adding loops

GrAnnoT/codes4publications/liftOffChainer.sh

@@ -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 
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