class ProteinGroup
Attributes
group_number[RW]
group_probability[RW]
proteins[RW]
Public Class Methods
from_mzid(groupnode,mzid_doc,minprob=0)
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Note: This is hacked together to work for a specific PeptideShaker output type Refactor and properly respect cvParams for real conversion
# File lib/protk/protein_group.rb, line 38 def from_mzid(groupnode,mzid_doc,minprob=0) group=new() group.group_number=groupnode.attributes['id'].split("_").last.to_i+1 group.group_probability=mzid_doc.get_cvParam(groupnode,"MS:1002470").attributes['value'].to_f # require 'byebug';byebug protein_nodes=mzid_doc.get_proteins_for_group(groupnode) group_members = protein_nodes.select do |e| mzid_doc.get_protein_probability(e)>=minprob end group.proteins = group_members.collect { |e| Protein.from_mzid(e,mzid_doc) } group end
new()
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# File lib/protk/protein_group.rb, line 64 def initialize() end
Public Instance Methods
as_protxml()
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# File lib/protk/protein_group.rb, line 68 def as_protxml() node = XML::Node.new('protein_group') node["group_number"] = self.group_number.to_s # require 'byebug';byebug node["group_probability"] = (self.group_probability * 0.01).to_s self.proteins.each { |prot| node << prot.as_protxml } node end