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
data/lib/bio/db/url.rb
ADDED
@@ -0,0 +1,42 @@
|
|
1
|
+
module Bio
|
2
|
+
# A module dedicated to providing URLs to common bioinformatic databases.
|
3
|
+
module URLGenerators
|
4
|
+
def pantherdb_panther_family_url(panther_id)
|
5
|
+
"http://www.pantherdb.org/panther/family.do?clsAccession=#{panther_id}"
|
6
|
+
end
|
7
|
+
|
8
|
+
def hhmi_pfam_family_url(pfam_family_id)
|
9
|
+
"http://pfam.janelia.org/family?entry=#{pfam_family_id}&type=Family"
|
10
|
+
end
|
11
|
+
|
12
|
+
def plasmodb_gene_url(plasmodb_id)
|
13
|
+
"http://plasmodb.org/gene/#{plasmodb_id}"
|
14
|
+
end
|
15
|
+
|
16
|
+
def pdb_url(pdbId)
|
17
|
+
"http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=#{pdbId}"
|
18
|
+
end
|
19
|
+
|
20
|
+
def pdbsum_url(pdbId)
|
21
|
+
"http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=#{pdbId}"
|
22
|
+
end
|
23
|
+
|
24
|
+
def cath_url(pdbId)
|
25
|
+
"http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/SearchPdb.pl?query=#{pdbId}&type=PDB"
|
26
|
+
end
|
27
|
+
|
28
|
+
def scop_url(pdbId)
|
29
|
+
"http://scop.mrc-lmb.cam.ac.uk/scop/pdb.cgi?disp=scop&id=#{pdbId}"
|
30
|
+
end
|
31
|
+
end
|
32
|
+
|
33
|
+
# Convenience class that allows easier creation of URLs.
|
34
|
+
# Use case: I have a gene name (PF11_0344) and I want to be able to generate
|
35
|
+
# a link to the corresponding PlasmoDB gene page, I can call Bio::URL.plasmodb_gene_url('PF11_0344')
|
36
|
+
class URL
|
37
|
+
# Include all the URL generators as static methods
|
38
|
+
class << self
|
39
|
+
include URLGenerators
|
40
|
+
end
|
41
|
+
end
|
42
|
+
end
|
data/lib/bio/feature.rb
ADDED
@@ -0,0 +1,139 @@
|
|
1
|
+
#
|
2
|
+
# = bio/feature.rb - Features/Feature class (GenBank Feature table)
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (c) 2002, 2005 Toshiaki Katayama <k@bioruby.org>
|
5
|
+
# 2006 Jan Aerts <jan.aerts@bbsrc.ac.uk>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: feature.rb,v 1.13.2.1 2008/03/04 10:12:22 ngoto Exp $
|
9
|
+
|
10
|
+
require 'bio/location'
|
11
|
+
|
12
|
+
module Bio
|
13
|
+
|
14
|
+
# = DESCRIPTION
|
15
|
+
# Container for the sequence annotation.
|
16
|
+
#
|
17
|
+
# = USAGE
|
18
|
+
# # Create a Bio::Feature object.
|
19
|
+
# # For example: the GenBank-formatted entry in genbank for accession M33388
|
20
|
+
# # contains the following feature:
|
21
|
+
# # exon 1532..1799
|
22
|
+
# # /gene="CYP2D6"
|
23
|
+
# # /note="cytochrome P450 IID6; GOO-132-127"
|
24
|
+
# # /number="1"
|
25
|
+
# feature = Bio::Feature.new('exon','1532..1799')
|
26
|
+
# feature.append(Bio::Feature::Qualifier.new('gene', 'CYP2D6'))
|
27
|
+
# feature.append(Bio::Feature::Qualifier.new('note', 'cytochrome P450 IID6'))
|
28
|
+
# feature.append(Bio::Feature::Qualifier.new('number', '1'))
|
29
|
+
#
|
30
|
+
# # or all in one go:
|
31
|
+
# feature2 = Bio::Feature.new('exon','1532..1799',
|
32
|
+
# [ Bio::Feature::Qualifier.new('gene', 'CYP2D6'),
|
33
|
+
# Bio::Feature::Qualifier.new('note', 'cytochrome P450 IID6; GOO-132-127'),
|
34
|
+
# Bio::Feature::Qualifier.new('number', '1')
|
35
|
+
# ])
|
36
|
+
#
|
37
|
+
# # Print the feature
|
38
|
+
# puts feature.feature + "\t" + feature.position
|
39
|
+
# feature.each do |qualifier|
|
40
|
+
# puts "- " + qualifier.qualifier + ": " + qualifier.value
|
41
|
+
# end
|
42
|
+
#
|
43
|
+
# = REFERENCES
|
44
|
+
# INSD feature table definition:: http://www.ddbj.nig.ac.jp/FT/full_index.html
|
45
|
+
class Feature
|
46
|
+
# Create a new Bio::Feature object.
|
47
|
+
# *Arguments*:
|
48
|
+
# * (required) _feature_: type of feature (e.g. "exon")
|
49
|
+
# * (required) _position_: position of feature (e.g. "complement(1532..1799)")
|
50
|
+
# * (opt) _qualifiers_: list of Bio::Feature::Qualifier objects (default: [])
|
51
|
+
# *Returns*:: Bio::Feature object
|
52
|
+
def initialize(feature = '', position = '', qualifiers = [])
|
53
|
+
@feature, @position, @qualifiers = feature, position, qualifiers
|
54
|
+
end
|
55
|
+
|
56
|
+
# Returns type of feature in String (e.g 'CDS', 'gene')
|
57
|
+
attr_accessor :feature
|
58
|
+
|
59
|
+
# Returns position of the feature in String (e.g. 'complement(123..146)')
|
60
|
+
attr_accessor :position
|
61
|
+
|
62
|
+
# Returns an Array of Qualifier objects.
|
63
|
+
attr_accessor :qualifiers
|
64
|
+
|
65
|
+
# Returns a Bio::Locations object translated from the position string.
|
66
|
+
def locations
|
67
|
+
Locations.new(@position)
|
68
|
+
end
|
69
|
+
|
70
|
+
# Appends a Qualifier object to the Feature.
|
71
|
+
#
|
72
|
+
# *Arguments*:
|
73
|
+
# * (required) _qualifier_: Bio::Feature::Qualifier object
|
74
|
+
# *Returns*:: Bio::Feature object
|
75
|
+
def append(a)
|
76
|
+
@qualifiers.push(a) if a.is_a? Qualifier
|
77
|
+
return self
|
78
|
+
end
|
79
|
+
|
80
|
+
# Iterates on each qualifier object.
|
81
|
+
#
|
82
|
+
# *Arguments*:
|
83
|
+
# * (optional) _key_: if specified, only iterates over qualifiers with this key
|
84
|
+
def each(arg = nil)
|
85
|
+
@qualifiers.each do |x|
|
86
|
+
next if arg and x.qualifier != arg
|
87
|
+
yield x
|
88
|
+
end
|
89
|
+
end
|
90
|
+
|
91
|
+
# Returns a Hash constructed from qualifier objects.
|
92
|
+
def assoc
|
93
|
+
STDERR.puts "Bio::Feature#assoc is deprecated, use Bio::Feature#to_hash instead" if $DEBUG
|
94
|
+
hash = Hash.new
|
95
|
+
@qualifiers.each do |x|
|
96
|
+
hash[x.qualifier] = x.value
|
97
|
+
end
|
98
|
+
return hash
|
99
|
+
end
|
100
|
+
|
101
|
+
# Returns a Hash constructed from qualifier objects.
|
102
|
+
def to_hash
|
103
|
+
hash = Hash.new
|
104
|
+
@qualifiers.each do |x|
|
105
|
+
hash[x.qualifier] ||= []
|
106
|
+
hash[x.qualifier] << x.value
|
107
|
+
end
|
108
|
+
return hash
|
109
|
+
end
|
110
|
+
|
111
|
+
# Short cut for the Bio::Feature#to_hash[key]
|
112
|
+
def [](key)
|
113
|
+
self.to_hash[key]
|
114
|
+
end
|
115
|
+
|
116
|
+
# Container for qualifier-value pairs for sequence features.
|
117
|
+
class Qualifier
|
118
|
+
# Creates a new Bio::Feature::Qualifier object
|
119
|
+
#
|
120
|
+
# *Arguments*:
|
121
|
+
# * (required) _key_: key of the qualifier (e.g. "gene")
|
122
|
+
# * (required) _value_: value of the qualifier (e.g. "CYP2D6")
|
123
|
+
# *Returns*:: Bio::Feature::Qualifier object
|
124
|
+
def initialize(key, value)
|
125
|
+
@qualifier, @value = key, value
|
126
|
+
end
|
127
|
+
|
128
|
+
# Qualifier name in String
|
129
|
+
attr_reader :qualifier
|
130
|
+
|
131
|
+
# Qualifier value in String
|
132
|
+
attr_reader :value
|
133
|
+
|
134
|
+
end #Qualifier
|
135
|
+
|
136
|
+
end #Feature
|
137
|
+
|
138
|
+
end # Bio
|
139
|
+
|
@@ -0,0 +1,64 @@
|
|
1
|
+
module Bio
|
2
|
+
class SQL
|
3
|
+
class Biodatabase < DummyBase
|
4
|
+
has_many :bioentries, :class_name =>"Bioentry", :foreign_key => "biodatabase_id"
|
5
|
+
validates_uniqueness_of :name
|
6
|
+
end
|
7
|
+
end #SQL
|
8
|
+
end #Bio
|
9
|
+
|
10
|
+
|
11
|
+
if __FILE__ == $0
|
12
|
+
require 'rubygems'
|
13
|
+
require 'composite_primary_keys'
|
14
|
+
require 'bio'
|
15
|
+
require 'pp'
|
16
|
+
|
17
|
+
# pp connection = Bio::SQL.establish_connection('bio/io/biosql/config/database.yml','development')
|
18
|
+
pp connection = Bio::SQL.establish_connection({'test'=>{'database'=>"bio_test", 'adapter'=>"postgresql", 'username'=>"rails", 'password'=>nil}},'test')
|
19
|
+
#pp YAML::load(ERB.new(IO.read('bio/io/biosql/config/database.yml')).result)
|
20
|
+
if true
|
21
|
+
pp Bio::SQL.list_entries
|
22
|
+
|
23
|
+
puts "### GenBank"
|
24
|
+
if ARGV.size > 0
|
25
|
+
gb = Bio::GenBank.new(ARGF.read)
|
26
|
+
else
|
27
|
+
require 'bio/io/fetch'
|
28
|
+
gb = Bio::GenBank.new(Bio::Fetch.query('gb', 'AJ224122'))
|
29
|
+
end
|
30
|
+
|
31
|
+
biosequence = gb.to_biosequence
|
32
|
+
db=Bio::SQL::Biodatabase.new(:biodatabase_id=>3,:name=>"JEFF", :authority=>"ME", :description=>"YOU")
|
33
|
+
db.save!
|
34
|
+
|
35
|
+
#sqlseq = Bio::SQL::Sequence.new(:biosequence=>biosequence,:biodatabase_id=>db.id)
|
36
|
+
|
37
|
+
# bioseq = Bio::SQL.fetch_accession('AJ224122')
|
38
|
+
# pp bioseq
|
39
|
+
# pp bioseq.entry_id
|
40
|
+
#TODO create a test only for tables not sequence here
|
41
|
+
# pp bioseq.molecule_type
|
42
|
+
#pp bioseq.molecule_type.class
|
43
|
+
#bioseq.molecule_type_update('dna', 1)
|
44
|
+
pp Bio::SQL::Taxon.find(8121).taxon_names
|
45
|
+
|
46
|
+
#sqlseq.to_biosequence
|
47
|
+
|
48
|
+
#sqlseq.delete
|
49
|
+
end
|
50
|
+
#pp bioseq.molecule_type
|
51
|
+
#term = Bio::SQL::Term.find_by_name('mol_type')
|
52
|
+
#pp term
|
53
|
+
#pp bioseq.entry.bioentry_qualifier_values.create(:term=>term, :rank=>2, :value=>'pippo')
|
54
|
+
#pp bioseq.entry.bioentry_qualifier_values.inspect
|
55
|
+
#pp bioseq.entry.bioentry_qualifier_values.find_all_by_term_id(26)
|
56
|
+
#pp primo.class
|
57
|
+
# pp primo.value='dna'
|
58
|
+
# pp primo.save
|
59
|
+
#pp bioseq.molecule_type= 'prova'
|
60
|
+
|
61
|
+
#Bio::SQL::BioentryQualifierValue.delete(delete.bioentry_id,delete.term_id,delete.rank)
|
62
|
+
|
63
|
+
|
64
|
+
end
|
@@ -0,0 +1,29 @@
|
|
1
|
+
module Bio
|
2
|
+
class SQL
|
3
|
+
class Bioentry < DummyBase
|
4
|
+
belongs_to :biodatabase, :class_name => "Biodatabase"
|
5
|
+
belongs_to :taxon, :class_name => "Taxon"
|
6
|
+
has_one :biosequence
|
7
|
+
#, :class_name => "Biosequence", :foreign_key => "bioentry_id"
|
8
|
+
has_many :comments, :class_name =>"Comment", :order =>'rank'
|
9
|
+
has_many :seqfeatures, :class_name => "Seqfeature", :order=>'rank'
|
10
|
+
has_many :bioentry_references, :class_name=>"BioentryReference" #, :foreign_key => "bioentry_id"
|
11
|
+
has_many :bioentry_dbxrefs, :class_name => "BioentryDbxref"
|
12
|
+
has_many :object_bioentry_relationships, :class_name=>"BioentryRelationship", :foreign_key=>"object_bioentry_id" #non mi convince molto credo non funzioni nel modo corretto
|
13
|
+
has_many :subject_bioentry_relationships, :class_name=>"BioentryRelationship", :foreign_key=>"subject_bioentry_id" #non mi convince molto credo non funzioni nel modo corretto
|
14
|
+
|
15
|
+
has_many :cdsfeatures, :class_name=>"Seqfeature", :foreign_key =>"bioentry_id", :conditions=>["term.name='CDS'"], :include=>"type_term"
|
16
|
+
|
17
|
+
has_many :terms, :through=>:bioentry_qualifier_values, :class_name => "Term"
|
18
|
+
#NOTE: added order_by for multiple hit and manage ranks correctly
|
19
|
+
has_many :bioentry_qualifier_values, :order=>"bioentry_id,term_id,rank", :class_name => "BioentryQualifierValue"
|
20
|
+
|
21
|
+
#per la creazione richiesti:
|
22
|
+
#name, accession, version
|
23
|
+
# validates_uniqueness_of :accession, :scope=>[:biodatabase_id]
|
24
|
+
# validates_uniqueness_of :name, :scope=>[:biodatabase_id]
|
25
|
+
# validates_uniqueness_of :identifier, :scope=>[:biodatabase_id]
|
26
|
+
|
27
|
+
end
|
28
|
+
end #SQL
|
29
|
+
end #Bio
|
@@ -0,0 +1,11 @@
|
|
1
|
+
module Bio
|
2
|
+
class SQL
|
3
|
+
class BioentryDbxref < DummyBase
|
4
|
+
#delete set_sequence_name nil
|
5
|
+
set_primary_key nil #bioentry_id,dbxref_id
|
6
|
+
belongs_to :bioentry, :class_name => "Bioentry"
|
7
|
+
belongs_to :dbxref, :class_name => "Dbxref"
|
8
|
+
end
|
9
|
+
end #SQL
|
10
|
+
end #Bio
|
11
|
+
|
@@ -0,0 +1,12 @@
|
|
1
|
+
module Bio
|
2
|
+
class SQL
|
3
|
+
class BioentryPath < DummyBase
|
4
|
+
set_primary_key nil
|
5
|
+
#delete set_sequence_name nil
|
6
|
+
belongs_to :term, :class_name => "Term"
|
7
|
+
#da sistemare per poter procedere.
|
8
|
+
belongs_to :object_bioentry, :class_name=>"Bioentry"
|
9
|
+
belongs_to :subject_bioentry, :class_name=>"Bioentry"
|
10
|
+
end #BioentryPath
|
11
|
+
end #SQL
|
12
|
+
end #Bio
|
@@ -0,0 +1,10 @@
|
|
1
|
+
module Bio
|
2
|
+
class SQL
|
3
|
+
class BioentryQualifierValue < DummyBase
|
4
|
+
#NOTE: added rank to primary_keys, now it's finished.
|
5
|
+
set_primary_keys :bioentry_id, :term_id, :rank
|
6
|
+
belongs_to :bioentry, :class_name => "Bioentry"
|
7
|
+
belongs_to :term, :class_name => "Term"
|
8
|
+
end #BioentryQualifierValue
|
9
|
+
end #SQL
|
10
|
+
end #Bio
|
@@ -0,0 +1,10 @@
|
|
1
|
+
module Bio
|
2
|
+
class SQL
|
3
|
+
class BioentryRelationship < DummyBase
|
4
|
+
#delete set_primary_key "bioentry_relationship_id"
|
5
|
+
set_sequence_name "bieontry_relationship_pk_seq"
|
6
|
+
belongs_to :object_bioentry, :class_name => "Bioentry"
|
7
|
+
belongs_to :subject_bioentry, :class_name => "Bioentry"
|
8
|
+
end
|
9
|
+
end #SQL
|
10
|
+
end #Bio
|
@@ -0,0 +1,11 @@
|
|
1
|
+
module Bio
|
2
|
+
class SQL
|
3
|
+
class Biosequence < DummyBase
|
4
|
+
set_primary_key "bioentry_id"
|
5
|
+
#delete set_sequence_name "biosequence_pk_seq"
|
6
|
+
belongs_to :bioentry, :foreign_key=>"bioentry_id"
|
7
|
+
#has_one :bioentry
|
8
|
+
#, :class_name => "Bioentry"
|
9
|
+
end
|
10
|
+
end #SQL
|
11
|
+
end #Bio
|
@@ -0,0 +1,20 @@
|
|
1
|
+
#This is the database configuration specific for BioSQL
|
2
|
+
#User can configure it's db here
|
3
|
+
|
4
|
+
development:
|
5
|
+
adapter: postgresql
|
6
|
+
database: biorails_development
|
7
|
+
username: rails
|
8
|
+
password:
|
9
|
+
|
10
|
+
test:
|
11
|
+
adapter: postgresql
|
12
|
+
database: biorails_test
|
13
|
+
username: rails
|
14
|
+
password:
|
15
|
+
|
16
|
+
production:
|
17
|
+
adapter: postgresql
|
18
|
+
database: biorails_production
|
19
|
+
username: rails
|
20
|
+
password:
|
@@ -0,0 +1,13 @@
|
|
1
|
+
module Bio
|
2
|
+
class SQL
|
3
|
+
class Dbxref < DummyBase
|
4
|
+
#set_sequence_name "dbxref_pk_seq"
|
5
|
+
has_many :dbxref_qualifier_values, :class_name => "DbxrefQualifierValue"
|
6
|
+
has_many :locations, :class_name => "Location"
|
7
|
+
has_many :references, :class_name=>"Reference"
|
8
|
+
has_many :term_dbxrefs, :class_name => "TermDbxref"
|
9
|
+
has_many :bioentry_dbxrefs, :class_name => "BioentryDbxref"
|
10
|
+
#TODO: check is with bioentry there is an has_and_belongs_to_many relationship has specified in schema overview.
|
11
|
+
end
|
12
|
+
end #SQL
|
13
|
+
end #Bio
|
@@ -0,0 +1,12 @@
|
|
1
|
+
module Bio
|
2
|
+
class SQL
|
3
|
+
class DbxrefQualifierValue < DummyBase
|
4
|
+
#think to use composite primary key
|
5
|
+
set_primary_key nil #dbxref_id, term_id, rank
|
6
|
+
#delete set_sequence_name nil
|
7
|
+
belongs_to :dbxref, :class_name => "Dbxref"
|
8
|
+
belongs_to :term, :class_name => "Term"
|
9
|
+
end
|
10
|
+
end #SQL
|
11
|
+
end #Bio
|
12
|
+
|
@@ -0,0 +1,32 @@
|
|
1
|
+
module Bio
|
2
|
+
class SQL
|
3
|
+
class Location < DummyBase
|
4
|
+
#set_sequence_name "location_pk_seq"
|
5
|
+
belongs_to :seqfeature, :class_name => "Seqfeature"
|
6
|
+
belongs_to :dbxref, :class_name => "Dbxref"
|
7
|
+
belongs_to :term, :class_name => "Term"
|
8
|
+
has_many :location_qualifier_values, :class_name => "LocationQualifierValue"
|
9
|
+
|
10
|
+
def to_s
|
11
|
+
if strand==-1
|
12
|
+
str="complement("+start_pos.to_s+".."+end_pos.to_s+")"
|
13
|
+
else
|
14
|
+
str=start_pos.to_s+".."+end_pos.to_s
|
15
|
+
end
|
16
|
+
return str
|
17
|
+
end
|
18
|
+
|
19
|
+
def sequence
|
20
|
+
seq=""
|
21
|
+
unless self.seqfeature.bioentry.biosequence.seq.nil?
|
22
|
+
seq=Bio::Sequence::NA.new(self.seqfeature.bioentry.biosequence.seq[start_pos-1..end_pos-1])
|
23
|
+
seq.reverse_complement! if strand==-1
|
24
|
+
end
|
25
|
+
return seq
|
26
|
+
end
|
27
|
+
|
28
|
+
|
29
|
+
|
30
|
+
end
|
31
|
+
end #SQL
|
32
|
+
end #Bio
|
@@ -0,0 +1,11 @@
|
|
1
|
+
module Bio
|
2
|
+
class SQL
|
3
|
+
class LocationQualifierValue < DummyBase
|
4
|
+
set_primary_key nil #location_id, term_id
|
5
|
+
#delete set_sequence_name nil
|
6
|
+
belongs_to :location, :class_name => "Location"
|
7
|
+
belongs_to :term, :class_name => "Term"
|
8
|
+
end
|
9
|
+
end #SQL
|
10
|
+
end #Bio
|
11
|
+
|