- data/lib/bio/io/fetch.rb +195 -0
- data/lib/bio/io/flatfile.rb +482 -0
- data/lib/bio/io/flatfile/autodetection.rb +545 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/buffer.rb +237 -0
- data/lib/bio/io/flatfile/index.rb +1381 -0
- data/lib/bio/io/flatfile/indexer.rb +805 -0
- data/lib/bio/io/flatfile/splitter.rb +297 -0
- data/lib/bio/io/higet.rb +73 -0
- data/lib/bio/io/hinv.rb +442 -0
- data/lib/bio/io/keggapi.rb +805 -0
- data/lib/bio/io/ncbirest.rb +733 -0
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +307 -0
- data/lib/bio/io/registry.rb +292 -0
- data/lib/bio/io/soapwsdl.rb +119 -0
- data/lib/bio/io/sql.rb +186 -0
- data/lib/bio/location.rb +867 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +960 -0
- data/lib/bio/reference.rb +602 -0
- data/lib/bio/sequence.rb +456 -0
- data/lib/bio/sequence/aa.rb +152 -0
- data/lib/bio/sequence/adapter.rb +108 -0
- data/lib/bio/sequence/common.rb +310 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/dblink.rb +54 -0
- data/lib/bio/sequence/format.rb +358 -0
- data/lib/bio/sequence/format_raw.rb +23 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +491 -0
- data/lib/bio/shell.rb +44 -0
- data/lib/bio/shell/core.rb +578 -0
- data/lib/bio/shell/demo.rb +146 -0
- data/lib/bio/shell/interface.rb +218 -0
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +71 -0
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +218 -0
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +105 -0
- data/lib/bio/shell/plugin/flatfile.rb +101 -0
- data/lib/bio/shell/plugin/keggapi.rb +181 -0
- data/lib/bio/shell/plugin/midi.rb +430 -0
- data/lib/bio/shell/plugin/obda.rb +45 -0
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +247 -0
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +102 -0
- data/lib/bio/tree.rb +852 -0
- data/lib/bio/util/color_scheme.rb +191 -0
- data/lib/bio/util/color_scheme/buried.rb +59 -0
- data/lib/bio/util/color_scheme/helix.rb +59 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +64 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +31 -0
- data/lib/bio/util/color_scheme/strand.rb +59 -0
- data/lib/bio/util/color_scheme/taylor.rb +50 -0
- data/lib/bio/util/color_scheme/turn.rb +59 -0
- data/lib/bio/util/color_scheme/zappo.rb +50 -0
- data/lib/bio/util/contingency_table.rb +370 -0
- data/lib/bio/util/restriction_enzyme.rb +228 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
- data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +200 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/aaindex/DAYM780301 +30 -0
- data/test/data/aaindex/PRAM900102 +20 -0
- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
- data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
- data/test/data/blast/2.2.15.blastp.m7 +876 -0
- data/test/data/blast/b0002.faa +15 -0
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- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/blast/blastp-multi.m7 +188 -0
- data/test/data/command/echoarg2.bat +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/embl/AB090716.embl.rel89 +63 -0
- data/test/data/fasta/example1.txt +75 -0
- data/test/data/fasta/example2.txt +21 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/paml/codeml/control_file.txt +30 -0
- data/test/data/paml/codeml/output.txt +78 -0
- data/test/data/paml/codeml/rates +217 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/rpsblast/misc.rpsblast +193 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/functional/bio/appl/test_pts1.rb +115 -0
- data/test/functional/bio/io/test_ensembl.rb +229 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -0
- data/test/functional/bio/sequence/test_output_embl.rb +51 -0
- data/test/functional/bio/test_command.rb +301 -0
- data/test/runner.rb +14 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_ncbioptions.rb +112 -0
- data/test/unit/bio/appl/blast/test_report.rb +1135 -0
- data/test/unit/bio/appl/blast/test_rpsblast.rb +398 -0
- data/test/unit/bio/appl/genscan/test_report.rb +182 -0
- data/test/unit/bio/appl/hmmer/test_report.rb +342 -0
- data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
- data/test/unit/bio/appl/mafft/test_report.rb +63 -0
- data/test/unit/bio/appl/paml/codeml/test_rates.rb +45 -0
- data/test/unit/bio/appl/paml/codeml/test_report.rb +45 -0
- data/test/unit/bio/appl/paml/test_codeml.rb +174 -0
- data/test/unit/bio/appl/sosui/test_report.rb +81 -0
- data/test/unit/bio/appl/targetp/test_report.rb +146 -0
- data/test/unit/bio/appl/test_blast.rb +277 -0
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_psort.rb +57 -0
- data/test/unit/bio/appl/test_pts1.rb +77 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +126 -0
- data/test/unit/bio/data/test_aa.rb +90 -0
- data/test/unit/bio/data/test_codontable.rb +107 -0
- data/test/unit/bio/data/test_na.rb +80 -0
- data/test/unit/bio/db/embl/test_common.rb +117 -0
- data/test/unit/bio/db/embl/test_embl.rb +214 -0
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +203 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1812 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +31 -0
- data/test/unit/bio/db/kegg/test_genes.rb +45 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +152 -0
- data/test/unit/bio/db/test_aaindex.rb +197 -0
- data/test/unit/bio/db/test_fasta.rb +250 -0
- data/test/unit/bio/db/test_gff.rb +1190 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_medline.rb +127 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +364 -0
- data/test/unit/bio/db/test_prosite.rb +1437 -0
- data/test/unit/bio/db/test_rebase.rb +101 -0
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/db/test_url.rb +36 -0
- data/test/unit/bio/io/flatfile/test_autodetection.rb +375 -0
- data/test/unit/bio/io/flatfile/test_buffer.rb +251 -0
- data/test/unit/bio/io/flatfile/test_splitter.rb +369 -0
- data/test/unit/bio/io/test_ddbjxml.rb +80 -0
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +42 -0
- data/test/unit/bio/io/test_flatfile.rb +505 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +115 -0
- data/test/unit/bio/sequence/test_common.rb +373 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -0
- data/test/unit/bio/sequence/test_dblink.rb +58 -0
- data/test/unit/bio/sequence/test_na.rb +330 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +185 -0
- data/test/unit/bio/test_alignment.rb +1025 -0
- data/test/unit/bio/test_command.rb +349 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +144 -0
- data/test/unit/bio/test_location.rb +599 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +499 -0
- data/test/unit/bio/test_reference.rb +252 -0
- data/test/unit/bio/test_sequence.rb +329 -0
- data/test/unit/bio/test_shell.rb +18 -0
- data/test/unit/bio/test_tree.rb +593 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +101 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
- data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
- data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
- data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
- data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
- data/test/unit/bio/util/test_color_scheme.rb +33 -0
- data/test/unit/bio/util/test_contingency_table.rb +94 -0
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +245 -0
- metadata +543 -0
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#
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# bio/util/restriction_enzyme.rb - Digests DNA based on restriction enzyme cut patterns
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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: restriction_enzyme.rb,v 1.16 2007/07/16 19:28:48 k Exp $
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#
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module Bio #:nodoc:
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autoload :REBASE, 'bio/db/rebase'
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# = Description
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#
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# Bio::RestrictionEnzyme allows you to fragment a DNA strand using one
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# or more restriction enzymes. Bio::RestrictionEnzyme is aware that
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# multiple enzymes may be competing for the same recognition site and
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# returns the various possible fragmentation patterns that result in
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# such circumstances.
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#
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# When using Bio::RestrictionEnzyme you may simply use the name of common
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# enzymes to cut your sequence or you may construct your own unique enzymes
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# to use.
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#
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# Visit the documentaion for individual classes for more information.
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#
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# An examination of the unit tests will also reveal several interesting uses
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# for the curious programmer.
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#
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# = Usage
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#
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# == Basic
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#
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# EcoRI cut pattern:
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# G|A A T T C
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# +-------+
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# C T T A A|G
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#
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# This can also be written as:
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# G^AATTC
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#
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# Note that to use the method +cut_with_enzyme+ from a Bio::Sequence object
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# you currently must +require+ +bio/util/restriction_enzyme+ directly. If
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# instead you're going to directly call Bio::RestrictionEnzyme::Analysis
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# then only +bio+ needs to be +required+.
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#
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# require 'bio'
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# require 'bio/util/restriction_enzyme'
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#
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# seq = Bio::Sequence::NA.new('gaattc')
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# cuts = seq.cut_with_enzyme('EcoRI')
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# cuts.primary # => ["aattc", "g"]
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# cuts.complement # => ["cttaa", "g"]
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# cuts.inspect # => "[#<struct Bio::RestrictionEnzyme::Fragment primary=\"g \", complement=\"cttaa\">, #<struct Bio::RestrictionEnzyme::Fragment primary=\"aattc\", complement=\" g\">]"
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#
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# seq = Bio::Sequence::NA.new('gaattc')
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# cuts = seq.cut_with_enzyme('g^aattc')
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# cuts.primary # => ["aattc", "g"]
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# cuts.complement # => ["cttaa", "g"]
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#
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# seq = Bio::Sequence::NA.new('gaattc')
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# cuts = seq.cut_with_enzyme('g^aattc', 'gaatt^c')
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# cuts.primary # => ["aattc", "c", "g", "gaatt"]
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# cuts.complement # => ["c", "cttaa", "g", "ttaag"]
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#
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# seq = Bio::Sequence::NA.new('gaattcgaattc')
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# cuts = seq.cut_with_enzyme('EcoRI')
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# cuts.primary # => ["aattc", "aattcg", "g"]
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# cuts.complement # => ["cttaa", "g", "gcttaa"]
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#
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# seq = Bio::Sequence::NA.new('gaattcgggaattc')
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# cuts = seq.cut_with_enzyme('EcoRI')
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# cuts.primary # => ["aattc", "aattcggg", "g"]
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# cuts.complement # => ["cttaa", "g", "gcccttaa"]
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#
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# cuts[0].inspect # => "#<struct Bio::RestrictionEnzyme::Fragment primary=\"g \", complement=\"cttaa\">"
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#
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# cuts[0].primary # => "g "
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# cuts[0].complement # => "cttaa"
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#
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# cuts[1].primary # => "aattcggg "
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# cuts[1].complement # => " gcccttaa"
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#
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# cuts[2].primary # => "aattc"
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# cuts[2].complement # => " g"
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#
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# == Advanced
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#
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# require 'bio'
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#
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# enzyme_1 = Bio::RestrictionEnzyme.new('anna', [1,1], [3,3])
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# enzyme_2 = Bio::RestrictionEnzyme.new('gg', [1,1])
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# a = Bio::RestrictionEnzyme::Analysis.cut('agga', enzyme_1, enzyme_2)
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# a.primary # => ["a", "ag", "g", "ga"]
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# a.complement # => ["c", "ct", "t", "tc"]
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#
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# a[0].primary # => "ag"
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# a[0].complement # => "tc"
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#
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# a[1].primary # => "ga"
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# a[1].complement # => "ct"
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#
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# a[2].primary # => "a"
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# a[2].complement # => "t"
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#
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# a[3].primary # => "g"
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# a[3].complement # => "c"
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#
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# = Todo / under development
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#
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# * Circular DNA cutting
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#
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class RestrictionEnzyme
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#require 'bio/util/restriction_enzyme/cut_symbol'
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autoload :CutSymbol, 'bio/util/restriction_enzyme/cut_symbol'
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autoload :StringFormatting, 'bio/util/restriction_enzyme/string_formatting'
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autoload :SingleStrand, 'bio/util/restriction_enzyme/single_strand'
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autoload :SingleStrandComplement, 'bio/util/restriction_enzyme/single_strand_complement'
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autoload :DoubleStranded, 'bio/util/restriction_enzyme/double_stranded'
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autoload :Analysis, 'bio/util/restriction_enzyme/analysis'
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autoload :Range, 'bio/util/restriction_enzyme/range/sequence_range'
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include CutSymbol
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extend CutSymbol
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# See Bio::RestrictionEnzyme::DoubleStranded.new for more information.
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#
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# ---
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# *Arguments*
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# * +users_enzyme_or_rebase_or_pattern+: One of three possible parameters: The name of an enzyme, a REBASE::EnzymeEntry object, or a nucleotide pattern with a cut mark.
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# * +cut_locations+: The cut locations in enzyme index notation.
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# *Returns*:: Bio::RestrictionEnzyme::DoubleStranded
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#--
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# Factory for DoubleStranded
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#++
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def self.new(users_enzyme_or_rebase_or_pattern, *cut_locations)
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DoubleStranded.new(users_enzyme_or_rebase_or_pattern, *cut_locations)
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end
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# REBASE enzyme data information
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#
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# Returns a Bio::REBASE object loaded with all of the enzyme data on file.
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#
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# ---
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# *Arguments*
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# * _none_
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# *Returns*:: Bio::REBASE
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def self.rebase
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enzymes_yaml_file = File.join(File.dirname(File.expand_path(__FILE__)), 'restriction_enzyme', 'enzymes.yaml')
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@@rebase_enzymes ||= Bio::REBASE.load_yaml(enzymes_yaml_file)
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@@rebase_enzymes
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end
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# Check if supplied name is the name of an available enzyme
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#
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# See Bio::REBASE.enzyme_name?
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#
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# ---
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# *Arguments*
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# * +name+: Enzyme name
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# *Returns*:: +true+ _or_ +false+
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def self.enzyme_name?( name )
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self.rebase.enzyme_name?(name)
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end
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# See Bio::RestrictionEnzyme::Analysis.cut
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def self.cut( sequence, enzymes )
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Bio::RestrictionEnzyme::Analysis.cut( sequence, enzymes )
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end
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+
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# A Bio::RestrictionEnzyme::Fragment is a DNA fragment composed of fused primary and
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# complementary strands that would be found floating in solution after a full
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# sequence is digested by one or more RestrictionEnzymes.
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#
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# You will notice that either the primary or complement strand will be
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# padded with spaces to make them line up according to the original DNA
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# configuration before they were cut.
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#
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# Example:
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#
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# Fragment 1:
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# primary = "attaca"
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# complement = " atga"
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#
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# Fragment 2:
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# primary = "g "
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# complement = "cta"
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#
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# View these with the +primary+ and +complement+ methods.
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#
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# Bio::RestrictionEnzyme::Fragment is a simple +Struct+ object.
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#
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# Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragment
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Fragment = Struct.new(:primary, :complement, :p_left, :p_right, :c_left, :c_right)
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+
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# Bio::RestrictionEnzyme::Fragments inherits from +Array+.
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#
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# Bio::RestrictionEnzyme::Fragments is a container for Fragment objects. It adds the
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# methods +primary+ and +complement+ which returns an +Array+ of all
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# respective strands from it's Fragment members in alphabetically sorted
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# order. Note that it will
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# not return duplicate items and does not return the spacing/padding
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# that you would
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# find by accessing the members directly.
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#
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# Example:
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#
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# primary = ['attaca', 'g']
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# complement = ['atga', 'cta']
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#
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# Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
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class Fragments < Array
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def primary; strip_and_sort(:primary); end
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def complement; strip_and_sort(:complement); end
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protected
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def strip_and_sort( sym_strand )
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self.map {|uf| uf.send( sym_strand ).tr(' ', '') }.sort
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end
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end
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end # RestrictionEnzyme
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end # Bio
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#
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# bio/util/restriction_enzyme/analysis.rb - Does the work of fragmenting the DNA from the enzymes
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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: analysis.rb,v 1.20 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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require 'bio/util/restriction_enzyme/analysis_basic'
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module Bio
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class RestrictionEnzyme
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class Analysis
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# See cut instance method
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def self.cut( sequence, *args )
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self.new.cut( sequence, *args )
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end
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# See main documentation for Bio::RestrictionEnzyme
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#
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#
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# +cut+ takes into account
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# permutations of cut variations based on competitiveness of enzymes for an
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# enzyme cutsite or enzyme bindsite on a sequence.
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#
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# Example:
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#
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# FIXME add output
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#
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# Bio::RestrictionEnzyme::Analysis.cut('gaattc', 'EcoRI')
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#
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# _same as:_
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#
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# Bio::RestrictionEnzyme::Analysis.cut('gaattc', 'g^aattc')
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# ---
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# *Arguments*
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# * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence.
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# * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects.
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# *Returns*:: Bio::RestrictionEnzyme::Fragments object populated with Bio::RestrictionEnzyme::Fragment objects. (Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragments) or a +Symbol+ containing an error code
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def cut( sequence, *args )
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view_ranges = false
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args.select { |i| i.class == Hash }.each do |hsh|
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hsh.each do |key, value|
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if key == :view_ranges
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unless ( value.kind_of?(TrueClass) or value.kind_of?(FalseClass) )
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raise ArgumentError, "view_ranges must be set to true or false, currently #{value.inspect}."
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end
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view_ranges = value
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end
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end
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end
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res = cut_and_return_by_permutations( sequence, *args )
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return res if res.class == Symbol
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# Format the fragments for the user
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fragments_for_display( res, view_ranges )
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end
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#########
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protected
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#########
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# See cut instance method
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#
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# ---
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# *Arguments*
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# * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence.
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# * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects.
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# May also supply a +Hash+ with the key ":max_permutations" to specificy how many permutations are allowed - a value of 0 indicates no permutations are allowed.
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# *Returns*:: +Hash+ Keys are a permutation ID, values are SequenceRange objects that have cuts applied.
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# _also_ may return the +Symbol+ ':sequence_empty', ':no_cuts_found', or ':too_many_permutations'
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def cut_and_return_by_permutations( sequence, *args )
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my_hash = {}
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|
+
maximum_permutations = nil
|
81
|
+
|
82
|
+
hashes_in_args = args.select { |i| i.class == Hash }
|
83
|
+
args.delete_if { |i| i.class == Hash }
|
84
|
+
hashes_in_args.each do |hsh|
|
85
|
+
hsh.each do |key, value|
|
86
|
+
case key
|
87
|
+
when :max_permutations, 'max_permutations', :maximum_permutations, 'maximum_permutations'
|
88
|
+
maximum_permutations = value.to_i unless value == nil
|
89
|
+
when :view_ranges
|
90
|
+
else
|
91
|
+
raise ArgumentError, "Received key #{key.inspect} in argument - I only know the key ':max_permutations' and ':view_ranges' currently. Hash passed: #{hsh.inspect}"
|
92
|
+
end
|
93
|
+
end
|
94
|
+
end
|
95
|
+
|
96
|
+
if !sequence.kind_of?(String) or sequence.empty?
|
97
|
+
logger.warn "The supplied sequence is empty." if defined?(logger)
|
98
|
+
return :sequence_empty
|
99
|
+
end
|
100
|
+
sequence = Bio::Sequence::NA.new( sequence )
|
101
|
+
|
102
|
+
enzyme_actions, initial_cuts = create_enzyme_actions( sequence, *args )
|
103
|
+
|
104
|
+
if enzyme_actions.empty? and initial_cuts.empty?
|
105
|
+
logger.warn "This enzyme does not make any cuts on this sequence." if defined?(logger)
|
106
|
+
return :no_cuts_found
|
107
|
+
end
|
108
|
+
|
109
|
+
# * When enzyme_actions.size is equal to '1' that means there are no permutations.
|
110
|
+
# * If enzyme_actions.size is equal to '2' there is one
|
111
|
+
# permutation ("[0, 1]")
|
112
|
+
# * If enzyme_actions.size is equal to '3' there are two
|
113
|
+
# permutations ("[0, 1, 2]")
|
114
|
+
# * and so on..
|
115
|
+
if maximum_permutations and enzyme_actions.size > 1
|
116
|
+
if (enzyme_actions.size - 1) > maximum_permutations.to_i
|
117
|
+
logger.warn "More permutations than maximum, skipping. Found: #{enzyme_actions.size-1} Max: #{maximum_permutations.to_i}" if defined?(logger)
|
118
|
+
return :too_many_permutations
|
119
|
+
end
|
120
|
+
end
|
121
|
+
|
122
|
+
if enzyme_actions.size > 1
|
123
|
+
permutations = permute(enzyme_actions.size)
|
124
|
+
|
125
|
+
permutations.each do |permutation|
|
126
|
+
previous_cut_ranges = []
|
127
|
+
# Primary and complement strands are both measured from '0' to 'sequence.size-1' here
|
128
|
+
sequence_range = Bio::RestrictionEnzyme::Range::SequenceRange.new( 0, 0, sequence.size-1, sequence.size-1 )
|
129
|
+
|
130
|
+
# Add the cuts to the sequence_range from each enzyme_action contained
|
131
|
+
# in initial_cuts. These are the cuts that have no competition so are
|
132
|
+
# not subject to permutations.
|
133
|
+
initial_cuts.each do |enzyme_action|
|
134
|
+
enzyme_action.cut_ranges.each do |cut_range|
|
135
|
+
sequence_range.add_cut_range(cut_range)
|
136
|
+
end
|
137
|
+
end
|
138
|
+
|
139
|
+
permutation.each do |id|
|
140
|
+
enzyme_action = enzyme_actions[id]
|
141
|
+
|
142
|
+
# conflict is false if the current enzyme action may cut in it's range.
|
143
|
+
# conflict is true if it cannot due to a previous enzyme action making
|
144
|
+
# a cut where this enzyme action needs a whole recognition site.
|
145
|
+
conflict = false
|
146
|
+
|
147
|
+
# If current size of enzyme_action overlaps with previous cut_range, don't cut
|
148
|
+
# note that the enzyme action may fall in the middle of a previous enzyme action
|
149
|
+
# so all cut locations must be checked that would fall underneath.
|
150
|
+
previous_cut_ranges.each do |cut_range|
|
151
|
+
next unless cut_range.class == Bio::RestrictionEnzyme::Range::VerticalCutRange # we aren't concerned with horizontal cuts
|
152
|
+
previous_cut_left = cut_range.range.first
|
153
|
+
previous_cut_right = cut_range.range.last
|
154
|
+
|
155
|
+
# Keep in mind:
|
156
|
+
# * The cut location is to the immediate right of the base located at the index.
|
157
|
+
# ex: at^gc -- the cut location is at index 1
|
158
|
+
# * The enzyme action location is located at the base of the index.
|
159
|
+
# ex: atgc -- 0 => 'a', 1 => 't', 2 => 'g', 3 => 'c'
|
160
|
+
# method create_enzyme_actions has similar commentary if interested
|
161
|
+
if (enzyme_action.right <= previous_cut_left) or
|
162
|
+
(enzyme_action.left > previous_cut_right) or
|
163
|
+
(enzyme_action.left > previous_cut_left and enzyme_action.right <= previous_cut_right) # in between cuts
|
164
|
+
# no conflict
|
165
|
+
else
|
166
|
+
conflict = true
|
167
|
+
end
|
168
|
+
end
|
169
|
+
|
170
|
+
next if conflict == true
|
171
|
+
enzyme_action.cut_ranges.each { |cut_range| sequence_range.add_cut_range(cut_range) }
|
172
|
+
previous_cut_ranges += enzyme_action.cut_ranges
|
173
|
+
end # permutation.each
|
174
|
+
|
175
|
+
# Fill in the source sequence for sequence_range so it knows what bases
|
176
|
+
# to use
|
177
|
+
sequence_range.fragments.primary = sequence
|
178
|
+
sequence_range.fragments.complement = sequence.forward_complement
|
179
|
+
my_hash[permutation] = sequence_range
|
180
|
+
end # permutations.each
|
181
|
+
|
182
|
+
else # if enzyme_actions.size == 1
|
183
|
+
# no permutations, just do it
|
184
|
+
sequence_range = Bio::RestrictionEnzyme::Range::SequenceRange.new( 0, 0, sequence.size-1, sequence.size-1 )
|
185
|
+
initial_cuts.each { |enzyme_action| enzyme_action.cut_ranges.each { |cut_range| sequence_range.add_cut_range(cut_range) } }
|
186
|
+
sequence_range.fragments.primary = sequence
|
187
|
+
sequence_range.fragments.complement = sequence.forward_complement
|
188
|
+
my_hash[0] = sequence_range
|
189
|
+
end
|
190
|
+
|
191
|
+
my_hash
|
192
|
+
end
|
193
|
+
|
194
|
+
|
195
|
+
# Returns permutation orders for a given number of elements.
|
196
|
+
#
|
197
|
+
# Examples:
|
198
|
+
# permute(0) # => [[0]]
|
199
|
+
# permute(1) # => [[0]]
|
200
|
+
# permute(2) # => [[1, 0], [0, 1]]
|
201
|
+
# permute(3) # => [[2, 1, 0], [2, 0, 1], [1, 2, 0], [0, 2, 1], [1, 0, 2], [0, 1, 2]]
|
202
|
+
# permute(4) # => [[3, 2, 1, 0],
|
203
|
+
# [3, 2, 0, 1],
|
204
|
+
# [3, 1, 2, 0],
|
205
|
+
# [3, 0, 2, 1],
|
206
|
+
# [3, 1, 0, 2],
|
207
|
+
# [3, 0, 1, 2],
|
208
|
+
# [2, 3, 1, 0],
|
209
|
+
# [2, 3, 0, 1],
|
210
|
+
# [1, 3, 2, 0],
|
211
|
+
# [0, 3, 2, 1],
|
212
|
+
# [1, 3, 0, 2],
|
213
|
+
# [0, 3, 1, 2],
|
214
|
+
# [2, 1, 3, 0],
|
215
|
+
# [2, 0, 3, 1],
|
216
|
+
# [1, 2, 3, 0],
|
217
|
+
# [0, 2, 3, 1],
|
218
|
+
# [1, 0, 3, 2],
|
219
|
+
# [0, 1, 3, 2],
|
220
|
+
# [2, 1, 0, 3],
|
221
|
+
# [2, 0, 1, 3],
|
222
|
+
# [1, 2, 0, 3],
|
223
|
+
# [0, 2, 1, 3],
|
224
|
+
# [1, 0, 2, 3],
|
225
|
+
# [0, 1, 2, 3]]
|
226
|
+
#
|
227
|
+
# ---
|
228
|
+
# *Arguments*
|
229
|
+
# * +count+: +Number+ of different elements to be permuted
|
230
|
+
# * +permutations+: ignore - for the recursive algorithm
|
231
|
+
# *Returns*:: +Array+ of +Array+ objects with different possible permutation orders. See examples.
|
232
|
+
def permute(count, permutations = [[0]])
|
233
|
+
return permutations if count <= 1
|
234
|
+
new_arrays = []
|
235
|
+
new_array = []
|
236
|
+
|
237
|
+
(permutations[0].size + 1).times do |n|
|
238
|
+
new_array.clear
|
239
|
+
permutations.each { |a| new_array << a.dup }
|
240
|
+
new_array.each { |e| e.insert(n, permutations[0].size) }
|
241
|
+
new_arrays += new_array
|
242
|
+
end
|
243
|
+
|
244
|
+
permute(count-1, new_arrays)
|
245
|
+
end
|
246
|
+
|
247
|
+
end # Analysis
|
248
|
+
end # RestrictionEnzyme
|
249
|
+
end # Bio
|