remove useless scripts extractpepandcheck.sh recalcGmapRescue.sh

bin/extractpepandcheck.sh

-#!/bin/bash
-#SBATCH --array=0-7
-#SBATCH -n1
-#SBATCH --mail-user=helene.rimbert@inrae.fr
-#SBATCH --mail-type=ALL
-#SBATCH --export=ALL
-
-chroms=($(echo TraesCS{1..7} TraesCSU))
-chrom=${chroms[$SLURM_ARRAY_TASK_ID]}
-
-# get the list of query and target file for gmap
-querylist=($(find  3_mapping_$chrom* -type f -name 'query.fasta'))
-targetlist=($(find 3_mapping_$chrom* -type f -name 'target.fasta'))
-
-numquery=${#querylist[@]}
-numtarget=${#targetlist[@]}
-
-echo "STARTING AT `date` FOR CHROM $chrom"
-echo "found $numquery query fasta file"
-echo "found $numtarget target fasta file"
-
-
-for i in "${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"
-
-
-	echo "1. indexing the query and target genomic"
-	if [ ! -s " $rootdir/query.fasta.fai" ]
-	then
-		samtools faidx $rootdir'/query.fasta'
-		samtools faidx $rootdir'/target.fasta'
-	else
-		echo " index already done"
-	fi
-
-	echo "2. running gffread to extract the pep sequence"
-
-	if [ ! -s " $rootdir/target.pep.faa" ]
-	then
-		gffread -x $rootdir'/target.cds.fasta' -y $rootdir'/target.pep.faa' -g $rootdir'/target.fasta' $rootdir'/gmap.target.gff3'
-		gffread -x $rootdir'/query.cds.fasta' -y $rootdir'/query.pep.faa' -g $rootdir'/query.fasta' $rootdir'/gmap.query.gff3'
-	else
-		echo "pep extraction already done"
-	fi
-
-	echo "3. running diff to check if the pep sequences are different or not"
-	diffresult=$(diff $rootdir'/target.pep.faa' $rootdir'/query.pep.faa')
-
-	if [ "$diffresult" != "" ]
-	then
-		echo "RESULTS pep of gene $geneid has changed"
-		echo $diffresults > $rootdir/CDS_CHANGED
-
-	elif [ ! -s "$rootdir/blat.txt" ]
-	then
-		echo "RESULTS no blat results here: no extraction to make"
-		touch $rootdir/UNMAPPED
-	else
-		echo "RESULTS pep of gene $geneid stays the same"
-		touch $rootdir/CDS_OK
-	fi
-
-done
-
-echo "ENDED AT `date`"

bin/recalcGmapRescue.sh

-#!/bin/bash
-##SBATCH --array=0-7
-##SBATCH -n1
-##SBATCH --mail-user=helene.rimbert@inrae.fr
-##SBATCH --mail-type=ALL
-
-inputDir=$1
-inputDescription=$2
-finalGFF=$3
-bindir=$4
-
-export TRANSFERTANNOT_PATH=$bindir
-
-querylist=($(find  $inputDir  -type f -name 'gmap.target.gff3'))
-
-numquery=${#querylist[@]}
-
-echo "STARTING AT `date` FOR DATASET $inputDir"
-echo "found $numquery query file"
-
-for inputgff in "${querylist[@]}";
-do
-	rootdir=`dirname $inputgff`
-	# extract the name of the gene
-    geneid=$(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 - $stop"
-
-    # check the status of the CDS: OK or CHANGED or UNKNOWN
-    mappingStatus='UNMAPPED'
-    cdsStatus='CDS_OK'
-    if [ -f "$rootdir/CDS_OK" ]
-    then
-        echo " CDS has not changed between target and reference"
-        cdsStatus='CDS_OK'
-
-    elif [ -f "$rootdir/CDS_CHANGED" ]
-    then
-        echo " WARNING : CDS has changed between target and reference"
-        cdsStatus='CDS_CHANGED'
-
-    elif [ -f "$rootdir/CDS_UNKNOWN" ]
-    then
-        echo " WARNING : we do not know if the CDS has changed or not"
-        cdsStatus='CDS_UNKNOWN'
-
-    else
-        echo " Assume gene is UNKNOWN"
-        echo " need to run gmap on entire genome"
-        cdsStatus='CDS_UNKNOWN'
-        continue
-    fi
-
-    echo " 1. convert gmap coordinates on new reference"
-    eval $TRANSFERTANNOT_PATH'/bin/convertGmapCoords.py' -G $inputgff -s $start -e $stop -c $cdsStatus -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> $rootdir'/recalc_clean.gff3'
-
-done
-
-# merge All recalc_clean.gff3 files
-gfflist=($(find  $inputDir  -type f -name 'recalc_clean.gff3'))
-gt gff3 -sort -tidy -retainids "${gfflist[@]}" 1> $finalGFF 2> $finalGFF.gt.log
-
-echo "ENDED AT `date`"