Merge branch 'master' of github.com:dieterich-lab/DCC

Author: tjakobi

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 < (

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)