Mercurial > repos > p.lucas > ssuisserotyping_pipeline

comparison Prepare_Ssuis_serotypingPipeline.py @ 3:f8e542216aea draft

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author p.lucas
date Thu, 08 Aug 2024 07:30:38 +0000
parents b4f2c9e7300b
children 8e5694208b79
comparison
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2:fc142f5cb6f1 3:f8e542216aea
50 MLSTdb = options.MLSTdb 50 MLSTdb = options.MLSTdb
51 ends = options.ends 51 ends = options.ends
52 f = options.f 52 f = options.f
53 r = options.r 53 r = options.r
54 54
55 way_pipeline = "/results/anses/bin/SsuisSerotyping_pipeline/" 55 # Need to clone repo from git : https://github.com/streplab/SsuisSerotyping_pipeline.git
56 way_pipeline = "/nfs/bin/SsuisSerotyping_pipeline/"
56 input_path = os.path.splitext(output2)[0]+"_input_file_test/" 57 input_path = os.path.splitext(output2)[0]+"_input_file_test/"
57 output_path = os.path.splitext(output2)[0]+"_Results/" 58 output_path = os.path.splitext(output2)[0]+"_Results/"
58 os.system("mkdir -p "+input_path) 59 os.system("mkdir -p "+input_path)
59 os.system("cp "+ffile+" "+input_path+"/file_test.fastq") 60 os.system("cp "+ffile+" "+input_path+"/file_test.fastq")
60 fdir = input_path 61 fdir = input_path