diff --git a/DCC/findcircRNA.py b/DCC/findcircRNA.py index 87d7c95..20d45b4 100644 --- a/DCC/findcircRNA.py +++ b/DCC/findcircRNA.py @@ -31,6 +31,8 @@ def printcircline(self, Chim_junc, output): outfile = open(output, 'w') for line in junctionfile: L = line.split('\t') + if L[0] == "chr_donorA": + continue if int(L[6]) >= 0 and L[0] == L[3] and L[2] == L[5] and ( (L[2] == '-' and int(L[4]) > int(L[1]) and self.minL < (int(L[4]) - int(L[1])) < self.maxL) or ( L[2] == '+' and int(L[1]) > int(L[4]) and self.minL < ( @@ -159,7 +161,8 @@ def findcirc(self, Chim_junc, output, strand=True): if len(L) < 14: print ("WARNING: File " + str(Chim_junc) + ", line " + str(linecnt) + " does not contain all features.") print ("WARNING: " + str(Chim_junc) + " is probably corrupt.") - + if L[0] == "chr_donorA": + continue if int(L[6]) >= 0 and L[0] == L[3] and L[2] == L[5] and ( (L[2] == '-' and int(L[4]) > int(L[1]) and self.minL < (int(L[4]) - int(L[1])) < self.maxL) or ( L[2] == '+' and int(L[1]) > int(L[4]) and self.minL < ( diff --git a/DCC/fix2chimera.py b/DCC/fix2chimera.py index 5fc75c9..84c63f1 100644 --- a/DCC/fix2chimera.py +++ b/DCC/fix2chimera.py @@ -51,6 +51,8 @@ def modify_junctiontype(junctiontype): line = line.rstrip() line_split = line.split('\t') + if line_split[0] == "chr_donorA": + continue # check if the row has all fields if len(line_split) < 14: print ("WARNING: File " + str(chimeric_junction_mate2) + ", line " + str(linecnt)