Mercurial > repos > charles_s_test > seqsero2

comparison SeqSero.py @ 7:3d6680af0bec draft

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planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author charles_s_test
date Mon, 27 Nov 2017 16:30:27 -0500
parents 6895de35a263
children 53efef402c51
comparison
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6:b6281a377a18 7:3d6680af0bec
24 os.system("cp -rf "+dirpath+"/database "+make_dir) 24 os.system("cp -rf "+dirpath+"/database "+make_dir)
25 mode_choice=args.m 25 mode_choice=args.m
26 mapping_mode=args.b 26 mapping_mode=args.b
27 dataset=args.i 27 dataset=args.i
28 if mode_choice=="1": 28 if mode_choice=="1":
29 print dataset[0] 29 print(dataset[0])
30 os.system("cp "+dataset[0]+" "+make_dir) 30 os.system("cp "+dataset[0]+" "+make_dir)
31 os.chdir(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") 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" 33 print("\n\n\nResult:\n")
34 os.system("cat Seqsero_result.txt") 34 os.system("cat Seqsero_result.txt")
35 os.system("rm "+dataset[0].split("/")[-1]) 35 os.system("rm "+dataset[0].split("/")[-1])
36 elif mode_choice=="2": 36 elif mode_choice=="2":
37 os.system("cp "+dataset[0]+" "+make_dir) 37 os.system("cp "+dataset[0]+" "+make_dir)
38 os.system("cp "+dataset[1]+" "+make_dir) 38 os.system("cp "+dataset[1]+" "+make_dir)
39 fnameA=dataset[0].split("/")[-1] 39 fnameA=dataset[0].split("/")[-1]
40 fnameB=dataset[1].split("/")[-1] 40 fnameB=dataset[1].split("/")[-1]
41 os.chdir(make_dir) 41 os.chdir(make_dir)
42 print "check fastq id and make them in accordance with each other...please wait..." 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") 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" 44 print("\n\n\nResult:\n")
45 os.system("cat Seqsero_result.txt") 45 os.system("cat Seqsero_result.txt")
46 elif mode_choice=="3": 46 elif mode_choice=="3":
47 os.system("cp "+dataset[0]+" "+make_dir) 47 os.system("cp "+dataset[0]+" "+make_dir)
48 os.chdir(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") 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" 50 print("\n\n\nResult:\n")
51 os.system("cat Seqsero_result.txt") 51 os.system("cat Seqsero_result.txt")
52 elif mode_choice=="4": 52 elif mode_choice=="4":
53 os.system("cp "+dataset[0]+" "+make_dir) 53 os.system("cp "+dataset[0]+" "+make_dir)
54 os.chdir(make_dir) 54 os.chdir(make_dir)
55 os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_assemblies.py "+dataset[0].split("/")[-1]) 55 os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_assemblies.py "+dataset[0].split("/")[-1])
56 print "\n\n\nResult:\n" 56 print("\n\n\nResult:\n")
57 os.system("cat Seqsero_result.txt") 57 os.system("cat Seqsero_result.txt")
58 58
59 if __name__ == '__main__': 59 if __name__ == '__main__':
60 main() 60 main()