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 +1,364 @@
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#
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# = test/bio/db/nexus.rb - Unit test for Bio::Nexus
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#
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# Copyright:: Copyright (C) 2006 Christian M Zmasek <cmzmasek@yahoo.com>
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#
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# License:: The Ruby License
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#
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# $Id:$
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#
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# == Description
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#
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# This file contains unit tests for Bio::Nexus.
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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/nexus'
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module Bio
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class TestNexus < Test::Unit::TestCase
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NEXUS_STRING_1 = <<-END_OF_NEXUS_STRING
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#NEXUS
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Begin Taxa;
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Dimensions [[comment]] ntax=4;
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TaxLabels "hag fish" [comment] 'african frog'
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[lots of different comment follow]
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[] [a] [[a]] [ a ] [[ a ]] [ [ a ] ] [a ]
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[[a ]] [ [a ] ] [ a] [[ a]] [ [ a] ] [ ]
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[[ ]] [ [ ] ] [ a b ] [[ a b ]] [ [ a b ] ]
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[x[ x [x[ x[[x[[xx[x[ x]] ]x ] []]][x]]x]]]
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[comment_1 comment_3] "rat snake" 'red
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mouse';
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End;
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[yet another comment End; ]
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Begin Characters;
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Dimensions nchar=20
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ntax=4;
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[ ntax=1000; ]
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Format DataType=DNA
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Missing=x
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Gap=- MatchChar=.;
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Matrix [comment]
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fish ACATA GAGGG
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TACCT CTAAG
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frog ACTTA GAGGC TACCT CTAGC
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snake ACTCA CTGGG TACCT TTGCG
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mouse ACTCA GACGG TACCT TTGCG;
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End;
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Begin Trees;
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[comment]
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Tree best=(fish,(frog,(snake,mo
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use)));
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[some long comment]
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Tree
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other=(snake,
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(frog,(fish,mo
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use
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)));
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End;
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Begin Trees;
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[comment]
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Tree worst=(A,(B,(C,D
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)));
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Tree bad=(a,
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(b,(c , d
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)
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) );
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End;
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Begin Distances;
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Dimensions nchar=20 ntax=5;
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Format Triangle=Both;
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Matrix
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taxon_1 0.0 1.0
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2.0 4.0 7.0
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taxon_2 1.0
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0.0 3.0 5.0 8.0
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taxon_3 3.0 4.0 0.0 6.0 9.0
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taxon_4 7.0 3.0 2.0 0.0 9.5
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taxon_5 1.2 1.3 1.4 1.5 0.0;
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End;
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Begin Data;
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Dimensions ntax=5 nchar=14;
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Format Datatype=RNA gap=# MISSING=x MatchChar=^;
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TaxLabels ciona
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cow [comment1 commentX] ape
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'purple urchin' "green lizard";
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Matrix
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[ comment [old comment] ]
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taxon_1 A- CCGTCGA-GTTA
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taxon_2 T- CCG-CGA-GATC
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taxon_3 A- C-GTCGA-GATG
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taxon_4 A- C C TC G
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A - -G T T
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T
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taxon_5
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T-CGGTCGT-CTTA;
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End;
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Begin Private1;
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Something foo=5 bar=20;
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Format Datatype=DNA;
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Matrix
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taxon_1 1111 1111111111
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taxon_2 2222 2222222222
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taxon_3 3333 3333333333
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taxon_4 4444 4444444444
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taxon_5 5555 5555555555;
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End;
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Begin Private1;
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some [boring]
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interesting [
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outdated
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] data be here
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End;
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END_OF_NEXUS_STRING
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DATA_BLOCK_OUTPUT_STRING = <<-DATA_BLOCK_OUTPUT_STRING
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Begin Data;
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Dimensions NTax=5 NChar=14;
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Format DataType=RNA Missing=x Gap=# MatchChar=^;
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TaxLabels ciona cow ape purple_urchin green_lizard;
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Matrix
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taxon_1 A-CCGTCGA-GTTA
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taxon_2 T-CCG-CGA-GATC
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taxon_3 A-C-GTCGA-GATG
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taxon_4 A-CCTCGA--GTTT
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taxon_5 T-CGGTCGT-CTTA;
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End;
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DATA_BLOCK_OUTPUT_STRING
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def test_nexus
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nexus = Bio::Nexus.new( NEXUS_STRING_1 )
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blocks = nexus.get_blocks
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assert_equal( 8, blocks.size )
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private_blocks = nexus.get_blocks_by_name( "private1" )
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data_blocks = nexus.get_data_blocks
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character_blocks = nexus.get_characters_blocks
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trees_blocks = nexus.get_trees_blocks
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distances_blocks = nexus.get_distances_blocks
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taxa_blocks = nexus.get_taxa_blocks
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assert_equal( 2, private_blocks.size )
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assert_equal( 1, data_blocks.size )
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assert_equal( 1, character_blocks.size )
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assert_equal( 2, trees_blocks.size )
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assert_equal( 1, distances_blocks.size )
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assert_equal( 1, taxa_blocks.size )
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taxa_block = taxa_blocks[ 0 ]
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assert_equal( taxa_block.get_number_of_taxa.to_i , 4 )
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assert_equal( taxa_block.get_taxa[ 0 ], "hag_fish" )
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assert_equal( taxa_block.get_taxa[ 1 ], "african_frog" )
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assert_equal( taxa_block.get_taxa[ 2 ], "rat_snake" )
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assert_equal( taxa_block.get_taxa[ 3 ], "red_mouse" )
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chars_block = character_blocks[ 0 ]
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assert_equal( chars_block.get_number_of_taxa.to_i, 4 )
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assert_equal( chars_block.get_number_of_characters.to_i, 20 )
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assert_equal( chars_block.get_datatype, "DNA" )
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assert_equal( chars_block.get_match_character, "." )
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assert_equal( chars_block.get_missing, "x" )
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assert_equal( chars_block.get_gap_character, "-" )
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assert_equal( chars_block.get_matrix.get_value( 0, 0 ), "fish" )
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assert_equal( chars_block.get_matrix.get_value( 1, 0 ), "frog" )
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assert_equal( chars_block.get_matrix.get_value( 2, 0 ), "snake" )
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assert_equal( chars_block.get_matrix.get_value( 3, 0 ), "mouse" )
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assert_equal( chars_block.get_matrix.get_value( 0, 20 ), "G" )
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assert_equal( chars_block.get_matrix.get_value( 1, 20 ), "C" )
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assert_equal( chars_block.get_matrix.get_value( 2, 20 ), "G" )
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assert_equal( chars_block.get_matrix.get_value( 3, 20 ), "G" )
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assert_equal( chars_block.get_characters_strings_by_name( "fish" )[ 0 ], "ACATAGAGGGTACCTCTAAG" )
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assert_equal( chars_block.get_characters_strings_by_name( "frog" )[ 0 ], "ACTTAGAGGCTACCTCTAGC" )
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assert_equal( chars_block.get_characters_strings_by_name( "snake" )[ 0 ], "ACTCACTGGGTACCTTTGCG" )
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assert_equal( chars_block.get_characters_strings_by_name( "mouse" )[ 0 ], "ACTCAGACGGTACCTTTGCG" )
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assert_equal( chars_block.get_characters_string( 0 ), "ACATAGAGGGTACCTCTAAG" )
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assert_equal( chars_block.get_characters_string( 1 ), "ACTTAGAGGCTACCTCTAGC" )
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assert_equal( chars_block.get_characters_string( 2 ), "ACTCACTGGGTACCTTTGCG" )
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assert_equal( chars_block.get_characters_string( 3 ), "ACTCAGACGGTACCTTTGCG" )
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assert_equal( chars_block.get_row_name( 1 ), "frog" )
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assert_equal( chars_block.get_sequences_by_name( "fish" )[ 0 ].seq.to_s.downcase, "ACATAGAGGGTACCTCTAAG".downcase )
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assert_equal( chars_block.get_sequences_by_name( "frog" )[ 0 ].seq.to_s.downcase, "ACTTAGAGGCTACCTCTAGC".downcase )
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assert_equal( chars_block.get_sequences_by_name( "snake" )[ 0 ].seq.to_s.downcase, "ACTCACTGGGTACCTTTGCG".downcase )
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assert_equal( chars_block.get_sequences_by_name( "mouse" )[ 0 ].seq.to_s.downcase, "ACTCAGACGGTACCTTTGCG".downcase )
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assert_equal( chars_block.get_sequences_by_name( "fish" )[ 0 ].definition, "fish" )
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assert_equal( chars_block.get_sequences_by_name( "frog" )[ 0 ].definition, "frog" )
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assert_equal( chars_block.get_sequences_by_name( "snake" )[ 0 ].definition, "snake" )
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assert_equal( chars_block.get_sequences_by_name( "mouse" )[ 0 ].definition, "mouse" )
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assert_equal( chars_block.get_sequence( 0 ).seq.to_s.downcase, "ACATAGAGGGTACCTCTAAG".downcase )
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assert_equal( chars_block.get_sequence( 1 ).seq.to_s.downcase, "ACTTAGAGGCTACCTCTAGC".downcase )
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assert_equal( chars_block.get_sequence( 2 ).seq.to_s.downcase, "ACTCACTGGGTACCTTTGCG".downcase )
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assert_equal( chars_block.get_sequence( 3 ).seq.to_s.downcase, "ACTCAGACGGTACCTTTGCG".downcase )
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assert_equal( chars_block.get_sequence( 0 ).definition, "fish" )
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assert_equal( chars_block.get_sequence( 1 ).definition, "frog" )
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assert_equal( chars_block.get_sequence( 2 ).definition, "snake" )
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assert_equal( chars_block.get_sequence( 3 ).definition, "mouse" )
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tree_block_0 = trees_blocks[ 0 ]
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tree_block_1 = trees_blocks[ 1 ]
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assert_equal( tree_block_0.get_tree_names[ 0 ], "best" )
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assert_equal( tree_block_0.get_tree_names[ 1 ], "other" )
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assert_equal( tree_block_0.get_tree_strings_by_name( "best" )[ 0 ], "(fish,(frog,(snake,mouse)));" )
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assert_equal( tree_block_0.get_tree_strings_by_name( "other" )[ 0 ], "(snake,(frog,(fish,mouse)));" )
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best_tree = tree_block_0.get_trees_by_name( "best" )[ 0 ]
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other_tree = tree_block_0.get_trees_by_name( "other" )[ 0 ]
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worst_tree = tree_block_1.get_tree( 0 )
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bad_tree = tree_block_1.get_tree( 1 )
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assert_equal( 6, best_tree.descendents( best_tree.root ).size )
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assert_equal( 4, best_tree.leaves.size)
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assert_equal( 6, other_tree.descendents( other_tree.root ).size )
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assert_equal( 4, other_tree.leaves.size)
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fish_leaf_best = best_tree.nodes.find { |x| x.name == 'fish' }
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assert_equal( 1, best_tree.ancestors( fish_leaf_best ).size )
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fish_leaf_other = other_tree.nodes.find { |x| x.name == 'fish' }
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assert_equal( 3, other_tree.ancestors( fish_leaf_other ).size )
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a_leaf_worst = worst_tree.nodes.find { |x| x.name == 'A' }
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assert_equal( 1, worst_tree.ancestors( a_leaf_worst ).size )
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c_leaf_bad = bad_tree.nodes.find { |x| x.name == 'c' }
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assert_equal( 3, bad_tree.ancestors( c_leaf_bad ).size )
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dist_block = distances_blocks[ 0 ]
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assert_equal( dist_block.get_number_of_taxa.to_i, 5 )
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assert_equal( dist_block.get_number_of_characters.to_i, 20 )
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assert_equal( dist_block.get_triangle, "Both" )
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assert_equal( dist_block.get_matrix.get_value( 0, 0 ), "taxon_1" )
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assert_equal( dist_block.get_matrix.get_value( 1, 0 ), "taxon_2" )
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assert_equal( dist_block.get_matrix.get_value( 2, 0 ), "taxon_3" )
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assert_equal( dist_block.get_matrix.get_value( 3, 0 ), "taxon_4" )
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assert_equal( dist_block.get_matrix.get_value( 4, 0 ), "taxon_5" )
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assert_equal( dist_block.get_matrix.get_value( 0, 5 ).to_f, 7.0 )
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assert_equal( dist_block.get_matrix.get_value( 1, 5 ).to_f, 8.0 )
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assert_equal( dist_block.get_matrix.get_value( 2, 5 ).to_f, 9.0 )
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assert_equal( dist_block.get_matrix.get_value( 3, 5 ).to_f, 9.5 )
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assert_equal( dist_block.get_matrix.get_value( 4, 5 ).to_f, 0.0 )
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data_block = data_blocks[ 0 ]
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assert_equal( data_block.get_number_of_taxa.to_i, 5 )
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assert_equal( data_block.get_number_of_characters.to_i, 14 )
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+
assert_equal( data_block.get_datatype, "RNA" )
|
279
|
+
assert_equal( data_block.get_match_character, "^" )
|
280
|
+
assert_equal( data_block.get_missing, "x" )
|
281
|
+
assert_equal( data_block.get_gap_character, "#" )
|
282
|
+
assert_equal( data_block.get_matrix.get_value( 0, 0 ), "taxon_1" )
|
283
|
+
assert_equal( data_block.get_matrix.get_value( 1, 0 ), "taxon_2" )
|
284
|
+
assert_equal( data_block.get_matrix.get_value( 2, 0 ), "taxon_3" )
|
285
|
+
assert_equal( data_block.get_matrix.get_value( 3, 0 ), "taxon_4" )
|
286
|
+
assert_equal( data_block.get_matrix.get_value( 4, 0 ), "taxon_5" )
|
287
|
+
assert_equal( data_block.get_matrix.get_value( 0, 14 ), "A" )
|
288
|
+
assert_equal( data_block.get_matrix.get_value( 1, 14 ), "C" )
|
289
|
+
assert_equal( data_block.get_matrix.get_value( 2, 14 ), "G" )
|
290
|
+
assert_equal( data_block.get_matrix.get_value( 3, 14 ), "T" )
|
291
|
+
assert_equal( data_block.get_matrix.get_value( 4, 14 ), "A" )
|
292
|
+
assert_equal( data_block.get_taxa[ 0 ], "ciona" )
|
293
|
+
assert_equal( data_block.get_taxa[ 1 ], "cow" )
|
294
|
+
assert_equal( data_block.get_taxa[ 2 ], "ape" )
|
295
|
+
assert_equal( data_block.get_taxa[ 3 ], "purple_urchin" )
|
296
|
+
assert_equal( data_block.get_taxa[ 4 ], "green_lizard" )
|
297
|
+
|
298
|
+
|
299
|
+
assert_equal( data_block.get_characters_strings_by_name( "taxon_1" )[ 0 ], "A-CCGTCGA-GTTA" )
|
300
|
+
assert_equal( data_block.get_characters_strings_by_name( "taxon_2" )[ 0 ], "T-CCG-CGA-GATC" )
|
301
|
+
assert_equal( data_block.get_characters_strings_by_name( "taxon_3" )[ 0 ], "A-C-GTCGA-GATG" )
|
302
|
+
assert_equal( data_block.get_characters_strings_by_name( "taxon_4" )[ 0 ], "A-CCTCGA--GTTT" )
|
303
|
+
assert_equal( data_block.get_characters_strings_by_name( "taxon_5" )[ 0 ], "T-CGGTCGT-CTTA" )
|
304
|
+
|
305
|
+
assert_equal( data_block.get_characters_string( 0 ), "A-CCGTCGA-GTTA" )
|
306
|
+
assert_equal( data_block.get_characters_string( 1 ), "T-CCG-CGA-GATC" )
|
307
|
+
assert_equal( data_block.get_characters_string( 2 ), "A-C-GTCGA-GATG" )
|
308
|
+
assert_equal( data_block.get_characters_string( 3 ), "A-CCTCGA--GTTT" )
|
309
|
+
assert_equal( data_block.get_characters_string( 4 ), "T-CGGTCGT-CTTA" )
|
310
|
+
|
311
|
+
assert_equal( data_block.get_row_name( 0 ), "taxon_1" )
|
312
|
+
assert_equal( data_block.get_row_name( 1 ), "taxon_2" )
|
313
|
+
assert_equal( data_block.get_row_name( 2 ), "taxon_3" )
|
314
|
+
assert_equal( data_block.get_row_name( 3 ), "taxon_4" )
|
315
|
+
assert_equal( data_block.get_row_name( 4 ), "taxon_5" )
|
316
|
+
|
317
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_1" )[ 0 ].seq.to_s.downcase, "A-CCGTCGA-GTTA".downcase )
|
318
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_2" )[ 0 ].seq.to_s.downcase, "T-CCG-CGA-GATC".downcase )
|
319
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_3" )[ 0 ].seq.to_s.downcase, "A-C-GTCGA-GATG".downcase )
|
320
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_4" )[ 0 ].seq.to_s.downcase, "A-CCTCGA--GTTT".downcase )
|
321
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_5" )[ 0 ].seq.to_s.downcase, "T-CGGTCGT-CTTA".downcase )
|
322
|
+
|
323
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_1" )[ 0 ].definition, "taxon_1" )
|
324
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_2" )[ 0 ].definition, "taxon_2" )
|
325
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_3" )[ 0 ].definition, "taxon_3" )
|
326
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_4" )[ 0 ].definition, "taxon_4" )
|
327
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_5" )[ 0 ].definition, "taxon_5" )
|
328
|
+
|
329
|
+
assert_equal( data_block.get_sequence( 0 ).seq.to_s.downcase, "A-CCGTCGA-GTTA".downcase )
|
330
|
+
assert_equal( data_block.get_sequence( 1 ).seq.to_s.downcase, "T-CCG-CGA-GATC".downcase )
|
331
|
+
assert_equal( data_block.get_sequence( 2 ).seq.to_s.downcase, "A-C-GTCGA-GATG".downcase )
|
332
|
+
assert_equal( data_block.get_sequence( 3 ).seq.to_s.downcase, "A-CCTCGA--GTTT".downcase )
|
333
|
+
assert_equal( data_block.get_sequence( 4 ).seq.to_s.downcase, "T-CGGTCGT-CTTA".downcase )
|
334
|
+
|
335
|
+
assert_equal( data_block.get_sequence( 0 ).definition, "taxon_1" )
|
336
|
+
assert_equal( data_block.get_sequence( 1 ).definition, "taxon_2" )
|
337
|
+
assert_equal( data_block.get_sequence( 2 ).definition, "taxon_3" )
|
338
|
+
assert_equal( data_block.get_sequence( 3 ).definition, "taxon_4" )
|
339
|
+
assert_equal( data_block.get_sequence( 4 ).definition, "taxon_5" )
|
340
|
+
|
341
|
+
assert_equal( DATA_BLOCK_OUTPUT_STRING, data_block.to_nexus() )
|
342
|
+
|
343
|
+
generic_0 = private_blocks[ 0 ]
|
344
|
+
generic_1 = private_blocks[ 1 ]
|
345
|
+
assert_equal( generic_0.get_tokens[ 0 ], "Something" )
|
346
|
+
assert_equal( generic_0.get_tokens[ 1 ], "foo" )
|
347
|
+
assert_equal( generic_0.get_tokens[ 2 ], "5" )
|
348
|
+
assert_equal( generic_0.get_tokens[ 3 ], "bar" )
|
349
|
+
assert_equal( generic_0.get_tokens[ 4 ], "20" )
|
350
|
+
assert_equal( generic_0.get_tokens[ 5 ], "Format" )
|
351
|
+
assert_equal( generic_0.get_tokens[ 6 ], "Datatype" )
|
352
|
+
assert_equal( generic_0.get_tokens[ 7 ], "DNA" )
|
353
|
+
assert_equal( generic_0.get_tokens[ 8 ], "Matrix" )
|
354
|
+
assert_equal( generic_0.get_tokens[ 9 ], "taxon_1" )
|
355
|
+
assert_equal( generic_0.get_tokens[10 ], "1111" )
|
356
|
+
assert_equal( generic_1.get_tokens[ 0 ], "some" )
|
357
|
+
assert_equal( generic_1.get_tokens[ 1 ], "interesting" )
|
358
|
+
assert_equal( generic_1.get_tokens[ 2 ], "data" )
|
359
|
+
assert_equal( generic_1.get_tokens[ 3 ], "be" )
|
360
|
+
assert_equal( generic_1.get_tokens[ 4 ], "here" )
|
361
|
+
|
362
|
+
end # test_nexus
|
363
|
+
end # class TestNexus
|
364
|
+
end # module Bio
|
@@ -0,0 +1,1437 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/db/test_prosite.rb - Unit test for Bio::PROSITE
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
|
5
|
+
# License:: The Ruby License
|
6
|
+
#
|
7
|
+
# $Id: test_prosite.rb,v 1.6 2007/04/05 23:35:43 trevor Exp $
|
8
|
+
#
|
9
|
+
|
10
|
+
require 'pathname'
|
11
|
+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
|
12
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
13
|
+
|
14
|
+
require 'test/unit'
|
15
|
+
require 'bio/db/prosite'
|
16
|
+
|
17
|
+
module Bio
|
18
|
+
class TestPROSITEConst < Test::Unit::TestCase
|
19
|
+
|
20
|
+
def test_delimiter
|
21
|
+
assert_equal("\n//\n", Bio::PROSITE::DELIMITER)
|
22
|
+
assert_equal("\n//\n", Bio::PROSITE::RS)
|
23
|
+
end
|
24
|
+
|
25
|
+
def test_tagsize
|
26
|
+
assert_equal(5, Bio::PROSITE::TAGSIZE)
|
27
|
+
end
|
28
|
+
|
29
|
+
end # class TestPROSITEConst
|
30
|
+
|
31
|
+
|
32
|
+
class TestPROSITE < Test::Unit::TestCase
|
33
|
+
|
34
|
+
def setup
|
35
|
+
bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4)).cleanpath.to_s
|
36
|
+
data = File.open(File.join(bioruby_root, 'test', 'data', 'prosite', 'prosite.dat')).read
|
37
|
+
data = data.split(Bio::PROSITE::RS)[0]
|
38
|
+
@obj = Bio::PROSITE.new(data)
|
39
|
+
end
|
40
|
+
|
41
|
+
def test_name
|
42
|
+
assert_equal("G_PROTEIN_RECEP_F1_1", @obj.name)
|
43
|
+
end
|
44
|
+
|
45
|
+
def test_division
|
46
|
+
data = "PATTERN"
|
47
|
+
assert_equal(data, @obj.division)
|
48
|
+
end
|
49
|
+
|
50
|
+
def test_ac
|
51
|
+
data = "PS00237"
|
52
|
+
assert_equal(data, @obj.ac)
|
53
|
+
end
|
54
|
+
|
55
|
+
def test_dt
|
56
|
+
assert_equal("APR-1990 (CREATED); NOV-1997 (DATA UPDATE); JUL-1998 (INFO UPDATE).", @obj.dt)
|
57
|
+
end
|
58
|
+
|
59
|
+
def test_de
|
60
|
+
data = "G-protein coupled receptors family 1 signature."
|
61
|
+
assert_equal(data, @obj.de)
|
62
|
+
end
|
63
|
+
|
64
|
+
def test_pa
|
65
|
+
pattern = "[GSTALIVMFYWC]-[GSTANCPDE]-{EDPKRH}-x(2)-[LIVMNQGA]-x(2)-[LIVMFT]-[GSTANC]-[LIVMFYWSTAC]-[DENH]-R-[FYWCSH]-x(2)-[LIVM]."
|
66
|
+
assert_equal(pattern, @obj.pa)
|
67
|
+
end
|
68
|
+
|
69
|
+
def test_ma
|
70
|
+
assert_equal('', @obj.ma)
|
71
|
+
end
|
72
|
+
|
73
|
+
def test_ru
|
74
|
+
assert_equal('', @obj.ru)
|
75
|
+
end
|
76
|
+
|
77
|
+
def test_nr
|
78
|
+
data = {"FALSE_NEG"=>112, "POSITIVE"=>[1057, 1057], "PARTIAL"=>48, "FALSE_POS"=>[64, 64], "RELEASE"=>["40.7", 103373], "TOTAL"=>[1121, 1121], "UNKNOWN"=>[0, 0]}
|
79
|
+
|
80
|
+
assert_equal(data, @obj.nr)
|
81
|
+
end
|
82
|
+
|
83
|
+
def test_release
|
84
|
+
assert_equal(['40.7', 103373], @obj.release)
|
85
|
+
end
|
86
|
+
|
87
|
+
def test_swissprot_release_number
|
88
|
+
assert_equal('40.7', @obj.swissprot_release_number)
|
89
|
+
end
|
90
|
+
|
91
|
+
def test_swissprot_release_sequences
|
92
|
+
assert_equal(103373, @obj.swissprot_release_sequences)
|
93
|
+
end
|
94
|
+
|
95
|
+
def test_total
|
96
|
+
assert_equal([1121, 1121], @obj.total)
|
97
|
+
end
|
98
|
+
|
99
|
+
def test_total_hits
|
100
|
+
assert_equal(1121, @obj.total_hits)
|
101
|
+
end
|
102
|
+
|
103
|
+
def test_total_sequences
|
104
|
+
assert_equal(1121, @obj.total_sequences)
|
105
|
+
end
|
106
|
+
|
107
|
+
def test_positive
|
108
|
+
assert_equal([1057, 1057], @obj.positive)
|
109
|
+
end
|
110
|
+
|
111
|
+
def test_positive_hits
|
112
|
+
assert_equal(1057, @obj.positive_hits)
|
113
|
+
end
|
114
|
+
|
115
|
+
def test_positive_sequences
|
116
|
+
assert_equal(1057, @obj.positive_sequences)
|
117
|
+
end
|
118
|
+
|
119
|
+
def test_unknown
|
120
|
+
assert_equal([0, 0], @obj.unknown)
|
121
|
+
end
|
122
|
+
|
123
|
+
def test_unknown_hits
|
124
|
+
assert_equal(0, @obj.unknown_hits)
|
125
|
+
end
|
126
|
+
|
127
|
+
def test_unknown_sequences
|
128
|
+
assert_equal(0, @obj.unknown_sequences)
|
129
|
+
end
|
130
|
+
|
131
|
+
def test_false_pos
|
132
|
+
assert_equal([64, 64], @obj.false_pos)
|
133
|
+
end
|
134
|
+
|
135
|
+
def test_false_positive_sequences
|
136
|
+
assert_equal(64, @obj.false_positive_sequences)
|
137
|
+
end
|
138
|
+
|
139
|
+
def test_false_neg
|
140
|
+
assert_equal(112, @obj.false_neg)
|
141
|
+
end
|
142
|
+
|
143
|
+
def test_partial
|
144
|
+
assert_equal(48, @obj.partial)
|
145
|
+
end
|
146
|
+
|
147
|
+
def test_cc
|
148
|
+
assert_equal({"TAXO-RANGE"=>"??E?V", "MAX-REPEAT"=>"1"}, @obj.cc)
|
149
|
+
end
|
150
|
+
|
151
|
+
def test_taxon_range
|
152
|
+
assert_equal('??E?V', @obj.taxon_range)
|
153
|
+
end
|
154
|
+
|
155
|
+
def test_max_repeat
|
156
|
+
assert_equal(1, @obj.max_repeat)
|
157
|
+
end
|
158
|
+
|
159
|
+
def test_site
|
160
|
+
assert_equal([0, nil], @obj.site)
|
161
|
+
end
|
162
|
+
|
163
|
+
def test_skip_flag
|
164
|
+
assert_equal(nil, @obj.skip_flag)
|
165
|
+
end
|
166
|
+
|
167
|
+
def test_dr
|
168
|
+
assert_equal(Hash, @obj.dr.class)
|
169
|
+
data = ['OPSD_LIMBE', 'T']
|
170
|
+
assert_equal(data, @obj.dr["O42427"])
|
171
|
+
end
|
172
|
+
|
173
|
+
def test_list_xref
|
174
|
+
flag = ''
|
175
|
+
assert_equal([], @obj.list_xref(flag))
|
176
|
+
end
|
177
|
+
|
178
|
+
def test_list_truepositive
|
179
|
+
data = ["O42427",
|
180
|
+
"P11617",
|
181
|
+
"P46090",
|
182
|
+
"P30939",
|
183
|
+
"P28336",
|
184
|
+
"Q9Z2J6",
|
185
|
+
"Q64326",
|
186
|
+
"P46092",
|
187
|
+
"P07550",
|
188
|
+
"Q9UKL2",
|
189
|
+
"P30940",
|
190
|
+
"P46093",
|
191
|
+
"Q61224",
|
192
|
+
"Q63384",
|
193
|
+
"P46094",
|
194
|
+
"Q28309",
|
195
|
+
"P22328",
|
196
|
+
"P46095",
|
197
|
+
"O77590",
|
198
|
+
"O02813",
|
199
|
+
"Q9R1C8",
|
200
|
+
"P22329",
|
201
|
+
"O93441",
|
202
|
+
"O42300",
|
203
|
+
"Q10904",
|
204
|
+
"O43613",
|
205
|
+
"Q9Z0D9",
|
206
|
+
"P18130",
|
207
|
+
"O42301",
|
208
|
+
"O43614",
|
209
|
+
"P22330",
|
210
|
+
"P22331",
|
211
|
+
"Q9GLJ8",
|
212
|
+
"O15552",
|
213
|
+
"O43193",
|
214
|
+
"P22332",
|
215
|
+
"O43194",
|
216
|
+
"Q9WV26",
|
217
|
+
"Q9TST4",
|
218
|
+
"Q62053",
|
219
|
+
"P58307",
|
220
|
+
"O42307",
|
221
|
+
"Q9TST5",
|
222
|
+
"P58308",
|
223
|
+
"Q9TST6",
|
224
|
+
"P41983",
|
225
|
+
"P30951",
|
226
|
+
"P41984",
|
227
|
+
"O02824",
|
228
|
+
"O88626",
|
229
|
+
"P91657",
|
230
|
+
"P30953",
|
231
|
+
"P18825",
|
232
|
+
"O62709",
|
233
|
+
"O42574",
|
234
|
+
"P30954",
|
235
|
+
"Q28585",
|
236
|
+
"O88628",
|
237
|
+
"P30955",
|
238
|
+
"P28221",
|
239
|
+
"Q9WU02",
|
240
|
+
"P28222",
|
241
|
+
"P32299",
|
242
|
+
"P70310",
|
243
|
+
"P28223",
|
244
|
+
"O76099",
|
245
|
+
"P04201",
|
246
|
+
"P35894",
|
247
|
+
"Q15722",
|
248
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249
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250
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251
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254
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255
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256
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257
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258
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259
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260
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261
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262
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263
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264
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265
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266
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267
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268
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269
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270
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271
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272
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273
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277
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278
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279
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280
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281
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282
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283
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284
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285
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286
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287
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288
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289
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290
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291
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292
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293
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294
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295
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296
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297
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298
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299
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301
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304
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305
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307
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308
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309
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310
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311
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312
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313
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314
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315
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316
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317
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318
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319
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320
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321
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322
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323
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324
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325
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326
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327
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328
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329
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330
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331
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332
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333
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334
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337
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341
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342
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395
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396
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568
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578
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671
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672
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673
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674
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675
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676
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677
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678
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679
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680
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681
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682
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683
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684
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685
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686
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687
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688
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689
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690
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691
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692
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693
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694
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695
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696
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698
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699
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700
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701
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702
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703
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704
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705
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706
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707
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708
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710
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711
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712
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713
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714
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715
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716
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718
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719
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720
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721
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722
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723
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724
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725
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727
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729
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730
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732
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733
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734
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735
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738
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740
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741
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742
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743
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744
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745
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746
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747
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748
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749
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750
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751
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759
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760
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761
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763
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764
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765
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767
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768
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769
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770
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771
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772
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773
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774
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775
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776
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777
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778
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780
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781
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782
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783
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784
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785
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786
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787
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788
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789
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790
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791
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792
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793
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794
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795
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796
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797
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798
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799
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800
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801
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802
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803
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804
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805
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806
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807
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808
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809
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810
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811
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812
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813
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814
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815
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816
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817
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818
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819
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820
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821
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822
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823
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825
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826
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827
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828
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829
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830
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831
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832
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833
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834
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835
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837
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838
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839
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840
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841
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842
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843
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845
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846
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847
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851
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860
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861
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862
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863
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864
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865
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866
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867
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868
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869
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870
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871
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873
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874
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875
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876
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877
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878
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879
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880
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881
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882
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883
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884
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885
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886
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887
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888
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889
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890
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891
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892
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893
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894
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895
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896
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897
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898
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899
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900
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901
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902
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903
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904
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905
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906
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907
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908
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909
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910
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911
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912
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913
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914
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915
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916
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917
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918
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919
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920
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921
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922
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923
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924
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925
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926
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927
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928
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929
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930
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931
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932
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933
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934
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935
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936
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937
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938
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939
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940
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941
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942
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943
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944
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945
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946
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947
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948
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949
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950
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951
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952
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953
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954
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955
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956
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957
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958
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959
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960
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961
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962
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963
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964
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965
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966
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967
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968
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969
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970
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971
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972
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973
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974
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975
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976
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977
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978
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979
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980
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981
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982
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983
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984
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985
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986
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987
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988
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989
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990
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991
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992
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993
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994
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995
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996
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997
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998
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999
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1000
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1001
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1002
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1003
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1004
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1005
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1006
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1007
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1008
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1009
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1010
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1011
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1012
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1013
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1014
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1015
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1016
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1017
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1018
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1019
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1020
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1021
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1022
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1023
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1024
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1025
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1026
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1027
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1028
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1029
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1030
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1031
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1032
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1033
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1034
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1035
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1036
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1037
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1038
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1039
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1040
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1041
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1042
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1043
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1044
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1045
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1046
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1047
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1048
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1049
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1050
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1051
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1052
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1053
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1054
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1055
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1056
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1057
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1058
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1059
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1060
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1061
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1062
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1063
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1064
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1065
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1066
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1067
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1068
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1069
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1070
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1071
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1072
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1073
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1074
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1075
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1076
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1077
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1078
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1079
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1080
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1081
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1082
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1083
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1084
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1085
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1086
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1087
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"Q9PUI7",
|
1088
|
+
"P28564",
|
1089
|
+
"P49650",
|
1090
|
+
"P32245",
|
1091
|
+
"P28565",
|
1092
|
+
"P49651",
|
1093
|
+
"P32246",
|
1094
|
+
"P28566",
|
1095
|
+
"P49652",
|
1096
|
+
"Q98894",
|
1097
|
+
"P32247",
|
1098
|
+
"Q9H255",
|
1099
|
+
"Q98895",
|
1100
|
+
"P32248",
|
1101
|
+
"P32249",
|
1102
|
+
"P20272",
|
1103
|
+
"P43088",
|
1104
|
+
"Q95170",
|
1105
|
+
"P50128",
|
1106
|
+
"P32250",
|
1107
|
+
"P50391",
|
1108
|
+
"P70658",
|
1109
|
+
"P08172",
|
1110
|
+
"P50129",
|
1111
|
+
"P08173",
|
1112
|
+
"P32251",
|
1113
|
+
"P46616",
|
1114
|
+
"Q9QYN8",
|
1115
|
+
"P50130",
|
1116
|
+
"P51470",
|
1117
|
+
"P14763",
|
1118
|
+
"P51471",
|
1119
|
+
"P50132",
|
1120
|
+
"Q27987",
|
1121
|
+
"P49660",
|
1122
|
+
"P51472",
|
1123
|
+
"P51473",
|
1124
|
+
"O60412",
|
1125
|
+
"P51474",
|
1126
|
+
"P51475",
|
1127
|
+
"Q90373",
|
1128
|
+
"Q95179",
|
1129
|
+
"P51476",
|
1130
|
+
"P58406",
|
1131
|
+
"O88853",
|
1132
|
+
"P70536",
|
1133
|
+
"Q17094",
|
1134
|
+
"O88854",
|
1135
|
+
"Q11082",
|
1136
|
+
"P37067",
|
1137
|
+
"Q90245",
|
1138
|
+
"P79785",
|
1139
|
+
"P37068",
|
1140
|
+
"O13076",
|
1141
|
+
"Q92633",
|
1142
|
+
"P46626",
|
1143
|
+
"Q91559",
|
1144
|
+
"P37069",
|
1145
|
+
"P46627",
|
1146
|
+
"P21917",
|
1147
|
+
"P23944",
|
1148
|
+
"O97967",
|
1149
|
+
"P46628",
|
1150
|
+
"P56971",
|
1151
|
+
"P43657",
|
1152
|
+
"O62809",
|
1153
|
+
"Q28553",
|
1154
|
+
"P21918",
|
1155
|
+
"P23945",
|
1156
|
+
"P20288",
|
1157
|
+
"O19091",
|
1158
|
+
"O15529",
|
1159
|
+
"P37070",
|
1160
|
+
"Q28422",
|
1161
|
+
"P29274",
|
1162
|
+
"P37071",
|
1163
|
+
"P29275",
|
1164
|
+
"Q9Z0Z6",
|
1165
|
+
"P29276",
|
1166
|
+
"Q25321",
|
1167
|
+
"Q18179",
|
1168
|
+
"P30372",
|
1169
|
+
"Q90252",
|
1170
|
+
"O14843",
|
1171
|
+
"Q9Z2I3",
|
1172
|
+
"Q25322",
|
1173
|
+
"Q08520",
|
1174
|
+
"Q28558",
|
1175
|
+
"P51488",
|
1176
|
+
"P41143",
|
1177
|
+
"P23265",
|
1178
|
+
"Q28691",
|
1179
|
+
"P51489",
|
1180
|
+
"P09241",
|
1181
|
+
"O18312",
|
1182
|
+
"P41144",
|
1183
|
+
"Q61212",
|
1184
|
+
"P23266",
|
1185
|
+
"Q9WV08",
|
1186
|
+
"P41145",
|
1187
|
+
"P46636",
|
1188
|
+
"P23267",
|
1189
|
+
"P56718",
|
1190
|
+
"P41146",
|
1191
|
+
"P21109",
|
1192
|
+
"P51490",
|
1193
|
+
"P79400",
|
1194
|
+
"Q9UPC5",
|
1195
|
+
"Q62035",
|
1196
|
+
"P56719",
|
1197
|
+
"P23269",
|
1198
|
+
"O14718",
|
1199
|
+
"P79798",
|
1200
|
+
"P51491",
|
1201
|
+
"O18315",
|
1202
|
+
"P41149",
|
1203
|
+
"P23270",
|
1204
|
+
"O60431",
|
1205
|
+
"P49681",
|
1206
|
+
"P23271",
|
1207
|
+
"P19327",
|
1208
|
+
"P30935",
|
1209
|
+
"P11613",
|
1210
|
+
"P49682",
|
1211
|
+
"P23272",
|
1212
|
+
"P41968",
|
1213
|
+
"O43603",
|
1214
|
+
"P19328",
|
1215
|
+
"Q63931",
|
1216
|
+
"P30936",
|
1217
|
+
"P49683",
|
1218
|
+
"P11614",
|
1219
|
+
"P23273",
|
1220
|
+
"P46089",
|
1221
|
+
"P28334",
|
1222
|
+
"P49684",
|
1223
|
+
"P30937",
|
1224
|
+
"P11615",
|
1225
|
+
"P23274",
|
1226
|
+
"P28335",
|
1227
|
+
"O13092",
|
1228
|
+
"O43869",
|
1229
|
+
"P97520",
|
1230
|
+
"Q01337",
|
1231
|
+
"P30938",
|
1232
|
+
"P49685",
|
1233
|
+
"P11616",
|
1234
|
+
"P23275",
|
1235
|
+
"Q01338"]
|
1236
|
+
assert_equal(data.sort, @obj.list_truepositive.sort)
|
1237
|
+
end
|
1238
|
+
|
1239
|
+
def test_list_falsenegative
|
1240
|
+
data = ["P18259",
|
1241
|
+
"Q13813",
|
1242
|
+
"Q55593",
|
1243
|
+
"Q00274",
|
1244
|
+
"P54466",
|
1245
|
+
"Q9HJA4",
|
1246
|
+
"P55687",
|
1247
|
+
"Q9W0K0",
|
1248
|
+
"Q42608",
|
1249
|
+
"P45873",
|
1250
|
+
"P45198",
|
1251
|
+
"P15828",
|
1252
|
+
"P18609",
|
1253
|
+
"Q51758",
|
1254
|
+
"P24151",
|
1255
|
+
"P23892",
|
1256
|
+
"P41510",
|
1257
|
+
"P22817",
|
1258
|
+
"P46457",
|
1259
|
+
"O15910",
|
1260
|
+
"P23515",
|
1261
|
+
"O59098",
|
1262
|
+
"P26560",
|
1263
|
+
"P26561",
|
1264
|
+
"P47551",
|
1265
|
+
"P22023",
|
1266
|
+
"P21503",
|
1267
|
+
"Q9VNB3",
|
1268
|
+
"P25147",
|
1269
|
+
"Q42675",
|
1270
|
+
"P21524",
|
1271
|
+
"P06882",
|
1272
|
+
"Q61647",
|
1273
|
+
"P42790",
|
1274
|
+
"Q10775",
|
1275
|
+
"O84877",
|
1276
|
+
"P51656",
|
1277
|
+
"P75548",
|
1278
|
+
"Q92839",
|
1279
|
+
"P51657",
|
1280
|
+
"P37274",
|
1281
|
+
"P34724",
|
1282
|
+
"P07751",
|
1283
|
+
"P00498",
|
1284
|
+
"P07886",
|
1285
|
+
"P26258",
|
1286
|
+
"O67284",
|
1287
|
+
"Q25410",
|
1288
|
+
"P46724",
|
1289
|
+
"P76097",
|
1290
|
+
"P16086",
|
1291
|
+
"P08032",
|
1292
|
+
"P14198",
|
1293
|
+
"P77916",
|
1294
|
+
"O60779",
|
1295
|
+
"P13688",
|
1296
|
+
"Q03834",
|
1297
|
+
"Q63912",
|
1298
|
+
"O68824",
|
1299
|
+
"P77932",
|
1300
|
+
"Q53547",
|
1301
|
+
"P77933",
|
1302
|
+
"P34529",
|
1303
|
+
"Q00126"]
|
1304
|
+
assert_equal(data.sort, @obj.list_falsenegative.sort)
|
1305
|
+
end
|
1306
|
+
|
1307
|
+
def test_list_falsepositive
|
1308
|
+
data =["P41985",
|
1309
|
+
"P41986",
|
1310
|
+
"P17645",
|
1311
|
+
"Q60612",
|
1312
|
+
"Q60879",
|
1313
|
+
"P52592",
|
1314
|
+
"Q60882",
|
1315
|
+
"Q60883",
|
1316
|
+
"Q60884",
|
1317
|
+
"Q60885",
|
1318
|
+
"Q60886",
|
1319
|
+
"Q60887",
|
1320
|
+
"Q60888",
|
1321
|
+
"Q60889",
|
1322
|
+
"Q60890",
|
1323
|
+
"P49218",
|
1324
|
+
"Q60891",
|
1325
|
+
"Q60892",
|
1326
|
+
"P49220",
|
1327
|
+
"Q60893",
|
1328
|
+
"Q60894",
|
1329
|
+
"Q60895",
|
1330
|
+
"O70430",
|
1331
|
+
"O70432",
|
1332
|
+
"P51046",
|
1333
|
+
"P51047",
|
1334
|
+
"P51048",
|
1335
|
+
"P51049",
|
1336
|
+
"P51051",
|
1337
|
+
"P51052",
|
1338
|
+
"Q98913",
|
1339
|
+
"Q98914",
|
1340
|
+
"Q61616",
|
1341
|
+
"Q61618",
|
1342
|
+
"P79250",
|
1343
|
+
"P14803",
|
1344
|
+
"P49287",
|
1345
|
+
"Q28602",
|
1346
|
+
"P97267",
|
1347
|
+
"Q90305",
|
1348
|
+
"Q29006",
|
1349
|
+
"Q95252",
|
1350
|
+
"P34985",
|
1351
|
+
"Q90456",
|
1352
|
+
"Q95136",
|
1353
|
+
"Q95137",
|
1354
|
+
"Q62953",
|
1355
|
+
"Q95195"]
|
1356
|
+
assert_equal(data.sort, @obj.list_falsepositive.sort)
|
1357
|
+
end
|
1358
|
+
|
1359
|
+
def test_list_potentialhit
|
1360
|
+
data = ["P41985",
|
1361
|
+
"P41986",
|
1362
|
+
"P17645",
|
1363
|
+
"Q60612",
|
1364
|
+
"Q60879",
|
1365
|
+
"P52592",
|
1366
|
+
"Q60882",
|
1367
|
+
"Q60883",
|
1368
|
+
"Q60884",
|
1369
|
+
"Q60885",
|
1370
|
+
"Q60886",
|
1371
|
+
"Q60887",
|
1372
|
+
"Q60888",
|
1373
|
+
"Q60889",
|
1374
|
+
"Q60890",
|
1375
|
+
"P49218",
|
1376
|
+
"Q60891",
|
1377
|
+
"Q60892",
|
1378
|
+
"P49220",
|
1379
|
+
"Q60893",
|
1380
|
+
"Q60894",
|
1381
|
+
"Q60895",
|
1382
|
+
"O70430",
|
1383
|
+
"O70432",
|
1384
|
+
"P51046",
|
1385
|
+
"P51047",
|
1386
|
+
"P51048",
|
1387
|
+
"P51049",
|
1388
|
+
"P51051",
|
1389
|
+
"P51052",
|
1390
|
+
"Q98913",
|
1391
|
+
"Q98914",
|
1392
|
+
"Q61616",
|
1393
|
+
"Q61618",
|
1394
|
+
"P79250",
|
1395
|
+
"P14803",
|
1396
|
+
"P49287",
|
1397
|
+
"Q28602",
|
1398
|
+
"P97267",
|
1399
|
+
"Q90305",
|
1400
|
+
"Q29006",
|
1401
|
+
"Q95252",
|
1402
|
+
"P34985",
|
1403
|
+
"Q90456",
|
1404
|
+
"Q95136",
|
1405
|
+
"Q95137",
|
1406
|
+
"Q62953",
|
1407
|
+
"Q95195"]
|
1408
|
+
assert_equal(data.sort, @obj.list_potentialhit.sort)
|
1409
|
+
end
|
1410
|
+
|
1411
|
+
def test_list_unknown
|
1412
|
+
data = []
|
1413
|
+
assert_equal(data, @obj.list_unknown)
|
1414
|
+
end
|
1415
|
+
|
1416
|
+
def test_pdb_xref
|
1417
|
+
data = ["1BOJ", "1BOK", "1F88"]
|
1418
|
+
assert_equal(data, @obj.pdb_xref)
|
1419
|
+
end
|
1420
|
+
|
1421
|
+
def test_pdoc_xref
|
1422
|
+
data = "PDOC00210"
|
1423
|
+
assert_equal(data, @obj.pdoc_xref)
|
1424
|
+
end
|
1425
|
+
|
1426
|
+
def test_pa2re
|
1427
|
+
pa = '[AC]-x-V-x(4)-{ED}.'
|
1428
|
+
assert_equal(/[AC].V.{4}[^ED]/i, @obj.pa2re(pa))
|
1429
|
+
end
|
1430
|
+
|
1431
|
+
def test_self_pa2re
|
1432
|
+
pa = '[AC]-x-V-x(4)-{ED}.'
|
1433
|
+
assert_equal(/[AC].V.{4}[^ED]/i, Bio::PROSITE.pa2re(pa))
|
1434
|
+
end
|
1435
|
+
|
1436
|
+
end # class TestPROSITE
|
1437
|
+
end
|