rbbt-study 0.2.4 → 0.2.5
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- checksums.yaml +8 -8
- data/lib/rbbt/entity/study/genotypes/knowledge_base.rb +6 -5
- metadata +1 -1
checksums.yaml
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@@ -1,15 +1,15 @@
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!binary "U0hBMQ==":
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metadata.gz: !binary |-
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@@ -21,24 +21,25 @@ module Study
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sample_mutations = study.knowledge_base.get_database(:sample_mutations, :source => "Sample")
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all_mutations = study.all_mutations
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mutations2mutated_isoforms = Misc.process_to_hash(all_mutations){|mutations| mutations.mutated_isoforms }
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mutations2mutated_isoforms = Misc.process_to_hash(all_mutations){|mutations| mutations.any? ? mutations.mutated_isoforms : [] }
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#mi2damaged = Misc.process_to_hash(MutatedIsoform.setup(mutations2mutated_isoforms.values.flatten.compact.uniq, study.organism)){|mis| mis.damaged? }
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mi2damaged = Misc.process_to_hash(MutatedIsoform.setup(mutations2mutated_isoforms.values.flatten.compact.uniq, study.organism)){|mis| [false] * mis.length }
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mi2consequence = Misc.process_to_hash(MutatedIsoform.setup(mutations2mutated_isoforms.values.flatten.compact.uniq, study.organism)){|mis| mis.consequence }
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gene_mutations = study.knowledge_base.get_database(:mutation_genes, :source => "Ensembl Gene ID")
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gene_mutations.unnamed = true
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gene_mutations.entity_options["Genomic Mutation"] = {:watson => study.watson, :organism => study.organism}
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study.samples.select_by(:has_genotype?).each do |sample|
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values = sample.affected_genes.collect do |gene|
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mutations = gene_mutations[gene]
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mutations = gene_mutations[gene] & (sample_mutations[sample] || [])
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if mutations.any?
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GenomicMutation.setup(mutations, "Mutations in #{ sample } over #{ gene }", study.organism, study.watson)
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junction = mutations.select_by(:in_exon_junction?).any?
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mis = Annotated.flatten mutations2mutated_isoforms.values_at(*mutations).compact
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affected = (mis.any? and mis.
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#damaged = (mis.any? and mis.select_by(:damaged?).any?)
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affected = (mis.any? and mis.select{|mi| c = mi2consequence[mi]; ! %w(UTR SYNONYMOUS).include? c}.any?)
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damaged = (mis.any? and mis.select{|mi| mi2damaged[mi] }.any?)
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[gene, mutations * ";;", affected, damaged, junction]
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