wwood-bioruby 1.2.11
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- data/README.rdoc +205 -0
- data/README_DEV.rdoc +285 -0
- data/VERSION.yml +4 -0
- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +293 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/lib/bio.rb +306 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +505 -0
- data/lib/bio/appl/blast/ddbj.rb +142 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/genomenet.rb +263 -0
- data/lib/bio/appl/blast/ncbioptions.rb +220 -0
- data/lib/bio/appl/blast/remote.rb +105 -0
- data/lib/bio/appl/blast/report.rb +767 -0
- data/lib/bio/appl/blast/rexml.rb +144 -0
- data/lib/bio/appl/blast/rpsblast.rb +277 -0
- data/lib/bio/appl/blast/wublast.rb +635 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blat/report.rb +530 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta.rb +235 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/gcg/msf.rb +212 -0
- data/lib/bio/appl/gcg/seq.rb +195 -0
- data/lib/bio/appl/genscan/report.rb +552 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/hmmer/report.rb +683 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/paml/baseml.rb +95 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/codeml.rb +242 -0
- data/lib/bio/appl/paml/codeml/rates.rb +67 -0
- data/lib/bio/appl/paml/codeml/report.rb +67 -0
- data/lib/bio/appl/paml/common.rb +348 -0
- data/lib/bio/appl/paml/common_report.rb +38 -0
- data/lib/bio/appl/paml/yn00.rb +103 -0
- data/lib/bio/appl/paml/yn00/report.rb +32 -0
- data/lib/bio/appl/phylip/alignment.rb +133 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/psort/report.rb +542 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +124 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sosui/report.rb +151 -0
- data/lib/bio/appl/spidey/report.rb +593 -0
- data/lib/bio/appl/targetp/report.rb +267 -0
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +231 -0
- data/lib/bio/command.rb +593 -0
- data/lib/bio/compat/features.rb +157 -0
- data/lib/bio/compat/references.rb +128 -0
- data/lib/bio/data/aa.rb +353 -0
- data/lib/bio/data/codontable.rb +722 -0
- data/lib/bio/data/na.rb +223 -0
- data/lib/bio/db.rb +329 -0
- data/lib/bio/db/aaindex.rb +357 -0
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +67 -0
- data/lib/bio/db/biosql/sequence.rb +508 -0
- data/lib/bio/db/embl/common.rb +352 -0
- data/lib/bio/db/embl/embl.rb +500 -0
- data/lib/bio/db/embl/embl_to_biosequence.rb +85 -0
- data/lib/bio/db/embl/format_embl.rb +190 -0
- data/lib/bio/db/embl/sptr.rb +1283 -0
- data/lib/bio/db/embl/swissprot.rb +42 -0
- data/lib/bio/db/embl/trembl.rb +41 -0
- data/lib/bio/db/embl/uniprot.rb +42 -0
- data/lib/bio/db/fantom.rb +597 -0
- data/lib/bio/db/fasta.rb +410 -0
- data/lib/bio/db/fasta/defline.rb +532 -0
- data/lib/bio/db/fasta/fasta_to_biosequence.rb +63 -0
- data/lib/bio/db/fasta/format_fasta.rb +97 -0
- data/lib/bio/db/genbank/common.rb +307 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/format_genbank.rb +187 -0
- data/lib/bio/db/genbank/genbank.rb +250 -0
- data/lib/bio/db/genbank/genbank_to_biosequence.rb +86 -0
- data/lib/bio/db/genbank/genpept.rb +60 -0
- data/lib/bio/db/genbank/refseq.rb +18 -0
- data/lib/bio/db/gff.rb +1846 -0
- data/lib/bio/db/go.rb +481 -0
- data/lib/bio/db/kegg/brite.rb +41 -0
- data/lib/bio/db/kegg/compound.rb +131 -0
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +148 -0
- data/lib/bio/db/kegg/expression.rb +155 -0
- data/lib/bio/db/kegg/genes.rb +263 -0
- data/lib/bio/db/kegg/genome.rb +241 -0
- data/lib/bio/db/kegg/glycan.rb +166 -0
- data/lib/bio/db/kegg/keggtab.rb +357 -0
- data/lib/bio/db/kegg/kgml.rb +256 -0
- data/lib/bio/db/kegg/orthology.rb +136 -0
- data/lib/bio/db/kegg/reaction.rb +82 -0
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +107 -0
- data/lib/bio/db/medline.rb +326 -0
- data/lib/bio/db/nbrf.rb +191 -0
- data/lib/bio/db/newick.rb +658 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +29 -0
- data/lib/bio/db/pdb/atom.rb +77 -0
- data/lib/bio/db/pdb/chain.rb +210 -0
- data/lib/bio/db/pdb/chemicalcomponent.rb +224 -0
- data/lib/bio/db/pdb/model.rb +148 -0
- data/lib/bio/db/pdb/pdb.rb +1911 -0
- data/lib/bio/db/pdb/residue.rb +176 -0
- data/lib/bio/db/pdb/utils.rb +399 -0
- data/lib/bio/db/prosite.rb +597 -0
- data/lib/bio/db/rebase.rb +456 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/db/url.rb +42 -0
- data/lib/bio/feature.rb +139 -0
- data/lib/bio/io/biosql/biodatabase.rb +64 -0
- data/lib/bio/io/biosql/bioentry.rb +29 -0
- data/lib/bio/io/biosql/bioentry_dbxref.rb +11 -0
- data/lib/bio/io/biosql/bioentry_path.rb +12 -0
- data/lib/bio/io/biosql/bioentry_qualifier_value.rb +10 -0
- data/lib/bio/io/biosql/bioentry_reference.rb +10 -0
- data/lib/bio/io/biosql/bioentry_relationship.rb +10 -0
- data/lib/bio/io/biosql/biosequence.rb +11 -0
- data/lib/bio/io/biosql/comment.rb +7 -0
- data/lib/bio/io/biosql/config/database.yml +20 -0
- data/lib/bio/io/biosql/dbxref.rb +13 -0
- data/lib/bio/io/biosql/dbxref_qualifier_value.rb +12 -0
- data/lib/bio/io/biosql/location.rb +32 -0
- data/lib/bio/io/biosql/location_qualifier_value.rb +11 -0
- data/lib/bio/io/biosql/ontology.rb +10 -0
- data/lib/bio/io/biosql/reference.rb +9 -0
- data/lib/bio/io/biosql/seqfeature.rb +32 -0
- data/lib/bio/io/biosql/seqfeature_dbxref.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_path.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_qualifier_value.rb +20 -0
- data/lib/bio/io/biosql/seqfeature_relationship.rb +11 -0
- data/lib/bio/io/biosql/taxon.rb +12 -0
- data/lib/bio/io/biosql/taxon_name.rb +9 -0
- data/lib/bio/io/biosql/term.rb +27 -0
- data/lib/bio/io/biosql/term_dbxref.rb +11 -0
- data/lib/bio/io/biosql/term_path.rb +12 -0
- data/lib/bio/io/biosql/term_relationship.rb +13 -0
- data/lib/bio/io/biosql/term_relationship_term.rb +11 -0
- data/lib/bio/io/biosql/term_synonym.rb +10 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +638 -0
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +163 -0
- data/lib/bio/io/fetch.rb +195 -0
- data/lib/bio/io/flatfile.rb +482 -0
- data/lib/bio/io/flatfile/autodetection.rb +545 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/buffer.rb +237 -0
- data/lib/bio/io/flatfile/index.rb +1381 -0
- data/lib/bio/io/flatfile/indexer.rb +805 -0
- data/lib/bio/io/flatfile/splitter.rb +297 -0
- data/lib/bio/io/higet.rb +73 -0
- data/lib/bio/io/hinv.rb +442 -0
- data/lib/bio/io/keggapi.rb +805 -0
- data/lib/bio/io/ncbirest.rb +733 -0
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +307 -0
- data/lib/bio/io/registry.rb +292 -0
- data/lib/bio/io/soapwsdl.rb +119 -0
- data/lib/bio/io/sql.rb +186 -0
- data/lib/bio/location.rb +867 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +960 -0
- data/lib/bio/reference.rb +602 -0
- data/lib/bio/sequence.rb +456 -0
- data/lib/bio/sequence/aa.rb +152 -0
- data/lib/bio/sequence/adapter.rb +108 -0
- data/lib/bio/sequence/common.rb +310 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/dblink.rb +54 -0
- data/lib/bio/sequence/format.rb +358 -0
- data/lib/bio/sequence/format_raw.rb +23 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +491 -0
- data/lib/bio/shell.rb +44 -0
- data/lib/bio/shell/core.rb +578 -0
- data/lib/bio/shell/demo.rb +146 -0
- data/lib/bio/shell/interface.rb +218 -0
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +71 -0
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +218 -0
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +105 -0
- data/lib/bio/shell/plugin/flatfile.rb +101 -0
- data/lib/bio/shell/plugin/keggapi.rb +181 -0
- data/lib/bio/shell/plugin/midi.rb +430 -0
- data/lib/bio/shell/plugin/obda.rb +45 -0
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +247 -0
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +102 -0
- data/lib/bio/tree.rb +852 -0
- data/lib/bio/util/color_scheme.rb +191 -0
- data/lib/bio/util/color_scheme/buried.rb +59 -0
- data/lib/bio/util/color_scheme/helix.rb +59 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +64 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +31 -0
- data/lib/bio/util/color_scheme/strand.rb +59 -0
- data/lib/bio/util/color_scheme/taylor.rb +50 -0
- data/lib/bio/util/color_scheme/turn.rb +59 -0
- data/lib/bio/util/color_scheme/zappo.rb +50 -0
- data/lib/bio/util/contingency_table.rb +370 -0
- data/lib/bio/util/restriction_enzyme.rb +228 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
- data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +200 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/aaindex/DAYM780301 +30 -0
- data/test/data/aaindex/PRAM900102 +20 -0
- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
- data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
- data/test/data/blast/2.2.15.blastp.m7 +876 -0
- data/test/data/blast/b0002.faa +15 -0
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- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/blast/blastp-multi.m7 +188 -0
- data/test/data/command/echoarg2.bat +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/embl/AB090716.embl.rel89 +63 -0
- data/test/data/fasta/example1.txt +75 -0
- data/test/data/fasta/example2.txt +21 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/paml/codeml/control_file.txt +30 -0
- data/test/data/paml/codeml/output.txt +78 -0
- data/test/data/paml/codeml/rates +217 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/rpsblast/misc.rpsblast +193 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/functional/bio/appl/test_pts1.rb +115 -0
- data/test/functional/bio/io/test_ensembl.rb +229 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -0
- data/test/functional/bio/sequence/test_output_embl.rb +51 -0
- data/test/functional/bio/test_command.rb +301 -0
- data/test/runner.rb +14 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_ncbioptions.rb +112 -0
- data/test/unit/bio/appl/blast/test_report.rb +1135 -0
- data/test/unit/bio/appl/blast/test_rpsblast.rb +398 -0
- data/test/unit/bio/appl/genscan/test_report.rb +182 -0
- data/test/unit/bio/appl/hmmer/test_report.rb +342 -0
- data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
- data/test/unit/bio/appl/mafft/test_report.rb +63 -0
- data/test/unit/bio/appl/paml/codeml/test_rates.rb +45 -0
- data/test/unit/bio/appl/paml/codeml/test_report.rb +45 -0
- data/test/unit/bio/appl/paml/test_codeml.rb +174 -0
- data/test/unit/bio/appl/sosui/test_report.rb +81 -0
- data/test/unit/bio/appl/targetp/test_report.rb +146 -0
- data/test/unit/bio/appl/test_blast.rb +277 -0
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_psort.rb +57 -0
- data/test/unit/bio/appl/test_pts1.rb +77 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +126 -0
- data/test/unit/bio/data/test_aa.rb +90 -0
- data/test/unit/bio/data/test_codontable.rb +107 -0
- data/test/unit/bio/data/test_na.rb +80 -0
- data/test/unit/bio/db/embl/test_common.rb +117 -0
- data/test/unit/bio/db/embl/test_embl.rb +214 -0
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +203 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1812 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +31 -0
- data/test/unit/bio/db/kegg/test_genes.rb +45 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +152 -0
- data/test/unit/bio/db/test_aaindex.rb +197 -0
- data/test/unit/bio/db/test_fasta.rb +250 -0
- data/test/unit/bio/db/test_gff.rb +1190 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_medline.rb +127 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +364 -0
- data/test/unit/bio/db/test_prosite.rb +1437 -0
- data/test/unit/bio/db/test_rebase.rb +101 -0
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/db/test_url.rb +36 -0
- data/test/unit/bio/io/flatfile/test_autodetection.rb +375 -0
- data/test/unit/bio/io/flatfile/test_buffer.rb +251 -0
- data/test/unit/bio/io/flatfile/test_splitter.rb +369 -0
- data/test/unit/bio/io/test_ddbjxml.rb +80 -0
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +42 -0
- data/test/unit/bio/io/test_flatfile.rb +505 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +115 -0
- data/test/unit/bio/sequence/test_common.rb +373 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -0
- data/test/unit/bio/sequence/test_dblink.rb +58 -0
- data/test/unit/bio/sequence/test_na.rb +330 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +185 -0
- data/test/unit/bio/test_alignment.rb +1025 -0
- data/test/unit/bio/test_command.rb +349 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +144 -0
- data/test/unit/bio/test_location.rb +599 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +499 -0
- data/test/unit/bio/test_reference.rb +252 -0
- data/test/unit/bio/test_sequence.rb +329 -0
- data/test/unit/bio/test_shell.rb +18 -0
- data/test/unit/bio/test_tree.rb +593 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +101 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
- data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
- data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
- data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
- data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
- data/test/unit/bio/util/test_color_scheme.rb +33 -0
- data/test/unit/bio/util/test_contingency_table.rb +94 -0
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +245 -0
- metadata +543 -0
@@ -0,0 +1,191 @@
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#
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# bio/util/color_scheme.rb - Popular color codings for nucleic and amino acids
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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: color_scheme.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
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#
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module Bio #:nodoc:
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#
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# bio/util/color_scheme.rb - Popular color codings for nucleic and amino acids
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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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#
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# = Description
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#
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# The Bio::ColorScheme module contains classes that return popular color codings
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# for nucleic and amino acids in RGB hex format suitable for HTML code.
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#
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# The current schemes supported are:
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# * Buried - Buried index
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# * Helix - Helix propensity
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# * Hydropathy - Hydrophobicity
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# * Nucleotide - Nucelotide color coding
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# * Strand - Strand propensity
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# * Taylor - Taylor color coding
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# * Turn - Turn propensity
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# * Zappo - Zappo color coding
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#
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# Planned color schemes include:
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# * BLOSUM62
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# * ClustalX
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# * Percentage Identity (PID)
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#
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# Color schemes BLOSUM62, ClustalX, and Percentage Identity are all dependent
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# on the alignment consensus.
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#
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# This data is currently referenced from the JalView alignment editor.
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# Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004),
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# "The Jalview Java Alignment Editor," Bioinformatics, 12, 426-7
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# http://www.jalview.org
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#
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# Currently the score data for things such as hydropathy, helix, turn, etc. are contained
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# here but should be moved to bio/data/aa once a good reference is found for these
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# values.
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#
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#
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# = Usage
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#
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# require 'bio'
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#
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# seq = 'gattaca'
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# scheme = Bio::ColorScheme::Zappo
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# postfix = '</span>'
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# html = ''
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# seq.each_byte do |c|
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# color = scheme[c.chr]
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# prefix = %Q(<span style="background:\##{color};">)
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# html += prefix + c.chr + postfix
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# end
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#
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# puts html
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#
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#
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# == Accessing colors
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#
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# puts Bio::ColorScheme::Buried['A'] # 00DC22
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# puts Bio::ColorScheme::Buried[:c] # 00BF3F
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# puts Bio::ColorScheme::Buried[nil] # nil
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# puts Bio::ColorScheme::Buried['-'] # FFFFFF
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# puts Bio::ColorScheme::Buried[7] # FFFFFF
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# puts Bio::ColorScheme::Buried['junk'] # FFFFFF
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# puts Bio::ColorScheme::Buried['t'] # 00CC32
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#
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module ColorScheme
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cs_location = File.join(File.dirname(File.expand_path(__FILE__)), 'color_scheme')
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# Score sub-classes
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autoload :Buried, File.join(cs_location, 'buried')
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autoload :Helix, File.join(cs_location, 'helix')
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autoload :Hydropathy, File.join(cs_location, 'hydropathy')
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autoload :Strand, File.join(cs_location, 'strand')
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autoload :Turn, File.join(cs_location, 'turn')
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# Simple sub-classes
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autoload :Nucleotide, File.join(cs_location, 'nucleotide')
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autoload :Taylor, File.join(cs_location, 'taylor')
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autoload :Zappo, File.join(cs_location, 'zappo')
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# Consensus sub-classes
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# NOTE todo
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# BLOSUM62
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# ClustalX
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# PID
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# A very basic class template for color code referencing.
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class Simple #:nodoc:
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def self.[](x)
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return if x.nil?
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# accept symbols and any case
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@colors[x.to_s.upcase]
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end
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def self.colors() @colors end
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#######
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private
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#######
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# Example
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@colors = {
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'A' => '64F73F',
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}
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@colors.default = 'FFFFFF' # return white by default
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end
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# A class template for color code referencing of color schemes
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# that are score based. This template is expected to change
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# when the scores are moved into bio/data/aa
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class Score #:nodoc:
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def self.[](x)
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return if x.nil?
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# accept symbols and any case
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@colors[x.to_s.upcase]
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end
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def self.min(x) @min end
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def self.max(x) @max end
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def self.scores() @scores end
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def self.colors() @colors end
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#########
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protected
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#########
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def self.percent_to_hex(percent)
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percent = percent.to_f if percent.is_a?(String)
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if (percent > 1.0) or (percent < 0.0) or percent.nil?
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raise 'Percentage must be between 0.0 and 1.0'
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end
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"%02X" % (percent * 255.0)
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end
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def self.rgb_percent_to_hex(red, green, blue)
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percent_to_hex(red) + percent_to_hex(green) + percent_to_hex(blue)
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end
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def self.score_to_percent(score, min, max)
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# .to_f to ensure every operation is float-aware
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percent = (score.to_f - min) / (max.to_f - min)
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percent = 1.0 if percent > 1.0
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percent = 0.0 if percent < 0.0
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percent
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end
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#######
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private
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#######
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# Example
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def self.score_to_rgb_hex(score, min, max)
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percent = score_to_percent(score, min, max)
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rgb_percent_to_hex(percent, 0.0, 1.0-percent)
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end
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@colors = {}
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@scores = {
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'A' => 0.83,
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}
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@min = 0.37
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@max = 1.7
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@scores.each { |k,s| @colors[k] = score_to_rgb_hex(s, @min, @max) }
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@colors.default = 'FFFFFF' # return white by default
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end
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# TODO
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class Consensus #:nodoc:
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end
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end # module ColorScheme
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end # module Bio
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#
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# bio/util/color_scheme/buried.rb - Color codings for buried amino acids
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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: buried.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
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#
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require 'bio/util/color_scheme'
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module Bio::ColorScheme
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class Buried < Score #:nodoc:
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#########
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protected
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#########
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def self.score_to_rgb_hex(score, min, max)
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percent = score_to_percent(score, min, max)
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rgb_percent_to_hex(0.0, 1.0-percent, percent)
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end
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@colors = {}
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@scores = {
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'A' => 0.66,
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'C' => 1.19,
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'D' => 1.46,
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'E' => 0.74,
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'F' => 0.6,
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'G' => 1.56,
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'H' => 0.95,
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'I' => 0.47,
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'K' => 1.01,
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'L' => 0.59,
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'M' => 0.6,
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'N' => 1.56,
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'P' => 1.52,
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'Q' => 0.98,
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'R' => 0.95,
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'S' => 1.43,
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'T' => 0.96,
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'U' => 0,
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'V' => 0.5,
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'W' => 0.96,
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'Y' => 1.14,
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'B' => 1.51,
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'X' => 1.0,
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'Z' => 0.86,
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}
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@min = 0.05
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@max = 4.6
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@scores.each { |k,s| @colors[k] = score_to_rgb_hex(s, @min, @max) }
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@colors.default = 'FFFFFF' # return white by default
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end
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end
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#
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# bio/util/color_scheme/helix.rb - Color codings for helix propensity
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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: helix.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
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#
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require 'bio/util/color_scheme'
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module Bio::ColorScheme
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class Helix < Score #:nodoc:
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#########
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protected
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#########
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def self.score_to_rgb_hex(score, min, max)
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percent = score_to_percent(score, min, max)
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rgb_percent_to_hex(percent, 1.0-percent, percent)
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end
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@colors = {}
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@scores = {
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'A' => 1.42,
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'C' => 0.7,
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'D' => 1.01,
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'E' => 1.51,
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'F' => 1.13,
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'G' => 0.57,
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'H' => 1.0,
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'I' => 1.08,
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'K' => 1.16,
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'L' => 1.21,
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'M' => 1.45,
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'N' => 0.67,
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'P' => 0.57,
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'Q' => 1.11,
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'R' => 0.98,
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'S' => 0.77,
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'T' => 0.83,
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'U' => 0.0,
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'V' => 1.06,
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'W' => 1.08,
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'Y' => 0.69,
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'B' => 0.84,
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'X' => 1.0,
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'Z' => 1.31,
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}
|
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@min = 0.57
|
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@max = 1.51
|
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@scores.each { |k,s| @colors[k] = score_to_rgb_hex(s, @min, @max) }
|
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@colors.default = 'FFFFFF' # return white by default
|
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end
|
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end
|
@@ -0,0 +1,64 @@
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#
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# bio/util/color_scheme/hydropathy.rb - Color codings for hydrophobicity
|
3
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#
|
4
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
|
5
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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6
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# License:: The Ruby License
|
7
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#
|
8
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# $Id: hydropathy.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
|
9
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#
|
10
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+
|
11
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require 'bio/util/color_scheme'
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12
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+
|
13
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module Bio::ColorScheme
|
14
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+
|
15
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# Hydropathy index
|
16
|
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# Kyte, J., and Doolittle, R.F., J. Mol. Biol.
|
17
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# 1157, 105-132, 1982
|
18
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+
|
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class Hydropathy < Score #:nodoc:
|
20
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+
|
21
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+
#########
|
22
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+
protected
|
23
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+
#########
|
24
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+
|
25
|
+
def self.score_to_rgb_hex(score, min, max)
|
26
|
+
percent = score_to_percent(score, min, max)
|
27
|
+
rgb_percent_to_hex(percent, 0.0, 1.0-percent)
|
28
|
+
end
|
29
|
+
|
30
|
+
@colors = {}
|
31
|
+
@scores = {
|
32
|
+
'A' => 1.8,
|
33
|
+
'C' => 2.5,
|
34
|
+
'D' => -3.5,
|
35
|
+
'E' => -3.5,
|
36
|
+
'F' => 2.8,
|
37
|
+
'G' => -0.4,
|
38
|
+
'H' => -3.2,
|
39
|
+
'I' => 4.5,
|
40
|
+
'K' => -3.9,
|
41
|
+
'L' => 3.8,
|
42
|
+
'M' => 1.9,
|
43
|
+
'N' => -3.5,
|
44
|
+
'P' => -1.6,
|
45
|
+
'Q' => -3.5,
|
46
|
+
'R' => -4.5,
|
47
|
+
'S' => -0.8,
|
48
|
+
'T' => -0.7,
|
49
|
+
'U' => 0.0,
|
50
|
+
'V' => 4.2,
|
51
|
+
'W' => -0.9,
|
52
|
+
'Y' => -1.3,
|
53
|
+
|
54
|
+
'B' => -3.5,
|
55
|
+
'X' => -0.49,
|
56
|
+
'Z' => -3.5,
|
57
|
+
}
|
58
|
+
@min = -3.9
|
59
|
+
@max = 4.5
|
60
|
+
@scores.each { |k,s| @colors[k] = score_to_rgb_hex(s, @min, @max) }
|
61
|
+
@colors.default = 'FFFFFF' # return white by default
|
62
|
+
|
63
|
+
end
|
64
|
+
end
|
@@ -0,0 +1,31 @@
|
|
1
|
+
#
|
2
|
+
# bio/util/color_scheme/nucleotide.rb - Color codings for nucleotides
|
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: nucleotide.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
require 'bio/util/color_scheme'
|
12
|
+
|
13
|
+
module Bio::ColorScheme
|
14
|
+
class Nucleotide < Simple #:nodoc:
|
15
|
+
|
16
|
+
#########
|
17
|
+
protected
|
18
|
+
#########
|
19
|
+
|
20
|
+
@colors = {
|
21
|
+
'A' => '64F73F',
|
22
|
+
'C' => 'FFB340',
|
23
|
+
'G' => 'EB413C',
|
24
|
+
'T' => '3C88EE',
|
25
|
+
'U' => '3C88EE',
|
26
|
+
}
|
27
|
+
@colors.default = 'FFFFFF' # return white by default
|
28
|
+
|
29
|
+
end
|
30
|
+
NA = Nuc = Nucleotide
|
31
|
+
end
|
@@ -0,0 +1,59 @@
|
|
1
|
+
#
|
2
|
+
# bio/util/color_scheme/strand.rb - Color codings for strand propensity
|
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: strand.rb,v 1.5 2007/04/05 23:35:41 trevor Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
require 'bio/util/color_scheme'
|
12
|
+
|
13
|
+
module Bio::ColorScheme
|
14
|
+
class Strand < Score #:nodoc:
|
15
|
+
|
16
|
+
#########
|
17
|
+
protected
|
18
|
+
#########
|
19
|
+
|
20
|
+
def self.score_to_rgb_hex(score, min, max)
|
21
|
+
percent = score_to_percent(score, min, max)
|
22
|
+
rgb_percent_to_hex(percent, percent, 1.0-percent)
|
23
|
+
end
|
24
|
+
|
25
|
+
@colors = {}
|
26
|
+
@scores = {
|
27
|
+
'A' => 0.83,
|
28
|
+
'C' => 1.19,
|
29
|
+
'D' => 0.54,
|
30
|
+
'E' => 0.37,
|
31
|
+
'F' => 1.38,
|
32
|
+
'G' => 0.75,
|
33
|
+
'H' => 0.87,
|
34
|
+
'I' => 1.6,
|
35
|
+
'K' => 0.74,
|
36
|
+
'L' => 1.3,
|
37
|
+
'M' => 1.05,
|
38
|
+
'N' => 0.89,
|
39
|
+
'P' => 0.55,
|
40
|
+
'Q' => 1.1,
|
41
|
+
'R' => 0.93,
|
42
|
+
'S' => 0.75,
|
43
|
+
'T' => 1.19,
|
44
|
+
'U' => 0.0,
|
45
|
+
'V' => 1.7,
|
46
|
+
'W' => 1.37,
|
47
|
+
'Y' => 1.47,
|
48
|
+
|
49
|
+
'B' => 0.72,
|
50
|
+
'X' => 1.0,
|
51
|
+
'Z' => 0.74,
|
52
|
+
}
|
53
|
+
@min = 0.37
|
54
|
+
@max = 1.7
|
55
|
+
@scores.each { |k,s| @colors[k] = score_to_rgb_hex(s, @min, @max) }
|
56
|
+
@colors.default = 'FFFFFF' # return white by default
|
57
|
+
|
58
|
+
end
|
59
|
+
end
|