NEW script to recalc coords of rescue with gmap

bin/recalcGmapRescue.sh

+#!/bin/bash
+##SBATCH --array=0-7
+##SBATCH -n1
+##SBATCH --mail-user=helene.rimbert@inrae.fr
+##SBATCH --mail-type=ALL
+
+# for use with slurm
+#chroms=($(echo TraesCS{1..7} TraesCSU))
+#chrom=${chroms[$SLURM_ARRAY_TASK_ID]}
+
+# get the list of query and target file for gmap
+
+inputDir=$1
+blastdb=$2
+
+querylist=($(find  $inputDir  -type f -name 'gmap.target.gff3'))
+
+numquery=${#querylist[@]}
+
+echo "STARTING AT `date` FOR DATASET $inputDir"
+echo "found $numquery query file"
+
+for i in "${querylist[@]}";
+do
+	rootdir=`dirname $i`
+	# extract the name of the gene
+    geneid=$(cat $rootdir'/query.fasta'|fgrep '>'|perl -ne 'print $1 if /^\>(TraesCS.+)\ coords/')
+	echo "\n\n================================================"
+    echo " gene is $geneid"
+	echo " datadir is $rootdir"
+
+    # extract the target chrom, start and stop
+    chrom=$(fgrep '>' $rootdir'/target.fasta'|sed "s/>//"|cut -d ' ' -f1|cut -d '_' -f2)
+    start=$(fgrep '>' $rootdir'/target.fasta'|sed "s/>//"|cut -d ' ' -f1|cut -d '_' -f3)
+    stop=$(fgrep '>' $rootdir'/target.fasta'|sed "s/>//"|cut -d ' ' -f1|cut -d '_' -f4)
+    echo " Target coords: $chrom from $start - $stop"
+
+    # check the status of the CDS: OK or CHANGED
+    mappingStatus='UNMAPPED'
+    if [ -f "$rootdir/CDS_OK" ]
+    then
+        echo " CDS has not changed between target and reference"
+        mappingStatus='CDS_OK'
+
+    elif [ -f "$rootdir/CDS_CHANGED" ]
+    then
+        echo " WARNING : CDS has changed between target and reference"
+        mappingStatus='CDS_CHANGED'
+
+    else
+        echo " Assume gene is unmapped"
+        echo " need to run gmap on entire genome"
+        mappingStatus='UNMAPPED'
+        #touch $rootdir/UNMAPPED
+        continue
+    fi
+
+    echo " 1. convert gmap coordinates on new reference"
+    eval $TRANSFERTANNOT_PATH'/bin/convertGmapCoords.py' -G $rootdir'/gmap.target.gff3' -s $start -e $stop -c $mappingStatus -o $rootdir'/recalc.gff3' -r $chrom -g $geneid -m GMAP_on_target &> $rootdir'/recalc.log'
+	
+    echo " 2. sort gff"
+    eval gt gff3 -sort -retainids -tidy $rootdir'/recalc.gff3' 1> $rootdir'/recalc_clean.gff3'
+
+done
+
+echo "ENDED AT `date`"