#!/bin/bash
#only for LONG READS mapping
#USAGE: runMapper.sh minimap2 ref.fa reads.fa/fq 48 ont
echo -e "This is a bash scrip to map your long reads and make it visualization ready !"
#Location of the tools
samtools=/home/urbe/anaconda3/bin/samtools
graphMapLoc=/home/urbe/Tools/graphmap/bin/Linux-x64/graphmap
minimap2Loc=/home/urbe/Tools/minimap2-2.3_x64-linux/minimap2
bwaMemLoc=/home/urbe/anaconda3/bin/bwa
ngmlrLoc=/home/urbe/Tools/ngmlr/bin/ngmlr-0.2.3/ngmlr
lamsaLoc=/home/urbe/Tools/LAMSA/lamsa
#Parameters accepted
toolName=$1
refFasta=$2
longReads=$3
thread=$4
readsType=$5
if [ $# -lt 5 ]; then
echo "No or less arguments provided"
echo "#USAGE: runMapper.sh minimap2 ref.fa reads.fa/fq 48 ont"
exit 1
fi
fileName=$(basename "$refFasta"); #fileName=$(basename "$refFasta" .fq);
echo "Name of the file used for mapping $fileName, present at $refFasta"
if [ $toolName == "bwa" ]; then
echo "Mapping with $toolName"
$bwaMemLoc index $refFasta
$bwaMemLoc mem $refFasta $longReads -t $thread > $fileName.out.sam
elif [ $toolName == "lamsa" ]; then
echo "Mapping with $toolName"
$lamsaLoc index $refFasta
if [ $readsType == "ont" ]; then
$lamsaLoc aln -t $thread -T ont2d $refFasta $longReads > $fileName.out.sam
elif [ $readsType == "pacbio" ]; then
$lamsaLoc aln -t $thread -T pacbio $refFasta $longReads > $fileName.out.sam
else
echo "LAMSA:Please specify reads type: ont, pacbio"
fi
elif [ $toolName == "minimap2" ]; then
echo "Mapping with $toolName"
if [ $readsType == "ont" ]; then
$minimap2Loc -ax map-ont $refFasta $longReads -t $thread > $fileName.out.sam
elif [ $readsType == "pacbio" ]; then
$minimap2Loc -ax map-pb $refFasta $longReads -t $thread > $fileName.out.sam
else
echo "MINIMAP2:Please specify reads type: ont, pacbio"
fi
elif [ $toolName == "ngmlr" ]; then
echo "Mapping with $toolName"
if [ $readsType == "ont" ]; then
$ngmlrLoc -t $thread -r $refFasta -q $longReads -o $fileName.out.sam -x $readsType
elif [ $readsType == "pacbio" ]; then
$ngmlrLoc -t $thread -r $refFasta -q $longReads -o $fileName.out.sam -x $readsType
else
echo "NGMLR:Please specify reads type: ont, pacbio"
fi
elif [ $toolName == "graphmap" ]; then
echo "Mapping with $toolName"
$graphMapLoc align -r $refFasta -d $longReads -t $thread -o $fileName.out.sam
else
echo "Unknown mapper name and parameter !"
fi
echo "Getting files ready for visualization !"
$samtools view -Sb $fileName.out.sam | $samtools sort -m 4G -@$thread -o $fileName.sorted.bam - && $samtools index -@$thread $fileName.sorted.bam
echo "All Done :)"
