rbbt-study 0.2.2 → 0.2.3

checksums.yaml

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

@@ -19,6 +19,7 @@ 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")
 
     all_mutations = study.all_mutations
@@ -27,6 +28,7 @@ module Study
     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?
 

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

@@ -23,7 +23,6 @@ module Study
                             if Proc === file
                               study = self
                               block = Proc.new{ file.call(self, database) }
-                              block.define_singleton_method(:filename) do [database, study] * "@" end
                               kb.register database, nil, {}, &block 
                             else
                               kb.register database, file

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

@@ -20,6 +20,7 @@ module Sample
     return nil if study.nil?
     study.organism
   end
+
 end
 
 module Study
@@ -42,14 +43,6 @@ module Study
     @samples
   end
 
-  def has_cnv?
-    study.has_cnv? and study.cnv_cohort.include? self
-  end
-  
-  def has_mutations?
-    study.cohort and study.cohort.include? self
-  end
-
   def match_samples(list)
     if donor_id_field = (sample_info = self.sample_info).fields.select{|f| f =~ /donor\s+id/i}.first
       list_donors = sample_info.select(list).slice(donor_id_field).values.compact.flatten

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-study
 version: !ruby/object:Gem::Version
-  version: 0.2.2
+  version: 0.2.3
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-10-25 00:00:00.000000000 Z
+date: 2013-10-29 00:00:00.000000000 Z
 dependencies: []
 description: This gem add the study entity with suport for NGS, Microarray and other
   types of data