rbbt-study 0.2.1 → 0.2.2
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- checksums.yaml +8 -8
- data/lib/rbbt/entity/study/genotypes/knowledge_base.rb +8 -5
- metadata +2 -2
checksums.yaml
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@@ -1,15 +1,15 @@
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---
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!binary "U0hBMQ==":
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metadata.gz: !binary |-
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data.tar.gz: !binary |-
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@@ -21,18 +21,21 @@ module Study
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gene_mutations = study.knowledge_base.get_database(:mutation_genes, :source => "Ensembl Gene ID")
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sample_mutations = study.knowledge_base.get_database(:sample_mutations, :source => "Sample")
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all_mutations = study.all_mutations
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mutations2mutated_isoforms = Misc.process_to_hash(all_mutations){|mutations| mutations.mutated_isoforms }
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mi2damaged = Misc.process_to_hash(MutatedIsoform.setup(mutations2mutated_isoforms.values.flatten.compact.uniq, study.organism)){|mis| mis.damaged? }
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study.samples.select_by(:has_genotype?).each do |sample|
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values = sample.affected_genes.collect do |gene|
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mutations = gene_mutations[gene].subset(sample_mutations[sample] || [])
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if mutations.any?
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junction = mutations.select_by(:in_exon_junction?).any?
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mis = Annotated.flatten mutations.
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mis = Annotated.flatten mutations2mutated_isoforms.values_at(*mutations).compact
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affected = (mis.any? and mis.select_by(:consequence){|c| ! %w(UTR SYNONYMOUS).include? c}.any?)
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damaged = (mis.any? and mis.select_by(:damaged?).any?)
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#damaged = (mis.any? and mis.select_by(:damaged?).any?)
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damaged = (mis.any? and mis.select{|mi| mi2damaged[mi] }.any?)
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[gene, mutations * ";;", affected, damaged, junction]
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else
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metadata
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--- !ruby/object:Gem::Specification
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name: rbbt-study
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version: !ruby/object:Gem::Version
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version: 0.2.
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version: 0.2.2
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platform: ruby
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authors:
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- Miguel Vazquez
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2013-10-
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date: 2013-10-25 00:00:00.000000000 Z
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dependencies: []
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description: This gem add the study entity with suport for NGS, Microarray and other
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types of data
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