jpayne@0: #!/usr/bin/env python
jpayne@0: 
jpayne@0: ############################################################################
jpayne@0: # Copyright (c) 2014-2015 University of Georgia
jpayne@0: # Developer: Shaokang Zhang, zskzsk@uga.edu
jpayne@0: # All Rights Reserved
jpayne@0: ############################################################################
jpayne@0: 
jpayne@0: import argparse,os,sys,time,random
jpayne@0: 
jpayne@0: def main():
jpayne@0:   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
jpayne@0:   parser.add_argument("-i",nargs="+", help="<string>: path/to/input_data")
jpayne@0:   parser.add_argument("-b",choices=['sam','mem'],default="mem",help="<string>: 'sam'(bwa samse/sampe), 'mem'(bwa mem),default=mem") 
jpayne@0:   parser.add_argument("-p",default="1",help="<int>: if p>4, only 4 threads will be used for assembly, default=1") 
jpayne@0:   args=parser.parse_args()
jpayne@0:   dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
jpayne@0:   if len(sys.argv)==1:
jpayne@0:     os.system(dirpath+"/SeqSero2.py -h")
jpayne@0:   else:
jpayne@0:     request_id = time.strftime("%m_%d_%Y_%H_%M_%S", time.localtime())
jpayne@0:     request_id += str(random.randint(1, 10000000))
jpayne@0:     make_dir="SeqSero_result_"+request_id
jpayne@0:     os.system("mkdir "+make_dir)
jpayne@0:     os.system("cp -rf "+dirpath+"/database/H_and_O_and_specific_genes.fasta "+make_dir)
jpayne@0:     #mode_choice=args.m
jpayne@0:     mapping_mode=args.b
jpayne@0:     threads=args.p
jpayne@0:     dataset=args.i
jpayne@0:     os.system("cp "+dataset[0]+" "+make_dir)
jpayne@0:    # print len(dataset)
jpayne@0:     os.system("cp "+dataset[1]+" "+make_dir)
jpayne@0:     fnameA=dataset[0].split("/")[-1]
jpayne@0:     fnameB=dataset[1].split("/")[-1]
jpayne@0:     os.chdir(make_dir)
jpayne@0:     os.system("python2.7 "+dirpath+"/libs/mapping_and_assembly_hybrid.py H_and_O_and_specific_genes.fasta "+mapping_mode+" "+str(threads)+" "+fnameA+" "+fnameB)
jpayne@0:     os.system("rm H_and_O_and_specific_genes.fasta* *.bam *.sam *.fastq *.fastq.gz *.fq temp.txt *.xml "+fnameA+"*_db* 2> /dev/null")
jpayne@0:     #print "Output_directory:",make_dir
jpayne@0:     #print "\n\n\nResult:\n"
jpayne@0:     #os.system("cat Seqsero_result.txt")
jpayne@0: 
jpayne@0: if __name__ == '__main__':
jpayne@0:   main()