--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SeqSero/SeqSero.py	Wed Dec 06 15:59:29 2017 -0500
@@ -0,0 +1,60 @@
+#!/usr/bin/env python
+
+############################################################################
+# Copyright (c) 2014-2015 University of Georgia
+# All Rights Reserved
+############################################################################
+
+import argparse,os,sys,time,random
+
+def main():
+  parser = argparse.ArgumentParser(usage='SeqSero.py -m <data_type> -i <input_data> [-b <BWA_algorithm>]\n\nDevelopper: Shaokang Zhang (zskzsk@uga.edu) and Xiangyu Deng (xdeng@uga.edu)\n\nContact email:seqsero@gmail.com')
+  parser.add_argument("-m", choices=['1','2','3', '4'],help="<int>: '1'(pair-end reads, interleaved),'2'(pair-end reads, seperated),'3'(single-end reads), '4'(assembly)")
+  parser.add_argument("-i", nargs="+", help="<string>: path/to/input_data")
+  parser.add_argument("-b",choices=['sam','mem','nanopore'],default="sam",help="<string>: 'sam'(bwa samse/sampe), 'mem'(bwa mem), default=sam") 
+  args=parser.parse_args()
+  dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
+  if len(sys.argv)==1:
+    os.system(dirpath+"/SeqSero.py -h")
+  else:
+    request_id = time.strftime("%m_%d_%Y_%H_%M_%S", time.localtime())
+    request_id += str(random.randint(1, 10000000))
+    make_dir="SeqSero_result_"+request_id
+    os.system("mkdir "+make_dir)
+    os.system("cp -rf "+dirpath+"/database "+make_dir)
+    mode_choice=args.m
+    mapping_mode=args.b
+    dataset=args.i
+    if mode_choice=="1":
+      print dataset[0]
+      os.system("cp "+dataset[0]+" "+make_dir)
+      os.chdir(make_dir)
+      os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 1")
+      print "\n\n\nResult:\n"
+      os.system("cat Seqsero_result.txt")
+      os.system("rm "+dataset[0].split("/")[-1])
+    elif mode_choice=="2":
+      os.system("cp "+dataset[0]+" "+make_dir)
+      os.system("cp "+dataset[1]+" "+make_dir)
+      fnameA=dataset[0].split("/")[-1]
+      fnameB=dataset[1].split("/")[-1]
+      os.chdir(make_dir)
+      print "check fastq id and make them in accordance with each other...please wait..."
+      os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+fnameA+" "+mapping_mode+" "+fnameB+" 2")
+      print "\n\n\nResult:\n"
+      os.system("cat Seqsero_result.txt")
+    elif mode_choice=="3":
+      os.system("cp "+dataset[0]+" "+make_dir)
+      os.chdir(make_dir)
+      os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 3")
+      print "\n\n\nResult:\n"
+      os.system("cat Seqsero_result.txt")
+    elif mode_choice=="4":
+      os.system("cp "+dataset[0]+" "+make_dir)
+      os.chdir(make_dir)
+      os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_assemblies.py "+dataset[0].split("/")[-1])
+      print "\n\n\nResult:\n"
+      os.system("cat Seqsero_result.txt")
+
+if __name__ == '__main__':
+  main()