class PeptideEvidence

Attributes

is_decoy[RW]

attr_accessor :peptide_sequence

peptide_next_aa[RW]
peptide_prev_aa[RW]
protein[RW]
protein_descr[RW]

Public Class Methods

from_mzid(pe_node,mzid_doc) click to toggle source
# File lib/protk/psm.rb, line 29
def from_mzid(pe_node,mzid_doc)
        pe = new()
        pe.peptide_prev_aa=pe_node.attributes['pre']
        pe.peptide_next_aa=pe_node.attributes['post']
        pe.is_decoy=pe_node.attributes['isDecoy'].to_bool

        # peptide_ref = pe_node.attributes['peptide_ref']
        prot_ref = pe_node.attributes['dBSequence_ref']
        # pep_node = MzIdentMLDoc.find(pe_node,"Peptide[@id=\'#{peptide_ref}\']",true)[0]
        prot_node = MzIdentMLDoc.find(pe_node,"DBSequence[@id=\'#{prot_ref}\']",true)[0]


        # <DBSequence id="JEMP01000193.1_rev_g3500.t1"
        # accession="JEMP01000193.1_rev_g3500.t1"
        # searchDatabase_ref="SearchDB_1">
        #   <cvParam cvRef="PSI-MS" accession="MS:1001088"
        #   name="protein description" value="280755|283436" />
        # </DBSequence>
        pe.protein=prot_node.attributes['accession']
        pe.protein_descr=mzid_doc.get_cvParam(prot_node,"MS:1001088")['value']


        # pe.peptide_sequence=pep_node

        pe
end
new() click to toggle source
# File lib/protk/psm.rb, line 60
def initialize()

end

Public Instance Methods

as_pepxml() click to toggle source
<alternative_protein protein="lcl|JEMP01000005.1_rev_g4624.t1"

protein_descr=“652491|654142” num_tol_term=“2” peptide_prev_aa=“K” peptide_next_aa=“Y”/> We use this only for alternative_proteins The first peptide_evidence item is baked into the attributes of a spectrum_query

# File lib/protk/psm.rb, line 68
def as_pepxml()
        alt_node = XML::Node.new('alternative_protein')
        alt_node['protein']=self.protein
        alt_node['protein_descr']=self.protein_descr
        alt_node['peptide_prev_aa']=self.peptide_prev_aa
        alt_node['peptide_next_aa']=self.peptide_next_aa


        alt_node
end