SRY_k

#!/bin/bash

script_abs=$(readlink -f "$0")
script_dir=$(dirname $script_abs)
export PATH=$PATH:$script_dir/script
export LC_ALL=C

usageHelp="\nUsage: ./${0##*/} (parameters with * must be supplied!)\n\n-m <string>*       Male (or female for W) short-read files with comma separated in sample and plus separated between samples\n-f <string>*       Female (or male for W) short-read files with comma separated in sample and plus separated between samples\n-i <int>           Minimum coverage of k-mers in each sample (default: 2)\n-a <int>           Maximum coverage of k-mers in each sample (default: unlimit)\n-k <int>           K-mer length (default: 21)\n-p <int>           CPU number (default: 1)\n-h                 Help and exit."
printHelpAndExit() {
	echo -e "$usageHelp"
	exit;
}

while getopts "m:f:l:g:i:a:k:p:h" opt; do
	case $opt in
		m) MSREAD=$OPTARG ;;
		f) FSREAD=$OPTARG ;;
		i) COV=$OPTARG ;;
		a) MCOV=$OPTARG ;;
		k) KLEN=$OPTARG ;;
		p) CPU=$OPTARG ;;
		h) printHelpAndExit 0;;
	esac
done

if [ -z "$MSREAD" ] || [ -z "$FSREAD" ];then
	printHelpAndExit
	exit
fi

if [ -z "$KLEN" ];then
	KLEN=21
fi

if [ -z "$COV" ];then
        COV=2
fi

if [ -z "$MCOV" ];then
        MCOV=0
fi

if [ -z "$CPU" ];then
        CPU=1
fi

if [ ! -d "output" ];then
	mkdir output
fi

#judge if the softwares needed are installed.

if ! type kmc >/dev/null 2>&1; then
	echo 'kmc is not installed!'
	exit
fi

if ! type samtools >/dev/null 2>&1; then
	echo 'samtools is not installed!'
	exit
fi

if ! type seqtk >/dev/null 2>&1; then
	echo 'seqtk is not installed!'
	exit
fi

if ! type parallel >/dev/null 2>&1; then
        echo 'parallel is not installed!'
        exit
fi

#obtain specific-Y kmers

echo "***********************************Preparation*************************************"
if [[ $MCOV == 0 ]]
then
	echo "Min coverage:$COV;max coverage:unlimit"
else
	echo "Min coverage:$COV;max coverage:$MCOV"
fi

call_kmc.pl $MSREAD $FSREAD $KLEN $COV $MCOV
parallel -j $CPU <output/kmer.sh
parallel -j 2 <output/ft.sh
KMER="output/SRY_kmer.txt"
filterx -k s -1 'cnt=1' output/Male_kmer.dat.gz:req=Y output/Female_kmer.dat.gz |cut -f 1 > $KMER
rm -r tmp_* output/M.kmer output/F.kmer