FASTQ_to_FASTA.py

import sys, subprocess, gzip

infile = sys.argv[1]
fasta = sys.argv[2]
gz = sys.argv[3]

## if gz is present open it with the gzip library else normal
if '.gz' in infile:
	print 'detected a .gz file '
	fastq = gzip.open(infile, 'rb')
else:
	fastq = open(infile, 'r')

## main function, skip line id 34 and rest counter to write out the fasta

def main(fastq, fasta, gz):
	line_n =0
	line_buffer = 0
	line_id = 1
	if gz == '1': ### if gz argument is provided it will write out a gz file else normal
		outfile = gzip.open(fasta+'.gz', 'w')
	else:
		outfile = open(fasta, 'w')
	fastas = 1
	fasta_length =0
	for line in fastq:
		line_n += 1
			#line_id += 1
		if line_n == 10000:
			line_buffer += 10000
			line_n =0
			print 'processed lines ', line_buffer
		if line_id == 4:
			line_id = 1
		elif line_id == 3:
			line_id += 1
		elif line_id == 2:
			line_id += 1
			fasta_line = line
			fasta_length += len(fasta_line.strip())
			outfile.write(fasta_line)
			fastas += 1
		else:
			if '@' not in line:
				print 'are you sure this is a fastq ??'
			else:
				fasta_header = line.replace('@', '>')
				line_id += 1
				outfile.write(fasta_header)
	outfile.close()
	print 'FASTA records written', fastas, 'average length of fasta sequences ', float(fasta_length//fastas)

if __name__ == '__main__':
	main(fastq, fasta, gz)