Eric Coissac
6015339839
Former-commit-id: 443a0446133850bb57211c27d2001241b03472bd Former-commit-id: 8af464a0786f81dddf795f0cbda9ada9974808bf
130 lines
3.3 KiB
Bash
Executable File
130 lines
3.3 KiB
Bash
Executable File
#!/bin/bash
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#
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# BUILD REFERENCE THE CAU TRNA LIBRARy
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#
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#========================================================================================
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
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function taxid {
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egrep '/db_xref="taxon:[0-9]+"' $1 | \
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sed -E 's@ +/db_xref="taxon:([0-9]+)"@\1@'
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}
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function ac {
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head -1 $1 | awk '{print $2}'
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}
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function definition {
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awk '/^DEFINITION/ {on=1} \
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(on==1) {printf("%s ",$0)} \
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(/\.$/ && (on==1)) {on=0;print ""}' $1 | \
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sed 's/^DEFINITION *//' | \
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sed 's/ *$//'
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}
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function gb2fasta {
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AC=`ac $1`
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TAXID=`taxid $1`
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DEFINITION=`definition $1`
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echo ">${AC} taxid=${TAXID}; ${DEFINITION}"
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awk '/^\/\// {on=0} \
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(on==1) {print $0} \
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/^ORIGIN / {on=1}' $1 | \
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sed -E 's/^ *[0-9]+ +//' | \
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sed 's/ //g'
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}
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function findCAUtrna {
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FASTATMP="$$.genome.fasta"
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gb2fasta $1 > ${FASTATMP}
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aragorn -i -w -seq ${FASTATMP} | \
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awk '(on==1) && /^ *[0-9]+/ {on=0;print ""} \
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(on==1) {printf($0)} \
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/\(cat\)$/ {on=1; printf("%s ",$0)} \
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END {print ""}' | \
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awk '{print $3,$6}' | \
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sed -E 's/c?\[([0-9]+),([0-9]+)\]/\1 \2/' | \
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sed 's/ /:/g'
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rm ${FASTATMP}
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}
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function trnaAnnotations {
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awk '/^ORIGIN/ {on=0} \
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(on==1) {print $0} \
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/^FEATURE/ {on=1}' $1 | \
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awk '/^ [^ ]/ {print ""} \
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{printf("%s ",$0)} \
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END {print ""}' | \
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sed 's/^ *//' | \
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sed -E 's/ +/ /g' | \
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grep '^tRNA' | grep '/gene="' | \
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sed -E 's/([0-9]+)\.\.([0-9]+)/\1 \2/g' | \
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sed -E 's/ [0-9]+,[0-9]+ / /g' | \
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grep -v '>' | \
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grep -v '<' | \
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sed -E 's/join\(([0-9]+ [0-9]+)\)/\1/' | \
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sed -E 's/complement\(([0-9]+ [0-9]+)\)/\1/' | \
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sed -E 's/join\(([0-9]+ [0-9]+)\)/\1/' | \
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sed 's/^tRNA *//' | \
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sed -E 's@([0-9]+) +([0-9]+).*/gene="([^"]+)"@\1 \2 \3@' | \
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awk '{print $1,$2,$3}'
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}
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function annotateCAU {
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DISTTMP="$$.trna.dist"
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trna=(`echo $1 | sed 's/:/ /g'`)
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awk -v b=${trna[0]} -v e=${trna[1]} \
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'{printf("sqrt((%d - %d)^2 + (%d - %d)^2)\n",$1,b,$2,e)}' $2 | \
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bc -l | \
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sed 's/\..*$//' > ${DISTTMP}
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paste ${DISTTMP} $2 | sort -nk 1 | head -1 | awk '{print $1,$4}'
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rm -f ${DISTTMP}
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}
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function writeTRNA {
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TAXID=`taxid $1`
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AC=`ac $1`
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DEFINITION=`definition $1`
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TRNATMP="$$.trna.txt"
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trnaAnnotations $1 > ${TRNATMP}
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ntrna=`wc -l ${TRNATMP} | awk '{print $1}'`
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if (( ntrna > 0 )); then
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trnacau=`findCAUtrna $1`
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for t in $trnacau; do
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AA=(`annotateCAU $t ${TRNATMP}`)
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distance=${AA[0]}
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aa=`echo ${AA[1]} | sed -E 's/(t(rn|RNA)-?)?(I|M|fM).*$/trn\3/'`
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if (( distance <= 10 )); then
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echo ">${aa}_${AC} gbac=${AC}; trna=${aa}; taxid=${TAXID}; distance=${distance}; ${DEFINITION}"
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echo "$t" | awk -F ':' '{print $3}'
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fi
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done
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fi
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rm -f ${TRNATMP}
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}
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pushTmpDir ORG.buildCAUtRNA
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for gb in $*; do
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writeTRNA $gb
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done
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popTmpDir
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