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Commit cca80b85 authored by francois.sabot_ird.fr's avatar francois.sabot_ird.fr
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adding loops

parent 264e1641
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......@@ -29,15 +29,16 @@
#SBATCH --export=ALL
#SBATCH --mail-user francois.sabot@ird.fr
#SBATCH --mail-type=ALL
#SBATCH -p gpu
#SBATCH -p temp
#SBATCH -A temp
#SBATCH -c 24
#SBATCH -J LOchain
#SBATCH -nodelist=node7
#Data recovery
ANNOTATION = $1
SEQFOLDER = $2
OUTPUT = $3
ANNOTATION=$1
SEQFOLDER=$2
REFERENCESEQ=$3
OUTPUT=$4
#Modules used
module load liftoff/1.6.3
......@@ -46,3 +47,31 @@ module load liftoff/1.6.3
# [-chroms TXT] [-unplaced TXT] [-copies] [-sc SC] [-overlap O] [-mismatch M] [-gap_open GO] [-gap_extend GE] [-polish] [-cds]
# target reference""
#Liftoff in GFF mode
echo -e "########################################\n\nRunning in GFF mode\n\n"
for TARGETSEQ in `ls $SEQFOLDER`; do
if [[ $TARGETSEQ == $REFERENCESEQ ]]; then
continue
fi
OUTFILE=$OUTPUT."/".$SEQFILE.".gff"
UNMAPPED==$OUTPUT."/".$SEQFILE."_unmapped.txt"
echo -e "\nRunning for $TARGETSEQ\n" >> timelog.txt
LIFTCOM='time liftoff -g $ANNOTATION -o $OUTFILE -u $UNMAPPED -p 1 $TARGETSEQ $REFERENCESEQ'
$LIFTCOM >> timelog.txt || exit 135
done
#Liftoff in DDB mode
echo -e "########################################\n\nRunning in DB mode\n\n"
for TARGETSEQ in `ls $SEQFOLDER`; do
if [[ $TARGETSEQ == $REFERENCESEQ ]]; then
continue
fi
DB=${ANNOTATION}"_db"
OUTFILE=$OUTPUT."/".$SEQFILE.".db.gff"
UNMAPPED==$OUTPUT."/".$SEQFILE."_unmappeddb.txt"
echo -e "\nRunning for $TARGETSEQ\n" >> timelog.txt
LIFTCOMDB='time liftoff -db $DB -o $OUTFILE -u $UNMAPPED -p 1 $TARGETSEQ $REFERENCESEQ'
$LIFTCOMDB >> timelog.txt || exit 135
done
#{ date ; time liftoff -o prout -g locus.gff IR64_GuppyFlyeMedakaRagtag.fasta irgsp5_complete.fasta ; } > time.log 2>&1 && tail -n 10 time.log > time2.log
\ No newline at end of file
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