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 +1,101 @@
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#
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# test/unit/bio/db/test_rebase.rb - Unit test for Bio::REBASE
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#
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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# License:: The Ruby License
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#
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# $Id: test_rebase.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
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#
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'test/unit'
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require 'bio/db/rebase'
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module Bio #:nodoc:
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class TestREBASE < Test::Unit::TestCase #:nodoc:
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def setup
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enzyme_data = <<END
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#
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# REBASE version 511 emboss_e.511
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#
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AarI CACCTGC 7 2 0 11 15 0 0
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AasI GACNNNNNNGTC 12 2 0 7 5 0 0
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AatI AGGCCT 6 2 1 3 3 0 0
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END
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reference_data = <<END
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#
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# REBASE version 511 emboss_r.511
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#
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#
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AarI
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Arthrobacter aurescens SS2-322
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A. Janulaitis
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F
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2
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Grigaite, R., Maneliene, Z., Janulaitis, A., (2002) Nucleic Acids Res., vol. 30.
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Maneliene, Z., Zakareviciene, L., Unpublished observations.
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//
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AasI
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Arthrobacter aurescens RFL3
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V. Butkus
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F
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1
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Kazlauskiene, R., Vaitkevicius, D., Maneliene, Z., Trinkunaite, L., Kiuduliene, L., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.
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//
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AatI
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Acetobacter aceti
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IFO 3281
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O
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2
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Sato, H., Yamada, Y., (1990) J. Gen. Appl. Microbiol., vol. 36, pp. 273-277.
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Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Nucleic Acids Res., vol. 10, pp. 5747-5752.
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//
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END
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supplier_data = <<END
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#
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# REBASE version 511 emboss_s.511
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#
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A GE Healthcare
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B Invitrogen Corporation
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C Minotech Biotechnology
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E Stratagene
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F Fermentas International Inc.
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G Qbiogene
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O Toyobo Biochemicals
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END
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@obj = Bio::REBASE.new(enzyme_data, reference_data, supplier_data)
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end
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def test_methods
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a = @obj
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assert_equal(a['AarI'].organism, 'Arthrobacter aurescens SS2-322')
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assert_equal(a['AarI'].references.size, 2)
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assert_equal(a['AarI'].supplier_names, ['Fermentas International Inc.'])
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assert_equal(a['AarI'].pattern, 'CACCTGC')
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assert_equal(a['AatI'].supplier_names, ['Toyobo Biochemicals'])
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assert_equal(a['AatI'].suppliers, ['O'])
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assert_equal(a.enzyme_name?('aasi'), true)
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assert_equal(a.enzyme_name?('AarI'), true)
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assert_equal(a.enzyme_name?('Aari'), true)
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assert_equal(a.enzyme_name?('AbrI'), false)
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end
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end
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end
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#
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# test/unit/bio/db/test_rebase.rb - Unit test for Bio::REBASE
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#
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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# License:: The Ruby License
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#
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# $Id: test_soft.rb,v 1.3 2007/04/05 23:35:43 trevor Exp $
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#
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'test/unit'
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require 'bio/db/soft'
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module Bio #:nodoc:
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class TestSOFT < Test::Unit::TestCase #:nodoc:
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def setup
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bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4)).cleanpath.to_s
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test_data_path = Pathname.new(File.join(bioruby_root, 'test', 'data', 'soft')).cleanpath.to_s
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series_filename = File.join(test_data_path, 'GSE3457_family_partial.soft')
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dataset_filename = File.join(test_data_path, 'GDS100_partial.soft')
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@obj_series = Bio::SOFT.new( IO.readlines(series_filename))
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@obj_dataset = Bio::SOFT.new( IO.readlines(dataset_filename))
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end
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def test_series
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assert_equal( @obj_series.platform[:geo_accession], 'GPL2092')
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assert_equal( @obj_series.platform[:organism], 'Populus')
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assert_equal( @obj_series.platform[:contributor], ["Jingyi,,Li", "Olga,,Shevchenko", "Steve,H,Strauss", "Amy,M,Brunner"])
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assert_equal( @obj_series.platform[:data_row_count], '240')
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assert_equal( @obj_series.platform.keys.sort {|a,b| a.to_s <=> b.to_s}[0..2], [:contact_address, :contact_city, :contact_country])
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assert_equal( @obj_series.platform[:"contact_zip/postal_code"], '97331')
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assert_equal( @obj_series.platform[:table].header, ["ID", "GB_ACC", "SPOT_ID", "Function/Family", "ORGANISM", "SEQUENCE"])
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assert_equal( @obj_series.platform[:table].header_description, {"ORGANISM"=>"sequence sources",
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"SEQUENCE"=>"oligo sequence used",
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"Function/Family"=>"gene functions and family",
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"ID"=>"",
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"SPOT_ID"=>"",
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"GB_ACC"=>"Gene bank accession number"})
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assert_equal( @obj_series.platform[:table].rows.size, 240)
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assert_equal( @obj_series.platform[:table].rows[5], ["A039P68U",
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"AI163321",
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"",
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"TF, flowering protein CONSTANS",
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"P. tremula x P. tremuloides",
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"AGAAAATTCGATATACTGTCCGTAAAGAGGTAGCACTTAGAATGCAACGGAATAAAGGGCAGTTCACCTC"])
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assert_equal( @obj_series.platform[:table].rows[5][4], 'P. tremula x P. tremuloides')
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assert_equal( @obj_series.platform[:table].rows[5][:organism], 'P. tremula x P. tremuloides')
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assert_equal( @obj_series.platform[:table].rows[5]['ORGANISM'], 'P. tremula x P. tremuloides')
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assert_equal( @obj_series.series[:geo_accession], 'GSE3457')
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assert_equal( @obj_series.series[:contributor], ["Jingyi,,Li",
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"Olga,,Shevchenko",
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"Ove,,Nilsson",
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"Steve,H,Strauss",
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"Amy,M,Brunner"])
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assert_equal( @obj_series.series[:platform_id], 'GPL2092')
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assert_equal( @obj_series.series[:sample_id].size, 74)
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assert_equal( @obj_series.series[:sample_id][0..4], ["GSM77557", "GSM77558", "GSM77559", "GSM77560", "GSM77561"])
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assert_equal( @obj_series.database[:name], 'Gene Expression Omnibus (GEO)')
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assert_equal( @obj_series.database[:ref], 'Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D562-6')
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assert_equal( @obj_series.database[:institute], 'NCBI NLM NIH')
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assert_equal( @obj_series.samples.size, 2)
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assert_equal( @obj_series.samples[:GSM77557][:series_id], 'GSE3457')
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assert_equal( @obj_series.samples['GSM77557'][:series_id], 'GSE3457')
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assert_equal( @obj_series.samples[:GSM77557][:platform_id], 'GPL2092')
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assert_equal( @obj_series.samples[:GSM77557][:type], 'RNA')
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assert_equal( @obj_series.samples[:GSM77557][:title], 'fb6a1')
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76
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assert_equal( @obj_series.samples[:GSM77557][:table].header, ["ID_REF", "VALUE"])
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77
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assert_equal( @obj_series.samples[:GSM77557][:table].header_description, {"ID_REF"=>"", "VALUE"=>"normalized signal intensities"})
|
78
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assert_equal( @obj_series.samples[:GSM77557][:table].rows.size, 217)
|
79
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assert_equal( @obj_series.samples[:GSM77557][:table].rows[5], ["A039P68U", "5.36"])
|
80
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assert_equal( @obj_series.samples[:GSM77557][:table].rows[5][0], 'A039P68U')
|
81
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assert_equal( @obj_series.samples[:GSM77557][:table].rows[5][:id_ref], 'A039P68U')
|
82
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assert_equal( @obj_series.samples[:GSM77557][:table].rows[5]['ID_REF'], 'A039P68U')
|
83
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+
end
|
84
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+
|
85
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def test_dataset
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86
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assert_equal( @obj_dataset.database[:name], 'Gene Expression Omnibus (GEO)')
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|
88
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assert_equal( @obj_dataset.database[:ref], 'Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D562-6')
|
89
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assert_equal( @obj_dataset.database[:institute], 'NCBI NLM NIH')
|
90
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+
|
91
|
+
assert_equal( @obj_dataset.subsets.size, 8)
|
92
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assert_equal( @obj_dataset.subsets.keys, ["GDS100_1",
|
93
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"GDS100_2",
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"GDS100_3",
|
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"GDS100_4",
|
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"GDS100_5",
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"GDS100_6",
|
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"GDS100_7",
|
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"GDS100_8"])
|
100
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assert_equal( @obj_dataset.subsets[:GDS100_7], {:sample_id=>"GSM548,GSM543",
|
101
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:dataset_id=>"GDS100",
|
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:description=>"60 minute",
|
103
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:type=>"time"})
|
104
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assert_equal( @obj_dataset.subsets['GDS100_7'][:sample_id], 'GSM548,GSM543')
|
105
|
+
assert_equal( @obj_dataset.subsets[:GDS100_7][:sample_id], 'GSM548,GSM543')
|
106
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assert_equal( @obj_dataset.subsets[:GDS100_7][:dataset_id], 'GDS100')
|
107
|
+
|
108
|
+
assert_equal( @obj_dataset.dataset[:order], 'none')
|
109
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+
assert_equal( @obj_dataset.dataset[:sample_organism], 'Escherichia coli')
|
110
|
+
assert_equal( @obj_dataset.dataset[:table].header, ["ID_REF",
|
111
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+
"IDENTIFIER",
|
112
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"GSM549",
|
113
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"GSM542",
|
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"GSM543",
|
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"GSM547",
|
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"GSM544",
|
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"GSM545",
|
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"GSM546",
|
119
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"GSM548"])
|
120
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assert_equal( @obj_dataset.dataset[:table].rows.size, 15)
|
121
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+
assert_equal( @obj_dataset.dataset[:table].rows[5], ["6",
|
122
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+
"EMPTY",
|
123
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"0.097",
|
124
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"0.217",
|
125
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"0.242",
|
126
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"0.067",
|
127
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"0.104",
|
128
|
+
"0.162",
|
129
|
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"0.104",
|
130
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+
"0.154"])
|
131
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assert_equal( @obj_dataset.dataset[:table].rows[5][4], '0.242')
|
132
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assert_equal( @obj_dataset.dataset[:table].rows[5][:gsm549], '0.097')
|
133
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assert_equal( @obj_dataset.dataset[:table].rows[5][:GSM549], '0.097')
|
134
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assert_equal( @obj_dataset.dataset[:table].rows[5]['GSM549'], '0.097')
|
135
|
+
end
|
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end
|
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|
138
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+
end
|
@@ -0,0 +1,36 @@
|
|
1
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|
2
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|
3
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$:.unshift File.join(File.dirname(__FILE__),['..'] * 4,'lib')
|
4
|
+
|
5
|
+
require 'test/unit'
|
6
|
+
require 'bio'
|
7
|
+
|
8
|
+
module Bio
|
9
|
+
# Test the static methods work correctly
|
10
|
+
class UrlTest < Test::Unit::TestCase
|
11
|
+
def test_hhmi_pfam_family_url
|
12
|
+
assert_equal "http://pfam.janelia.org/family?entry=PF00001&type=Family",
|
13
|
+
Bio::URL.hhmi_pfam_family_url('PF00001')
|
14
|
+
end
|
15
|
+
|
16
|
+
def test_pantherdb_panther_family_url
|
17
|
+
assert_equal "http://www.pantherdb.org/panther/family.do?clsAccession=PTHR10003",
|
18
|
+
Bio::URL.pantherdb_panther_family_url('PTHR10003')
|
19
|
+
end
|
20
|
+
|
21
|
+
def test_plasmodb_gene_url
|
22
|
+
assert_equal "http://plasmodb.org/gene/PfCRT",
|
23
|
+
Bio::URL.plasmodb_gene_url('PfCRT')
|
24
|
+
end
|
25
|
+
end
|
26
|
+
|
27
|
+
# Test that inclusion of the module works correctly
|
28
|
+
class UrlGeneratorsTest < Test::Unit::TestCase
|
29
|
+
include Bio::URLGenerators
|
30
|
+
|
31
|
+
def test_module_include
|
32
|
+
assert_equal "http://www.pantherdb.org/panther/family.do?clsAccession=PTHR10003",
|
33
|
+
pantherdb_panther_family_url('PTHR10003')
|
34
|
+
end
|
35
|
+
end
|
36
|
+
end
|
@@ -0,0 +1,375 @@
|
|
1
|
+
#
|
2
|
+
# = test/unit/bio/io/flatfile/test_autodetection.rb - unit test for Bio::FlatFile::AutoDetect
|
3
|
+
#
|
4
|
+
# Copyright (C) 2006 Naohisa Goto <ng@bioruby.org>
|
5
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#
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# License:: The Ruby License
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#
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# $Id: test_flatfile.rb,v 1.2 2007/04/05 23:35:43 trevor Exp $
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#
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'test/unit'
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require 'bio'
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module Bio::TestFlatFile
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19
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20
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# testing default AutoDetect's behavior
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class TestDefaultAutoDetect < Test::Unit::TestCase
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bioruby_root = Pathname.new(File.join(File.dirname(__FILE__),
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['..'] * 5)).cleanpath.to_s
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TestDataPath = Pathname.new(File.join(bioruby_root,
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'test', 'data')).cleanpath.to_s
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def setup
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@ad = Bio::FlatFile::AutoDetect.default
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end
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32
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def test_genbank
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# modified from GenBank AB009803.1
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# (E-mail and telephone/FAX numbers are removed from original entry)
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text = <<__END_OF_TEXT__
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LOCUS AB009803 81 bp DNA linear PRI 14-APR-2000
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DEFINITION Homo sapiens gene for osteonidogen, intron 4.
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+
ACCESSION AB009803
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+
VERSION AB009803.1 GI:2749808
|
40
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+
KEYWORDS osteonidogen.
|
41
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+
SOURCE Homo sapiens (human)
|
42
|
+
ORGANISM Homo sapiens
|
43
|
+
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
|
44
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+
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
|
45
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+
Catarrhini; Hominidae; Homo.
|
46
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+
REFERENCE 1
|
47
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+
AUTHORS Ohno,I., Okubo,K. and Matsubara,K.
|
48
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TITLE Human osteonidogen gene: intron-exon junctions and chromosomal
|
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+
localization
|
50
|
+
JOURNAL Published Only in Database (1998)
|
51
|
+
REFERENCE 2 (bases 1 to 81)
|
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AUTHORS Ohno,I., Okubo,K. and Matsubara,K.
|
53
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TITLE Direct Submission
|
54
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JOURNAL Submitted (13-DEC-1997) Ikko Ohno, Institute for Molecular and
|
55
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+
Cellular Biology, Osaka University, Molecular Genetics; 1-3
|
56
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+
Yamada-oka, Suita, Osaka 565, Japan
|
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+
FEATURES Location/Qualifiers
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source 1..81
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/organism="Homo sapiens"
|
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/mol_type="genomic DNA"
|
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/db_xref="taxon:9606"
|
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/chromosome="14"
|
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/map="14q21-22"
|
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/clone_lib="Lambda FIX II STRATAGENE"
|
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intron 1..81
|
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/number=4
|
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+
ORIGIN
|
68
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+
1 gtaggatctc ccctccagat tctgatctgt cctccccctt gcatccaaca cctacttatt
|
69
|
+
61 ggccattcta tcctgaaaca g
|
70
|
+
//
|
71
|
+
__END_OF_TEXT__
|
72
|
+
assert_equal(Bio::GenBank, @ad.autodetect(text))
|
73
|
+
end
|
74
|
+
|
75
|
+
def test_genpept
|
76
|
+
# modified from: NCBI: P04637.2 GI:129369
|
77
|
+
# (to shorten data, many elements are omitted)
|
78
|
+
text = <<__END_OF_TEXT__
|
79
|
+
LOCUS P04637 393 aa linear PRI 01-JUL-2008
|
80
|
+
DEFINITION Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein
|
81
|
+
p53) (Antigen NY-CO-13).
|
82
|
+
ACCESSION P04637
|
83
|
+
VERSION P04637.2 GI:129369
|
84
|
+
KEYWORDS 3D-structure; Acetylation; Activator; Alternative splicing;
|
85
|
+
Anti-oncogene; Apoptosis; Cell cycle; Covalent protein-RNA linkage;
|
86
|
+
Cytoplasm; Disease mutation; DNA-binding; Endoplasmic reticulum;
|
87
|
+
Glycoprotein; Host-virus interaction; Li-Fraumeni syndrome;
|
88
|
+
Metal-binding; Methylation; Nucleus; Phosphoprotein; Polymorphism;
|
89
|
+
Transcription; Transcription regulation; Ubl conjugation; Zinc.
|
90
|
+
SOURCE Homo sapiens (human)
|
91
|
+
ORGANISM Homo sapiens
|
92
|
+
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
|
93
|
+
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
|
94
|
+
Catarrhini; Hominidae; Homo.
|
95
|
+
REFERENCE 1 (residues 1 to 393)
|
96
|
+
AUTHORS Zakut-Houri,R., Bienz-Tadmor,B., Givol,D. and Oren,M.
|
97
|
+
TITLE Human p53 cellular tumor antigen: cDNA sequence and expression in
|
98
|
+
COS cells
|
99
|
+
JOURNAL EMBO J. 4 (5), 1251-1255 (1985)
|
100
|
+
PUBMED 4006916
|
101
|
+
REMARK NUCLEOTIDE SEQUENCE [MRNA].
|
102
|
+
FEATURES Location/Qualifiers
|
103
|
+
source 1..393
|
104
|
+
/organism="Homo sapiens"
|
105
|
+
/db_xref="taxon:9606"
|
106
|
+
gene 1..393
|
107
|
+
/gene="TP53"
|
108
|
+
/note="synonym: P53"
|
109
|
+
Protein 1..393
|
110
|
+
/gene="TP53"
|
111
|
+
/product="Cellular tumor antigen p53"
|
112
|
+
ORIGIN
|
113
|
+
1 meepqsdpsv epplsqetfs dlwkllpenn vlsplpsqam ddlmlspddi eqwftedpgp
|
114
|
+
61 deaprmpeaa ppvapapaap tpaapapaps wplsssvpsq ktyqgsygfr lgflhsgtak
|
115
|
+
121 svtctyspal nkmfcqlakt cpvqlwvdst pppgtrvram aiykqsqhmt evvrrcphhe
|
116
|
+
181 rcsdsdglap pqhlirvegn lrveylddrn tfrhsvvvpy eppevgsdct tihynymcns
|
117
|
+
241 scmggmnrrp iltiitleds sgnllgrnsf evrvcacpgr drrteeenlr kkgephhelp
|
118
|
+
301 pgstkralpn ntssspqpkk kpldgeyftl qirgrerfem frelnealel kdaqagkepg
|
119
|
+
361 gsrahsshlk skkgqstsrh kklmfktegp dsd
|
120
|
+
//
|
121
|
+
__END_OF_TEXT__
|
122
|
+
|
123
|
+
assert_equal(Bio::GenPept, @ad.autodetect(text))
|
124
|
+
end
|
125
|
+
|
126
|
+
def test_medline
|
127
|
+
# PMID: 13054692
|
128
|
+
text = <<__END_OF_TEXT__
|
129
|
+
PMID- 13054692
|
130
|
+
OWN - NLM
|
131
|
+
STAT- MEDLINE
|
132
|
+
DA - 19531201
|
133
|
+
DCOM- 20030501
|
134
|
+
LR - 20061115
|
135
|
+
PUBM- Print
|
136
|
+
IS - 0028-0836 (Print)
|
137
|
+
VI - 171
|
138
|
+
IP - 4356
|
139
|
+
DP - 1953 Apr 25
|
140
|
+
TI - Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid.
|
141
|
+
PG - 737-8
|
142
|
+
FAU - WATSON, J D
|
143
|
+
AU - WATSON JD
|
144
|
+
FAU - CRICK, F H
|
145
|
+
AU - CRICK FH
|
146
|
+
LA - eng
|
147
|
+
PT - Journal Article
|
148
|
+
PL - Not Available
|
149
|
+
TA - Nature
|
150
|
+
JT - Nature
|
151
|
+
JID - 0410462
|
152
|
+
RN - 0 (Nucleic Acids)
|
153
|
+
SB - OM
|
154
|
+
MH - *Nucleic Acids
|
155
|
+
OID - CLML: 5324:25254:447
|
156
|
+
OTO - NLM
|
157
|
+
OT - *NUCLEIC ACIDS
|
158
|
+
EDAT- 1953/04/25
|
159
|
+
MHDA- 1953/04/25 00:01
|
160
|
+
PST - ppublish
|
161
|
+
SO - Nature. 1953 Apr 25;171(4356):737-8.
|
162
|
+
__END_OF_TEXT__
|
163
|
+
|
164
|
+
assert_equal(Bio::MEDLINE, @ad.autodetect(text))
|
165
|
+
end
|
166
|
+
|
167
|
+
def test_embl_oldrelease
|
168
|
+
fn = File.join(TestDataPath, 'embl', 'AB090716.embl')
|
169
|
+
text = File.read(fn)
|
170
|
+
assert_equal(Bio::EMBL, @ad.autodetect(text))
|
171
|
+
end
|
172
|
+
|
173
|
+
def test_embl
|
174
|
+
fn = File.join(TestDataPath, 'embl', 'AB090716.embl.rel89')
|
175
|
+
text = File.read(fn)
|
176
|
+
assert_equal(Bio::EMBL, @ad.autodetect(text))
|
177
|
+
end
|
178
|
+
|
179
|
+
def test_sptr
|
180
|
+
fn = File.join(TestDataPath, 'uniprot', 'p53_human.uniprot')
|
181
|
+
text = File.read(fn)
|
182
|
+
assert_equal(Bio::SPTR, @ad.autodetect(text))
|
183
|
+
end
|
184
|
+
|
185
|
+
def test_prosite
|
186
|
+
fn = File.join(TestDataPath, 'prosite', 'prosite.dat')
|
187
|
+
text = File.read(fn)
|
188
|
+
assert_equal(Bio::PROSITE, @ad.autodetect(text))
|
189
|
+
end
|
190
|
+
|
191
|
+
def test_transfac
|
192
|
+
# Dummy data; Generated from random data
|
193
|
+
text = <<__END_OF_TEXT__
|
194
|
+
AC M99999
|
195
|
+
XX
|
196
|
+
ID V$XXXX_99
|
197
|
+
XX
|
198
|
+
DT 13.01.98 (created); ewi.
|
199
|
+
DT 31.12.99 (updated); ewi.
|
200
|
+
XX
|
201
|
+
NA XXXX
|
202
|
+
XX
|
203
|
+
DE example gene protein
|
204
|
+
XX
|
205
|
+
BF T99998; XXXX; Species: human, Homo sapiens.
|
206
|
+
BF T99999; XXXX; Species: mouse, Mus musculus.
|
207
|
+
XX
|
208
|
+
P0 A C G T
|
209
|
+
01 1 2 2 2 N
|
210
|
+
02 0 2 2 3 N
|
211
|
+
03 1 1 5 0 G
|
212
|
+
04 3 1 1 2 N
|
213
|
+
05 7 0 0 0 A
|
214
|
+
06 2 0 1 4 W
|
215
|
+
07 0 1 6 0 G
|
216
|
+
08 0 3 0 4 Y
|
217
|
+
09 6 1 0 0 A
|
218
|
+
10 1 1 0 5 T
|
219
|
+
XX
|
220
|
+
BA 7 functional elements in 3 genes
|
221
|
+
XX
|
222
|
+
CC compiled sequences
|
223
|
+
XX
|
224
|
+
RN [1]
|
225
|
+
RA Anonymou S., Whoam I.
|
226
|
+
RT Example article title for XXXX
|
227
|
+
RL J. Example. 99:990-999 (1999).
|
228
|
+
__END_OF_TEXT__
|
229
|
+
|
230
|
+
assert_equal(Bio::TRANSFAC, @ad.autodetect(text))
|
231
|
+
end
|
232
|
+
|
233
|
+
def test_aaindex1
|
234
|
+
fn = File.join(TestDataPath, 'aaindex', 'PRAM900102')
|
235
|
+
text = File.read(fn)
|
236
|
+
assert_equal(Bio::AAindex1, @ad.autodetect(text))
|
237
|
+
end
|
238
|
+
|
239
|
+
def test_aaindex2
|
240
|
+
fn = File.join(TestDataPath, 'aaindex', 'DAYM780301')
|
241
|
+
text = File.read(fn)
|
242
|
+
assert_equal(Bio::AAindex2, @ad.autodetect(text))
|
243
|
+
end
|
244
|
+
|
245
|
+
# def test_litdb
|
246
|
+
# end
|
247
|
+
|
248
|
+
# def test_brite
|
249
|
+
# end
|
250
|
+
|
251
|
+
# def test_orthology
|
252
|
+
# end
|
253
|
+
|
254
|
+
# def test_drug
|
255
|
+
# end
|
256
|
+
|
257
|
+
# def test_glycan
|
258
|
+
# end
|
259
|
+
|
260
|
+
# def test_enzyme
|
261
|
+
# end
|
262
|
+
|
263
|
+
# def test_compound
|
264
|
+
# end
|
265
|
+
|
266
|
+
# def test_reaction
|
267
|
+
# end
|
268
|
+
|
269
|
+
# def test_genes
|
270
|
+
# end
|
271
|
+
|
272
|
+
# def test_genome
|
273
|
+
# end
|
274
|
+
|
275
|
+
def test_maxml_cluster
|
276
|
+
# dummy empty data
|
277
|
+
text = <<__END_OF_TEXT__
|
278
|
+
<?xml version="1.0"?>
|
279
|
+
<!DOCTYPE maxml-clusters SYSTEM "http://fantom.gsc.riken.go.jp/maxml/maxml.dtd"><maxml-clusters>
|
280
|
+
</maxml-clusters>
|
281
|
+
__END_OF_TEXT__
|
282
|
+
assert_equal(Bio::FANTOM::MaXML::Cluster, @ad.autodetect(text))
|
283
|
+
end
|
284
|
+
|
285
|
+
def test_maxml_sequence
|
286
|
+
# dummy empty data
|
287
|
+
text = <<__END_OF_TEXT__
|
288
|
+
<?xml version="1.0"?>
|
289
|
+
<!DOCTYPE maxml-sequences SYSTEM "http://fantom.gsc.riken.go.jp/maxml/maxml.dtd">
|
290
|
+
<maxml-sequences>
|
291
|
+
</maxml-sequences>
|
292
|
+
__END_OF_TEXT__
|
293
|
+
assert_equal(Bio::FANTOM::MaXML::Sequence, @ad.autodetect(text))
|
294
|
+
end
|
295
|
+
|
296
|
+
# def test_pdb
|
297
|
+
# end
|
298
|
+
|
299
|
+
# def test_chemicalcomponent
|
300
|
+
# end
|
301
|
+
|
302
|
+
# def test_clustal
|
303
|
+
# end
|
304
|
+
|
305
|
+
# def test_gcg_msf
|
306
|
+
# end
|
307
|
+
|
308
|
+
# def test_gcg_seq
|
309
|
+
# end
|
310
|
+
|
311
|
+
def test_blastxml
|
312
|
+
fn = File.join(TestDataPath, 'blast', '2.2.15.blastp.m7')
|
313
|
+
text = File.read(fn)
|
314
|
+
assert_equal(Bio::Blast::Report, @ad.autodetect(text))
|
315
|
+
end
|
316
|
+
|
317
|
+
# def test_wublast
|
318
|
+
# end
|
319
|
+
|
320
|
+
# def test_wutblast
|
321
|
+
# end
|
322
|
+
|
323
|
+
def test_blast
|
324
|
+
fn = File.join(TestDataPath, 'blast', 'b0002.faa.m0')
|
325
|
+
text = File.read(fn)
|
326
|
+
assert_equal(Bio::Blast::Default::Report, @ad.autodetect(text))
|
327
|
+
end
|
328
|
+
|
329
|
+
# def test_tblast
|
330
|
+
# end
|
331
|
+
|
332
|
+
# def test_blat
|
333
|
+
# end
|
334
|
+
|
335
|
+
# def test_spidey
|
336
|
+
# end
|
337
|
+
|
338
|
+
def test_hmmer
|
339
|
+
fn = File.join(TestDataPath, 'HMMER', 'hmmpfam.out')
|
340
|
+
text = File.read(fn)
|
341
|
+
assert_equal(Bio::HMMER::Report, @ad.autodetect(text))
|
342
|
+
|
343
|
+
fn = File.join(TestDataPath, 'HMMER', 'hmmsearch.out')
|
344
|
+
text = File.read(fn)
|
345
|
+
assert_equal(Bio::HMMER::Report, @ad.autodetect(text))
|
346
|
+
end
|
347
|
+
|
348
|
+
# def test_sim4
|
349
|
+
# end
|
350
|
+
|
351
|
+
def test_fastaformat
|
352
|
+
fn = File.join(TestDataPath, 'fasta', 'example1.txt')
|
353
|
+
text = File.read(fn)
|
354
|
+
assert_equal(Bio::FastaFormat, @ad.autodetect(text))
|
355
|
+
|
356
|
+
fn = File.join(TestDataPath, 'fasta', 'example2.txt')
|
357
|
+
text = File.read(fn)
|
358
|
+
assert_equal(Bio::FastaFormat, @ad.autodetect(text))
|
359
|
+
end
|
360
|
+
|
361
|
+
def test_fastanumericformat
|
362
|
+
text = <<__END_OF_TEXT__
|
363
|
+
>sample
|
364
|
+
30 21 16 11 8 6 3 34 28 34 28 28 35 28 28 37 33 15 27 28 28
|
365
|
+
27 37 33 17 27 27 28 28 33 26 33 26 28 27 37 33 15 27 26 27
|
366
|
+
28 37 33 16 34 26 27 33 26 28 33 25 28 28 38 34 23 13 2
|
367
|
+
__END_OF_TEXT__
|
368
|
+
|
369
|
+
assert_equal(Bio::FastaNumericFormat, @ad.autodetect(text))
|
370
|
+
end
|
371
|
+
|
372
|
+
end #class TestDefaultAutoDetect
|
373
|
+
|
374
|
+
end #module Bio::TestFlatFile
|
375
|
+
|