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 +1,42 @@
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#
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# = bio/db/embl/swissprot.rb - SwissProt database class
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#
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# Copyright:: Copyright (C) 2001, 2002 Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: swissprot.rb,v 1.7 2007/04/05 23:35:40 trevor Exp $
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#
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require 'bio/db/embl/sptr'
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module Bio
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# == Description
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#
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# Parser class for SwissProt database entry. See also Bio::SPTR class.
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# This class holds name space for SwissProt specific methods.
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#
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# SwissProt (before UniProtKB/SwissProt) specific methods are defined in
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# this class. Shared methods for UniProtKB/SwissProt and TrEMBL classes
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# are defined in Bio::SPTR class.
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#
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# == Examples
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#
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# str = File.read("p53_human.swiss")
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# obj = Bio::SwissProt.new(str)
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# obj.entry_id #=> "P53_HUMAN"
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#
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# == Referencees
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#
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# * Swiss-Prot Protein knowledgebase
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# http://au.expasy.org/sprot/
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#
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# * Swiss-Prot Protein Knowledgebase User Manual
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# http://au.expasy.org/sprot/userman.html
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#
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class SwissProt < SPTR
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# Nothing to do (SwissProt format is abstracted in SPTR)
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end
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end
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#
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# = bio/db/embl/trembl.rb - TrEMBL database class
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#
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# Copyright:: Copyright (C) 2001, 2002 Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: trembl.rb,v 1.7 2007/04/05 23:35:40 trevor Exp $
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#
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require 'bio/db/embl/sptr'
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module Bio
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# == Description
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#
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# Parser class for TrEMBL database entry. See also Bio::SPTR class.
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# This class holds name space for TrEMBL specific methods.
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#
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# UniProtKB/SwissProt specific methods are defined in this class.
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# Shared methods for UniProtKB/SwissProt and TrEMBL classes are
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# defined in Bio::SPTR class.
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#
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# == Examples
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#
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# str = File.read("Q2UNG2_ASPOR.trembl")
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# obj = Bio::TrEMBL.new(str)
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# obj.entry_id #=> "Q2UNG2_ASPOR"
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#
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# == Referencees
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#
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# * TrEMBL Computer-annotated supplement to Swiss-Prot
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# http://au.expasy.org/sprot/
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#
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# * TrEMBL Computer-annotated supplement to Swiss-Prot User Manual
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# http://au.expasy.org/sprot/userman.html
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#
|
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class TrEMBL < SPTR
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# Nothing to do (TrEMBL format is abstracted in SPTR)
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end
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end
|
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#
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# = bio/db/embl/uniprot.rb - UniProt database class
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#
|
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# Copyright:: Copyright (C) 2005 Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: uniprot.rb,v 1.5 2007/04/05 23:35:40 trevor Exp $
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#
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require 'bio/db/embl/sptr'
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module Bio
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# == Description
|
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#
|
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# Parser class for SwissProt database entry.# See also Bio::SPTR class.
|
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# This class holds name space for UniProtKB/SwissProt specific methods.
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#
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# UniProtKB/SwissProt specific methods are defined in this class.
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# Shared methods for UniProtKB/SwissProt and TrEMBL classes are
|
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# defined in Bio::SPTR class.
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#
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# == Examples
|
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#
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# str = File.read("p53_human.swiss")
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# obj = Bio::UniProt.new(str)
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# obj.entry_id #=> "P53_HUMAN"
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#
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# == Referencees
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#
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# * UniProt
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# http://uniprot.org/
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#
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# * The UniProtKB/SwissProt/TrEMBL User Manual
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# http://www.expasy.org/sprot/userman.html
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#
|
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class UniProt < SPTR
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# Nothing to do (UniProt format is abstracted in SPTR)
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end
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end
|
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#
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# bio/db/fantom.rb - RIKEN FANTOM2 database classes
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#
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# Copyright:: Copyright (C) 2003 GOTO Naohisa <ng@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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require 'rexml/document'
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require 'cgi'
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require 'uri'
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require 'net/http'
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require 'bio/db'
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require 'bio/command'
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#require 'bio/sequence'
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|
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module Bio
|
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|
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module FANTOM
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|
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def query(idstr, http_proxy = nil)
|
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xml = get_by_id(idstr, http_proxy)
|
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seqs = MaXML::Sequences.new(xml.to_s)
|
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seqs[0]
|
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end
|
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module_function :query
|
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|
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def get_by_id(idstr, http_proxy = nil)
|
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addr = 'fantom.gsc.riken.go.jp'
|
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port = 80
|
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path = "/db/maxml/maxmlseq.cgi?masterid=#{CGI.escape(idstr.to_s)}&style=xml"
|
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xml = ''
|
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if http_proxy then
|
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proxy = URI.parse(http_proxy.to_s)
|
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Net::HTTP.start(addr, port, proxy.host, proxy.port) do |http|
|
38
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response = http.get(path)
|
39
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xml = response.body
|
40
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end
|
41
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else
|
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Bio::Command.start_http(addr, port) do |http|
|
43
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response = http.get(path)
|
44
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xml = response.body
|
45
|
+
end
|
46
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+
end
|
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xml
|
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end
|
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module_function :get_by_id
|
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|
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|
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class MaXML < DB
|
53
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# DTD of MaXML(Mouse annotation XML)
|
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# http://fantom.gsc.riken.go.jp/maxml/maxml.dtd
|
55
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|
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DELIMITER = RS = "\n--EOF--\n"
|
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# This class is for {allseq|repseq|allclust}.sep.xml,
|
58
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# not for {allseq|repseq|allclust}.xml.
|
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|
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Data_XPath = ''
|
61
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|
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def initialize(x)
|
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if x.is_a?(REXML::Element) then
|
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@elem = x
|
65
|
+
else
|
66
|
+
if x.is_a?(String) then
|
67
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x = x.sub(/#{Regexp.escape(DELIMITER)}\z/om, "\n")
|
68
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+
end
|
69
|
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doc = REXML::Document.new(x)
|
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@elem = doc.elements[self.class::Data_XPath]
|
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#raise 'element is null' unless @elem
|
72
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@elem = REXML::Document.new('') unless @elem
|
73
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+
end
|
74
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end
|
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attr_reader :elem
|
76
|
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|
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|
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def to_s
|
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@elem.to_s
|
79
|
+
end
|
80
|
+
|
81
|
+
def gsub_entities(str)
|
82
|
+
# workaround for bug?
|
83
|
+
if str then
|
84
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str.gsub(/\&\#(\d{1,3})\;/) { sprintf("%c", $1.to_i) }
|
85
|
+
else
|
86
|
+
str
|
87
|
+
end
|
88
|
+
end
|
89
|
+
|
90
|
+
def entry_id
|
91
|
+
unless defined?(@entry_id)
|
92
|
+
@entry_id = @elem.attributes['id']
|
93
|
+
end
|
94
|
+
@entry_id
|
95
|
+
end
|
96
|
+
def self.define_element_text_method(array)
|
97
|
+
array.each do |tagstr|
|
98
|
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module_eval("
|
99
|
+
def #{tagstr}
|
100
|
+
unless defined?(@#{tagstr})
|
101
|
+
@#{tagstr} = gsub_entities(@elem.text('#{tagstr}'))
|
102
|
+
end
|
103
|
+
@#{tagstr}
|
104
|
+
end
|
105
|
+
")
|
106
|
+
end
|
107
|
+
end
|
108
|
+
private_class_method :define_element_text_method
|
109
|
+
|
110
|
+
class Cluster < MaXML
|
111
|
+
# (MaXML cluster)
|
112
|
+
# ftp://fantom2.gsc.riken.go.jp/fantom/2.1/allclust.sep.xml.gz
|
113
|
+
|
114
|
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Data_XPath = 'maxml-clusters/cluster'
|
115
|
+
|
116
|
+
def representative_seqid
|
117
|
+
unless defined?(@representative_seqid)
|
118
|
+
@representative_seqid =
|
119
|
+
gsub_entities(@elem.text('representative-seqid'))
|
120
|
+
end
|
121
|
+
@representative_seqid
|
122
|
+
end
|
123
|
+
|
124
|
+
def sequences
|
125
|
+
unless defined?(@sequences)
|
126
|
+
@sequences = MaXML::Sequences.new(@elem)
|
127
|
+
end
|
128
|
+
@sequences
|
129
|
+
end
|
130
|
+
|
131
|
+
def sequence(idstr = nil)
|
132
|
+
idstr ? sequences[idstr] : representative_sequence
|
133
|
+
end
|
134
|
+
|
135
|
+
def representative_sequence
|
136
|
+
unless defined?(@representative_sequence)
|
137
|
+
rid = representative_seqid
|
138
|
+
@representative_sequence =
|
139
|
+
rid ? sequences[representative_seqid] : nil
|
140
|
+
end
|
141
|
+
@representative_sequence
|
142
|
+
end
|
143
|
+
alias representative_clone representative_sequence
|
144
|
+
|
145
|
+
def representative_annotations
|
146
|
+
e = representative_sequence
|
147
|
+
e ? e.annotations : nil
|
148
|
+
end
|
149
|
+
|
150
|
+
def representative_cloneid
|
151
|
+
e = representative_sequence
|
152
|
+
e ? e.cloneid : nil
|
153
|
+
end
|
154
|
+
|
155
|
+
define_element_text_method(%w(fantomid))
|
156
|
+
end #class MaXML::Cluster
|
157
|
+
|
158
|
+
class Sequences < MaXML
|
159
|
+
Data_XPath = 'maxml-sequences'
|
160
|
+
|
161
|
+
include Enumerable
|
162
|
+
def each
|
163
|
+
to_a.each { |x| yield x }
|
164
|
+
end
|
165
|
+
|
166
|
+
def to_a
|
167
|
+
unless defined?(@sequences)
|
168
|
+
@sequences = @elem.get_elements('sequence')
|
169
|
+
@sequences.collect! { |e| MaXML::Sequence.new(e) }
|
170
|
+
end
|
171
|
+
@sequences
|
172
|
+
end
|
173
|
+
|
174
|
+
def get(idstr)
|
175
|
+
unless defined?(@hash)
|
176
|
+
@hash = {}
|
177
|
+
end
|
178
|
+
unless @hash.member?(idstr) then
|
179
|
+
@hash[idstr] = self.find do |x|
|
180
|
+
x.altid.values.index(idstr)
|
181
|
+
end
|
182
|
+
end
|
183
|
+
@hash[idstr]
|
184
|
+
end
|
185
|
+
|
186
|
+
def [](*arg)
|
187
|
+
if arg[0].is_a?(String) and arg.size == 1 then
|
188
|
+
get(arg[0])
|
189
|
+
else
|
190
|
+
to_a[*arg]
|
191
|
+
end
|
192
|
+
end
|
193
|
+
|
194
|
+
def cloneids
|
195
|
+
unless defined?(@cloneids)
|
196
|
+
@cloneids = to_a.collect { |x| x.cloneid }
|
197
|
+
end
|
198
|
+
@cloneids
|
199
|
+
end
|
200
|
+
|
201
|
+
def id_strings
|
202
|
+
unless defined?(@id_strings)
|
203
|
+
@id_strings = to_a.collect { |x| x.id_strings }
|
204
|
+
@id_strings.flatten!
|
205
|
+
@id_strings.sort!
|
206
|
+
@id_strings.uniq!
|
207
|
+
end
|
208
|
+
@id_strings
|
209
|
+
end
|
210
|
+
end #class MaXML::Sequences
|
211
|
+
|
212
|
+
class Sequence < MaXML
|
213
|
+
# (MaXML sequence)
|
214
|
+
# ftp://fantom2.gsc.riken.go.jp/fantom/2.1/allseq.sep.xml.gz
|
215
|
+
# ftp://fantom2.gsc.riken.go.jp/fantom/2.1/repseq.sep.xml.gz
|
216
|
+
|
217
|
+
Data_XPath = 'maxml-sequences/sequence'
|
218
|
+
|
219
|
+
def altid(t = nil)
|
220
|
+
unless defined?(@altid)
|
221
|
+
@altid = {}
|
222
|
+
@elem.each_element('altid') do |e|
|
223
|
+
@altid[e.attributes['type']] = gsub_entities(e.text)
|
224
|
+
end
|
225
|
+
end
|
226
|
+
if t then
|
227
|
+
@altid[t]
|
228
|
+
else
|
229
|
+
@altid
|
230
|
+
end
|
231
|
+
end
|
232
|
+
|
233
|
+
def id_strings
|
234
|
+
altid.values.sort.uniq
|
235
|
+
end
|
236
|
+
|
237
|
+
def library_id
|
238
|
+
entry_id[0,2]
|
239
|
+
end
|
240
|
+
|
241
|
+
def annotations
|
242
|
+
unless defined?(@annotations)
|
243
|
+
@annotations =
|
244
|
+
MaXML::Annotations.new(@elem.elements['annotations'])
|
245
|
+
end
|
246
|
+
@annotations
|
247
|
+
end
|
248
|
+
|
249
|
+
define_element_text_method(%w(annotator version modified_time comment))
|
250
|
+
|
251
|
+
def self.define_id_method(array)
|
252
|
+
array.each do |tagstr|
|
253
|
+
module_eval("
|
254
|
+
def #{tagstr}
|
255
|
+
unless defined?(@#{tagstr})
|
256
|
+
@#{tagstr} = gsub_entities(@elem.text('#{tagstr}'))
|
257
|
+
@#{tagstr} = altid('#{tagstr}') unless @#{tagstr}
|
258
|
+
end
|
259
|
+
@#{tagstr}
|
260
|
+
end
|
261
|
+
")
|
262
|
+
end
|
263
|
+
end
|
264
|
+
private_class_method :define_id_method
|
265
|
+
|
266
|
+
define_id_method(%w(seqid fantomid cloneid rearrayid accession))
|
267
|
+
end #class MaXML::Sequence
|
268
|
+
|
269
|
+
class Annotations < MaXML
|
270
|
+
Data_XPath = nil
|
271
|
+
|
272
|
+
include Enumerable
|
273
|
+
def each
|
274
|
+
to_a.each { |x| yield x }
|
275
|
+
end
|
276
|
+
|
277
|
+
def to_a
|
278
|
+
unless defined?(@a)
|
279
|
+
@a = @elem.get_elements('annotation')
|
280
|
+
@a.collect! { |e| MaXML::Annotation.new(e) }
|
281
|
+
end
|
282
|
+
@a
|
283
|
+
end
|
284
|
+
|
285
|
+
def get_all_by_qualifier(qstr)
|
286
|
+
unless defined?(@hash)
|
287
|
+
@hash = {}
|
288
|
+
end
|
289
|
+
unless @hash.member?(qstr) then
|
290
|
+
@hash[qstr] = self.find_all do |x|
|
291
|
+
x.qualifier == qstr
|
292
|
+
end
|
293
|
+
end
|
294
|
+
@hash[qstr]
|
295
|
+
end
|
296
|
+
|
297
|
+
def get_by_qualifier(qstr)
|
298
|
+
a = get_all_by_qualifier(qstr)
|
299
|
+
a ? a[0] : nil
|
300
|
+
end
|
301
|
+
|
302
|
+
def [](*arg)
|
303
|
+
if arg[0].is_a?(String) and arg.size == 1 then
|
304
|
+
get_by_qualifier(arg[0])
|
305
|
+
else
|
306
|
+
to_a[*arg]
|
307
|
+
end
|
308
|
+
end
|
309
|
+
|
310
|
+
def cds_start
|
311
|
+
unless defined?(@cds_start)
|
312
|
+
e = get_by_qualifier('cds_start')
|
313
|
+
@cds_start = e ? e.anntext.to_i : nil
|
314
|
+
end
|
315
|
+
@cds_start
|
316
|
+
end
|
317
|
+
|
318
|
+
def cds_stop
|
319
|
+
unless defined?(@cds_stop)
|
320
|
+
e = get_by_qualifier('cds_stop')
|
321
|
+
@cds_stop = e ? e.anntext.to_i : nil
|
322
|
+
end
|
323
|
+
@cds_stop
|
324
|
+
end
|
325
|
+
|
326
|
+
def gene_name
|
327
|
+
unless defined?(@gene_name)
|
328
|
+
e = get_by_qualifier('gene_name')
|
329
|
+
@gene_name = e ? e.anntext : nil
|
330
|
+
end
|
331
|
+
@gene_name
|
332
|
+
end
|
333
|
+
|
334
|
+
def data_source
|
335
|
+
unless defined?(@data_source)
|
336
|
+
e = get_by_qualifier('gene_name')
|
337
|
+
@data_source = e ? e.datasrc[0] : nil
|
338
|
+
end
|
339
|
+
@data_source
|
340
|
+
end
|
341
|
+
|
342
|
+
def evidence
|
343
|
+
unless defined?(@evidence)
|
344
|
+
e = get_by_qualifier('gene_name')
|
345
|
+
@evidence = e ? e.evidence : nil
|
346
|
+
end
|
347
|
+
@evidence
|
348
|
+
end
|
349
|
+
end #class MaXML::Annotations
|
350
|
+
|
351
|
+
class Annotation < MaXML
|
352
|
+
def entry_id
|
353
|
+
nil
|
354
|
+
end
|
355
|
+
|
356
|
+
class DataSrc < String
|
357
|
+
def initialize(text, href)
|
358
|
+
super(text)
|
359
|
+
@href = href
|
360
|
+
end
|
361
|
+
attr_reader :href
|
362
|
+
end
|
363
|
+
|
364
|
+
def datasrc
|
365
|
+
unless defined?(@datasrc)
|
366
|
+
@datasrc = []
|
367
|
+
@elem.each_element('datasrc') do |e|
|
368
|
+
text = e.text
|
369
|
+
href = e.attributes['href']
|
370
|
+
@datasrc << DataSrc.new(gsub_entities(text), gsub_entities(href))
|
371
|
+
end
|
372
|
+
end
|
373
|
+
@datasrc
|
374
|
+
end
|
375
|
+
|
376
|
+
define_element_text_method(%w(qualifier srckey anntext evidence))
|
377
|
+
end #class MaXML::Annotation
|
378
|
+
|
379
|
+
end #class MaXML
|
380
|
+
|
381
|
+
end #module FANTOM
|
382
|
+
|
383
|
+
end #module Bio
|
384
|
+
|
385
|
+
=begin
|
386
|
+
|
387
|
+
Bio::FANTOM are database classes (and modules) treating RIKEN FANTOM2 data.
|
388
|
+
FANTOM2 is available at ((<URL:http://fantom2.gsc.riken.go.jp/>)).
|
389
|
+
|
390
|
+
= Bio::FANTOM
|
391
|
+
|
392
|
+
This module contains useful methods to access databases.
|
393
|
+
|
394
|
+
--- Bio::FANTOM.query(idstr, http_proxy=nil)
|
395
|
+
|
396
|
+
Get MaXML sequence data corresponding to given ID through the internet
|
397
|
+
from ((<URL:http://fantom.gsc.riken.go.jp/db/maxml/)).
|
398
|
+
Returns Bio::FANTOM::MaXML::Sequence object.
|
399
|
+
|
400
|
+
--- Bio::FANTOM.get_by_id(idstr, http_proxy=nil)
|
401
|
+
|
402
|
+
Same as FANTOM.query, but returns XML document as a string.
|
403
|
+
(Reference: bio/io/registry.rb)
|
404
|
+
|
405
|
+
|
406
|
+
= Bio::FANTOM::MaXML::Cluster
|
407
|
+
|
408
|
+
This class is for 'allclust.sep.xml' found at
|
409
|
+
((<URL:ftp://fantom2.gsc.riken.go.jp/fantom/2.1/allclust.sep.xml.gz>)).
|
410
|
+
Not that this class is not suitable for 'allclust.xml'.
|
411
|
+
|
412
|
+
--- Bio::FANTOM::MaXML::Cluster.new(str)
|
413
|
+
|
414
|
+
--- Bio::FANTOM::MaXML::Cluster#entry_id
|
415
|
+
|
416
|
+
--- Bio::FANTOM::MaXML::Cluster#fantomid
|
417
|
+
|
418
|
+
--- Bio::FANTOM::MaXML::Cluster#representative_seqid
|
419
|
+
|
420
|
+
--- Bio::FANTOM::MaXML::Cluster#sequences
|
421
|
+
|
422
|
+
Lists sequences in this cluster.
|
423
|
+
Returns Bio::FANTOM::MaXML::Sequences object.
|
424
|
+
|
425
|
+
--- Bio::FANTOM::MaXML::Cluster#sequence(id_str)
|
426
|
+
|
427
|
+
Shows a sequence information of given id.
|
428
|
+
Returns Bio::FANTOM::MaXML::Sequence object or nil.
|
429
|
+
|
430
|
+
--- Bio::FANTOM::MaXML::Cluster#representataive_sequence
|
431
|
+
--- Bio::FANTOM::MaXML::Cluster#representataive_clone
|
432
|
+
|
433
|
+
Shows a sequence of repesentative_seqid.
|
434
|
+
Returns Bio::FANTOM::MaXML::Sequence object (or nil).
|
435
|
+
|
436
|
+
-- Bio::FANTOM::MaXML::Cluster#representative_annotations
|
437
|
+
|
438
|
+
Shows annotations of repesentative sequence.
|
439
|
+
Returns Bio::FANTOM::MaXML::Annotations object (or nil).
|
440
|
+
|
441
|
+
-- Bio::FANTOM::MaXML::Cluster#representative_cloneid
|
442
|
+
|
443
|
+
Shows cloneid of repesentative sequence.
|
444
|
+
Returns String (or nil).
|
445
|
+
|
446
|
+
|
447
|
+
= Bio::FANTOM::MaXML::Sequences
|
448
|
+
|
449
|
+
The instances of this class are automatically created
|
450
|
+
by Bio::FANTOM::MaXML::Cluster class.
|
451
|
+
|
452
|
+
This class can also be used for 'allseq.sep.xml' and 'repseq.sep.xml',
|
453
|
+
but you'd better using Bio::FANTOM::MaXML::Sequence class.
|
454
|
+
|
455
|
+
In addition, this class can be used for 'allseq.xml' and 'repseq.xml',
|
456
|
+
but you'd better not to use them, becase of the speed is very slow.
|
457
|
+
|
458
|
+
--- Bio::FANTOM::MaXML::Sequences#to_a
|
459
|
+
|
460
|
+
Returns an Array of Bio::FANTOM::MaXML::Sequence objects.
|
461
|
+
|
462
|
+
--- Bio::FANTOM::MaXML::Sequences#each
|
463
|
+
|
464
|
+
--- Bio::FANTOM::MaXML::Sequences#[](x)
|
465
|
+
|
466
|
+
Same as to_a[x] when x is a integer.
|
467
|
+
Same as get[x] when x is a string.
|
468
|
+
|
469
|
+
--- Bio::FANTOM::MaXML::Sequences#get(id_str)
|
470
|
+
|
471
|
+
Shows a sequence information of given id.
|
472
|
+
Returns Bio::FANTOM::MaXML::Sequence object or nil.
|
473
|
+
|
474
|
+
--- Bio::FANTOM::MaXML::Sequences#cloneids
|
475
|
+
|
476
|
+
Shows clone ID list.
|
477
|
+
Returns an array of strings.
|
478
|
+
|
479
|
+
--- Bio::FANTOM::MaXML::Sequences#id_strings
|
480
|
+
|
481
|
+
Shows ID list.
|
482
|
+
Returns an array of strings.
|
483
|
+
|
484
|
+
|
485
|
+
= Bio::FANTOM::MaXML::Sequence
|
486
|
+
|
487
|
+
This class is for 'allseq.sep.xml' and 'repseq.sep.xml' found at
|
488
|
+
((<URL:ftp://fantom2.gsc.riken.go.jp/fantom/2.1/allseq.sep.xml.gz>)) and
|
489
|
+
((<URL:ftp://fantom2.gsc.riken.go.jp/fantom/2.1/repseq.sep.xml.gz>)).
|
490
|
+
Not that this class is not suitable for 'allseq.xml' and 'repseq.xml'.
|
491
|
+
|
492
|
+
In addition, the instances of this class are automatically created
|
493
|
+
by Bio::FANTOM::MaXML::Sequences class.
|
494
|
+
|
495
|
+
--- Bio::FANTOM::MaXML::Sequence.new(str)
|
496
|
+
|
497
|
+
--- Bio::FANTOM::MaXML::Sequence#entry_id
|
498
|
+
|
499
|
+
--- Bio::FANTOM::MaXML::Sequence#altid(type_str = nil)
|
500
|
+
|
501
|
+
Returns hash of altid if no arguments are given.
|
502
|
+
Returns ID as a string if a type of ID (string) is given.
|
503
|
+
|
504
|
+
--- Bio::FANTOM::MaXML::Sequence#annotations
|
505
|
+
|
506
|
+
Gets lists of annotation data.
|
507
|
+
Returns a Bio::FANTOM::MaXML::Annotations object.
|
508
|
+
|
509
|
+
--- Bio::FANTOM::MaXML::Sequence#id_strings
|
510
|
+
|
511
|
+
Gets lists of ID. (same as altid.values)
|
512
|
+
Returns an array of strings.
|
513
|
+
|
514
|
+
--- Bio::FANTOM::MaXML::Sequence#library_id
|
515
|
+
|
516
|
+
Shows library ID. (same as cloneid[0,2])
|
517
|
+
Library IDs are listed at:
|
518
|
+
((<URL:http://fantom2.gsc.riken.go.jp/fantom2/SI/sup01_est_3r_libraryinfo.pdf))
|
519
|
+
((<URL:http://fantom2.gsc.riken.go.jp/fantom2/SI/sup01_est_5f_libraryinfo.pdf))
|
520
|
+
|
521
|
+
--- Bio::FANTOM::MaXML::Sequence#seqid
|
522
|
+
|
523
|
+
--- Bio::FANTOM::MaXML::Sequence#fantomid
|
524
|
+
|
525
|
+
--- Bio::FANTOM::MaXML::Sequence#cloneid
|
526
|
+
|
527
|
+
--- Bio::FANTOM::MaXML::Sequence#rearrayid
|
528
|
+
|
529
|
+
--- Bio::FANTOM::MaXML::Sequence#accession
|
530
|
+
|
531
|
+
--- Bio::FANTOM::MaXML::Sequence#annotator
|
532
|
+
|
533
|
+
--- Bio::FANTOM::MaXML::Sequence#version
|
534
|
+
|
535
|
+
--- Bio::FANTOM::MaXML::Sequence#modified_time
|
536
|
+
|
537
|
+
--- Bio::FANTOM::MaXML::Sequence#comment
|
538
|
+
|
539
|
+
|
540
|
+
= Bio::FANTOM::MaXML::Annotations
|
541
|
+
|
542
|
+
The instances of this class are automatically created
|
543
|
+
by Bio::FANTOM::MaXML::Sequence class.
|
544
|
+
|
545
|
+
--- Bio::FANTOM::MaXML::Annotations#to_a
|
546
|
+
|
547
|
+
Returns an Array of Bio::FANTOM::MaXML::Annotations objects.
|
548
|
+
|
549
|
+
--- Bio::FANTOM::MaXML::Annotations#each
|
550
|
+
|
551
|
+
--- Bio::FANTOM::MaXML::Annotations#get_all_by_qualifier(qstr)
|
552
|
+
|
553
|
+
--- Bio::FANTOM::MaXML::Annotations#get_by_qualifier(qstr)
|
554
|
+
|
555
|
+
--- Bio::FANTOM::MaXML::Annotations#[](x)
|
556
|
+
|
557
|
+
Same as to_a[x] when x is a integer.
|
558
|
+
Same as get_by_qualifier[x] when x is a string.
|
559
|
+
|
560
|
+
--- Bio::FANTOM::MaXML::Annotations#cds_start
|
561
|
+
--- Bio::FANTOM::MaXML::Annotations#cds_stop
|
562
|
+
--- Bio::FANTOM::MaXML::Annotations#gene_name
|
563
|
+
--- Bio::FANTOM::MaXML::Annotations#data_source
|
564
|
+
--- Bio::FANTOM::MaXML::Annotations#evidence
|
565
|
+
|
566
|
+
|
567
|
+
= Bio::FANTOM::MaXML::Annotation
|
568
|
+
|
569
|
+
The instances of this class are automatically created
|
570
|
+
by Bio::FANTOM::MaXML::Annotations class.
|
571
|
+
|
572
|
+
--- Bio::FANTOM::MaXML::Annotation#datasrc
|
573
|
+
|
574
|
+
Returns an Array of Bio::FANTOM::MaXML::Annotation::DataSrc objects.
|
575
|
+
|
576
|
+
--- Bio::FANTOM::MaXML::Annotation#qualifier
|
577
|
+
|
578
|
+
--- Bio::FANTOM::MaXML::Annotation#srckey
|
579
|
+
|
580
|
+
--- Bio::FANTOM::MaXML::Annotation#anntext
|
581
|
+
|
582
|
+
--- Bio::FANTOM::MaXML::Annotation#evidence
|
583
|
+
|
584
|
+
= Bio::FANTOM::MaXML::Annotation::DataSrc < String
|
585
|
+
|
586
|
+
The instances of this class are automatically created
|
587
|
+
by Bio::FANTOM::MaXML::Annotation class.
|
588
|
+
|
589
|
+
---- Bio::FANTOM::MaXML::Annotation::DataSrc#href
|
590
|
+
|
591
|
+
Shows a link URL to database web page as an String.
|
592
|
+
|
593
|
+
= References
|
594
|
+
|
595
|
+
* ((<URL:http://fantom2.gsc.riken.go.jp/>))
|
596
|
+
|
597
|
+
=end
|