--- a/multigps.py	Tue Jan 05 08:19:30 2016 -0500
+++ b/multigps.py	Tue Jan 05 08:19:39 2016 -0500
@@ -1,4 +1,4 @@
-import optparse
+import argparse
 import os
 import shutil
 import subprocess
@@ -57,119 +57,119 @@
     sys.stderr.write(msg)
     sys.exit(1)
 
-parser = optparse.OptionParser()
-parser.add_option('--input_item', dest='input_items', action='append', nargs=7, help="Input datasets and associated parameters")
-parser.add_option('--threads', dest='threads', type="int", default=4, help='The number of threads to run')
-parser.add_option('--multigps_jar', dest='multigps_jar', help='Path to the MultiGPS jar file')
-parser.add_option('--geninfo', dest='geninfo', help='File listing the lengths of all chromosomes')
-parser.add_option('--use_motif', dest='use_motif', help='Perform motif-finding or use a motif-prior')
-parser.add_option('--seq_dir', dest='seq_dir', default=None, help='Directory containing fasta files corresponding to every named chromosome')
-parser.add_option('--positional_prior', dest='positional_prior', default=None, help='Perform inter-experiment positional prior')
-parser.add_option('--events_shared_probability', dest='events_shared_probability', type=float, default=0.9, help='Probability that events are shared across conditions')
-parser.add_option('--motifs', dest='motifs', default=None, help='Perform motif-finding and motif priors')
-parser.add_option('--motif_finding_only', dest='motif_finding_only', default=None, help='Perform motif-finding only')
-parser.add_option('--num_motifs', dest='num_motifs', type="int", default=None, help='Number of motifs MEME should find for each condition')
-parser.add_option('--mememinw', dest='mememinw', type="int", default=None, help='Minimum motif width for MEME')
-parser.add_option('--mememaxw', dest='mememaxw', type="int", default=None, help='Maximum motif width for MEME')
-parser.add_option('--fixedpb', dest='fixedpb', type="int", default=None, help='Fixed per-base limit')
-parser.add_option('--poissongausspb', dest='poissongausspb', type="int", default=None, help='Poisson threshold for filtering per base')
-parser.add_option('--non_unique_reads', dest='non_unique_reads', default=None, help='Use non-unique reads')
-parser.add_option('--minqvalue', dest='minqvalue', type="int", default=None, help='Minimum Q-value (corrected p-value) of reported binding events')
-parser.add_option('--minfold', dest='minfold', type="int", default=None, help='Minimum event fold-change vs scaled control')
-parser.add_option('--diff_enrichment_tests', dest='diff_enrichment_tests', help='Run differential enrichment tests')
-parser.add_option('--edgerod', dest='edgerod', type="int", default=None, help='EdgeR over-dispersion parameter value')
-parser.add_option('--diffp', dest='diffp', type="int", default=None, help='Minimum p-value for reporting differential enrichment')
-parser.add_option('--noscaling', dest='noscaling', default=None, help='Do not use signal vs control scaling')
-parser.add_option('--medianscale', dest='medianscale', default=None, help='Use the median signal/control ratio as the scaling factor')
-parser.add_option('--sesscale', dest='sesscale', default=None, help='Estimate scaling factor by SES')
-parser.add_option('--scalewin', dest='scalewin', type="int", default=None, help='Window size for estimating scaling ratios')
-parser.add_option('--max_training_rounds', dest='max_training_rounds', type="int", default=None, help='Maximum number of training rounds for updating binding event read distributions')
-parser.add_option('--exclude_file', dest='exclude_file', default=None, help='File containing a set of regions to ignore during MultiGPS training')
-parser.add_option('--binding_model_updates', dest='binding_model_updates', default=None, help='Perform binding model updates')
-parser.add_option('--minmodelupdateevents', dest='minmodelupdateevents', type="int", default=None, help='Minimum number of events to support an update of the read distribution')
-parser.add_option('--binding_model_smoothing', dest='binding_model_smoothing', default=None, help='Binding model smoothing')
-parser.add_option('--spline_smooth', dest='spline_smooth', type="int", default=None, help='Binding model smoothing value')
-parser.add_option('--gauss_smooth', dest='gauss_smooth', type="int", default=None, help='Gaussian smoothing std dev')
-parser.add_option('--joint_in_model', dest='joint_in_model', default=None, help='Allow joint events in model updates')
-parser.add_option('--ml_config_not_shared', dest='ml_config_not_shared', default=None, help='Share component configs in the ML step')
-parser.add_option('--output_html_path', dest='output_html_path', help='Output html results file')
-parser.add_option('--output_html_files_path', dest='output_html_files_path', help='Output html extra files')
-parser.add_option('--output_process_path', dest='output_process_path', default=None, help='Output file for capturing stdout')
-options, args = parser.parse_args()
+parser = argparse.ArgumentParser()
+parser.add_argument('--input_item', dest='input_items', action='append', nargs=7, help="Input datasets and associated parameters")
+parser.add_argument('--threads', dest='threads', type=int, default=4, help='The number of threads to run')
+parser.add_argument('--multigps_jar', dest='multigps_jar', help='Path to the MultiGPS jar file')
+parser.add_argument('--geninfo', dest='geninfo', help='File listing the lengths of all chromosomes')
+parser.add_argument('--use_motif', dest='use_motif', help='Perform motif-finding or use a motif-prior')
+parser.add_argument('--seq_dir', dest='seq_dir', default=None, help='Directory containing fasta files corresponding to every named chromosome')
+parser.add_argument('--positional_prior', dest='positional_prior', default=None, help='Perform inter-experiment positional prior')
+parser.add_argument('--events_shared_probability', dest='events_shared_probability', type=float, default=0.9, help='Probability that events are shared across conditions')
+parser.add_argument('--motifs', dest='motifs', default=None, help='Perform motif-finding and motif priors')
+parser.add_argument('--motif_finding_only', dest='motif_finding_only', default=None, help='Perform motif-finding only')
+parser.add_argument('--num_motifs', dest='num_motifs', type=int, default=None, help='Number of motifs MEME should find for each condition')
+parser.add_argument('--mememinw', dest='mememinw', type=int, default=None, help='Minimum motif width for MEME')
+parser.add_argument('--mememaxw', dest='mememaxw', type=int, default=None, help='Maximum motif width for MEME')
+parser.add_argument('--fixedpb', dest='fixedpb', type=int, default=None, help='Fixed per-base limit')
+parser.add_argument('--poissongausspb', dest='poissongausspb', type=int, default=None, help='Poisson threshold for filtering per base')
+parser.add_argument('--non_unique_reads', dest='non_unique_reads', default=None, help='Use non-unique reads')
+parser.add_argument('--minqvalue', dest='minqvalue', type=int, default=None, help='Minimum Q-value (corrected p-value) of reported binding events')
+parser.add_argument('--minfold', dest='minfold', type=int, default=None, help='Minimum event fold-change vs scaled control')
+parser.add_argument('--diff_enrichment_tests', dest='diff_enrichment_tests', help='Run differential enrichment tests')
+parser.add_argument('--edgerod', dest='edgerod', type=int, default=None, help='EdgeR over-dispersion parameter value')
+parser.add_argument('--diffp', dest='diffp', type=int, default=None, help='Minimum p-value for reporting differential enrichment')
+parser.add_argument('--noscaling', dest='noscaling', default=None, help='Do not use signal vs control scaling')
+parser.add_argument('--medianscale', dest='medianscale', default=None, help='Use the median signal/control ratio as the scaling factor')
+parser.add_argument('--sesscale', dest='sesscale', default=None, help='Estimate scaling factor by SES')
+parser.add_argument('--scalewin', dest='scalewin', type=int, default=None, help='Window size for estimating scaling ratios')
+parser.add_argument('--max_training_rounds', dest='max_training_rounds', type=int, default=None, help='Maximum number of training rounds for updating binding event read distributions')
+parser.add_argument('--exclude_file', dest='exclude_file', default=None, help='File containing a set of regions to ignore during MultiGPS training')
+parser.add_argument('--binding_model_updates', dest='binding_model_updates', default=None, help='Perform binding model updates')
+parser.add_argument('--minmodelupdateevents', dest='minmodelupdateevents', type=int, default=None, help='Minimum number of events to support an update of the read distribution')
+parser.add_argument('--binding_model_smoothing', dest='binding_model_smoothing', default=None, help='Binding model smoothing')
+parser.add_argument('--spline_smooth', dest='spline_smooth', type=int, default=None, help='Binding model smoothing value')
+parser.add_argument('--gauss_smooth', dest='gauss_smooth', type=int, default=None, help='Gaussian smoothing std dev')
+parser.add_argument('--joint_in_model', dest='joint_in_model', default=None, help='Allow joint events in model updates')
+parser.add_argument('--ml_config_not_shared', dest='ml_config_not_shared', default=None, help='Share component configs in the ML step')
+parser.add_argument('--output_html_path', dest='output_html_path', help='Output html results file')
+parser.add_argument('--output_html_files_path', dest='output_html_files_path', help='Output html extra files')
+parser.add_argument('--output_process_path', dest='output_process_path', default=None, help='Output file for capturing stdout')
+args = parser.parse_args()
 
 try:
     # Preparation.
     tmp_dir = tempfile.mkdtemp(prefix="tmp-multigps-")
-    generate_design_file(options.input_items, DESIGN_FILE)
+    generate_design_file(args.input_items, DESIGN_FILE)
     # Build the command line.
-    cmd_list = ['java -jar %s --verbose' % options.multigps_jar]
-    cmd_list.append('--threads %d' % options.threads)
-    cmd_list.append('--geninfo %s' % options.geninfo)
-    if options.use_motif == 'yes':
-        cmd_list.append('--seq %s' % options.seq_dir)
-        if options.positional_prior == 'no':
+    cmd_list = ['java -jar %s --verbose' % args.multigps_jar]
+    cmd_list.append('--threads %d' % args.threads)
+    cmd_list.append('--geninfo %s' % args.geninfo)
+    if args.use_motif == 'yes':
+        cmd_list.append('--seq %s' % args.seq_dir)
+        if args.positional_prior == 'no':
             cmd_list.append('--noposprior')
-        cmd_list.append('--probshared %3f' % options.events_shared_probability)
-        if options.motifs == 'no':
+        cmd_list.append('--probshared %3f' % args.events_shared_probability)
+        if args.motifs == 'no':
             cmd_list.append('--nomotifs')
-        if options.motif_finding_only == 'yes':
+        if args.motif_finding_only == 'yes':
             cmd_list.append('--nomotifprior')
-        if options.num_motifs is not None:
-            cmd_list.append('--memenmotifs %d' % options.num_motifs)
-        if options.mememinw is not None:
-            cmd_list.append('--mememinw %d' % options.mememinw)
-        if options.mememaxw is not None:
-            cmd_list.append('--mememaxw %d' % options.mememaxw)
-    if options.fixedpb is not None:
-        cmd_list.append('--fixedpb %d' % options.fixedpb)
-    if options.poissongausspb is not None:
-        cmd_list.append('--poissongausspb %d' % options.poissongausspb)
-    if options.non_unique_reads == 'yes':
+        if args.num_motifs is not None:
+            cmd_list.append('--memenmotifs %d' % args.num_motifs)
+        if args.mememinw is not None:
+            cmd_list.append('--mememinw %d' % args.mememinw)
+        if args.mememaxw is not None:
+            cmd_list.append('--mememaxw %d' % args.mememaxw)
+    if args.fixedpb is not None:
+        cmd_list.append('--fixedpb %d' % args.fixedpb)
+    if args.poissongausspb is not None:
+        cmd_list.append('--poissongausspb %d' % args.poissongausspb)
+    if args.non_unique_reads == 'yes':
         cmd_list.append('--nonunique')
-    if options.minqvalue is not None:
-        cmd_list.append('--q %d' % options.minqvalue)
-    if options.minfold is not None:
-        cmd_list.append('--minfold %d' % options.minfold)
-    if options.diff_enrichment_tests == 'no':
+    if args.minqvalue is not None:
+        cmd_list.append('--q %d' % args.minqvalue)
+    if args.minfold is not None:
+        cmd_list.append('--minfold %d' % args.minfold)
+    if args.diff_enrichment_tests == 'no':
         cmd_list.append('--nodifftests')
-    if options.edgerod is not None:
-        cmd_list.append('--edgerod %d' % options.edgerod)
-    if options.diffp is not None:
-        cmd_list.append('--diffp %d' % options.diffp)
-    if options.noscaling == 'no':
+    if args.edgerod is not None:
+        cmd_list.append('--edgerod %d' % args.edgerod)
+    if args.diffp is not None:
+        cmd_list.append('--diffp %d' % args.diffp)
+    if args.noscaling == 'no':
         cmd_list.append('--noscaling')
-    if options.medianscale == "yes":
+    if args.medianscale == "yes":
         cmd_list.append('--medianscale')
-    if options.sesscale == "yes":
+    if args.sesscale == "yes":
         cmd_list.append('--sesscale')
-    if options.scalewin is not None:
-        cmd_list.append('--scalewin %d' % options.scalewin)
-    if options.max_training_rounds is not None:
-        cmd_list.append('--r %d' % options.max_training_rounds)
-    if options.exclude_file not in [None, 'None']:
-        cmd_list.append('--exclude %s' % options.exclude_file)
-    if options.binding_model_updates == 'no':
+    if args.scalewin is not None:
+        cmd_list.append('--scalewin %d' % args.scalewin)
+    if args.max_training_rounds is not None:
+        cmd_list.append('--r %d' % args.max_training_rounds)
+    if args.exclude_file not in [None, 'None']:
+        cmd_list.append('--exclude %s' % args.exclude_file)
+    if args.binding_model_updates == 'no':
         cmd_list.append('--nomodelupdate')
-    if options.minmodelupdateevents is not None:
-        cmd_list.append('--minmodelupdateevents %d' % options.minmodelupdateevents)
-    if options.binding_model_smoothing == 'yes':
-        if options.spline_smooth is not None:
-            cmd_list.append('--splinesmoothparam %d' % options.spline_smooth)
+    if args.minmodelupdateevents is not None:
+        cmd_list.append('--minmodelupdateevents %d' % args.minmodelupdateevents)
+    if args.binding_model_smoothing == 'yes':
+        if args.spline_smooth is not None:
+            cmd_list.append('--splinesmoothparam %d' % args.spline_smooth)
     else:
         cmd_list.append('--nomodelsmoothing')
-        if options.gauss_smooth is not None:
+        if args.gauss_smooth is not None:
             cmd_list.append('--gaussmodelsmoothing')
-            cmd_list.append('--gausssmoothparam %d' % options.gauss_smooth)
-    if options.joint_in_model == 'yes':
+            cmd_list.append('--gausssmoothparam %d' % args.gauss_smooth)
+    if args.joint_in_model == 'yes':
         cmd_list.append('--jointinmodel')
-    if options.ml_config_not_shared == 'no':
+    if args.ml_config_not_shared == 'no':
         cmd_list.append('--mlconfignotshared')
     cmd_list.append('--design %s' % DESIGN_FILE)
-    cmd_list.append('--out %s' % options.output_html_files_path)
-    if options.output_process_path is None:
+    cmd_list.append('--out %s' % args.output_html_files_path)
+    if args.output_process_path is None:
         cmd_list.append('2>/dev/null')
     else:
-        cmd_list.append('2>%s' % options.output_process_path)
+        cmd_list.append('2>%s' % args.output_process_path)
     cmd = ' '.join(cmd_list)
     # Define command response buffers.
     tmp_out = tempfile.NamedTemporaryFile(dir=tmp_dir).name
@@ -184,8 +184,8 @@
         error_message = get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout)
         stop_err(error_message)
     # Move the output HTML file to the output dataset path.
-    output_html_filename = 'multiGPS_%s_results.html' % os.path.split(options.output_html_files_path)[1]
-    shutil.move(os.path.join(options.output_html_files_path, output_html_filename), options.output_html_path)
+    output_html_filename = 'multiGPS_%s_results.html' % os.path.split(args.output_html_files_path)[1]
+    shutil.move(os.path.join(args.output_html_files_path, output_html_filename), args.output_html_path)
 except Exception, e:
     stop_err('Error running MultiGPS\n%s\n' % str(e))
 finally: