Mercurial > repos > iss > eurl_vtec_wgs_pt
changeset 5:fd9093b9368f draft
planemo upload commit 9af296d380b81335353ebfb8bb6de831e1fbebe1
| author | iss |
|---|---|
| date | Thu, 19 Oct 2023 20:27:22 +0000 |
| parents | 32b5625795ea |
| children | 20ff3dca457f |
| files | EURL_VTEC_WGS_PT.py |
| diffstat | 1 files changed, 1 insertions(+), 1 deletions(-) [+] |
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--- a/EURL_VTEC_WGS_PT.py Thu Oct 19 19:07:24 2023 +0000 +++ b/EURL_VTEC_WGS_PT.py Thu Oct 19 20:27:22 2023 +0000 @@ -121,7 +121,7 @@ log.write("parameters: minGeneCoverage=90, minGeneIdentity=90, minGeneDepth=15\n\n") log.write(os.popen("cat " + TOOL_DIR + "/data/ViruloTyping_db.txt").read()) # SEQUENCETYPER - subprocess.call("mlst --legacy --scheme ecoli_4 " + args.contigs + " | cut -f3,4,5,6,7,8,9,10 > " + args.mlstsevenloci, shell=True) + subprocess.call("mlst --legacy --scheme ecoli_achtman_4 " + args.contigs + " | cut -f3,4,5,6,7,8,9,10 > " + args.mlstsevenloci, shell=True) sequence_typing = openFileAsTable(args.mlstsevenloci) log.write("\n\nSequence Typer\n==============\n") log.write(os.popen("mlst -v").read())