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#!/usr/bin/python3
import glob
import os
import sys
helpMessage = """
This script will convert all fastq files in the current directory to fasta.
Invoke without arguments.
"""
if not len(sys.argv)==1:
print(helpMessage)
exit(1)
# Loop over fastq files in the current directory.
for fastqFileName in glob.glob('*.fastq'):
print(fastqFileName)
fastaFileName = fastqFileName[:-1] + 'a'
command = 'cat ' + fastqFileName + ' | awk \'{if(NR%4==1) {printf(">%s\\n",substr($0,2));} else if(NR%4==2) print;}\' > ' + fastaFileName
os.system(command)
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