BB_SmallRnaFqToPiRnaFq

#!/bin/bash

#########--function--#########
help_info(){
	echo "usage:"
	echo "SmallRnaFqToPiRnaFq.sh <option>* [-a adapter] [-i in.fq] [-o out.directory]"
	echo ""
	echo "necessary parameter:"
	echo "-a adapter sequence used for small RNA experiment"
	echo "-i small RNA file input"
	echo "-m bowtie2 index file for remove"
	echo "unnecessary parameter:"
	echo "-l len range you want to filter, default: 23-35"
	echo "-o piRNA fastq file output, default: stored in ./"
	echo "-p prefix name for output files, default: prefix"
	echo "-O the -O parameter used for cutadapt"
	echo "-c CPU used for the program, default: 1"
	echo "-s input file format sra, default: fq"
	echo "caution: the cutadapt parameter -O need modification"
}

#########--arguments--#########
if [ $# -lt 1 ]; then
	help_info
	exit 1
fi

len_filt="24-31"
dire="./"
prefix="prefix"
CPU="1"
sra=0

while getopts "a:i:m:o:l:p:c:O:s" opt
do
	case $opt in
		a) adap=$OPTARG;;
		i) smrn=$OPTARG;;
		o) dire=$OPTARG;;
		l) len_filt=$OPTARG;;
		p) prefix=$OPTARG;;
		c) CPU=$OPTARG;;
		s) sra=1;;
		m) index=$OPTARG;;
		O) cut_o=$OPTARG;;
		?) echo "Wrong parameter!!!"
		exit 1;;
	esac
done

#########--process--#########

######-sra dump-######
##fastq-dump: dump sra file to fq
if [ ${sra} -eq 1 ]; then
	fastq-dump ${smrn} -O temp_fq_${prefix}.fq
	smrn=temp_fq_${prefix}.fq
fi

######-adapter remove-######
##cutadapt: remove adapter from primary small RNA fastq
cutadapt -a ${adap} -e 0.15 -m 15 -O ${cut_o} -o temp_${prefix}.fq ${smrn} > ${dire}${prefix}_log_cutadapt 2>&1

##prinseq: filter len from temp.fa
perl /home/tongji2/piRNA/Software/prinseq-lite-0.20.4/prinseq-lite.pl \
-fastq temp_${prefix}.fq -range_len ${len_filt} -out_good temp_good_${prefix} -out_bad temp_bad_${prefix} \
> ${dire}${prefix}_log_prinseq 2>&1

##fastqc: quality control

/home/tongji2/piRNA/Software/FastQC/fastqc temp_good_${prefix}*

mv temp_good_${prefix}*.html ${dire}${prefix}_fastqc.html

##bowtie: remove reads mapped to known ncRNA
bowtie2 -q -N 0 -S temp_${prefix}.sam -p ${CPU} --un ${dire}${prefix}_piRNA.fq -U temp_good_${prefix}.fastq -x ${index} > ${dire}${prefix}_log_bowtie 2>&1

##remove temp file
#rm -rf temp*