protk 1.4.4.beta1 → 1.4.4.beta2

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checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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@@ -71,7 +71,8 @@ protein_groups.each do |group_node|
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  if group_prob >= tool.minprob.to_f
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  $stdout.write "\n" if tool.debug
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  $protk.log "Writing group with probability #{group_prob}" , :info
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- group = ProteinGroup.from_mzid(group_node,mzid_doc,tool.minprob.to_f)
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+ group = ProteinGroup.from_mzid(group_node,mzid_doc,tool.minprob.to_f)
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+ # require 'byebug';byebug
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  prot_xml_writer.append_protein_group(group.as_protxml)
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  n_written+=1
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  end
@@ -127,8 +127,9 @@ class MzIdentMLDoc < Object
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  # Memoized because it gets called for every protein in a group
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  def get_proteins_for_group(group_node)
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+ # puts group_node.attributes['group_number']
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  @proteins_for_group_cache ||= Hash.new do |h,key|
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- h[key] = self.find(group_node,"ProteinDetectionHypothesis")
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+ h[key] = self.find(key,"ProteinDetectionHypothesis")
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  end
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  @proteins_for_group_cache[group_node]
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  end
@@ -68,7 +68,8 @@ class ProteinGroup
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  def as_protxml()
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  node = XML::Node.new('protein_group')
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  node["group_number"] = self.group_number.to_s
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- node["group_probability"] = self.group_probability.to_s
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+ # require 'byebug';byebug
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+ node["group_probability"] = (self.group_probability * 0.01).to_s
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  self.proteins.each { |prot| node << prot.as_protxml }
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  node
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  end
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: protk
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  version: !ruby/object:Gem::Version
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- version: 1.4.4.beta1
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+ version: 1.4.4.beta2
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  platform: ruby
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  authors:
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  - Ira Cooke