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 +1,38 @@
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#
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# = bio/appl/paml/common_report.rb - basic report class for PAML results
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#
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# Copyright:: Copyright (C) 2008
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# Naohisa Goto <ng@bioruby.org>
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#
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# License:: The Ruby License
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#
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# == Description
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#
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# This file contains Bio::PAML::Common::Report, a basic report class
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# for PAML program's results.
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#
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# == References
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#
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# * http://abacus.gene.ucl.ac.uk/software/paml.html
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#
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require 'bio/appl/paml/common'
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module Bio::PAML
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class Common
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# UNDER CONSTRUCTION.
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#
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# Bio::PAML::Common::Report is a basic report class for PAML program's
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# results. It will have common function for baseml and codeml.
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#
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# Normally, users should not use this class directly.
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class Report
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# Creates a new Report object.
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def initialize(str)
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end
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end #class Report
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end #class Common
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end #module Bio::PAML
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#
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# = bio/appl/paml/baseml.rb - Wrapper for running PAML program yn00
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#
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# Copyright:: Copyright (C) 2008
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# Naohisa Goto <ng@bioruby.org>
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#
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# License:: The Ruby License
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#
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# == Description
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#
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# This file contains Bio::PAML::Yn00, a wrapper class running yn00.
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#
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# == References
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#
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# * http://abacus.gene.ucl.ac.uk/software/paml.html
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#
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require 'bio/appl/paml/common'
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module Bio::PAML
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# == Description
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#
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# Bio::PAML::Yn00 is a wrapper for running PAML yn00 program.
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#
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# Because most of the methods in this class are inherited from
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# Bio::PAML::Common, see documents of Bio::PAML::Common for details.
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#
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# == Examples
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#
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# Example 1:
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#
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# require 'bio'
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# # Reads multi-fasta formatted file and gets a Bio::Alignment object.
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# alignment = Bio::FlatFile.open(Bio::Alignment::MultiFastaFormat,
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# 'example.fst').alignment
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# # Creates a Yn00 object
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# baseml = Bio::PAML::Yn00.new
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# # Sets parameters
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# baseml.parameters[:verbose] = 1
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# baseml.parameters[:icode] = 0
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# # You can also set many parameters at a time.
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# baseml.parameters.update({ :weighting => 0, :commonf3x4 => 0 })
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# # Executes yn00 with the alignment
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# report = yn00.query(alignment)
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#
|
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class Yn00 < Common
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autoload :Report, 'bio/appl/paml/yn00/report'
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# Default program name
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DEFAULT_PROGRAM = 'yn00'.freeze
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# Default parameters when running baseml.
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#
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# The parameters whose values are different from the baseml defalut
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# value (described in pamlDOC.pdf) in PAML 4.1 are:
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# seqfile, outfile, treefile, ndata, noisy, verbose
|
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#
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DEFAULT_PARAMETERS = {
|
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# Essential argumemts
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:seqfile => nil,
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:outfile => nil,
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# Optional arguments
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:verbose => 1,
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:icode => 0,
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:weighting => 0,
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:commonf3x4 => 0
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}
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# Runs the program on the internal parameters with the specified
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# sequence alignment.
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# Note that parameters[:seqfile] and parameters[:outfile]
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# are always modified.
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#
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# For other important information, see the document of
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# Bio::PAML::Common#query.
|
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#
|
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# ---
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# *Arguments*:
|
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# * (required) _alignment_: Bio::Alignment object or similar object
|
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# *Returns*:: Report object
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def query(alignment)
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super(alignment)
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end
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# Runs the program on the internal parameters with the specified
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# sequence alignment as a String object.
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#
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# For other important information, see the document of
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# query and Bio::PAML::Common#query_by_string methods.
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#
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# ---
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# *Arguments*:
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# * (required) _alignment_: Bio::Alignment object or similar object
|
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# *Returns*:: Report object
|
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def query_by_string(alignment = nil)
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super(alignment)
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end
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end #class Yn00
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end #module Bio::PAML
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#
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# = bio/appl/paml/baseml/report.rb - parser class for PAML program yn00
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#
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# Copyright:: Copyright (C) 2008
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# Naohisa Goto <ng@bioruby.org>
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#
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# License:: The Ruby License
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#
|
9
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# == Description
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#
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# This file contains Bio::PAML::Yn00::Report, a parser class for a result
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# of yn00.
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#
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# == References
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#
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# * http://abacus.gene.ucl.ac.uk/software/paml.html
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#
|
18
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require 'bio/appl/paml/yn00'
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module Bio::PAML
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class Yn00
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# UNDER CONSTRUCTION.
|
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#
|
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# Bio::PAML::Yn00::Report is a parser class for a yn00 result.
|
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#
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class Report < Bio::PAML::Common::Report
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end #class Report
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end #class Yn00
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end #module Bio::PAML
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#
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# = bio/appl/phylip/alignment.rb - phylip multiple alignment format parser
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#
|
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# Copyright:: Copyright (C) 2006
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# GOTO Naohisa <ng@bioruby.org>
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#
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# License:: The Ruby License
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#
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# $Id: alignment.rb,v 1.2 2007/04/05 23:35:40 trevor Exp $
|
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#
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# = About Bio::Phylip::PhylipFormat
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#
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# Please refer document of Bio::Phylip::PhylipFormat class.
|
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#
|
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module Bio
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module Phylip
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# This is phylip multiple alignment format parser.
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# The two formats, interleaved and non-interleaved, are
|
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# automatically determined.
|
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#
|
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class PhylipFormat
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|
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# create a new object from a string
|
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def initialize(str)
|
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@data = str.strip.split(/(?:\r\n|\r|\n)/)
|
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@first_line = @data.shift
|
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@number_of_sequences, @alignment_length =
|
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@first_line.to_s.strip.split(/\s+/).collect { |x| x.to_i }
|
31
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end
|
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|
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# number of sequences
|
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attr_reader :number_of_sequences
|
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|
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# alignment length
|
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attr_reader :alignment_length
|
38
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+
|
39
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# If the alignment format is "interleaved", returns true.
|
40
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+
# If not, returns false.
|
41
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+
# It would mistake to determine if the alignment is very short.
|
42
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+
def interleaved?
|
43
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+
unless defined? @interleaved_flag then
|
44
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+
if /\A +/ =~ @data[1].to_s then
|
45
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+
@interleaved_flag = false
|
46
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+
else
|
47
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+
@interleaved_flag = true
|
48
|
+
end
|
49
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+
end
|
50
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+
@interleaved_flag
|
51
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+
end
|
52
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+
|
53
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# Gets the alignment. Returns a Bio::Alignment object.
|
54
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+
def alignment
|
55
|
+
unless defined? @alignment then
|
56
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+
do_parse
|
57
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+
a = Bio::Alignment.new
|
58
|
+
(0...@number_of_sequences).each do |i|
|
59
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+
a.add_seq(@sequences[i], @sequence_names[i])
|
60
|
+
end
|
61
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@alignment = a
|
62
|
+
end
|
63
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+
@alignment
|
64
|
+
end
|
65
|
+
|
66
|
+
private
|
67
|
+
|
68
|
+
def do_parse
|
69
|
+
if interleaved? then
|
70
|
+
do_parse_interleaved
|
71
|
+
else
|
72
|
+
do_parse_noninterleaved
|
73
|
+
end
|
74
|
+
end
|
75
|
+
|
76
|
+
def do_parse_interleaved
|
77
|
+
first_block = @data[0, @number_of_sequences]
|
78
|
+
@data[0, @number_of_sequences] = ''
|
79
|
+
@sequence_names = Array.new(@number_of_sequences) { '' }
|
80
|
+
@sequences = Array.new(@number_of_sequences) do
|
81
|
+
' ' * @alignment_length
|
82
|
+
end
|
83
|
+
first_block.each_with_index do |x, i|
|
84
|
+
n, s = x.split(/ +/, 2)
|
85
|
+
if s.nil? # if there is no space separator, assume 10 character name
|
86
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+
n = x[0..9]
|
87
|
+
s = x[10..(x.length-1)]
|
88
|
+
end
|
89
|
+
@sequence_names[i] = n
|
90
|
+
@sequences[i].replace(s.gsub(/\s+/, ''))
|
91
|
+
end
|
92
|
+
i = 0
|
93
|
+
@data.each do |x|
|
94
|
+
if x.strip.length <= 0 then
|
95
|
+
i = 0
|
96
|
+
else
|
97
|
+
@sequences[i] << x.gsub(/\s+/, '')
|
98
|
+
i = (i + 1) % @number_of_sequences
|
99
|
+
end
|
100
|
+
end
|
101
|
+
@data.clear
|
102
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+
true
|
103
|
+
end
|
104
|
+
|
105
|
+
def do_parse_noninterleaved
|
106
|
+
@sequence_names = Array.new(@number_of_sequences) { '' }
|
107
|
+
@sequences = Array.new(@number_of_sequences) do
|
108
|
+
' ' * @alignment_length
|
109
|
+
end
|
110
|
+
curseq = nil
|
111
|
+
i = 0
|
112
|
+
@data.each do |x|
|
113
|
+
next if x.strip.length <= 0
|
114
|
+
if !curseq or
|
115
|
+
curseq.length > @alignment_length or /^\s/ !~ x then
|
116
|
+
p i
|
117
|
+
n, s = x.strip.split(/ +/, 2)
|
118
|
+
@sequence_names[i] = n
|
119
|
+
curseq = @sequences[i]
|
120
|
+
curseq.replace(s.gsub(/\s+/, ''))
|
121
|
+
i += 1
|
122
|
+
else
|
123
|
+
curseq << x.gsub(/\s+/, '')
|
124
|
+
end
|
125
|
+
end
|
126
|
+
@data.clear
|
127
|
+
true
|
128
|
+
end
|
129
|
+
|
130
|
+
end #class PhylipFormat
|
131
|
+
end #module Phylip
|
132
|
+
end #module Bio
|
133
|
+
|
@@ -0,0 +1,96 @@
|
|
1
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#
|
2
|
+
# = bio/appl/phylip/distance_matrix.rb - phylip distance matrix parser
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2006
|
5
|
+
# GOTO Naohisa <ng@bioruby.org>
|
6
|
+
#
|
7
|
+
# License:: The Ruby License
|
8
|
+
#
|
9
|
+
# $Id: distance_matrix.rb,v 1.3 2007/04/05 23:35:40 trevor Exp $
|
10
|
+
#
|
11
|
+
# = About Bio::Phylip::DistanceMatrix
|
12
|
+
#
|
13
|
+
# Please refer document of Bio::Phylip::DistanceMatrix class.
|
14
|
+
#
|
15
|
+
|
16
|
+
require 'matrix'
|
17
|
+
|
18
|
+
module Bio
|
19
|
+
module Phylip
|
20
|
+
|
21
|
+
# This is a parser class for phylip distance matrix data
|
22
|
+
# created by dnadist, protdist, or restdist commands.
|
23
|
+
#
|
24
|
+
class DistanceMatrix
|
25
|
+
|
26
|
+
# creates a new distance matrix object
|
27
|
+
def initialize(str)
|
28
|
+
data = str.strip.split(/(?:\r\n|\r|\n)/)
|
29
|
+
@otus = data.shift.to_s.strip.to_i
|
30
|
+
prev = nil
|
31
|
+
data.collect! do |x|
|
32
|
+
if /\A +/ =~ x and prev then
|
33
|
+
prev.concat x.strip.split(/\s+/)
|
34
|
+
nil
|
35
|
+
else
|
36
|
+
prev = x.strip.split(/\s+/)
|
37
|
+
prev
|
38
|
+
end
|
39
|
+
end
|
40
|
+
data.compact!
|
41
|
+
if data.size != @otus then
|
42
|
+
raise "inconsistent data (OTUs=#{@otus} but #{data.size} rows)"
|
43
|
+
end
|
44
|
+
@otu_names = data.collect { |x| x.shift }
|
45
|
+
mat = data.collect do |x|
|
46
|
+
if x.size != @otus then
|
47
|
+
raise "inconsistent data (OTUs=#{@otus} but #{x.size} columns)"
|
48
|
+
end
|
49
|
+
x.collect { |y| y.to_f }
|
50
|
+
end
|
51
|
+
@matrix = Matrix.rows(mat, false)
|
52
|
+
@original_matrix = Matrix.rows(data, false)
|
53
|
+
end
|
54
|
+
|
55
|
+
# distance matrix (returns Ruby's Matrix object)
|
56
|
+
attr_reader :matrix
|
57
|
+
|
58
|
+
# matrix contains values as original strings.
|
59
|
+
# Use it when you doubt precision of floating-point numbers.
|
60
|
+
attr_reader :original_matrix
|
61
|
+
|
62
|
+
# number of OTUs
|
63
|
+
attr_reader :otus
|
64
|
+
|
65
|
+
# names of OTUs
|
66
|
+
attr_reader :otu_names
|
67
|
+
|
68
|
+
# Generates a new phylip distance matrix formatted text as a string.
|
69
|
+
def self.generate(matrix, otu_names = nil, options = {})
|
70
|
+
if matrix.row_size != matrix.column_size then
|
71
|
+
raise "must be a square matrix"
|
72
|
+
end
|
73
|
+
otus = matrix.row_size
|
74
|
+
names = (0...otus).collect do |i|
|
75
|
+
name = ((otu_names and otu_names[i]) or "OTU#{i.to_s}")
|
76
|
+
name
|
77
|
+
end
|
78
|
+
data = (0...otus).collect do |i|
|
79
|
+
x = (0...otus).collect { |j| sprintf("%9.6f", matrix[i, j]) }
|
80
|
+
x.unshift(sprintf("%-10s", names[i])[0, 10])
|
81
|
+
|
82
|
+
str = x[0, 7].join(' ') + "\n"
|
83
|
+
7.step(otus + 1, 7) do |k|
|
84
|
+
str << ' ' + x[k, 7].join(' ') + "\n"
|
85
|
+
end
|
86
|
+
str
|
87
|
+
end
|
88
|
+
sprintf("%5d\n", otus) + data.join('')
|
89
|
+
end
|
90
|
+
|
91
|
+
end #class DistanceMatrix
|
92
|
+
|
93
|
+
end #module Phylip
|
94
|
+
|
95
|
+
end #module Bio
|
96
|
+
|
@@ -0,0 +1,41 @@
|
|
1
|
+
#
|
2
|
+
# = bio/appl/probcons.rb - ProbCons application wrapper class
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2006-2007
|
5
|
+
# Jeffrey Blakeslee and John Conery University of Oregon <jeffb@uoregon.edu>
|
6
|
+
# Naohisa Goto <ng@bioruby.org>
|
7
|
+
# License:: The Ruby License
|
8
|
+
#
|
9
|
+
# $Id: probcons.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $
|
10
|
+
#
|
11
|
+
# Bio::Probcons is a wrapper class to execute ProbCons
|
12
|
+
# (Probabilistic Consistency-based Multiple Alignment
|
13
|
+
# of Amino Acid Sequences).
|
14
|
+
#
|
15
|
+
# == References
|
16
|
+
#
|
17
|
+
# * http://probcons.stanford.edu/
|
18
|
+
# * Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S.
|
19
|
+
# ProbCons: Probabilistic Consistency-based Multiple Sequence Alignment.
|
20
|
+
# Genome Research 15: 330-340, 2005.
|
21
|
+
#
|
22
|
+
|
23
|
+
|
24
|
+
module Bio
|
25
|
+
|
26
|
+
# Bio::Probcons is a wrapper class to execute PROBCONS
|
27
|
+
# (Probabilistic Consistency-based Multiple Alignment
|
28
|
+
# of Amino Acid Sequences).
|
29
|
+
#
|
30
|
+
# Please refer documents in bio/apple/probcons.rb for references.
|
31
|
+
class Probcons < Bio::Alignment::FactoryTemplate::FileInStdoutOut
|
32
|
+
|
33
|
+
# default program name
|
34
|
+
DEFAULT_PROGRAM = 'probcons'.freeze
|
35
|
+
|
36
|
+
# default report parser
|
37
|
+
DEFAULT_PARSER = Bio::Alignment::MultiFastaFormat
|
38
|
+
|
39
|
+
end #class Probcons
|
40
|
+
|
41
|
+
end #module Bio
|