Mercurial > repos > iss > eurl_vtec_wgs_pt
diff EURL_VTEC_WGS_PT.py @ 4:32b5625795ea draft
planemo upload commit 906fafe94520fdbabb0fb94cdbe93ffeab43867a
| author | iss |
|---|---|
| date | Thu, 19 Oct 2023 19:07:24 +0000 |
| parents | 444b0421bbdc |
| children | fd9093b9368f |
line wrap: on
line diff
--- a/EURL_VTEC_WGS_PT.py Thu Oct 19 12:31:29 2023 +0000 +++ b/EURL_VTEC_WGS_PT.py Thu Oct 19 19:07:24 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 " + args.contigs + " | cut -f3,4,5,6,7,8,9,10 > " + args.mlstsevenloci, shell=True) + subprocess.call("mlst --legacy --scheme ecoli_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()) @@ -204,14 +204,14 @@ report.write("</p>\n") if args.virulotyping: subprocess.call("sort " + args.virulotyper + " | awk '/eae_|stx1._|stx2._|ehxa_/ && $2>50 && !seen[substr($1, 1, index($1, \"_\")-2)]++ { printf(\"%s%s\",sep,substr($1, 1, index($1, \"_\")-1));sep=\", \" }END{print \"\"}' > virulotyper_rep", shell=True) - for line in fileinput.input("virulotyper_rep", inplace=True): - print(line.replace("1a", "1"),) - for line in fileinput.input("virulotyper_rep", inplace=True): - print(line.replace("2a", "2"),) - for line in fileinput.input("virulotyper_rep", inplace=True): - print(line.replace("1b", "1"),) - for line in fileinput.input("virulotyper_rep", inplace=True): - print(line.replace("2b", "2"),) + # for line in fileinput.input("virulotyper_rep", inplace=True): + # print(line.replace("1a", "1"),) + # for line in fileinput.input("virulotyper_rep", inplace=True): + # print(line.replace("2a", "2"),) + # for line in fileinput.input("virulotyper_rep", inplace=True): + # print(line.replace("1b", "1"),) + # for line in fileinput.input("virulotyper_rep", inplace=True): + # print(line.replace("2b", "2"),) report.write("<p>Virulotypes: ") insertFile("virulotyper_rep", report) report.write("</p>\n")