Mercurial > repos > iss > eurl_vtec_wgs_pt
diff scripts/stx_subtype_fa.sh @ 0:c6bab5103a14 draft
"planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"
author | iss |
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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; \ No newline at end of file