根据提供的fastq文件列表，针对单个fastq文件并行计算reads的长度，全部完成后计算N50

#!/usr/bin/env python
#-*- encoding=UTF-8 -*-
import multiprocessing
import gzip
import sys
## this function cal the sequence length per file
def cal_length(f):
	seq = []
	reads = 0
	tt = gzip.open(f).readlines()
	tlen = len(tt)
	plen = tlen/4
	for i in range(0,plen):
		start,end = (i*4,(i+1)*4)
		pdna = tt[start:end][1]
		reads += 1
		seq.append(len(pdna))
	return (f,reads,seq)

if __name__ == '__main__':
	fasta_files = sys.argv[1]## fasta files input list
	flist = [  f.strip() for f in open(fasta_files).readlines() if f.strip()] ## read the list file
	pool = multiprocessing.Pool(10) ## multi processing cal the sequence length
	results = pool.map(cal_length,flist) ## get the calulate results

	lengths = [] ### the seqences list
	pool.close() ## close the processing
	pool.join()
	for res in results: ## read results
		#print ('fasta file',res[0],'reads number:',res[1])
		for r in res[2]:
			lengths.append(int(r))

	## the N50 calculate
	N50_pos = sum(lengths)/2.0    
	lengths.sort()  
	lengths.reverse() 
	ValueSum,N50 = 0,0
	for value in lengths: 
		ValueSum += value
		if N50_pos <= ValueSum:
			N50 = value
			break
	print ("fasta files N50:",N50)

1.使用示例：

python n50_cal_batch.py f.list

f.list是fastq文件的绝对路径的列表。

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