# HG changeset patch
# User greg
# Date 1493991034 14400
# Node ID 9d58af3e459d4ebe0eba6e7311dd1689f33a4fc1
# Parent  564163c7afd855829492f77a199472001a0598b2
Uploaded

diff -r 564163c7afd8 -r 9d58af3e459d assembly_post_processor.py
--- a/assembly_post_processor.py	Fri May 05 09:30:26 2017 -0400
+++ b/assembly_post_processor.py	Fri May 05 09:30:34 2017 -0400
@@ -1,12 +1,8 @@
 #!/usr/bin/env python
 import argparse
-import os
-import subprocess
 
 import utils
 
-OUTPUT_DIR = 'assemblyPostProcessor_dir'
-
 parser = argparse.ArgumentParser()
 parser.add_argument('--dereplicate', dest='dereplicate', default=None, help='Remove duplicate sequences')
 parser.add_argument('--gap_trimming', dest='gap_trimming', type=float, default=0, help='Trim alignments')
@@ -43,8 +39,5 @@
 if args.strand_specific is not None:
     cmd += ' --strand_specific'
 cmd += ' --transcripts %s' % args.transcripts
-
 # Run the command.
-proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)
-rc = proc.wait()
-utils.check_execution_errors(rc, proc.stderr, proc.stdout)
+utils.run_command(cmd)