--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SeqSero2/scripts/SeqSero2.py	Thu Apr 18 15:18:14 2019 -0400
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+############################################################################
+# Copyright (c) 2014-2015 University of Georgia
+# Developer: Shaokang Zhang, zskzsk@uga.edu
+# All Rights Reserved
+############################################################################
+
+import argparse,os,sys,time,random
+
+def main():
+  parser = argparse.ArgumentParser(usage='SeqSero2.py -i <input_data> [-p <number of threads>] [-b <BWA_algorithm>]\n\nDevelopper: Shaokang Zhang (zskzsk@uga.edu) and Xiangyu Deng (xdeng@uga.edu)\n\nContact email:seqsero@gmail.com')#add "-m <data_type>" in future
+  parser.add_argument("-i",nargs="+", help="<string>: path/to/input_data")
+  parser.add_argument("-b",choices=['sam','mem'],default="mem",help="<string>: 'sam'(bwa samse/sampe), 'mem'(bwa mem),default=mem") 
+  parser.add_argument("-p",default="1",help="<int>: if p>4, only 4 threads will be used for assembly, default=1") 
+  args=parser.parse_args()
+  dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
+  if len(sys.argv)==1:
+    os.system(dirpath+"/SeqSero2.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/H_and_O_and_specific_genes.fasta "+make_dir)
+    #mode_choice=args.m
+    mapping_mode=args.b
+    threads=args.p
+    dataset=args.i
+    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)
+    os.system("python2.7 "+dirpath+"/libs/mapping_and_assembly_hybrid.py H_and_O_and_specific_genes.fasta "+mapping_mode+" "+str(threads)+" "+fnameA+" "+fnameB)
+    os.system("rm H_and_O_and_specific_genes.fasta* *.bam *.sam *.fastq *.fastq.gz *.fq temp.txt *.xml "+fnameA+"*_db* 2> /dev/null")
+    print "Output_directory:",make_dir
+    #print "\n\n\nResult:\n"
+    #os.system("cat Seqsero_result.txt")
+
+if __name__ == '__main__':
+  main()