rbbt-study 0.2.2 → 0.2.3
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@@ -19,6 +19,7 @@ module Study
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self.study_registry[:sample_genes] = Proc.new{|study,database|
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tsv = TSV.setup({}, :key_field => "Sample", :fields => ["Ensembl Gene ID", "Genomic Mutation", "Affected isoform", "Damaged isoform", "Exon Junction"], :type => :double, :namespace => study.organism)
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gene_mutations = study.knowledge_base.get_database(:mutation_genes, :source => "Ensembl Gene ID")
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gene_mutations.entity_options["Genomic Mutation"] = {:watson => study.watson, :organism => study.organism}
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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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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].subset(sample_mutations[sample] || [])
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if mutations.any?
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junction = mutations.select_by(:in_exon_junction?).any?
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return nil if study.nil?
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study.organism
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end
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end
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module Study
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@samples
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end
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def has_cnv?
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study.has_cnv? and study.cnv_cohort.include? self
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end
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def has_mutations?
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study.cohort and study.cohort.include? self
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end
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def match_samples(list)
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if donor_id_field = (sample_info = self.sample_info).fields.select{|f| f =~ /donor\s+id/i}.first
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list_donors = sample_info.select(list).slice(donor_id_field).values.compact.flatten
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metadata
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--- !ruby/object:Gem::Specification
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name: rbbt-study
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version: !ruby/object:Gem::Version
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version: 0.2.
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version: 0.2.3
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platform: ruby
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authors:
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- Miguel Vazquez
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2013-10-
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date: 2013-10-29 00:00:00.000000000 Z
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dependencies: []
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description: This gem add the study entity with suport for NGS, Microarray and other
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types of data
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