Mercurial > repos > iss > eurl_vtec_wgs_pt
comparison 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 |
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| 3:0506503db01d | 4:32b5625795ea |
|---|---|
| 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 " + args.contigs + " | cut -f3,4,5,6,7,8,9,10 > " + args.mlstsevenloci, shell=True) | 124 subprocess.call("mlst --legacy --scheme ecoli_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()) |
| 202 else: | 202 else: |
| 203 report.write("ST%s" % sequence_typing[1][0]) | 203 report.write("ST%s" % sequence_typing[1][0]) |
| 204 report.write("</p>\n") | 204 report.write("</p>\n") |
| 205 if args.virulotyping: | 205 if args.virulotyping: |
| 206 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) | 206 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) |
| 207 for line in fileinput.input("virulotyper_rep", inplace=True): | 207 # for line in fileinput.input("virulotyper_rep", inplace=True): |
| 208 print(line.replace("1a", "1"),) | 208 # print(line.replace("1a", "1"),) |
| 209 for line in fileinput.input("virulotyper_rep", inplace=True): | 209 # for line in fileinput.input("virulotyper_rep", inplace=True): |
| 210 print(line.replace("2a", "2"),) | 210 # print(line.replace("2a", "2"),) |
| 211 for line in fileinput.input("virulotyper_rep", inplace=True): | 211 # for line in fileinput.input("virulotyper_rep", inplace=True): |
| 212 print(line.replace("1b", "1"),) | 212 # print(line.replace("1b", "1"),) |
| 213 for line in fileinput.input("virulotyper_rep", inplace=True): | 213 # for line in fileinput.input("virulotyper_rep", inplace=True): |
| 214 print(line.replace("2b", "2"),) | 214 # print(line.replace("2b", "2"),) |
| 215 report.write("<p>Virulotypes: ") | 215 report.write("<p>Virulotypes: ") |
| 216 insertFile("virulotyper_rep", report) | 216 insertFile("virulotyper_rep", report) |
| 217 report.write("</p>\n") | 217 report.write("</p>\n") |
| 218 if args.shigatoxintyping: | 218 if args.shigatoxintyping: |
| 219 report.write("<p>Stx Subtypes: ") | 219 report.write("<p>Stx Subtypes: ") |