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Do correct renaming of RPS12 genes if several

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Former-commit-id: 8ddbfaea302c440aa0992f3443632cf026b0d3a9
Former-commit-id: 2559779ab79d1b52d5193e1a60b443f6290dda48
This commit is contained in:
Eric Coissac
2022-02-14 15:29:02 +01:00
parent 616fd2bb44
commit 90b3ee9b04
1 changed files with 13 additions and 3 deletions
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16
detectors/cds/bin/do_rps12.sh
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@ -263,12 +263,13 @@ blastx \
# #
export PASS1_SPEEDUP=0 export PASS1_SPEEDUP=0
cp $DBROOT/Annot.lst RPS12 cp $DBROOT/Annot.lst RPS12
nbseq = 0
for fasta in rps12_fragments_*.fasta ; do for fasta in rps12_fragments_*.fasta ; do
tcsh -f ${PROG_DIR}/do_exonerate.csh \ tcsh -f ${PROG_DIR}/do_exonerate.csh \
$fasta \ $fasta \
"RPS12/rps12.fasta" \ "RPS12/rps12.fasta" \
$DBROOT/../models $(pwd) $DBROOT/../models $(pwd)
((nbseq=nbseq+1))
done done
# #
@ -276,8 +277,9 @@ blastx \
# fragment to the chloroplaste genome coordinates # fragment to the chloroplaste genome coordinates
# #
n=0
for f in *.res ; do for f in *.res ; do
((n=n+1))
mv $f $f.ori mv $f $f.ori
if [[ -z "$TEMP" ]] ; then if [[ -z "$TEMP" ]] ; then
dest="/dev/stdout" dest="/dev/stdout"
@ -382,9 +384,17 @@ blastx \
$0 = line $0 = line
} }
{print $0} {print $0}
' | \
$AwkCmd -v n=$n -v nbseq=$nbseq '
/^FT +\/gene="rps12"/ && (nbseq > 1) {
sub(/rps12/,"rps12_" n,$0)
}
{
print $0
}
' > $dest ' > $dest
done done
popTmpDir popTmpDir