rbbt-study 0.2.1 → 0.2.2

checksums.yaml

@@ -1,15 +1,15 @@
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data/lib/rbbt/entity/study/genotypes/knowledge_base.rb

@@ -21,18 +21,21 @@ module Study
     gene_mutations = study.knowledge_base.get_database(:mutation_genes, :source => "Ensembl Gene ID")
     sample_mutations = study.knowledge_base.get_database(:sample_mutations, :source => "Sample")
 
-    require 'progress-monitor'
-    Progress.monitor "Mon", :stack_depth => 1
-    study.samples.select_by(:has_genotype?)[0..3].each do |sample|
+    all_mutations = study.all_mutations
+    mutations2mutated_isoforms = Misc.process_to_hash(all_mutations){|mutations| mutations.mutated_isoforms }
+    mi2damaged = Misc.process_to_hash(MutatedIsoform.setup(mutations2mutated_isoforms.values.flatten.compact.uniq, study.organism)){|mis| mis.damaged? }
+    study.samples.select_by(:has_genotype?).each do |sample|
       values = sample.affected_genes.collect do |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
+          mis = Annotated.flatten mutations2mutated_isoforms.values_at(*mutations).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?) 
+          #damaged = (mis.any? and mis.select_by(:damaged?).any?) 
+          
+          damaged = (mis.any? and mis.select{|mi| mi2damaged[mi]  }.any?) 
 
           [gene, mutations * ";;", affected, damaged, junction]
         else

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-study
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.2.2
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-10-23 00:00:00.000000000 Z
+date: 2013-10-25 00:00:00.000000000 Z
 dependencies: []
 description: This gem add the study entity with suport for NGS, Microarray and other
   types of data