--- a/gene_family_classifier.py	Fri May 05 09:32:14 2017 -0400
+++ b/gene_family_classifier.py	Fri May 05 09:32:21 2017 -0400
@@ -2,7 +2,6 @@
 import argparse
 import os
 import shutil
-import subprocess
 
 import utils
 
@@ -11,7 +10,7 @@
 OUTPUT_DIR = 'geneFamilyClassification_dir'
 
 parser = argparse.ArgumentParser()
-parser.add_argument('--input', dest='input', help="Input dataset")
+parser.add_argument('--input', dest='input', help='Input dataset')
 parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold')
 parser.add_argument('--method', dest='method', help='Protein clustering method')
 parser.add_argument('--classifier', dest='classifier', help='Protein classification method')
@@ -19,7 +18,7 @@
 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
 parser.add_argument('--super_orthogroups', dest='super_orthogroups', default=None, help='Super orthogroups clustering specification')
 parser.add_argument('--single_copy_custom', dest='single_copy_custom', default=None, help='Custom single copy orthogroup configuration')
-parser.add_argument('--single_copy_taxa', dest='single_copy_taxa', type=int, default=0, help='"Minimum single copy taxa required in orthogroup')
+parser.add_argument('--single_copy_taxa', dest='single_copy_taxa', type=int, default=0, help='Minimum single copy taxa required in orthogroup')
 parser.add_argument('--taxa_present', dest='taxa_present', type=int, default=0, help='Minimum taxa required in single copy orthogroup')
 parser.add_argument('--orthogroup_fasta', dest='orthogroup_fasta', default=None, help='Flag to create orthogroup sequences')
 parser.add_argument('--coding_sequences', dest='coding_sequences', default=None, help='Flag to create orthogroup coding sequences')
@@ -34,7 +33,6 @@
 
 args = parser.parse_args()
 
-
 # Build the command line.
 cmd = 'GeneFamilyClassifier'
 cmd += ' --proteins %s' % args.input
@@ -61,10 +59,10 @@
 else:
     create_corresponding_coding_sequences = True
     cmd += ' --coding_sequences %s' % args.coding_sequences
+
 # 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 hmmscan.log output.
 if args.classifier in ['hmmscan', 'both']:
     src_hmmscan_log = os.path.join(OUTPUT_DIR, 'hmmscan.log')
@@ -73,6 +71,7 @@
             os.remove(src_hmmscan_log)
         else:
             shutil.move(src_hmmscan_log, args.hmmscan_log)
+
 # Handle orthogroups outputs.
 if create_ortho_sequences:
     if create_corresponding_coding_sequences:
@@ -86,6 +85,7 @@
     orthogroups_fasta_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_fasta')
     utils.move_directory_files(orthogroups_fasta_src_dir, orthogroups_fasta_dest_dir)
     utils.write_html_output(out_file, title, orthogroups_fasta_dest_dir)
+
 # Handle single copy orthogroup outputs.
 if args.output_ptsco is not None:
     single_copy_fasta_src_dir = os.path.join(OUTPUT_DIR, 'single_copy_fasta')