rbbt-study 0.2.0

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data/LICENSE.txt

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+Copyright (c) 2013 Miguel Vazquez
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= rbbt-study
+
+Description goes here.
+
+== Contributing to rbbt-study
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.
+* Fork the project.
+* Start a feature/bugfix branch.
+* Commit and push until you are happy with your contribution.
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2013 Miguel Vazquez. See LICENSE.txt for
+further details.
+

data/lib/rbbt/entity/study/cnv/genes.rb

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+module Study
+
+  property :samples_with_gene_gained => :single do
+    samples_with_gene_gained = {}
+    self.job(:cnv_overview).run.through do |gene, values|
+      values.fields.zip(values).each do |sample, value|
+        next unless value == "Gained"
+        samples_with_gene_gained[gene] ||= []
+        samples_with_gene_gained[gene] << sample
+      end
+    end
+    samples_with_gene_gained
+  end
+  
+
+  property :samples_with_gene_lost => :single do
+    samples_with_gene_lost = {}
+    self.job(:cnv_overview).run.through do |gene, values|
+      values.fields.zip(values).each do |sample, value|
+        next unless value == "Lost"
+        samples_with_gene_lost[gene] ||= []
+        samples_with_gene_lost[gene] << sample
+      end
+    end
+    samples_with_gene_lost
+  end
+  
+end

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

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+module Sample
+  property :cnvs => :array2single do
+    study.cnv_cohort
+  end
+
+  property :has_cnv? => :array2single do
+    study.cnv_cohort.values_at(*self).collect{|cnvs| not cnvs.nil?}
+  end
+
+  property :gene_CN => :single do
+    gene_CN = {}
+    cnvs.variation.zip(cnvs.genes).each do |var, genes|
+      genes = genes.clean_annotations
+      case var
+      when "loss"
+        genes.each{|gene| gene_CN[gene] = "Lost"}
+      when "gain"
+        genes.each{|gene| gene_CN[gene] = "Gained"}
+      end
+    end
+    gene_CN
+  end
+  persist :gene_CN
+  
+  property :gained_cnvs => :single do
+    return nil if cnvs.nil?
+    return [] if cnvs.empty?
+    cnvs.select_by(:gain?)
+  end
+ 
+  property :lost_cnvs => :single do
+    return nil if cnvs.nil?
+    return [] if cnvs.empty?
+    cnvs.select_by(:loss?)
+  end
+  
+  property :gained_genes => :single do
+    Gene.setup(gene_CN.select{|g,v| v == "Gained"}.collect{|g,v| g}, "Ensembl Gene ID", self.study.organism)
+  end
+
+
+  property :lost_genes => :single do
+    Gene.setup(gene_CN.select{|g,v| v == "Lost"}.collect{|g,v| g}, "Ensembl Gene ID", self.study.organism)
+  end
+
+
+  property :cnv_genes => :single do
+    return nil if lost_genes.nil? or gained_genes.nil?
+    organism = study.metadata[:organism]
+    Gene.setup((lost_genes + gained_genes).uniq, "Ensembl Gene ID", lost_genes.organism)
+  end
+
+end
+
+

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

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+require 'rbbt/entity/cnv'
+
+require 'rbbt/entity/study/cnv/genes'
+require 'rbbt/entity/study/cnv/samples'
+
+module StudyWorkflow
+  helper :organism do
+    study.metadata[:organism]
+  end
+
+  task :cnv_overview => :tsv do
+    gene_overview = TSV.setup({}, 
+                          :key_field => "Ensembl Gene ID", 
+                          :fields => ["Samples with gene lost", "Samples with gene gained"],
+                          :type => :double
+                         )
+
+    cnv_samples = study.samples.select_by(:has_cnv?)
+
+    log :samples, "Gathering affected samples"
+    samples_gene_status = {}
+    all_genes = []
+    cnv_samples.each do |sample|
+      samples_gene_status[sample] = {}
+
+      lost_genes = sample.lost_genes
+      lost_genes.clean_annotations.each do |gene|
+        samples_gene_status[sample][gene] ||= [false, false]
+        samples_gene_status[sample][gene][0] = true
+        all_genes << gene
+      end if lost_genes.any?
+
+      gained_genes = sample.gained_genes
+      gained_genes.clean_annotations.each do |gene|
+        samples_gene_status[sample][gene] ||= [false, false]
+        samples_gene_status[sample][gene][1] = true
+        all_genes << gene
+      end if gained_genes.any?
+    end
+
+    log :compiling, "Compiling result"
+    all_genes.uniq.sort.each do |gene|
+      gene_overview[gene] = []
+      gene_overview[gene] << samples_gene_status.select{|sample, gene_status| gene_status.include? gene and gene_status[gene][0]}.collect{|sample, gene_status| sample}
+      gene_overview[gene] << samples_gene_status.select{|sample, gene_status| gene_status.include? gene and gene_status[gene][1]}.collect{|sample, gene_status| sample} 
+    end
+
+    gene_overview
+  end
+end
+
+module Study
+  def has_cnv?
+    dir.cnv.exists?
+  end
+
+  def cnv_files
+    dir.cnv.find.glob("*")
+  end
+
+  def cnv_cohort
+    if @cnv_cohort.nil?
+      @cnv_cohort = {}
+      cnv_files.each do |f| 
+        sample = File.basename(f)
+        Sample.setup(sample, self)
+        cnvs = Open.read(f).split("\n").sort
+        CNV.setup(cnvs, organism)
+        @cnv_cohort[sample] =  cnvs
+      end
+    end
+    @cnv_cohort
+  end
+end
+
+module Study
+  property :recurrently_lost_genes => :single do |threshold|
+    counts = {}
+    self.samples.each do |sample|
+      next unless sample.has_cnvs?
+      puts sample
+
+      genes = nil
+      genes = sample.lost_genes.clean_annotations
+      genes.each do |gene|
+        counts[gene] ||= 0
+        counts[gene] += 1 
+      end
+    end
+
+    recurrent = counts.select{|k,c| c >= threshold }.collect{|k,v| k }
+    Gene.setup(recurrent, "Ensembl Gene ID", organism)
+  end
+
+  property :recurrently_gained_genes => :single do |threshold|
+    counts = {}
+    self.samples.each do |sample|
+      next unless sample.has_cnvs?
+      puts sample
+
+      genes = nil
+      genes = sample.gained_genes.clean_annotations
+      genes.each do |gene|
+        counts[gene] ||= 0
+        counts[gene] += 1 
+      end
+    end
+
+    recurrent = counts.select{|k,c| c >= threshold }.collect{|k,v| k }
+    Gene.setup(recurrent, "Ensembl Gene ID", organism)
+  end
+
+  property :gene_sample_cnv_matrix => :single do
+    tsv = TSV.setup({}, :key_field => "Ensembl Gene ID", :namespace => organism, :type => :list)
+    samples = []
+    i = 0
+    num_samples = cohort.length
+    cnv_cohort.each do |sample,cnvs|
+      cnvs.genes.compact.flatten.uniq.each do |gene|
+        tsv[gene] ||= ["FALSE"] * num_samples
+        tsv[gene][i] = "TRUE"
+      end
+      samples << sample
+      i += 1
+    end
+
+    tsv.fields = samples
+
+    tsv
+  end
+
+  property :gene_sample_gain_matrix => :single do
+    tsv = TSV.setup({}, :key_field => "Ensembl Gene ID", :namespace => organism, :type => :list)
+    samples = []
+    i = 0
+    num_samples = cohort.length
+    cnv_cohort.each do |sample,cnvs|
+      cnvs.select_by(:gain?).genes.compact.flatten.uniq.each do |gene|
+        tsv[gene] ||= ["FALSE"] * num_samples
+        tsv[gene][i] = "TRUE"
+      end
+      samples << sample
+      i += 1
+    end
+
+    tsv.fields = samples
+
+    tsv
+  end
+
+
+  property :gene_sample_loss_matrix => :single do
+    tsv = TSV.setup({}, :key_field => "Ensembl Gene ID", :namespace => organism, :type => :list)
+    samples = []
+    i = 0
+    num_samples = cohort.length
+    cnv_cohort.each do |sample,cnvs|
+      cnvs.select_by(:loss?).genes.compact.flatten.uniq.each do |gene|
+        tsv[gene] ||= ["FALSE"] * num_samples
+        tsv[gene][i] = "TRUE"
+      end
+      samples << sample
+      i += 1
+    end
+
+    tsv.fields = samples
+
+    tsv
+  end
+end