Mercurial > repos > p.lucas > ssuisserotyping_pipeline
changeset 7:07cf23fc69c8 draft default tip
Uploaded
| author | p.lucas |
|---|---|
| date | Thu, 08 Aug 2024 08:01:21 +0000 |
| parents | 76c82b2a43d2 |
| children | |
| files | Prepare_Ssuis_serotypingPipeline.py |
| diffstat | 1 files changed, 3 insertions(+), 4 deletions(-) [+] |
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--- a/Prepare_Ssuis_serotypingPipeline.py Thu Aug 08 08:01:10 2024 +0000 +++ b/Prepare_Ssuis_serotypingPipeline.py Thu Aug 08 08:01:21 2024 +0000 @@ -3,14 +3,12 @@ #Libraries: import os, os.path, argparse, sys, gzip, re - - ##### MAIN def __main__(): ### Arguments: parser = argparse.ArgumentParser(description='''Launch Ssuis_serotypingPipeline.pl with correct argument''', epilog="""This script needs few options use -h to see it.""") - parser.add_argument('--fastq_file', dest='ffile') + parser.add_argument('--fastq_file2', dest='ffile2') parser.add_argument('--scoreName', dest='sname') parser.add_argument('--output2', dest='o2') parser.add_argument('--output3', dest='o3') @@ -33,6 +31,7 @@ ### Get argument in variable: options = parser.parse_args() ffile = options.ffile + ffile2 = options.ffile2 sname = options.sname output2 = options.o2 output3 = options.o3 @@ -66,7 +65,7 @@ elif ends == "pe": os.system("cp "+ffile+" "+input_path+"/file_test"+f+".fastq") - os.system("cp "+ffile+" "+input_path+"/file_test"+r+".fastq") + os.system("cp "+ffile2+" "+input_path+"/file_test"+r+".fastq") if sd is None: 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))