python 随机抽取Fastq文件

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参考 http://pythonforbiologists.com/index.php/randomly-sampling-reads-from-a-fastq-file/

最近要做一个二代测序的模拟，所以网上找了个小脚本，做了些注释，希望能够帮助大家。

from __future__ import division
import randomnumber_to_sample = 3000000
number_of_replicates = 10#计算行数 
with open("test.fastq") as input:num_lines = sum([1 for line in input])# 全部reads数目
total_records = int(num_lines / 4)
print("sampling " + str(number_to_sample) + " out of " + str(total_records) + " records")# 可以设置多个输出文件
output_files = []
output_sequence_sets = []#打开10个文件
for i in range(number_of_replicates):output_files.append(open("sample.fastq." + str(i), "w"))# 随机抽取    output_sequence_sets.append(set(random.sample(xrange(total_records + 1), number_to_sample)))# 一次读取4行
record_number = 0
with open("test.fastq") as input:for line1 in input:line2 = input.next()line3 = input.next()line4 = input.next()for i, output in enumerate(output_files):if record_number in output_sequence_sets[i]:output.write(line1)output.write(line2)output.write(line3)output.write(line4)record_number += 1for output in output_files:output.close()

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