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annotate scripts/stx_subtype_fa.sh @ 6:20ff3dca457f draft default tip

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planemo upload commit 6857c749c21f580c828aba3543e294b69d32b662
author iss
date Mon, 23 Oct 2023 11:45:36 +0000
parents c6bab5103a14
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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c6bab5103a14 "planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"
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1 tooldir="$1";
c6bab5103a14 "planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"
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2 fastafile="$2";
c6bab5103a14 "planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"
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3
c6bab5103a14 "planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"
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4 # SEQUENCE SEARCH
c6bab5103a14 "planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"
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5 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;
c6bab5103a14 "planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"
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6 # SHIGATOXINTYPER: FILTER, CUT AND CONCATENATE SEQUENCE SEARCH OUTPUT
c6bab5103a14 "planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"
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7 awk -F '\t' '($3>95 && $4>1200) { print $2 FS $3 FS $4 FS $16 }' shigatoxin > shigatoxin_fc;