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 +1,292 @@
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#
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# = bio/io/registry.rb - OBDA BioRegistry module
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#
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# Copyright:: Copyright (C) 2002, 2003, 2004, 2005
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# Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
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# $Id:$
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#
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# == Description
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#
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# BioRegistry read the OBDA (Open Bio Database Access) configuration file
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# (seqdatabase.ini) and create a registry object. OBDA is created during
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# the BioHackathon held in Tucson and South Africa in 2002 as a project
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# independent set of protocols to access biological databases. The spec
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# is refined in the BioHackathon 2003 held in Singapore.
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#
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# By using the OBDA, user can access to the database by get_database method
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# without knowing where and how the database is stored, and each database
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# has the get_by_id method to obtain a sequence entry.
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#
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# Sample configuration file is distributed with BioRuby package which
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# consists of stanza format entries as following:
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#
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# VERSION=1.00
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#
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# [myembl]
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# protocol=biofetch
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# location=http://www.ebi.ac.uk/cgi-bin/dbfetch
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# dbname=embl
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#
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# [mysp]
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# protocol=biosql
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# location=db.bioruby.org
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# dbname=biosql
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# driver=mysql
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# user=root
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# pass=
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# biodbname=swissprot
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#
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# The first line means that this configration file is version 1.00.
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#
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# The [myembl] line defines a user defined database name 'myembl' and
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# following block indicates how the database can be accessed.
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# In this example, the 'myembl' database is accecced via the OBDA's
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# BioFetch protocol to the dbfetch server at EBI, where the EMBL
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# database is accessed by the name 'embl' on the server side.
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#
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# The [mysp] line defines another database 'mysp' which accesses the
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# RDB (Relational Database) at the db.bioruby.org via the OBDA's
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# BioSQL protocol. This BioSQL server is running MySQL database as
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# its backend and stores the SwissProt database by the name 'swissprot'
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# and which can be accessed by 'root' user without password.
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# Note that the db.bioruby.org server is a dummy for the explanation.
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#
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# The configuration file is searched by the following order.
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#
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# 1. Local file name given to the Bio::Registry.new(filename).
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#
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# 2. Remote or local file list given by the environmenetal variable
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# 'OBDA_SEARCH_PATH', which is a '+' separated string of the
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# remote (HTTP) and/or local files.
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#
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# e.g. OBDA_SEARCH_PATH="http://example.org/obda.ini+$HOME/lib/myobda.ini"
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#
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# 3. Local file "$HOME/.bioinformatics/seqdatabase.ini" in the user's
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# home directory.
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#
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# 4. Local file "/etc/bioinformatics/seqdatabase.ini" in the system
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# configuration directry.
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#
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# All these configuration files are loaded. If there are database
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# definitions having the same name, the first one is used.
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#
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# If none of these files can be found, Bio::Registry.new will try
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# to use http://www.open-bio.org/registry/seqdatabase.ini file.
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#
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# == References
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#
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# * http://obda.open-bio.org/
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# * http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/obda-specs/?cvsroot=obf-common
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# * http://www.open-bio.org/registry/seqdatabase.ini
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#
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require 'uri'
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require 'net/http'
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require 'bio/command'
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module Bio
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autoload :Fetch, 'bio/io/fetch'
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autoload :SQL, 'bio/io/sql'
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autoload :FlatFile, 'bio/io/flatfile'
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autoload :FlatFileIndex, 'bio/io/flatfile/index'
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class Registry
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def initialize(file = nil)
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@spec_version = nil
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@databases = Array.new
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read_local(file) if file
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env_path = ENV['OBDA_SEARCH_PATH']
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if env_path and env_path.size > 0
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read_env(env_path)
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else
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read_local("#{ENV['HOME']}/.bioinformatics/seqdatabase.ini")
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read_local("/etc/bioinformatics/seqdatabase.ini")
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if @databases.empty?
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read_remote("http://www.open-bio.org/registry/seqdatabase.ini")
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end
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end
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end
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# Version string of the first configulation file
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attr_reader :spec_version
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# List of databases (Array of Bio::Registry::DB)
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attr_reader :databases
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# Returns a dababase handle (Bio::SQL, Bio::Fetch etc.) or nil
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# if not found (case insensitive).
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# The handles should have get_by_id method.
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def get_database(dbname)
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@databases.each do |db|
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if db.database == dbname.downcase
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case db.protocol
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when 'biofetch'
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return serv_biofetch(db)
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when 'biosql'
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return serv_biosql(db)
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when 'flat', 'index-flat', 'index-berkeleydb'
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return serv_flat(db)
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when 'bsane-corba', 'biocorba'
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raise NotImplementedError
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when 'xembl'
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raise NotImplementedError
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end
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end
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end
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return nil
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end
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alias db get_database
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# Returns a Registry::DB object corresponding to the first dbname
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# entry in the registry records (case insensitive).
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def query(dbname)
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@databases.each do |db|
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return db if db.database == dbname.downcase
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end
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end
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private
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def read_env(path)
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path.split('+').each do |elem|
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if /:/.match(elem)
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read_remote(elem)
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else
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read_local(elem)
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end
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end
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end
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def read_local(file)
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if File.readable?(file)
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stanza = File.read(file)
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parse_stanza(stanza)
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end
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end
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def read_remote(url)
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schema, user, host, port, reg, path, = URI.split(url)
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Bio::Command.start_http(host, port) do |http|
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response = http.get(path)
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parse_stanza(response.body)
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end
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end
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def parse_stanza(stanza)
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return unless stanza
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if stanza[/.*/] =~ /VERSION\s*=\s*(\S+)/
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@spec_version ||= $1 # for internal use (may differ on each file)
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stanza[/.*/] = '' # remove VERSION line
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end
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stanza.each_line do |line|
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case line
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when /^\[(.*)\]/
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dbname = $1.downcase
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db = Bio::Registry::DB.new($1)
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@databases.push(db)
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when /=/
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tag, value = line.chomp.split(/\s*=\s*/)
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@databases.last[tag] = value
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end
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end
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end
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def serv_biofetch(db)
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serv = Bio::Fetch.new(db.location)
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serv.database = db.dbname
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return serv
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end
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def serv_biosql(db)
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location, port = db.location.split(':')
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port = db.port unless port
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case db.driver
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when /mysql/i
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driver = 'Mysql'
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when /pg|postgres/i
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driver = 'Pg'
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when /oracle/
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when /sybase/
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when /sqlserver/
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when /access/
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when /csv/
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when /informix/
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when /odbc/
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when /rdb/
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end
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dbi = [ "dbi", driver, db.dbname, location ].compact.join(':')
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dbi += ';port=' + port if port
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serv = Bio::SQL.new(dbi, db.user, db.pass)
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# We can not manage biodbname (for name space) in BioSQL yet.
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# use db.biodbname here!!
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return serv
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end
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def serv_flat(db)
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path = db.location
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path = File.join(path, db.dbname) if db.dbname
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serv = Bio::FlatFileIndex.open(path)
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return serv
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end
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class DB
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def initialize(dbname)
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@database = dbname
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@property = Hash.new
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end
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attr_reader :database
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def method_missing(meth_id)
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@property[meth_id.id2name]
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end
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def []=(tag, value)
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@property[tag] = value
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end
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end
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end # class Registry
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end # module Bio
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if __FILE__ == $0
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begin
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require 'pp'
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alias p pp
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rescue
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end
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# Usually, you don't need to pass ARGV.
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reg = Bio::Registry.new(ARGV[0])
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p reg
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p reg.query('genbank_biosql')
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serv = reg.get_database('genbank_biofetch')
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puts serv.get_by_id('AA2CG')
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serv = reg.get_database('genbank_biosql')
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puts serv.get_by_id('AA2CG')
|
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|
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serv = reg.get_database('swissprot_biofetch')
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puts serv.get_by_id('CYC_BOVIN')
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|
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serv = reg.get_database('swissprot_biosql')
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puts serv.get_by_id('CYC_BOVIN')
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end
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|
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@@ -0,0 +1,119 @@
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#
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# = bio/io/soapwsdl.rb - SOAP/WSDL interface class
|
3
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#
|
4
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# Copyright:: Copyright (C) 2004
|
5
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# Toshiaki Katayama <k@bioruby.org>
|
6
|
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# License:: The Ruby License
|
7
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+
#
|
8
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# $Id: soapwsdl.rb,v 1.7 2007/04/05 23:35:41 trevor Exp $
|
9
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+
#
|
10
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+
begin
|
11
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require 'soap/wsdlDriver'
|
12
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+
rescue LoadError
|
13
|
+
end
|
14
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+
|
15
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+
module Bio
|
16
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+
|
17
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# == Examples
|
18
|
+
#
|
19
|
+
# class API < Bio::SOAPWSDL
|
20
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+
# def initialize
|
21
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+
# @wsdl = 'http://example.com/example.wsdl'
|
22
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+
# @log = File.new("soap_log", 'w')
|
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# create_driver
|
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+
# end
|
25
|
+
# end
|
26
|
+
#
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27
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+
# == Use HTTP proxy
|
28
|
+
#
|
29
|
+
# You need to set following two environmental variables
|
30
|
+
# (case might be insensitive) as required by SOAP4R.
|
31
|
+
#
|
32
|
+
# --- soap_use_proxy
|
33
|
+
#
|
34
|
+
# Set the value of this variable to 'on'.
|
35
|
+
#
|
36
|
+
# --- http_proxy
|
37
|
+
#
|
38
|
+
# Set the URL of your proxy server (http://myproxy.com:8080 etc.).
|
39
|
+
#
|
40
|
+
# === Example to use HTTP proxy
|
41
|
+
#
|
42
|
+
# % export soap_use_proxy=on
|
43
|
+
# % export http_proxy=http://localhost:8080
|
44
|
+
#
|
45
|
+
class SOAPWSDL
|
46
|
+
|
47
|
+
# Returns URL of the current WSDL file.
|
48
|
+
attr_reader :wsdl
|
49
|
+
|
50
|
+
# Returns current logging IO.
|
51
|
+
attr_reader :log
|
52
|
+
|
53
|
+
|
54
|
+
def initialize(wsdl = nil)
|
55
|
+
@wsdl = wsdl
|
56
|
+
@log = nil
|
57
|
+
create_driver
|
58
|
+
end
|
59
|
+
|
60
|
+
|
61
|
+
def create_driver
|
62
|
+
if RUBY_VERSION > "1.8.2"
|
63
|
+
@driver = SOAP::WSDLDriverFactory.new(@wsdl).create_rpc_driver
|
64
|
+
else
|
65
|
+
@driver = SOAP::WSDLDriverFactory.new(@wsdl).create_driver
|
66
|
+
end
|
67
|
+
@driver.generate_explicit_type = true # Ruby obj <-> SOAP obj
|
68
|
+
end
|
69
|
+
private :create_driver
|
70
|
+
|
71
|
+
|
72
|
+
# Change the URL for WSDL file
|
73
|
+
#
|
74
|
+
# serv = Bio::SOAPWSDL.new("http://soap.genome.jp/KEGG.wsdl")
|
75
|
+
#
|
76
|
+
# or
|
77
|
+
#
|
78
|
+
# serv = Bio::SOAPWSDL.new
|
79
|
+
# serv.wsdl = "http://soap.genome.jp/KEGG.wsdl"
|
80
|
+
#
|
81
|
+
# Note that you can't read two or more different WSDL files at once.
|
82
|
+
# In that case, create Bio::SOAPWSDL object for each.
|
83
|
+
#
|
84
|
+
def wsdl=(url)
|
85
|
+
@wsdl = url
|
86
|
+
create_driver
|
87
|
+
end
|
88
|
+
|
89
|
+
|
90
|
+
# Change the IO for logging. The argument is passed to wiredump_dev method
|
91
|
+
# of the SOAP4R, thus
|
92
|
+
#
|
93
|
+
# serv = Bio::SOAPWSDL.new
|
94
|
+
# serv.log = STDERR
|
95
|
+
#
|
96
|
+
# will print all the SOAP transactions in standard error.
|
97
|
+
# This feature is especially useful for debug.
|
98
|
+
#
|
99
|
+
def log=(io)
|
100
|
+
@log = io
|
101
|
+
@driver.wiredump_dev = @log
|
102
|
+
end
|
103
|
+
|
104
|
+
|
105
|
+
# List of methods defined by WSDL
|
106
|
+
def list_methods
|
107
|
+
@driver.methods(false)
|
108
|
+
end
|
109
|
+
|
110
|
+
|
111
|
+
def method_missing(*arg)
|
112
|
+
@driver.send(*arg)
|
113
|
+
end
|
114
|
+
private :method_missing
|
115
|
+
|
116
|
+
end # SOAPWSDL
|
117
|
+
|
118
|
+
end # Bio
|
119
|
+
|
data/lib/bio/io/sql.rb
ADDED
@@ -0,0 +1,186 @@
|
|
1
|
+
|
2
|
+
require 'rubygems'
|
3
|
+
require 'erb'
|
4
|
+
require 'composite_primary_keys'
|
5
|
+
# BiosqlPlug
|
6
|
+
|
7
|
+
=begin
|
8
|
+
Ok Hilmar gives to me some clarification
|
9
|
+
1) "EMBL/GenBank/SwissProt" name in term table, is only a convention assuming data loaded by genbank embl ans swissprot formats.
|
10
|
+
If your features come from others ways for example blast or alignment ... whatever.. the user as to take care about the source.
|
11
|
+
|
12
|
+
|
13
|
+
=end
|
14
|
+
=begin
|
15
|
+
TODO:
|
16
|
+
1) source_term_id => surce_term and check before if the source term is present or not and the level, the root should always be something "EMBL/GenBank/SwissProt" or contestualized.
|
17
|
+
2) Into DummyBase class delete connection there and use Bio::ArSQL.establish_connection which reads info from a yml file.
|
18
|
+
3) Chk Locations in Biofeatures ArSQL
|
19
|
+
=end
|
20
|
+
module Bio
|
21
|
+
class SQL
|
22
|
+
#no check is made
|
23
|
+
def self.establish_connection(configurations, env)
|
24
|
+
#configurations is an hash similar what YAML returns.
|
25
|
+
#{:database=>"biorails_development", :adapter=>"postgresql", :username=>"rails", :password=>nil}
|
26
|
+
configurations.assert_valid_keys('development', 'production','test')
|
27
|
+
configurations[env].assert_valid_keys('hostname','database','adapter','username','password')
|
28
|
+
DummyBase.configurations = configurations
|
29
|
+
DummyBase.establish_connection "#{env}"
|
30
|
+
end
|
31
|
+
|
32
|
+
def self.fetch_id(id)
|
33
|
+
Bio::SQL::Bioentry.find(id)
|
34
|
+
end
|
35
|
+
|
36
|
+
def self.fetch_accession(accession)
|
37
|
+
accession = accession.upcase
|
38
|
+
Bio::SQL::Bioentry.exists?(:accession => accession) ? Bio::SQL::Sequence.new(:entry=>Bio::SQL::Bioentry.find_by_accession(accession)) : nil
|
39
|
+
end
|
40
|
+
|
41
|
+
def self.exists_accession(accession)
|
42
|
+
Bio::SQL::Bioentry.find_by_accession(accession.upcase).nil? ? false : true
|
43
|
+
end
|
44
|
+
|
45
|
+
def self.exists_database(name)
|
46
|
+
Bio::SQL::Biodatabase.find_by_name(name).nil? ? false : true
|
47
|
+
end
|
48
|
+
|
49
|
+
def self.list_entries
|
50
|
+
Bio::SQL::Bioentry.find(:all).collect{|entry|
|
51
|
+
{:id=>entry.bioentry_id, :accession=>entry.accession}
|
52
|
+
}
|
53
|
+
end
|
54
|
+
|
55
|
+
def self.list_databases
|
56
|
+
Bio::SQL::Biodatabase.find(:all).collect{|entry|
|
57
|
+
{:id=>entry.biodatabase_id, :name => entry.name}
|
58
|
+
}
|
59
|
+
end
|
60
|
+
|
61
|
+
def self.delete_entry_id(id)
|
62
|
+
Bioentry.delete(id)
|
63
|
+
end
|
64
|
+
|
65
|
+
def self.delete_entry_accession(accession)
|
66
|
+
Bioentry.delete(Bioentry.find_by_accession(accession))
|
67
|
+
end
|
68
|
+
|
69
|
+
|
70
|
+
class DummyBase < ActiveRecord::Base
|
71
|
+
#NOTE: Using postgresql, not setting sequence name, system will discover the name by default.
|
72
|
+
#NOTE: this class will not establish the connection automatically
|
73
|
+
self.abstract_class = true
|
74
|
+
self.pluralize_table_names = false
|
75
|
+
#prepend table name to the usual id, avoid to specify primary id for every table
|
76
|
+
self.primary_key_prefix_type = :table_name_with_underscore
|
77
|
+
#biosql_configurations=YAML::load(ERB.new(IO.read(File.join(File.dirname(__FILE__),'../config', 'database.yml'))).result)
|
78
|
+
#self.configurations=biosql_configurations
|
79
|
+
#self.establish_connection "development"
|
80
|
+
end #DummyBase
|
81
|
+
|
82
|
+
autoload :Biodatabase, 'bio/io/biosql/biodatabase'
|
83
|
+
autoload :Bioentry, 'bio/io/biosql/bioentry'
|
84
|
+
autoload :BioentryDbxref, 'bio/io/biosql/bioentry_dbxref'
|
85
|
+
autoload :BioentryPath, 'bio/io/biosql/bioentry_path'
|
86
|
+
autoload :BioentryQualifierValue, 'bio/io/biosql/bioentry_qualifier_value'
|
87
|
+
autoload :BioentryReference, 'bio/io/biosql/bioentry_reference'
|
88
|
+
autoload :BioentryRelationship, 'bio/io/biosql/bioentry_relationship'
|
89
|
+
autoload :Biosequence, 'bio/io/biosql/biosequence'
|
90
|
+
autoload :Comment, 'bio/io/biosql/comment'
|
91
|
+
autoload :Dbxref, 'bio/io/biosql/dbxref'
|
92
|
+
autoload :DbxrefQualifierValue, 'bio/io/biosql/dbxref_qualifier_value'
|
93
|
+
autoload :Location, 'bio/io/biosql/location'
|
94
|
+
autoload :LocationQualifierValue, 'bio/io/biosql/location_qualifier_value'
|
95
|
+
autoload :Ontology, 'bio/io/biosql/ontology'
|
96
|
+
autoload :Reference, 'bio/io/biosql/reference'
|
97
|
+
autoload :Seqfeature, 'bio/io/biosql/seqfeature'
|
98
|
+
autoload :SeqfeatureDbxref, 'bio/io/biosql/seqfeature_dbxref'
|
99
|
+
autoload :SeqfeaturePath, 'bio/io/biosql/seqfeature_path'
|
100
|
+
autoload :SeqfeatureQualifierValue, 'bio/io/biosql/seqfeature_qualifier_value'
|
101
|
+
autoload :SeqfeatureRelationship, 'bio/io/biosql/seqfeature_relationship'
|
102
|
+
autoload :Taxon, 'bio/io/biosql/taxon'
|
103
|
+
autoload :TaxonName, 'bio/io/biosql/taxon_name'
|
104
|
+
autoload :Term, 'bio/io/biosql/term'
|
105
|
+
autoload :TermDbxref, 'bio/io/biosql/term_dbxref'
|
106
|
+
autoload :TermPath, 'bio/io/biosql/term_path'
|
107
|
+
autoload :TermRelationship, 'bio/io/biosql/term_relationship'
|
108
|
+
autoload :TermRelationshipTerm, 'bio/io/biosql/term_relationship_term'
|
109
|
+
autoload :Sequence, 'bio/db/biosql/sequence'
|
110
|
+
end #biosql
|
111
|
+
|
112
|
+
end #Bio
|
113
|
+
|
114
|
+
if __FILE__ == $0
|
115
|
+
require 'rubygems'
|
116
|
+
require 'composite_primary_keys'
|
117
|
+
require 'bio'
|
118
|
+
require 'pp'
|
119
|
+
|
120
|
+
# pp connection = Bio::SQL.establish_connection('bio/io/biosql/config/database.yml','development')
|
121
|
+
connection = Bio::SQL.establish_connection({'development'=>{'database'=>"bio_test", 'adapter'=>"postgresql", 'username'=>"rails", 'password'=>nil}},'development')
|
122
|
+
#pp YAML::load(ERB.new(IO.read('bio/io/biosql/config/database.yml')).result)
|
123
|
+
if true
|
124
|
+
#Bio::SQL.list_entries
|
125
|
+
|
126
|
+
# biosequence = data.to_biosequence
|
127
|
+
# puts biosequence.output(:genbank)
|
128
|
+
db=Bio::SQL::Biodatabase.new(:name=>'JEFF', :authority=>'ME', :description=>'YOU')
|
129
|
+
db.save!
|
130
|
+
|
131
|
+
puts "### FileFile.auto"
|
132
|
+
if ARGV.size > 0
|
133
|
+
#embl = Bio::FlatFile.auto(ARGF.read)
|
134
|
+
Bio::FlatFile.auto(ARGF) do |ff|
|
135
|
+
ff.each do |data|
|
136
|
+
biosequence=data.to_biosequence
|
137
|
+
puts biosequence.output(:fasta)
|
138
|
+
sqlseq = Bio::SQL::Sequence.new(:biosequence=>biosequence,:biodatabase_id=>db.biodatabase_id)
|
139
|
+
sqlseq.save
|
140
|
+
sqlseq.to_biosequence.output(:fasta)
|
141
|
+
end
|
142
|
+
end
|
143
|
+
else
|
144
|
+
require 'bio/io/fetch'
|
145
|
+
server = Bio::Fetch.new('http://www.ebi.ac.uk/cgi-bin/dbfetch')
|
146
|
+
data = Bio::EMBL.new(server.fetch('embl','AJ224123'))
|
147
|
+
end
|
148
|
+
|
149
|
+
|
150
|
+
# sqlseq = Bio::SQL::Sequence.new(:biosequence=>biosequence,:biodatabase_id=>db.biodatabase_id)
|
151
|
+
# sqlseq.save
|
152
|
+
# sqlseq_bioseq=sqlseq.to_biosequence
|
153
|
+
# puts sqlseq_bioseq.output(:genbank)
|
154
|
+
|
155
|
+
|
156
|
+
|
157
|
+
# bioseq = Bio::SQL.fetch_accession('AJ224122')
|
158
|
+
# pp bioseq
|
159
|
+
# pp bioseq.entry_id
|
160
|
+
#TODO create a test only for tables not sequence here
|
161
|
+
# pp bioseq.molecule_type
|
162
|
+
#pp bioseq.molecule_type.class
|
163
|
+
#bioseq.molecule_type_update('dna', 1)
|
164
|
+
## pp Bio::SQL::Taxon.find(8121).taxon_names
|
165
|
+
|
166
|
+
#sqlseq.to_biosequence
|
167
|
+
|
168
|
+
# sqlseq.delete
|
169
|
+
|
170
|
+
# db.destroy
|
171
|
+
end
|
172
|
+
#pp bioseq.molecule_type
|
173
|
+
#term = Bio::SQL::Term.find_by_name('mol_type')
|
174
|
+
#pp term
|
175
|
+
#pp bioseq.entry.bioentry_qualifier_values.create(:term=>term, :rank=>2, :value=>'pippo')
|
176
|
+
#pp bioseq.entry.bioentry_qualifier_values.inspect
|
177
|
+
#pp bioseq.entry.bioentry_qualifier_values.find_all_by_term_id(26)
|
178
|
+
#pp primo.class
|
179
|
+
# pp primo.value='dna'
|
180
|
+
# pp primo.save
|
181
|
+
#pp bioseq.molecule_type= 'prova'
|
182
|
+
|
183
|
+
#Bio::SQL::BioentryQualifierValue.delete(delete.bioentry_id,delete.term_id,delete.rank)
|
184
|
+
|
185
|
+
|
186
|
+
end
|