Mercurial > repos > p.lucas > ssuisserotyping_pipeline

comparison Prepare_Ssuis_serotypingPipeline.py @ 7:07cf23fc69c8 draft default tip

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author p.lucas
date Thu, 08 Aug 2024 08:01:21 +0000
parents 8e5694208b79
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6:76c82b2a43d2 7:07cf23fc69c8
1 #!/usr/bin/python 1 #!/usr/bin/python
2 #-*- coding: utf-8 -*- 2 #-*- coding: utf-8 -*-
3 #Libraries: 3 #Libraries:
4 import os, os.path, argparse, sys, gzip, re 4 import os, os.path, argparse, sys, gzip, re
5 5
6
7
8 ##### MAIN 6 ##### MAIN
9 def __main__(): 7 def __main__():
10 ### Arguments: 8 ### Arguments:
11 parser = argparse.ArgumentParser(description='''Launch Ssuis_serotypingPipeline.pl with correct argument''', epilog="""This script needs few options use -h to see it.""") 9 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') 10 parser.add_argument('--fastq_file', dest='ffile')
11 parser.add_argument('--fastq_file2', dest='ffile2')
14 parser.add_argument('--scoreName', dest='sname') 12 parser.add_argument('--scoreName', dest='sname')
15 parser.add_argument('--output2', dest='o2') 13 parser.add_argument('--output2', dest='o2')
16 parser.add_argument('--output3', dest='o3') 14 parser.add_argument('--output3', dest='o3')
17 parser.add_argument('--output4', dest='o4') 15 parser.add_argument('--output4', dest='o4')
18 parser.add_argument('--output5', dest='o5') 16 parser.add_argument('--output5', dest='o5')
31 parser.add_argument('--reverse', dest='r') 29 parser.add_argument('--reverse', dest='r')
32 30
33 ### Get argument in variable: 31 ### Get argument in variable:
34 options = parser.parse_args() 32 options = parser.parse_args()
35 ffile = options.ffile 33 ffile = options.ffile
34 ffile2 = options.ffile2
36 sname = options.sname 35 sname = options.sname
37 output2 = options.o2 36 output2 = options.o2
38 output3 = options.o3 37 output3 = options.o3
39 output4 = options.o4 38 output4 = options.o4
40 output5 = options.o5 39 output5 = options.o5
64 r = "SINGLE" 63 r = "SINGLE"
65 os.system("cp "+ffile+" "+input_path+"/file_test.fastq") 64 os.system("cp "+ffile+" "+input_path+"/file_test.fastq")
66 65
67 elif ends == "pe": 66 elif ends == "pe":
68 os.system("cp "+ffile+" "+input_path+"/file_test"+f+".fastq") 67 os.system("cp "+ffile+" "+input_path+"/file_test"+f+".fastq")
69 os.system("cp "+ffile+" "+input_path+"/file_test"+r+".fastq") 68 os.system("cp "+ffile2+" "+input_path+"/file_test"+r+".fastq")
70 69
71 if sd is None: 70 if sd is None:
72 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)) 71 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))
73 else: 72 else:
74 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)) 73 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))