Mercurial > repos > iss > eurl_vtec_wgs_pt

diff scripts/stx_subtype_fa.sh @ 0:c6bab5103a14 draft

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"planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"
author iss
date Mon, 21 Mar 2022 15:23:09 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/stx_subtype_fa.sh	Mon Mar 21 15:23:09 2022 +0000
@@ -0,0 +1,7 @@
+tooldir="$1";
+fastafile="$2";
+
+# SEQUENCE SEARCH
+blastn -query $fastafile -db $tooldir/data/stx -task blastn -evalue 0.001 -out shigatoxin -outfmt '6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles' -num_threads 8 -strand both -dust yes -max_target_seqs 1 -perc_identity 95.0;
+# SHIGATOXINTYPER: FILTER, CUT AND CONCATENATE SEQUENCE SEARCH OUTPUT
+awk -F '\t' '($3>95 && $4>1200) { print $2 FS $3 FS $4 FS $16 }' shigatoxin > shigatoxin_fc;
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