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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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13
detectors/trna/tools/buildCAURefDB.sh
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@@ -11,7 +11,7 @@ source "${THIS_DIR}/../../../scripts/bash_init.sh"
function fasta1li {
awk '/^>/ {if (sequence) \
$AwkCmd '/^>/ {if (sequence) \
{print sequence}; \
print $0; \
sequence=""} \
@@ -28,7 +28,7 @@ function dereplicate {
grep -v -- -- | \
sed -E "s/count=[0-9]+; //" | \
sed 's/cluster_weight/count/' | \
awk ' /^>/ {SEQ++;$1=$1"_"SEQ;print $0} \
$AwkCmd ' /^>/ {SEQ++;$1=$1"_"SEQ;print $0} \
!/^>/ {print $0}'
}
@@ -52,15 +52,16 @@ function goodtrna {
sumatra -t 0.90 -x $QUERY $REF | \
sed -E 's/.(trn.M?)[_A-Z0-9]+/ \1 /' | \
sort -k 1,2 | \
awk '(OLD) && ($1!=OLD) {print OLD,c["trnM"],c["trnfM"],c["trnI"]} \
$AwkCmd '(OLD) && ($1!=OLD) {print OLD,c["trnM"],c["trnfM"],c["trnI"]} \
(OLD !=$1) {c["trnM"]=0;c["trnfM"]=0;c["trnI"]=0;OLD=$1} \
{c[$2]+=$5}' | awk '{p=0;} \
{c[$2]+=$5}' | \
$AwkCmd '{p=0;} \
($2 > $3) && ($2 > $4) { print $0,"trnM";p=1 } \
($3 > $2) && ($3 > $4) {print $0,"trnfM";p=1} \
($4 > $2) && ($4 > $3) {print $0,"trnI";p=1} \
(p==0) {print $0,"----"}' | sed 's/_/ /' | \
awk '{print $1"_"$2,$3,$4,$5,$1,$6}' | \
awk '(($2+$3+$4) > 1) && ($5==$6) {print $1}'
$AwkCmd '{print $1"_"$2,$3,$4,$5,$1,$6}' | \
$AwkCmd '(($2+$3+$4) > 1) && ($5==$6) {print $1}'
}
pushTmpDir ORG.buildSCDB