rbbt-study 0.2.3 → 0.2.4

checksums.yaml

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

@@ -18,13 +18,15 @@ module Study
 
   self.study_registry[:sample_genes] = Proc.new{|study,database|
     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")
-    gene_mutations.entity_options["Genomic Mutation"] = {:watson => study.watson, :organism => study.organism}
-    sample_mutations = study.knowledge_base.get_database(:sample_mutations, :source => "Sample")
 
+    sample_mutations = study.knowledge_base.get_database(:sample_mutations, :source => "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? }
+    #mi2damaged = Misc.process_to_hash(MutatedIsoform.setup(mutations2mutated_isoforms.values.flatten.compact.uniq, study.organism)){|mis| mis.damaged? }
+    mi2damaged = Misc.process_to_hash(MutatedIsoform.setup(mutations2mutated_isoforms.values.flatten.compact.uniq, study.organism)){|mis| [false] * mis.length }
+
+    gene_mutations = study.knowledge_base.get_database(:mutation_genes, :source => "Ensembl Gene ID")
+    gene_mutations.entity_options["Genomic Mutation"] = {:watson => study.watson, :organism => study.organism}
     study.samples.select_by(:has_genotype?).each do |sample|
       values = sample.affected_genes.collect do |gene|
         mutations = gene_mutations[gene].subset(sample_mutations[sample] || [])

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-study
 version: !ruby/object:Gem::Version
-  version: 0.2.3
+  version: 0.2.4
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-10-29 00:00:00.000000000 Z
+date: 2013-10-30 00:00:00.000000000 Z
 dependencies: []
 description: This gem add the study entity with suport for NGS, Microarray and other
   types of data