Class: Protein

Inherits:
Object
  • Object
show all
Defined in:
lib/protk/protein.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Protein

Returns a new instance of Protein.



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# File 'lib/protk/protein.rb', line 121

def initialize()

end

Instance Attribute Details

#group_number ⇒ Object

Returns the value of attribute group_number.



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# File 'lib/protk/protein.rb', line 9

def group_number
  @group_number
end

#group_probability ⇒ Object

Returns the value of attribute group_probability.



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# File 'lib/protk/protein.rb', line 10

def group_probability
  @group_probability
end

#n_indistinguishable_proteins ⇒ Object

Returns the value of attribute n_indistinguishable_proteins.



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# File 'lib/protk/protein.rb', line 14

def n_indistinguishable_proteins
  @n_indistinguishable_proteins
end

#peptides ⇒ Object

Returns the value of attribute peptides.



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# File 'lib/protk/protein.rb', line 16

def peptides
  @peptides
end

#percent_coverage ⇒ Object

Returns the value of attribute percent_coverage.



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# File 'lib/protk/protein.rb', line 15

def percent_coverage
  @percent_coverage
end

#probability ⇒ Object

Returns the value of attribute probability.



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# File 'lib/protk/protein.rb', line 11

def probability
  @probability
end

#protein_name ⇒ Object

Returns the value of attribute protein_name.



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# File 'lib/protk/protein.rb', line 13

def protein_name
  @protein_name
end

#sequence ⇒ Object

Returns the value of attribute sequence.



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# File 'lib/protk/protein.rb', line 12

def sequence
  @sequence
end

Class Method Details

.from_mzid(xmlnode, mzid_doc) ⇒ Object

Note: This is hacked together to work for a specific PeptideShaker output type Refactor and properly respect cvParams for real conversion



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# File 'lib/protk/protein.rb', line 87

def from_mzid(xmlnode,mzid_doc)

  coverage_cvparam=""
  prot=new()
  groupnode = xmlnode.parent

  prot.group_number=groupnode.attributes['id'].split("_").last.to_i+1
  prot.protein_name=mzid_doc.get_dbsequence(xmlnode,xmlnode.attributes['dBSequence_ref']).attributes['accession']

  prot.n_indistinguishable_proteins=mzid_doc.get_proteins_for_group(groupnode).length


  prot.group_probability=mzid_doc.get_cvParam(groupnode,"MS:1002470").attributes['value'].to_f


  coverage_node=mzid_doc.get_cvParam(xmlnode,"MS:1001093")

  prot.percent_coverage=coverage_node.attributes['value'].to_f if coverage_node
  prot.probability = mzid_doc.get_protein_probability(xmlnode)
  # require 'byebug';byebug

  peptide_nodes=mzid_doc.get_peptides_for_protein(xmlnode)

  prot.peptides = peptide_nodes.collect { |e| Peptide.from_mzid(e,mzid_doc) }

  Constants.instance.log "Generated protein entry with probability #{prot.probability}" , :debug

  prot
end

.from_protxml(xmlnode) ⇒ Object 



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# File 'lib/protk/protein.rb', line 51

def from_protxml(xmlnode)
  prot=new()
  groupnode = xmlnode.parent
  prot.group_probability = groupnode['probability'].to_f
  prot.group_number = groupnode['group_number'].to_i
  prot.probability = xmlnode['probability'].to_f
  prot.protein_name = xmlnode['protein_name']
  prot.n_indistinguishable_proteins = xmlnode['n_indistinguishable_proteins'].to_i
  prot.percent_coverage = xmlnode['percent_coverage'].to_f

  peptide_nodes = xmlnode.find('protxml:peptide','protxml:http://regis-web.systemsbiology.net/protXML')
  prot.peptides = peptide_nodes.collect { |e| Peptide.from_protxml(e) }
  prot
end

Instance Method Details

#as_protxml ⇒ Object 



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# File 'lib/protk/protein.rb', line 18

def as_protxml
  node = XML::Node.new('protein')
    node['protein_name']=self.protein_name.to_s
    node['n_indistinguishable_proteins']=self.n_indistinguishable_proteins.to_s
    node['probability']=self.probability.to_s
    node['percent_coverage']=self.percent_coverage.to_s
    node['unique_stripped_peptides']=self.peptides.collect {|p| p.sequence }.join("+")
    node['total_number_peptides']=self.peptides.length.to_s
    self.peptides.each do |peptide|  
      node<<peptide.as_protxml
    end
    node
end

#representative_peptides ⇒ Object

Return just one peptide for each unique sequence choosing the peptide with highest probability



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# File 'lib/protk/protein.rb', line 127

def representative_peptides()
  best_peptides={}
  self.peptides.each do |peptide|
    seq = peptide.sequence
    if best_peptides[seq].nil?
      best_peptides[seq]=peptide       
    else
      best_peptides[seq]=peptide if peptide.probability > best_peptides[seq].probability
    end
  end

  best_peptides.values
end