rbbt-study 0.2.0 → 0.2.1

checksums.yaml

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data/lib/rbbt/entity/study/cnv/samples.rb

@@ -10,6 +10,7 @@ module Sample
   property :gene_CN => :single do
     gene_CN = {}
     cnvs.variation.zip(cnvs.genes).each do |var, genes|
+      next if genes.empty?
       genes = genes.clean_annotations
       case var
       when "loss"

data/lib/rbbt/entity/study/genotypes/knowledge_base.rb

@@ -17,20 +17,29 @@ module Study
   }
 
   self.study_registry[:sample_genes] = Proc.new{|study,database|
-    tsv = TSV.setup({}, :key_field => "Sample", :fields => ["Ensembl Gene ID"], :type => :flat, :namespace => study.organism)
-    study.samples.select_by(:has_genotype?).each do |sample|
-      tsv[sample] = sample.affected_genes
-    end
-    tsv
-  }
+    tsv = TSV.setup({}, :key_field => "Sample", :fields => ["Ensembl Gene ID", "Genomic Mutation", "Affected isoform", "Damaged isoform", "Exon Junction"], :type => :double, :namespace => study.organism)
+    gene_mutations = study.knowledge_base.get_database(:mutation_genes, :source => "Ensembl Gene ID")
+    sample_mutations = study.knowledge_base.get_database(:sample_mutations, :source => "Sample")
 
-  self.study_registry[:sample_genes2] = Proc.new{|study,database|
-    tsv = TSV.setup({}, :key_field => "Sample", :fields => ["Ensembl Gene ID", "Genomic Mutation"], :type => :double, :namespace => study.organism)
-    kb = study.knowledge_base.get_database(:mutation_genes, :source => "Ensembl Gene ID")
-    study.samples.select_by(:has_genotype?).each do |sample|
+    require 'progress-monitor'
+    Progress.monitor "Mon", :stack_depth => 1
+    study.samples.select_by(:has_genotype?)[0..3].each do |sample|
       values = sample.affected_genes.collect do |gene|
-        [gene, kb[gene] * ";;"]
+        mutations = gene_mutations[gene].subset(sample_mutations[sample] || [])
+        if mutations.any?
+          junction = mutations.select_by(:in_exon_junction?).any?
+
+          mis = Annotated.flatten mutations.mutated_isoforms.compact
+
+          affected = (mis.any? and mis.select_by(:consequence){|c| ! %w(UTR SYNONYMOUS).include? c}.any?) 
+          damaged = (mis.any? and mis.select_by(:damaged?).any?) 
+
+          [gene, mutations * ";;", affected, damaged, junction]
+        else
+          [gene, "", false, false, false]
+        end
       end
+
       tsv[sample] = Misc.zip_fields values
     end
     tsv

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-study
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.2.1
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-10-21 00:00:00.000000000 Z
+date: 2013-10-23 00:00:00.000000000 Z
 dependencies: []
 description: This gem add the study entity with suport for NGS, Microarray and other
   types of data