ngoto-bio 1.2.9.9001
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- data/ChangeLog +2046 -0
- data/README.rdoc +223 -0
- data/README_DEV.rdoc +285 -0
- data/Rakefile +70 -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/bioruby.gemspec +463 -0
- data/bioruby.gemspec.erb +79 -0
- data/doc/Changes-0.7.rd +369 -0
- data/doc/Changes-1.3.rdoc +195 -0
- data/doc/KEGG_API.rd +1843 -0
- data/doc/KEGG_API.rd.ja +1834 -0
- data/doc/Tutorial.rd +1296 -0
- data/doc/Tutorial.rd.ja +2640 -0
- data/etc/bioinformatics/seqdatabase.ini +210 -0
- data/extconf.rb +2 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -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 +671 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blast.rb +505 -0
- data/lib/bio/appl/blat/report.rb +530 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/fasta.rb +235 -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/report.rb +683 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/baseml.rb +95 -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/codeml.rb +242 -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/report.rb +32 -0
- data/lib/bio/appl/paml/yn00.rb +103 -0
- data/lib/bio/appl/phylip/alignment.rb +129 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort/report.rb +457 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sim4.rb +124 -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 +349 -0
- data/lib/bio/data/codontable.rb +722 -0
- data/lib/bio/data/na.rb +223 -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/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/fasta.rb +410 -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/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/pdb.rb +29 -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.rb +329 -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/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/flatfile.rb +473 -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/aa.rb +125 -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/sequence.rb +456 -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
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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
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- 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/shell.rb +44 -0
- data/lib/bio/tree.rb +852 -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/color_scheme.rb +191 -0
- data/lib/bio/util/contingency_table.rb +370 -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/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/double_stranded.rb +321 -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/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/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -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.rb +200 -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/restriction_enzyme.rb +228 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/lib/bio.rb +300 -0
- data/rdoc.zsh +8 -0
- data/sample/any2fasta.rb +59 -0
- data/sample/biofetch.rb +475 -0
- data/sample/color_scheme_na.rb +91 -0
- data/sample/dbget +37 -0
- data/sample/demo_sequence.rb +158 -0
- data/sample/enzymes.rb +78 -0
- data/sample/fasta2tab.rb +99 -0
- data/sample/fastagrep.rb +72 -0
- data/sample/fastasort.rb +54 -0
- data/sample/fsplit.rb +51 -0
- data/sample/gb2fasta.rb +30 -0
- data/sample/gb2tab.rb +325 -0
- data/sample/gbtab2mysql.rb +161 -0
- data/sample/genes2nuc.rb +33 -0
- data/sample/genes2pep.rb +33 -0
- data/sample/genes2tab.rb +81 -0
- data/sample/genome2rb.rb +29 -0
- data/sample/genome2tab.rb +76 -0
- data/sample/goslim.rb +303 -0
- data/sample/gt2fasta.rb +47 -0
- data/sample/na2aa.rb +34 -0
- data/sample/pmfetch.rb +42 -0
- data/sample/pmsearch.rb +42 -0
- data/sample/psortplot_html.rb +214 -0
- data/sample/ssearch2tab.rb +96 -0
- data/sample/tdiary.rb +158 -0
- data/sample/tfastx2tab.rb +100 -0
- data/sample/vs-genes.rb +212 -0
- data/setup.rb +1596 -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
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- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
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- data/test/data/fasta/example1.txt +75 -0
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- data/test/data/genscan/sample.report +63 -0
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- 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
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- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
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- 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 +23 -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
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- 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/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 +488 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +103 -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 +484 -0
@@ -0,0 +1,24 @@
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#
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# bio/util/restriction_enzyme/range/cut_range.rb - Abstract base class for HorizontalCutRange and VerticalCutRange
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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_range.rb,v 1.4 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 Range
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# Abstract base class for HorizontalCutRange and VerticalCutRange
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#
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class CutRange
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end # CutRange
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end # Range
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end # RestrictionEnzyme
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end # Bio
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#
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# bio/util/restriction_enzyme/range/cut_ranges.rb - Container for many CutRange objects or CutRange child 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: cut_ranges.rb,v 1.5 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 Range
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# Container for many CutRange objects or CutRange child objects. Inherits from array.
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#
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class CutRanges < Array
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def min; self.collect{|a| a.min}.flatten.sort.first; end
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def max; self.collect{|a| a.max}.flatten.sort.last; end
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def include?(i); self.collect{|a| a.include?(i)}.include?(true); end
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def min_vertical
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vertical_min_max_helper( :min )
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end
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def max_vertical
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vertical_min_max_helper( :max )
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end
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protected
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def vertical_min_max_helper( sym_which )
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tmp = []
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self.each do |a|
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next unless a.class == Bio::RestrictionEnzyme::Range::VerticalCutRange
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tmp << a.send( sym_which )
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end
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z = (sym_which == :max) ? :last : :first
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tmp.flatten.sort.send(z)
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end
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end # CutRanges
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end # Range
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end # RestrictionEnzyme
|
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end # Bio
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#
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# bio/util/restriction_enzyme/range/horizontal_cut_range.rb -
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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: horizontal_cut_range.rb,v 1.5 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 Range
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class HorizontalCutRange < CutRange
|
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attr_reader :p_cut_left, :p_cut_right
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attr_reader :c_cut_left, :c_cut_right
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attr_reader :min, :max
|
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attr_reader :hcuts
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def initialize( left, right=left )
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raise "left > right" if left > right
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# The 'range' here is actually off by one on the left
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# side in relation to a normal CutRange, so using the normal
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# variables from CutRange would result in bad behavior.
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#
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# See below - the first horizontal cut is the primary cut plus one.
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#
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# 1 2 3 4 5 6 7
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# G A|T T A C A
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# +-----+
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# C T A A T|G T
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# 1 2 3 4 5 6 7
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#
|
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# Primary cut = 2
|
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# Complement cut = 5
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# Horizontal cuts = 3, 4, 5
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|
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@p_cut_left = nil
|
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@p_cut_right = nil
|
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@c_cut_left = nil
|
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@c_cut_right = nil
|
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@min = left # NOTE this used to be 'nil', make sure all tests work
|
47
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@max = right # NOTE this used to be 'nil', make sure all tests work
|
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@range = (@min..@max) unless @min == nil or @max == nil # NOTE this used to be 'nil', make sure all tests work
|
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@hcuts = (left..right)
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end
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# Check if a location falls within the minimum or maximum values of this
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# range.
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#
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# ---
|
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# *Arguments*
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# * +i+: Location to check if it is included in the range
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# *Returns*:: +true+ _or_ +false+
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def include?(i)
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@range.include?(i)
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end
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end # HorizontalCutRange
|
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end # Range
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end # RestrictionEnzyme
|
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end # Bio
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#
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# bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb -
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#
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4
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
|
5
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
|
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# License:: The Ruby License
|
7
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#
|
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# $Id: calculated_cuts.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
|
14
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class RestrictionEnzyme
|
15
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class Range
|
16
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class SequenceRange
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|
18
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# cc = CalculatedCuts.new(@size)
|
19
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# cc.add_cuts_from_cut_ranges(@cut_ranges)
|
20
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# cc.remove_incomplete_cuts
|
21
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#
|
22
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# 1 2 3 4 5 6 7
|
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# G A|T T A C A
|
24
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# +-----+
|
25
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# C T A A T|G T
|
26
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# 1 2 3 4 5 6 7
|
27
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#
|
28
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# Primary cut = 2
|
29
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# Complement cut = 5
|
30
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# Horizontal cuts = 3, 4, 5
|
31
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#
|
32
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class CalculatedCuts
|
33
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include CutSymbol
|
34
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include StringFormatting
|
35
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+
|
36
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# +Array+ of vertical cuts on the primary strand in 0-based index notation
|
37
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attr_reader :vc_primary
|
38
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+
|
39
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# +Array+ of vertical cuts on the complementary strand in 0-based index notation
|
40
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attr_reader :vc_complement
|
41
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+
|
42
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# +Array+ of horizontal cuts between strands in 0-based index notation
|
43
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attr_reader :hc_between_strands
|
44
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+
|
45
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# Set to +true+ if the fragment CalculatedCuts is working on is circular
|
46
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attr_accessor :circular
|
47
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+
|
48
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# An +Array+ with the primary strand with vertical cuts, the horizontal cuts, and the complementary strand with vertical cuts.
|
49
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+
attr_reader :strands_for_display
|
50
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+
|
51
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# If +false+ the strands_for_display method needs to be called to update the contents
|
52
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# of @strands_for_display. Becomes out of date whenever add_cuts_from_cut_ranges is called.
|
53
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attr_reader :strands_for_display_current
|
54
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+
|
55
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+
# Size of the sequence being digested.
|
56
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attr_reader :size
|
57
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+
|
58
|
+
def initialize(size=nil, circular=false)
|
59
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+
@size = size
|
60
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+
@circular = circular
|
61
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+
@vc_primary = []
|
62
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+
@vc_complement = []
|
63
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@hc_between_strands = []
|
64
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+
end
|
65
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+
|
66
|
+
# Accepts an +Array+ of CutRange type objects and applies them to
|
67
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+
# @vc_complement, @vc_primary, and @hc_between_strands.
|
68
|
+
#
|
69
|
+
# ---
|
70
|
+
# *Arguments*
|
71
|
+
# * +cut_ranges+: An +Array+ of HorizontalCutRange or VerticalCutRange objects
|
72
|
+
# *Returns*:: nothing
|
73
|
+
def add_cuts_from_cut_ranges(cut_ranges)
|
74
|
+
@strands_for_display_current = false
|
75
|
+
|
76
|
+
cut_ranges.each do |cut_range|
|
77
|
+
@vc_primary += [cut_range.p_cut_left, cut_range.p_cut_right]
|
78
|
+
@vc_complement += [cut_range.c_cut_left, cut_range.c_cut_right]
|
79
|
+
|
80
|
+
# Add horizontal cut ranges. This may happen from cuts made inbetween a
|
81
|
+
# VerticalCutRange or may be specifically defined by a HorizontalCutRange.
|
82
|
+
if cut_range.class == VerticalCutRange
|
83
|
+
( cut_range.min + 1 ).upto( cut_range.max ){|i| @hc_between_strands << i} if cut_range.min < cut_range.max
|
84
|
+
elsif cut_range.class == HorizontalCutRange
|
85
|
+
( cut_range.hcuts.first ).upto( cut_range.hcuts.last ){|i| @hc_between_strands << i}
|
86
|
+
end
|
87
|
+
end
|
88
|
+
clean_all
|
89
|
+
#return
|
90
|
+
end
|
91
|
+
|
92
|
+
# There may be incomplete cuts made, this method removes the cuts that don't
|
93
|
+
# create sub-sequences for easier processing.
|
94
|
+
#
|
95
|
+
# For example, stray horizontal cuts that do not end with a left
|
96
|
+
# and right separation:
|
97
|
+
#
|
98
|
+
# G A T T A C A
|
99
|
+
# +-- ---
|
100
|
+
# C T|A A T G T
|
101
|
+
#
|
102
|
+
# Or stray vertical cuts:
|
103
|
+
#
|
104
|
+
# G A T T A C A
|
105
|
+
# +-- +
|
106
|
+
# C T|A A T|G T
|
107
|
+
#
|
108
|
+
# However note that for non-circular sequences this would be a successful
|
109
|
+
# cut which would result in a floating 'GT' sub-sequence:
|
110
|
+
#
|
111
|
+
# G A T T A C A
|
112
|
+
# +---
|
113
|
+
# C T A A T|G T
|
114
|
+
#
|
115
|
+
# Blunt cuts are also complete cuts.
|
116
|
+
# ---
|
117
|
+
# *Arguments*
|
118
|
+
# * +size+: (_optional_) Size of the sequence being digested. Defined here or during initalization of CalculatedCuts.
|
119
|
+
# *Returns*:: nothing
|
120
|
+
def remove_incomplete_cuts(size=nil)
|
121
|
+
@strands_for_display_current = false
|
122
|
+
@size = size if size
|
123
|
+
raise IndexError, "Size of the strand must be provided here or during initalization." if !@size.kind_of?(Fixnum) and not @circular
|
124
|
+
|
125
|
+
vcuts = (@vc_primary + @vc_complement).uniq.sort
|
126
|
+
hcuts = @hc_between_strands
|
127
|
+
last_index = @size - 1
|
128
|
+
good_hcuts = []
|
129
|
+
potential_hcuts = []
|
130
|
+
|
131
|
+
if @circular
|
132
|
+
# NOTE
|
133
|
+
# if it's circular we should start at the beginning of a cut for orientation,
|
134
|
+
# scan for it, hack off the first set of hcuts and move them to the back
|
135
|
+
else
|
136
|
+
vcuts.unshift(-1) unless vcuts.include?(-1)
|
137
|
+
vcuts.push(last_index) unless vcuts.include?(last_index)
|
138
|
+
end
|
139
|
+
|
140
|
+
hcuts.each do |hcut|
|
141
|
+
raise IndexError if hcut < -1 or hcut > last_index
|
142
|
+
# skipped a nucleotide
|
143
|
+
potential_hcuts.clear if !potential_hcuts.empty? and (hcut - potential_hcuts.last).abs > 1
|
144
|
+
|
145
|
+
if potential_hcuts.empty?
|
146
|
+
if vcuts.include?( hcut ) and vcuts.include?( hcut - 1 )
|
147
|
+
good_hcuts += [hcut]
|
148
|
+
elsif vcuts.include?( hcut - 1 )
|
149
|
+
potential_hcuts << hcut
|
150
|
+
end
|
151
|
+
else
|
152
|
+
if vcuts.include?( hcut )
|
153
|
+
good_hcuts += potential_hcuts + [hcut]
|
154
|
+
potential_hcuts.clear
|
155
|
+
else
|
156
|
+
potential_hcuts << hcut
|
157
|
+
end
|
158
|
+
end
|
159
|
+
end
|
160
|
+
|
161
|
+
check_vc = lambda do |vertical_cuts, opposing_vcuts|
|
162
|
+
# opposing_vcuts is here only to check for blunt cuts, so there shouldn't
|
163
|
+
# be any out-of-order problems with this
|
164
|
+
good_vc = []
|
165
|
+
vertical_cuts.each { |vc| good_vc << vc if good_hcuts.include?( vc ) or good_hcuts.include?( vc + 1 ) or opposing_vcuts.include?( vc ) }
|
166
|
+
good_vc
|
167
|
+
end
|
168
|
+
|
169
|
+
@vc_primary = check_vc.call(@vc_primary, @vc_complement)
|
170
|
+
@vc_complement = check_vc.call(@vc_complement, @vc_primary)
|
171
|
+
@hc_between_strands = good_hcuts
|
172
|
+
|
173
|
+
clean_all
|
174
|
+
end
|
175
|
+
|
176
|
+
# Sets @strands_for_display_current to +true+ and populates @strands_for_display.
|
177
|
+
#
|
178
|
+
# ---
|
179
|
+
# *Arguments*
|
180
|
+
# * +str1+: (_optional_) For displaying a primary strand. If +nil+ a numbered sequence will be used in place.
|
181
|
+
# * +str2+: (_optional_) For displaying a complementary strand. If +nil+ a numbered sequence will be used in place.
|
182
|
+
# * +vcp+: (_optional_) An array of vertical cut locations on the primary strand. If +nil+ the contents of @vc_primary is used.
|
183
|
+
# * +vcc+: (_optional_) An array of vertical cut locations on the complementary strand. If +nil+ the contents of @vc_complementary is used.
|
184
|
+
# * +hc+: (_optional_) An array of horizontal cut locations between strands. If +nil+ the contents of @hc_between_strands is used.
|
185
|
+
# *Returns*:: +Array+ An array with the primary strand with vertical cuts, the horizontal cuts, and the complementary strand with vertical cuts.
|
186
|
+
#
|
187
|
+
def strands_for_display(str1 = nil, str2 = nil, vcp=nil, vcc=nil, hc=nil)
|
188
|
+
return @strands_for_display if @strands_for_display_current
|
189
|
+
vcs = '|' # Vertical cut symbol
|
190
|
+
hcs = '-' # Horizontal cut symbol
|
191
|
+
vhcs = '+' # Intersection of vertical and horizontal cut symbol
|
192
|
+
|
193
|
+
num_txt_repeat = lambda { num_txt = '0123456789'; (num_txt * ( @size / num_txt.size.to_f ).ceil)[0..@size-1] }
|
194
|
+
(str1 == nil) ? a = num_txt_repeat.call : a = str1.dup
|
195
|
+
(str2 == nil) ? b = num_txt_repeat.call : b = str2.dup
|
196
|
+
|
197
|
+
vcp = @vc_primary if vcp==nil
|
198
|
+
vcc = @vc_complement if vcc==nil
|
199
|
+
hc = @hc_between_strands if hc==nil
|
200
|
+
|
201
|
+
vcuts = (vcp + vcc).uniq.sort
|
202
|
+
|
203
|
+
vcp.reverse.each { |c| a.insert(c+1, vcs) }
|
204
|
+
vcc.reverse.each { |c| b.insert(c+1, vcs) }
|
205
|
+
|
206
|
+
between = ' ' * @size
|
207
|
+
hc.each {|hcut| between[hcut,1] = hcs }
|
208
|
+
|
209
|
+
s_a = add_spacing(a, vcs)
|
210
|
+
s_b = add_spacing(b, vcs)
|
211
|
+
s_bet = add_spacing(between)
|
212
|
+
|
213
|
+
# NOTE watch this for circular
|
214
|
+
i = 0
|
215
|
+
0.upto( s_a.size-1 ) do
|
216
|
+
if (s_a[i,1] == vcs) or (s_b[i,1] == vcs)
|
217
|
+
s_bet[i] = vhcs
|
218
|
+
elsif i != 0 and s_bet[i-1,1] == hcs and s_bet[i+1,1] == hcs
|
219
|
+
s_bet[i] = hcs
|
220
|
+
end
|
221
|
+
i+=1
|
222
|
+
end
|
223
|
+
|
224
|
+
@strands_for_display_current = true
|
225
|
+
@strands_for_display = [s_a, s_bet, s_b]
|
226
|
+
end
|
227
|
+
|
228
|
+
#########
|
229
|
+
protected
|
230
|
+
#########
|
231
|
+
|
232
|
+
# remove nil values, remove duplicate values, and
|
233
|
+
# sort @vc_primary, @vc_complement, and @hc_between_strands
|
234
|
+
def clean_all
|
235
|
+
[@vc_primary, @vc_complement, @hc_between_strands].collect { |a| a.delete(nil); a.uniq!; a.sort! }
|
236
|
+
end
|
237
|
+
|
238
|
+
end # CalculatedCuts
|
239
|
+
end # SequenceRange
|
240
|
+
end # Range
|
241
|
+
end # RestrictionEnzyme
|
242
|
+
end # Bio
|
@@ -0,0 +1,51 @@
|
|
1
|
+
#
|
2
|
+
# bio/util/restriction_enzyme/range/sequence_range/fragment.rb -
|
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: fragment.rb,v 1.6 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 Range
|
16
|
+
class SequenceRange
|
17
|
+
|
18
|
+
class Fragment
|
19
|
+
|
20
|
+
attr_reader :size
|
21
|
+
|
22
|
+
def initialize( primary_bin, complement_bin )
|
23
|
+
@primary_bin = primary_bin
|
24
|
+
@complement_bin = complement_bin
|
25
|
+
end
|
26
|
+
|
27
|
+
DisplayFragment = Struct.new(:primary, :complement, :p_left, :p_right, :c_left, :c_right)
|
28
|
+
|
29
|
+
def for_display(p_str=nil, c_str=nil)
|
30
|
+
df = DisplayFragment.new
|
31
|
+
df.primary = ''
|
32
|
+
df.complement = ''
|
33
|
+
|
34
|
+
both_bins = (@primary_bin + @complement_bin).sort.uniq
|
35
|
+
both_bins.each do |item|
|
36
|
+
@primary_bin.include?(item) ? df.primary << p_str[item] : df.primary << ' '
|
37
|
+
@complement_bin.include?(item) ? df.complement << c_str[item] : df.complement << ' '
|
38
|
+
end
|
39
|
+
|
40
|
+
df.p_left = @primary_bin.first
|
41
|
+
df.p_right = @primary_bin.last
|
42
|
+
df.c_left = @complement_bin.first
|
43
|
+
df.c_right = @complement_bin.last
|
44
|
+
|
45
|
+
df
|
46
|
+
end
|
47
|
+
end # Fragment
|
48
|
+
end # SequenceRange
|
49
|
+
end # Range
|
50
|
+
end # RestrictionEnzyme
|
51
|
+
end # Bio
|
@@ -0,0 +1,41 @@
|
|
1
|
+
#
|
2
|
+
# bio/util/restriction_enzyme/analysis/fragments.rb -
|
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: fragments.rb,v 1.5 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 Range
|
16
|
+
class SequenceRange
|
17
|
+
|
18
|
+
class Fragments < Array
|
19
|
+
|
20
|
+
attr_accessor :primary
|
21
|
+
attr_accessor :complement
|
22
|
+
|
23
|
+
def initialize(primary, complement)
|
24
|
+
@primary = primary
|
25
|
+
@complement = complement
|
26
|
+
end
|
27
|
+
|
28
|
+
DisplayFragment = Struct.new(:primary, :complement)
|
29
|
+
|
30
|
+
def for_display(p_str=nil, c_str=nil)
|
31
|
+
p_str ||= @primary
|
32
|
+
c_str ||= @complement
|
33
|
+
pretty_fragments = []
|
34
|
+
self.each { |fragment| pretty_fragments << fragment.for_display(p_str, c_str) }
|
35
|
+
pretty_fragments
|
36
|
+
end
|
37
|
+
end # Fragments
|
38
|
+
end # SequenceRange
|
39
|
+
end # Range
|
40
|
+
end # RestrictionEnzyme
|
41
|
+
end # Bio
|