Mercurial > repos > estrain > seqsero_v1

comparison SeqSero/SeqSero.py @ 0:c577b57b7c74 draft

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author estrain
date Wed, 06 Dec 2017 15:59:29 -0500
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-1:000000000000 0:c577b57b7c74
1 #!/usr/bin/env python
2
3 ############################################################################
4 # Copyright (c) 2014-2015 University of Georgia
5 # All Rights Reserved
6 ############################################################################
7
8 import argparse,os,sys,time,random
9
10 def main():
11 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')
12 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)")
13 parser.add_argument("-i", nargs="+", help="<string>: path/to/input_data")
14 parser.add_argument("-b",choices=['sam','mem','nanopore'],default="sam",help="<string>: 'sam'(bwa samse/sampe), 'mem'(bwa mem), default=sam")
15 args=parser.parse_args()
16 dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
17 if len(sys.argv)==1:
18 os.system(dirpath+"/SeqSero.py -h")
19 else:
20 request_id = time.strftime("%m_%d_%Y_%H_%M_%S", time.localtime())
21 request_id += str(random.randint(1, 10000000))
22 make_dir="SeqSero_result_"+request_id
23 os.system("mkdir "+make_dir)
24 os.system("cp -rf "+dirpath+"/database "+make_dir)
25 mode_choice=args.m
26 mapping_mode=args.b
27 dataset=args.i
28 if mode_choice=="1":
29 print dataset[0]
30 os.system("cp "+dataset[0]+" "+make_dir)
31 os.chdir(make_dir)
32 os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 1")
33 print "\n\n\nResult:\n"
34 os.system("cat Seqsero_result.txt")
35 os.system("rm "+dataset[0].split("/")[-1])
36 elif mode_choice=="2":
37 os.system("cp "+dataset[0]+" "+make_dir)
38 os.system("cp "+dataset[1]+" "+make_dir)
39 fnameA=dataset[0].split("/")[-1]
40 fnameB=dataset[1].split("/")[-1]
41 os.chdir(make_dir)
42 print "check fastq id and make them in accordance with each other...please wait..."
43 os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+fnameA+" "+mapping_mode+" "+fnameB+" 2")
44 print "\n\n\nResult:\n"
45 os.system("cat Seqsero_result.txt")
46 elif mode_choice=="3":
47 os.system("cp "+dataset[0]+" "+make_dir)
48 os.chdir(make_dir)
49 os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 3")
50 print "\n\n\nResult:\n"
51 os.system("cat Seqsero_result.txt")
52 elif mode_choice=="4":
53 os.system("cp "+dataset[0]+" "+make_dir)
54 os.chdir(make_dir)
55 os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_assemblies.py "+dataset[0].split("/")[-1])
56 print "\n\n\nResult:\n"
57 os.system("cat Seqsero_result.txt")
58
59 if __name__ == '__main__':
60 main()