fastq to tasta using linux shell script

#!/bin/bash
usage()
{       echo " ";    echo "#################################################"; echo " ";
        printf "# "; echo "Usage: ./`basename $0` -i input.fa -o out.fa"
        echo " ";    echo "#################################################"; echo " ";
        exit 1
}
[ $# -eq 0 ] && usage

while getopts :i:o: OPTION
do
   case $OPTION in
        i)
         input_file=$OPTARG
        ;;
        o)
         output_file=$OPTARG
        ;;
        \?)
        usage
        ;;
   esac
done
awk '{if (NR%4==1) {print ">" substr($0,2)}}{if (NR%4==2) {print}}' $input_file > $output_file
time ./awk_fq_to_fa.sh -i ../sample_data/fastQ_data/reads.left.fq -o test.fa

real    0m0.065s
user    0m0.039s
sys     0m0.014s
time perl fastQ_to_fastA.pl -I ../sample_data/fastQ_data/reads.left.fq > test_1.fa

real    0m1.562s
user    0m1.550s
sys     0m0.004s
posted @ 2015-11-23 11:18  liuhui_pine  阅读(213)  评论(0)    收藏  举报