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Switch from awk to gawk

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Former-commit-id: 70b104ab89d4c90a35925dbbcacdafaf6c1f2836
Former-commit-id: bf29abf66345cbc0ca81461064dcca63dfd4c15c
This commit is contained in:
Eric Coissac
2015-11-08 19:33:00 +01:00
parent 6fa63daf3f
commit 2261fa1c48
16 changed files with 52 additions and 49 deletions
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24
detectors/trna/tools/extract_refCAUtRNA.sh
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@ -15,11 +15,11 @@ function taxid {
}
function ac {
head -1 $1 | awk '{print $2}'
head -1 $1 | $AwkCmd '{print $2}'
}
function definition {
awk '/^DEFINITION/ {on=1} \
$AwkCmd '/^DEFINITION/ {on=1} \
(on==1) {printf("%s ",$0)} \
(/\.$/ && (on==1)) {on=0;print ""}' $1 | \
sed 's/^DEFINITION *//' | \
@ -33,7 +33,7 @@ function gb2fasta {
echo ">${AC} taxid=${TAXID}; ${DEFINITION}"
awk '/^\/\// {on=0} \
$AwkCmd '/^\/\// {on=0} \
(on==1) {print $0} \
/^ORIGIN / {on=1}' $1 | \
sed -E 's/^ *[0-9]+ +//' | \
@ -46,11 +46,11 @@ function findCAUtrna {
gb2fasta $1 > ${FASTATMP}
aragorn -i -w -seq ${FASTATMP} | \
awk '(on==1) && /^ *[0-9]+/ {on=0;print ""} \
$AwkCmd '(on==1) && /^ *[0-9]+/ {on=0;print ""} \
(on==1) {printf($0)} \
/\(cat\)$/ {on=1; printf("%s ",$0)} \
END {print ""}' | \
awk '{print $3,$6}' | \
$AwkCmd '{print $3,$6}' | \
sed -E 's/c?\[([0-9]+),([0-9]+)\]/\1 \2/' | \
sed 's/ /:/g'
@ -58,10 +58,10 @@ function findCAUtrna {
}
function trnaAnnotations {
awk '/^ORIGIN/ {on=0} \
$AwkCmd '/^ORIGIN/ {on=0} \
(on==1) {print $0} \
/^FEATURE/ {on=1}' $1 | \
awk '/^ [^ ]/ {print ""} \
$AwkCmd '/^ [^ ]/ {print ""} \
{printf("%s ",$0)} \
END {print ""}' | \
sed 's/^ *//' | \
@ -76,17 +76,17 @@ function trnaAnnotations {
sed -E 's/join\(([0-9]+ [0-9]+)\)/\1/' | \
sed 's/^tRNA *//' | \
sed -E 's@([0-9]+) +([0-9]+).*/gene="([^"]+)"@\1 \2 \3@' | \
awk '{print $1,$2,$3}'
$AwkCmd '{print $1,$2,$3}'
}
function annotateCAU {
DISTTMP="$$.trna.dist"
trna=(`echo $1 | sed 's/:/ /g'`)
awk -v b=${trna[0]} -v e=${trna[1]} \
$AwkCmd -v b=${trna[0]} -v e=${trna[1]} \
'{printf("sqrt((%d - %d)^2 + (%d - %d)^2)\n",$1,b,$2,e)}' $2 | \
bc -l | \
sed 's/\..*$//' > ${DISTTMP}
paste ${DISTTMP} $2 | sort -nk 1 | head -1 | awk '{print $1,$4}'
paste ${DISTTMP} $2 | sort -nk 1 | head -1 | $AwkCmd '{print $1,$4}'
rm -f ${DISTTMP}
}
@ -98,7 +98,7 @@ function writeTRNA {
TRNATMP="$$.trna.txt"
trnaAnnotations $1 > ${TRNATMP}
ntrna=`wc -l ${TRNATMP} | awk '{print $1}'`
ntrna=`wc -l ${TRNATMP} | $AwkCmd '{print $1}'`
if (( ntrna > 0 )); then
trnacau=`findCAUtrna $1`
@ -110,7 +110,7 @@ function writeTRNA {
if (( distance <= 10 )); then
echo ">${aa}_${AC} gbac=${AC}; trna=${aa}; taxid=${TAXID}; distance=${distance}; ${DEFINITION}"
echo "$t" | awk -F ':' '{print $3}'
echo "$t" | $AwkCmd -F ':' '{print $3}'
fi
done
fi