--- a/gene_family_aligner.py	Fri May 05 09:31:23 2017 -0400
+++ b/gene_family_aligner.py	Fri May 05 09:31:30 2017 -0400
@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 import argparse
 import os
-import subprocess
 
 import utils
 
@@ -9,15 +8,15 @@
 
 parser = argparse.ArgumentParser()
 parser.add_argument('--alignment_method', dest='alignment_method', help='Multiple sequence alignments method')
-parser.add_argument('--automated_trimming', dest='automated_trimming', default=None, help="Trims alignments using trimAl's ML heuristic trimming approach")
-parser.add_argument('--codon_alignments', dest='codon_alignments', default=None, help="Flag for constructing orthogroup multiple codon alignments")
+parser.add_argument('--automated_trimming', dest='automated_trimming', default=None, help='Trims alignments using trimAls ML heuristic trimming approach')
+parser.add_argument('--codon_alignments', dest='codon_alignments', default=None, help='Flag for constructing orthogroup multiple codon alignments')
 parser.add_argument('--gap_trimming', dest='gap_trimming', default=0, type=float, help='Remove sites in alignments with gaps of')
-parser.add_argument('--iterative_realignment', dest='iterative_realignment', type=int, default=0, help='"Maximum number of iterations')
+parser.add_argument('--iterative_realignment', dest='iterative_realignment', type=int, default=0, help='Maximum number of iterations')
 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
-parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help="Directory of input fasta datasets")
-parser.add_argument('--output', dest='output', help="Output dataset")
-parser.add_argument('--output_dir', dest='output_dir', help="Output dataset files_path directory")
-parser.add_argument('--pasta_iter_limit', dest='pasta_iter_limit', type=int, default=None, help='"Maximum number of iteration that the PASTA algorithm will execute')
+parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help='Directory of input fasta datasets')
+parser.add_argument('--output', dest='output', help='Output dataset')
+parser.add_argument('--output_dir', dest='output_dir', help='Output dataset files_path directory')
+parser.add_argument('--pasta_iter_limit', dest='pasta_iter_limit', type=int, default=None, help='Maximum number of iteration that the PASTA algorithm will execute')
 parser.add_argument('--pasta_script_path', dest='pasta_script_path', default=None, help='Path to script for executing pasta')
 parser.add_argument('--remove_sequences', dest='remove_sequences', default=0, type=float, help='Remove sequences with gaps of')
 
@@ -43,10 +42,11 @@
     cmd += ' --remove_sequences %4f' % args.remove_sequences
 if args.iterative_realignment > 0:
     cmd += ' --iterative_realignment %d' % args.iterative_realignment
+
 # 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)
+utils.run_command(cmd)
+
+# Handle outputs.
 if args.codon_alignments is None:
     src_output_dir = OUTPUT_DIR
 else: