--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cnv-sim.py	Sat Aug 06 15:29:48 2016 -0400
@@ -0,0 +1,79 @@
+#!/usr/bin/python
+
+__author__ = 'Abdelrahman Hosny'
+
+import os.path
+import datetime
+import argparse
+import shutil
+
+from cnvsim.fileio import *
+from cnvsim.exome_simulator import *
+from cnvsim.genome_simulator import *
+
+def log(message):
+    print '[CNV SIM {:%Y-%m-%d %H:%M:%S}'.format(datetime.datetime.now()) + "] " + message
+
+def main():
+    parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument("simulation_type", type=str, choices=['genome', 'exome'], \
+                        help="simulate copy number variations in whole genome or exome regions")
+    parser.add_argument("genome", type=file, \
+                        help="path to the referece genome file in FASTA format ")
+    parser.add_argument("target", type=file, nargs='?', default=None, \
+                        help="path to the target regions file in BED format (if using exome)")
+
+    parser.add_argument("-o", "--output_dir_name",type=str, default="test", \
+                        help="a name to be used to create the output directory (overrides existing directory with the same name).")
+    parser.add_argument("-n", "--n_reads", type=int, default=10000, \
+                        help="total number of reads without variations")
+    parser.add_argument("-l", "--read_length", type=int, default=100, \
+                        help="read length (bp)")
+    parser.add_argument("--cnv_list", type=file, default=None, \
+                        help="path to a CNV list file in BED format chr | start | end | variation. If not passed, it is randomly generated using CNV list parameters below")
+
+    cnv_sim_group = parser.add_argument_group('CNV list parameters', "parameters to be used if CNV list is not passed")
+    cnv_sim_group.add_argument("-g", "--regions_count", type=int, default=30, \
+                        help="number of CNV regions to be randomly generated")
+    cnv_sim_group.add_argument("-a", "--amplifications", type=float, default=0.30, \
+                        help="percentage of amplifications in range [0.0: 1.0].")
+    cnv_sim_group.add_argument("-d", "--deletions", type=float, default=0.20, \
+                        help="percentage of deletions in range [0.0: 1.0].")
+    cnv_sim_group.add_argument("-min", "--minimum", type=float, default=3, \
+                        help="minimum number of amplifications/deletions introduced")
+    cnv_sim_group.add_argument("-max", "--maximum", type=float, default=10, \
+                        help="maximum number of amplifications/deletions introduced")
+
+    args = parser.parse_args()
+
+    simulation_parameters = {}
+    simulation_parameters['type'] = args.simulation_type
+    simulation_parameters['genome_file'] = args.genome.name
+    if args.target is not None:
+        simulation_parameters['target_file'] = args.target.name
+    else:
+        simulation_parameters['target_file'] = None
+    simulation_parameters['output_dir'] = os.path.join(os.getcwd(), args.output_dir_name)
+    simulation_parameters['number_of_reads'] = args.n_reads
+    simulation_parameters['read_length'] = args.read_length
+    if args.cnv_list is not None:
+        simulation_parameters['cnv_list_file'] = args.cnv_list.name
+    else:
+        simulation_parameters['cnv_list_file'] = None
+    simulation_parameters['tmp_dir'] = os.path.join(os.getcwd(), args.output_dir_name , "tmp")
+
+    cnv_list_parameters = {}
+    cnv_list_parameters['regions_count'] = args.regions_count
+    cnv_list_parameters['amplifications'] = args.amplifications
+    cnv_list_parameters['deletions'] = args.deletions
+    cnv_list_parameters['minimum_variations'] = args.minimum
+    cnv_list_parameters['maximum_variations'] = args.maximum
+
+    if simulation_parameters['type'] == 'genome':
+        simulate_genome_cnv(simulation_parameters, cnv_list_parameters)
+    else:
+        simulate_exome_cnv(simulation_parameters, cnv_list_parameters)
+
+
+if __name__ == '__main__':
+    main()
\ No newline at end of file