#!/usr/bin/env python 

from Bio import SeqIO

from Bio import SeqRecord

import sys 

import argparse 

def open_either(file, mode='r'):
	'''open either compressed or not compressed files'''
	
	if file.endswith('.gz'): 
		import gzip 
		return gzip.open(file, mode)
		
	else:
	
		return open(file, mode)
		
		
def calc_percentA(List):

	BaseList = ['A'] 
	for Base in BaseList:
		Percent = 100 * List.count(Base) / float(len(List))
		
		PercentA = float(Percent)
		
	return PercentA  

def calc_percentC(List):
	
	BaseList = ['C']
	for Base in BaseList:
		Percent = 100 * List.count(Base) / float(len(List))
	
		PercentC = float(Percent)
	
	return PercentC		
	
def calc_percentG(List): 

	BaseList = ['G']	
	for Base in BaseList:
		Percent = 100 * List.count(Base) / float(len(List))
	
		PercentG = float(Percent)
		
	return PercentG
	
def calc_percentT(List):
	
	BaseList = ['T']	
	for Base in BaseList:
		Percent = 100 * List.count(Base) / float(len(List))
	
		PercentT = float(Percent)
		
	return PercentT
	
		
if __name__ == '__main__' :

	parser = argparse.ArgumentParser(description='Filter paired-end read quality based on percent base composition.',)	
	
	parser.add_argument('-1', '--fastq1',
											help='The input read1 fastq file.',
											required=True)


	parser.add_argument('-2', '--fastq2', 
											help='The input read2 fastq file.', 
											required=True)
																					
	parser.add_argument('-p', '--minPercent',
											help='Any base must account for this percent of read. Or read will be discarded.',
											type=float,
											default=5.0)


	parser.add_argument('-o1', '--outFile1', 
											help='fastq1 output file.',
											required=True)
											
											
	parser.add_argument('-o2', '--outFile2',
											help='fastq2 output file.',
											required=True)
											
																					
											
	args = parser.parse_args()
												

	fastqFormat = 'fastq' 
	


	fastq1handle = open_either(args.fastq1, 'rU')
	fastq2handle = open_either(args.fastq2, 'rU')

	fastq1out = open_either(args.outFile1, 'wb')
	fastq2out = open_either(args.outFile2, 'wb')
	
	fastq1SeqIO = SeqIO.parse(fastq1handle, fastqFormat)
	fastq2SeqIO = SeqIO.parse(fastq2handle, fastqFormat)
	
	
	while True:
		
		try: 
			
			fastq1record = fastq1SeqIO.next()
			fastq2record = fastq2SeqIO.next()
			
		except:
		
			break
			
		Seq_ListR1 = fastq1record.seq
		Seq_ListR2 = fastq2record.seq		
	
	
		if (calc_percentA(Seq_ListR1) < args.minPercent) or (calc_percentA(Seq_ListR2) < args.minPercent):
			continue 
			
		if (calc_percentC(Seq_ListR1) < args.minPercent) or (calc_percentC(Seq_ListR2) < args.minPercent): 
			continue 
			
		if (calc_percentG(Seq_ListR1) < args.minPercent) or (calc_percentG(Seq_ListR2) < args.minPercent):
			continue			
		 
		if (calc_percentT(Seq_ListR1) < args.minPercent) or (calc_percentT(Seq_ListR2) < args.minPercent):
			continue
				
		
		fastq1out.write(fastq1record.format(fastqFormat))
		fastq2out.write(fastq2record.format(fastqFormat))
		
		
	
	fastq1out.close()
	fastq2out.close()
		
		
	print "Filtering complete!"