Mercurial > repos > p.lucas > ssuisserotyping_pipeline

comparison Prepare_Ssuis_serotypingPipeline.py @ 1:8164dae8b281 draft

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author p.lucas
date Thu, 09 May 2019 04:14:32 -0400
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0:135510a99b5a 1:8164dae8b281
1 #!/usr/bin/python
2 #-*- coding: utf-8 -*-
3 #Libraries:
4 import os, os.path, argparse, sys, gzip, re
5
6
7
8 ##### MAIN
9 def __main__():
10 ### Arguments:
11 parser = argparse.ArgumentParser(description='''Launch Ssuis_serotypingPipeline.pl with correct argument''', epilog="""This script needs few options use -h to see it.""")
12
13 parser.add_argument('--fastq_file', dest='ffile')
14 parser.add_argument('--scoreName', dest='sname')
15 parser.add_argument('--output2', dest='o2')
16 parser.add_argument('--output3', dest='o3')
17 parser.add_argument('--output4', dest='o4')
18 parser.add_argument('--output5', dest='o5')
19 parser.add_argument('--output6', dest='o6')
20 parser.add_argument('--output7', dest='o7')
21 parser.add_argument('--output8', dest='o8')
22 parser.add_argument('--serotype_db', dest='sd')
23 parser.add_argument('--serotype_definitions', dest='sdef')
24 parser.add_argument('--cps2K', dest='cps')
25 parser.add_argument('--Virulence_db', dest='Vdb')
26 parser.add_argument('--recN_db', dest='recdb')
27 parser.add_argument('--MLST_definitions', dest='MLSTdef')
28 parser.add_argument('--MLST_db', dest='MLSTdb')
29 parser.add_argument('--ends', dest='ends')
30 parser.add_argument('--forward', dest='f')
31 parser.add_argument('--reverse', dest='r')
32
33 ### Get argument in variable:
34 options = parser.parse_args()
35 ffile = options.ffile
36 sname = options.sname
37 output2 = options.o2
38 output3 = options.o3
39 output4 = options.o4
40 output5 = options.o5
41 output6 = options.o6
42 output7 = options.o7
43 output8 = options.o8
44 sd = options.sd
45 sdef = options.sdef
46 cps = options.cps
47 Vdb = options.Vdb
48 recdb = options.recdb
49 MLSTdef = options.MLSTdef
50 MLSTdb = options.MLSTdb
51 ends = options.ends
52 f = options.f
53 r = options.r
54
55 way_pipeline = "/results/anses/bin/SsuisSerotyping_pipeline/"
56 input_path = os.path.splitext(output2)[0]+"_input_file_test/"
57 output_path = os.path.splitext(output2)[0]+"_Results/"
58 os.system("mkdir -p "+input_path)
59 os.system("cp "+ffile+" "+input_path+"/file_test.fastq")
60 fdir = input_path
61
62 if ends == "se":
63 f = "SINGLE"
64 r = "SINGLE"
65
66 if sd is None:
67 os.system("perl "+way_pipeline+"/Ssuis_serotypingPipeline.pl --fastq_directory "+str(fdir)+" --scoreName "+output_path+"Results --ends "+str(ends)+" --forward "+str(f)+" --reverse "+str(r))
68 else:
69 os.system("perl "+way_pipeline+"/Ssuis_serotypingPipeline.pl --fastq_directory "+str(fdir)+" --scoreName "+output_path+"Results --serotype_db "+str(sd)+" --serotype_definitions "+str(sdef)+" --cps2K "+str(cps)+" --Virulence_db "+str(Vdb)+" --recN_db "+str(recdb)+" --MLST_definitions "+str(MLSTdef)+" --MLST_db "+str(MLSTdb)+" --ends "+str(ends)+" --forward "+str(f)+" --reverse "+str(r))
70
71 os.system("rm -r "+fdir)
72 os.system("mv "+output_path+"/Results_FinalResults.txt "+sname)
73 os.system("mv "+output_path+"/Results_MLSTResults.txt "+output2)
74 os.system("mv "+output_path+"/Results_recN__fullgenes__recN_full__results.txt "+output3)
75 os.system("mv "+output_path+"/Results_speciesConfirmation.txt "+output4)
76 os.system("mv "+output_path+"/Results_FinalSerotypingResults.txt "+output5)
77 os.system("mv "+output_path+"/Results_InitialCapsuleResults.txt "+output6)
78 os.system("mv "+output_path+"/Results_VirulenceFactors__fullgenes__Virulence__results.txt "+output7)
79 os.system("mv "+output_path+"/Results_VirulenceFactorResults.txt "+output8)
80 #### MAIN END
81 if __name__ == "__main__": __main__()
82