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
@@ -27,6 +28,7 @@ module Study
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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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+
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  if mutations.any?
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  junction = mutations.select_by(:in_exon_junction?).any?
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@@ -23,7 +23,6 @@ module Study
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  if Proc === file
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  study = self
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  block = Proc.new{ file.call(self, database) }
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- block.define_singleton_method(:filename) do [database, study] * "@" end
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  kb.register database, nil, {}, &block
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  else
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  kb.register database, file
@@ -20,6 +20,7 @@ module Sample
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  return nil if study.nil?
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  study.organism
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  end
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+
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  end
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  module Study
@@ -42,14 +43,6 @@ 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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-
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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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-
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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
metadata CHANGED
@@ -1,14 +1,14 @@
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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: 0.2.2
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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: 2013-10-25 00:00:00.000000000 Z
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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