Mercurial > repos > p.lucas > ssuisserotyping_pipeline

comparison Prepare_Ssuis_serotypingPipeline.py @ 4:8e5694208b79 draft

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author p.lucas
date Thu, 08 Aug 2024 07:40:42 +0000
parents f8e542216aea
children 07cf23fc69c8
comparison
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3:f8e542216aea 4:8e5694208b79
55 # Need to clone repo from git : https://github.com/streplab/SsuisSerotyping_pipeline.git 55 # Need to clone repo from git : https://github.com/streplab/SsuisSerotyping_pipeline.git
56 way_pipeline = "/nfs/bin/SsuisSerotyping_pipeline/" 56 way_pipeline = "/nfs/bin/SsuisSerotyping_pipeline/"
57 input_path = os.path.splitext(output2)[0]+"_input_file_test/" 57 input_path = os.path.splitext(output2)[0]+"_input_file_test/"
58 output_path = os.path.splitext(output2)[0]+"_Results/" 58 output_path = os.path.splitext(output2)[0]+"_Results/"
59 os.system("mkdir -p "+input_path) 59 os.system("mkdir -p "+input_path)
60 os.system("cp "+ffile+" "+input_path+"/file_test.fastq")
61 fdir = input_path 60 fdir = input_path
62 61
63 if ends == "se": 62 if ends == "se":
64 f = "SINGLE" 63 f = "SINGLE"
65 r = "SINGLE" 64 r = "SINGLE"
65 os.system("cp "+ffile+" "+input_path+"/file_test.fastq")
66
67 elif ends == "pe":
68 os.system("cp "+ffile+" "+input_path+"/file_test"+f+".fastq")
69 os.system("cp "+ffile+" "+input_path+"/file_test"+r+".fastq")
66 70
67 if sd is None: 71 if sd is None:
68 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)) 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))
69 else: 73 else:
70 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)) 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))