コード例 #1
0
        except Exception, inst:
            sys.stderr.write("Unexpected error opening %s: %s\n" % (infile, inst))
            sys.exit()
             
        if(verbose):
            print "Reading " + str(argv[0])   
                         
        elems = tree.getroot()     
        
        proteins_percolator= per.getProteins(elems)
        peptides = per.getPeptides(elems)
        
        ntarget_percolator = len([prot for prot in [prot for prot in proteins_percolator if not prot.isdecoy]])
        ndecoy_percolator = len([prot for prot in [prot for prot in proteins_percolator if prot.isdecoy]])
        
        print "Found " + str(ntarget_percolator) + " proteins"
        
        print "doing parsimony at " + str(fdr)
        
        parsimony_tmp = [prot for prot,pep in parsimony.getParsimony(peptides, fdr, True)]
        ntarget_parsimony = len([prot for prot in parsimony_tmp if prot.find("random") == -1])
        ndecoy_parsimony = len([prot for prot in parsimony_tmp if prot.find("random") != -1])
        
        print "Found " + str(ntarget_parsimony) + " proteins at " + str(fdr) + " fdr doing parsimony"
        
        print "Computed Gamma is " + str(float(ntarget_parsimony) / float(ntarget_percolator))
        
if __name__ == "__main__":
    main(sys.argv[1:]) 
    
    
コード例 #2
0
            two_hit_thresholds_unique.append(fdr_2hit_unique)

            print "Unique two peptide rule gives " + str(
                ntarget_2peprule_unique) + " target proteins and " + str(
                    ndecoy_2peprule_unique) + " decoy proteins and " + str(
                        fdr_2hit_unique) + " qvalue"
            if (maxtarget < ntarget_2peprule_unique):
                maxtarget = ntarget_2peprule_unique
            if (maxdecoy < ndecoy_2peprule_unique):
                maxdecoy = ndecoy_2peprule_unique

            print "doing parsimony at " + str(t)
            parsimony_tmp = [
                prot
                for prot, pep in parsimony.getParsimony(peptides, t, qvalue)
            ]
            ntarget_parsimony = len(
                [prot for prot in parsimony_tmp if prot.find("random") == -1])
            ndecoy_parsimony = len(
                [prot for prot in parsimony_tmp if prot.find("random") != -1])
            parsimony_proteins_target.append(ntarget_parsimony)
            parsimony_proteins_decoy.append(ndecoy_parsimony)

            if (num_targets_mayus > 0):
                tmp_target = float(ntarget_parsimony) / float(
                    num_targets_mayus)
            else:
                tmp_target = 0

            if (num_decoys_mayus > 0):
コード例 #3
0
 
 if(tmp_target > 0):
     fdr_2hit_unique = float((tmp_decoy / tmp_target) * prot_fdr_mayus)
 else:
     fdr_2hit_unique = 0
     
 two_hit_thresholds_unique.append(fdr_2hit_unique)
 
 print "Unique two peptide rule gives " + str(ntarget_2peprule_unique) + " target proteins and " + str(ndecoy_2peprule_unique) + " decoy proteins and " +str(fdr_2hit_unique) + " qvalue" 
 if(maxtarget < ntarget_2peprule_unique):
     maxtarget = ntarget_2peprule_unique
 if(maxdecoy < ndecoy_2peprule_unique):
     maxdecoy = ndecoy_2peprule_unique
     
 print "doing parsimony at " + str(t)
 parsimony_tmp = [prot for prot,pep in parsimony.getParsimony(peptides, t, qvalue)]
 ntarget_parsimony = len([prot for prot in parsimony_tmp if prot.find("random") == -1])
 ndecoy_parsimony = len([prot for prot in parsimony_tmp if prot.find("random") != -1])
 parsimony_proteins_target.append(ntarget_parsimony)
 parsimony_proteins_decoy.append(ndecoy_parsimony)
 
 if(num_targets_mayus > 0 ):
     tmp_target = float(ntarget_parsimony) / float(num_targets_mayus)
 else:
     tmp_target = 0
 
 if(num_decoys_mayus > 0 ):
     tmp_decoy = float(ndecoy_parsimony) / float(num_decoys_mayus)
 else:
     tmp_decoy = 0