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Change setup for the blast filtering before exonerate

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Former-commit-id: 139685eca58c1fb2272854dee31de3821c54af80
Former-commit-id: dc5c345ce72e9895cbdcc3321499b869040a24da
This commit is contained in:
Eric Coissac
2022-02-17 18:41:27 +01:00
parent 3b584dbebd
commit 9d93a68b3a
3 changed files with 26 additions and 18 deletions
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12
detectors/cds/bin/go_cds.sh
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@ -66,15 +66,15 @@ Fasta="$temp/genome.fasta"
#
if [[ "$cdsdetection_pass1" == "yes" ]] ; then
for dir in "core" ; do
( for dir in "core" ; do
if [[ -d $DbRoot/$dir ]] ; then
fams=$(ls $DbRoot/$dir/*.fst)
loginfo "running pass1:$dir exonerate of $Genome on $DbRoot"
for f in $fams ; do
tcsh -f $PROG_DIR/do_exonerate.csh Pass1 $Fasta $f $AnnotFile $DbRoot/models $temp
echo tcsh -f $PROG_DIR/do_exonerate.csh Pass1 $Fasta $f $AnnotFile $DbRoot/models $temp
done
fi
done
done ) | parallel -j 8
mv $temp/genome.cds.fasta $Genome.cds_pass1.fasta
fi
@ -94,16 +94,16 @@ fi
#
if [[ "$cdsdetection_pass3" == "yes" ]] ; then
for dir in "shell" ; do
(for dir in "shell" ; do
if [[ -d $DbRoot/$dir ]] ; then
fams=$(ls $DbRoot/$dir/*.fst)
loginfo $fams
loginfo "running pass3:$dir exonerate of $Genome on $DbRoot"
for f in $fams ; do
tcsh -f $PROG_DIR/do_exonerate.csh Pass3 $Fasta $f $AnnotFile $DbRoot/models $temp
echo tcsh -f $PROG_DIR/do_exonerate.csh Pass3 $Fasta $f $AnnotFile $DbRoot/models $temp
done
fi
done
done) | parallel -j 8
mv $temp/genome.cds.fasta $Genome.cds_pass2.fasta
fi