rbbt-study 0.2.20 → 0.2.21

checksums.yaml

@@ -1,15 +1,15 @@
 ---
 !binary "U0hBMQ==":
   metadata.gz: !binary |-
-    MmU0YmUxZDUxOTZhMmU1MjJlMmI3MWUwYzU4NzYxODY1NWZhNjk0NQ==
+    N2VkYmEwMzZlMjkzMDdkODVjZDVhNGQ0M2E1ZjY4YmFlYTQ1Yzg5Nw==
   data.tar.gz: !binary |-
-    NGI4ODVjZThmOTk5ODI2NTRhYzRlN2RlNDA0NTc0ZWIyNDk4NGYzOA==
+    MTQyMTYxNTE4OGUzZDlmN2EzYzk3OWU4NWMyZDNjZjQ2MTgxZmY4Ng==
 SHA512:
   metadata.gz: !binary |-
-    MjI1Yzc5YmZjM2ZhY2NmNzI0Zjk3MTZhNTFlMzM0YWZkZWZkZjEwNDVkZGI0
-    NjVkM2Q4ZTY5OGQwZjkyMDRkYWM4Yzg0YmU3MWVjNzY4OGNjNWNiMDM2M2U4
-    YTQxYmZiMDQwM2VjNzI3MTNjOTgzNjdmNzg5ZTQ2NDM4OTJmYTM=
+    YTE2NjRlZWRmZGNiMmQwNDJjY2Y4Y2IxNGYxM2FhMWQ0YjI3ODhmMGZmYjUz
+    NjBlMDkwMWI5Y2RhYzEzOWM3ZTdjZTc4M2Q0MTA3M2YzMDhjOWJlYmU0YWEx
+    NTUzN2M4ZGU3YjZlYWRlYzA5MTdjNGUyODViNTg1MGMxMDBjODk=
   data.tar.gz: !binary |-
-    MTk5MjBlZTc1NDQ4OTZiNjE0M2VlZGVkYWE0YWZiM2VhYzJkNjk0MjhjYTI2
-    OTc2YzhiZTAxMTBmOWQwZGI0OGNiZjM5NmZiZjk3ODMxMjYwNzYzNDJmZGRj
-    ZTMyY2EzZjg1Y2I2MDkwNzM0OGRhOGJkYTllMmVmNTEwNzQzODY=
+    MDQxN2RiZDJmYTI3NTZjZDc4NDc5MjQ2ZDc3MDRjZDIzMTAxNDE3NzMzODI1
+    MjNiYWIxNDEzYTc1NWExNjJiMGRmMTkyZGFjNDkxYTZkNTFmYTc2YTgwMzQx
+    YjZkYmY0MmJmZDJlNjJiMzQxN2MzMGE3MTA4NzY4MTQzOWQwZTg=

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

@@ -15,9 +15,11 @@ module Study
 
   self.study_registry[:sample_mutations] = Proc.new{|study,database|
     tsv = TSV.setup({}, :key_field => "Sample", :fields => ["Genomic Mutation"], :type => :flat, :namespace => study.organism)
+
     study.samples.select_by(:has_genotype?).each do |sample|
       tsv[sample] = sample.mutations
     end
+
     tsv
   }
 

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

@@ -28,7 +28,7 @@ module StudyWorkflow
 
     genes.each do |gene|
       mutations = study.knowledge_base.parents(:mutation_genes, gene).target
-      mutations = study.knowledge_base.subset(:sample_mutations, "Genomic Mutation" => mutations).source
+      mutations = study.knowledge_base.subset(:sample_mutations, "Genomic Mutation" => mutations, "Sample" => :all).source
       next if mutations.empty?
       matches = mutations.length
       exon_bases = gene2exon_size[gene]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-study
 version: !ruby/object:Gem::Version
-  version: 0.2.20
+  version: 0.2.21
 platform: ruby
 authors:
 - Miguel Vazquez