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#!/bin/bash
sam2wig(){
chrlen=$1
chr=$2
infi=$3
nosingle=$4
minins=$5
maxins=$6
threads=$7
outfi="$infi.$chr.wig"
tmp="$infi.$chr.sam"
samtools view -@ $threads $infi $chr | \
./genwig2.py $chrlen $chr - $outfi $nosingle $minins $maxins
echo "completed: $chr"
}
export -f sam2wig
while getopts ":b:m:n:o:p:q:" opt; do
case $opt in
b)
if [ ! -f $OPTARG ]
then
echo "ERROR: Unable to find input bam $OPTARG" >&2
exit 1
else
inbam="$OPTARG"
fi
;;
m)
maxins=$OPTARG
;;
n)
minins=$OPTARG
;;
o)
if [ ! -d $OPTARG ];
then
echo "ERROR: Unable to find output directory $OPTARG" >&2
exit 1
else
outdir="$OPTARG"
fi
;;
p)
nproc=$OPTARG
;;
q)
nosingle=$OPTARG
;;
\?)
echo "ERROR: Unknown argument $opt" >&2
exit 1
;;
esac
done
#dump chromosome info from bam index
chrinfo="$inbam.chr"
#sort is required to preserve order between trinity and here
samtools idxstats $inbam | grep -v "^*" | cut -f1,2 | sort > $chrinfo
#generate wigs for segs/chrs
parallel -j $nproc --xapply \
sam2wig {1} {2} $inbam $nosingle $minins $maxins $nproc \
::: `cut -f2 $chrinfo` ::: `cut -f1 $chrinfo`
#cat to final wig and remove file
if [ -f "$inbam.wig" ]
then
rm "$inbam.wig"
fi
while read chr len
do
cat "$inbam.$chr.wig" >> "$inbam.wig"
rm "$inbam.$chr.wig"
done < $chrinfo
|
