Eric Coissac
7eb55b5d0b
Former-commit-id: 8c4c1d0391ad06ed67e748e0f837399e9b3de7ad Former-commit-id: 5af9ed909a6f6bed7bae86c77bd770ae4b5fc14e
24 lines
642 B
Bash
Executable File
24 lines
642 B
Bash
Executable File
#!/bin/bash
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SUMATRA=`dirname $0`/sumatra
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function annotateCAU {
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QUERY="$$.query.fasta"
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echo $1 | sed 's/&/ /' | tr '@' '\n' > ${QUERY}
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${SUMATRA} -d -n ${QUERY} $2 2> /dev/null | \
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awk ' {n[$2]+=1;d[$2]+=$3} \
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END {for (i in n) \
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print i, n[i],d[i], d[i]/n[i]\
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}' | \
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sort -rnk4 | \
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egrep '^trn(I|M|fM)' | \
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tail -1 | \
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awk '{print $1,$NF}'
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rm -rf ${QUERY}
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}
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for seq in `awk '(on==1) && /^>/ {print "";on=0} /^>/ {printf("%s@",$0)} ! /^>/ {on=1;printf($0)}' $1 | tr ' ' '&'`; do
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new=(`annotateCAU ${seq} $1`)
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echo $seq | sed 's/&/ /g' | sed -E 's/>([^ ]+) />'${new[0]}' /' | tr '@' '\n'
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done |