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#!/usr/bin/python3
import os
import sys
helpMessage = """
This script will unzip a fastq.gz file
and convert it to fasta format on the fly,
without having to store the uncompressed fastq
file on disk.
Invoke with two arguments:
- Name of the input fastq.gz file.
- Name of the output fasta file.
"""
if not len(sys.argv)==3:
print(helpMessage)
exit(1)
inputFileName = sys.argv[1]
outputFileName = sys.argv[2]
command = 'gunzip -c ' + inputFileName +' | awk \'{if(NR%4==1) {printf(">%s\\n",substr($0,2));} else if(NR%4==2) print;}\' > ' + outputFileName
os.system(command)
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