Merge branch '7-gmap-rescue-on-target-only-for-genes-with-gmaprescue-file-tag' into 'master'

BUG : fixed bad rescue on target with gmap

Closes #7

See merge request !9

bin/gmapRescue.sh

@@ -53,16 +53,21 @@ do
 		echo " Gene $geneid has status UNMAPPED: mapping on the whole genome"
 
 		cat $rootdir'/query.mrna.fasta' >> $unmappedMrnaFasta && rm $rootdir'/query.mrna.fasta'
-		#targetindex=$gmapdb
-		#targetindexdir=$gmapdbdir
-		#targetgff=$rootdir'/gmap.wholeGenome.gff3'
-		#gmapexe='gmapl'
-		#eval $gmapexe --min-identity 0.80 --min-trimmed-coverage 0.50 --ordered -n 1 -d $targetindex -D $targetindexdir -f 2 $rootdir'/query.mrna.fasta' 1> $targetgff 2> $rootdir'/gmap.wg.log' && rm $rootdir'/query.mrna.fasta'
-	else
-		echo "running gmap on target"
+
+	elif [ -f "$rootdir/GMAPRESCUE" ]
+	then
+		echo " Gene $geneid has status GMAPRESCUE: mapping on the target with gmap"
 		eval gmap --ordered --min-identity 0.80 --min-trimmed-coverage 0.50 -n 1 -g $rootdir'/target.fasta' -f 2 $rootdir'/query.mrna.fasta' 1> $targetgff 2> $rootdir'/gmap.target.log' && rm $rootdir'/query.mrna.fasta'
+
+
+	elif [ -f "$rootdir/FULLPERFECTMATCH" ] || [ -f "$rootdir/FULLMATCHWITHMISSMATCHES" ]
+	then
+		echo " Gene $geneid has been mapped on the target with BLAT: next"
+
+	else
+		echo " FAIL TO EVAL THE ANCHORING STATUS OF GENE $geneid: rescue on whole genome"
+		cat $rootdir'/query.mrna.fasta' >> $unmappedMrnaFasta && rm $rootdir'/query.mrna.fasta'
 	fi
-	eval gmap --ordered --min-identity 0.80 --min-trimmed-coverage 0.50 -n 1 -g $rootdir'/query.fasta' -f 2 $rootdir'/query.mrna.fasta' 1> $rootdir'/gmap.query.gff3' && rm $rootdir'/query.mrna.fasta'
 
 	echo "3. indexing the query and target genomic"
 	samtools faidx $rootdir'/query.fasta' &

config.yaml

@@ -19,9 +19,9 @@ transferType: 'first'
 # FASTA of the target genome
 targetFasta: 'data/Triticum_aestivum_arinalrfor.PGSBv2.1.dna.toplevel.fa'
 #GMAP index of the genome for -d option
-targetGmapIndex: 'ensembl_Triticum_aestivum_julius_2022-9-16'
+targetGmapIndex: 'ensembl_Triticum_aestivum_arinalrfor_2023-2-17'
 #GMAP index: path to the gmapindex directory, for -D option
-targetGmapIndexPath: '/home/herimbert/gdec/shared/triticum_aestivum/julius/current/gmapdb/all/'
+targetGmapIndexPath: '/home/herimbert/gdec/shared/triticum_aestivum/arinalrfor/current/gmapdb/all/'
 
 ##### ISBP/markers related config and parameters
 # BAM file of markers/ISBPs mapped on the target genome