Mercurial > repos > iss > eurl_vtec_wgs_pt

comparison EURL_VTEC_WGS_PT.py @ 5:fd9093b9368f draft

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planemo upload commit 9af296d380b81335353ebfb8bb6de831e1fbebe1
author iss
date Thu, 19 Oct 2023 20:27:22 +0000
parents 32b5625795ea
children
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4:32b5625795ea 5:fd9093b9368f
119 subprocess.call("(head -n 1 pathotyper_rep_tot_tab && tail -n +2 pathotyper_rep_tot_tab | sort -k 2rn) > " + args.virulotyper, shell=True) 119 subprocess.call("(head -n 1 pathotyper_rep_tot_tab && tail -n +2 pathotyper_rep_tot_tab | sort -k 2rn) > " + args.virulotyper, shell=True)
120 log.write("\n\nViruloTyper\n===========\npatho_typing v1.0\n") 120 log.write("\n\nViruloTyper\n===========\npatho_typing v1.0\n")
121 log.write("parameters: minGeneCoverage=90, minGeneIdentity=90, minGeneDepth=15\n\n") 121 log.write("parameters: minGeneCoverage=90, minGeneIdentity=90, minGeneDepth=15\n\n")
122 log.write(os.popen("cat " + TOOL_DIR + "/data/ViruloTyping_db.txt").read()) 122 log.write(os.popen("cat " + TOOL_DIR + "/data/ViruloTyping_db.txt").read())
123 # SEQUENCETYPER 123 # SEQUENCETYPER
124 subprocess.call("mlst --legacy --scheme ecoli_4 " + args.contigs + " | cut -f3,4,5,6,7,8,9,10 > " + args.mlstsevenloci, shell=True) 124 subprocess.call("mlst --legacy --scheme ecoli_achtman_4 " + args.contigs + " | cut -f3,4,5,6,7,8,9,10 > " + args.mlstsevenloci, shell=True)
125 sequence_typing = openFileAsTable(args.mlstsevenloci) 125 sequence_typing = openFileAsTable(args.mlstsevenloci)
126 log.write("\n\nSequence Typer\n==============\n") 126 log.write("\n\nSequence Typer\n==============\n")
127 log.write(os.popen("mlst -v").read()) 127 log.write(os.popen("mlst -v").read())
128 log.write("\n") 128 log.write("\n")
129 log.write(os.popen("cat " + TOOL_DIR + "/data/SequenceTyping_db.txt").read()) 129 log.write(os.popen("cat " + TOOL_DIR + "/data/SequenceTyping_db.txt").read())