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)
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# 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()
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# File lib/protk/psm.rb, line 60 def initialize() end
Public Instance Methods
as_pepxml()
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<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