+ using new parsers now
[qpalma.git] / scripts / perform_remapping.py
index 609e449..cd546c5 100644 (file)
@@ -22,10 +22,10 @@ class Remapping:
       self.chromosomes = chromos
       self.result_dir = result_d
 
-      self.max_mismatch    = 2
+      self.max_mismatch    = 1
       self.max_equal_hits  = 100
-      self.max_gap_size    = 2
-      self.seed_size       = 12
+      self.max_gap_size    = 6000
+      self.seed_size       = 5
 
 
    def performRemapping(self):
@@ -39,9 +39,11 @@ class Remapping:
          cmd +=' -r 2 -v %d -w %d -g %d -s %d' %\
          (self.max_mismatch,self.max_equal_hits,self.max_gap_size,self.seed_size)
 
-         os.system('echo \"%s\" | qsub -l h_vmem=2.0G -cwd -j y -N \"%s.log\"'%(cmd,chromId))
-         #obj = subprocess.Popen(cmd,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
-         #out,err = obj.communicate()
+         #os.system('echo \"%s\" | qsub -l h_vmem=5.0G -cwd -j y -N \"%s.log\"'%(cmd,chromId))
+         obj = subprocess.Popen(cmd,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
+         out,err = obj.communicate()
+         print out
+         print err
 
 
 if __name__ == '__main__':