Mercurial > repos > iss > eurl_vtec_wgs_pt
view scripts/stx_subtype_fa.sh @ 6:20ff3dca457f draft default tip
planemo upload commit 6857c749c21f580c828aba3543e294b69d32b662
author | iss |
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date | Mon, 23 Oct 2023 11:45:36 +0000 |
parents | c6bab5103a14 |
children |
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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;