博主也是刚刚接触生信,会将自己平时练习用到的python脚本发布到博客上,用来记录自己的学习之路。
介绍
测序回来的fastq文件通常在分析之前,需要进行过滤,该脚本利用python实现fastq文件中提取指定ID的序列,并保存为新fastq文件,脚本一所有输入文件和输出文件都必须是压缩文件格式,脚本二是否压缩均可,但输出的过滤后的文件会和原始fastq文件保持一致。
说明
脚本一:
- 输入文件为fq.gz文件,压缩的ID list文件。
- 必须是压缩格式的文件才可以,如果非压缩格式,可以压缩成gz格式后使用该脚本,或者将该脚本改写。
脚本二:
- 自动识别input文件格式,无论fq文件是否压缩都可以打开。
- 输出文件格式默认与fq文件一致,即fq是压缩文件,过滤后的输出文件也是压缩文件,fq没有压缩,输出文件也是普通格式。
脚本如下
脚本一
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#Author: gyw
#Date: 2019-03-07
#E-mail: willgyw@126.com
#Description:Filter reads from fastq.gz
import gzip
import argparse
parser = argparse.ArgumentParser(description='filter reads from fastq.gz')
parser.add_argument('--fastq', '-q', dest='fastq', help='input a fastq.gz file')
parser.add_argument('--idlist', '-i', dest='idlist', help='input idlist.gz file')
parser.add_argument('--outfile', '-o', dest='outfile', help='input outfile name,end by gz')
args = parser.parse_args()
fastqdict = {}
with gzip.open(args.fastq, 'rb') as fastq:
for line in fastq:
if line.decode().startswith('@'):
fastqid = line.decode().strip().split()[0][1:]
fastqdict[fastqid] = ''
else:
fastqdict[fastqid] += line.decode()
outfile = gzip.open(args.outfile, 'wb')
with gzip.open(args.idlist, 'rb') as idfile:
for line in idfile:
readsid = line.decode().strip()
for key in fastqdict.keys():
if readsid == key:
res = '@' + key + '\n' + fastqdict[key]
outfile.write(res.encode())
outfile.close()
脚本二
import filetype
import gzip
import argparse
parser = argparse.ArgumentParser(description='filter reads from fastq')
parser.add_argument('--fastq', '-q', dest='fastq', help='input a fastq file')
parser.add_argument('--idlist', '-i', dest='idlist', help='input idlist file')
parser.add_argument('--outfile', '-o', dest='outfile', help='input outfile name')
args = parser.parse_args()
fastqdict = {}
kind1 = filetype.guess(args.fastq)
kind2 = filetype.guess(args.idlist)
if kind1 is None:
with open(args.fastq,'r') as fastq:
for line in fastq:
if line.startswith('@'):
fastqid = line.strip().split()[0][1:]
fastqdict[fastqid] = ''
else:
fastqdict[fastqid] += line
elif kind1.extension == 'gz':
with gzip.open(args.fastq, 'rb') as fastq:
for line in fastq:
if line.decode().startswith('@'):
fastqid = line.decode().strip().split()[0][1:]
fastqdict[fastqid] = ''
else:
fastqdict[fastqid] += line.decode()
if kind1 is None:
outfile = open(args.outfile, 'w')
elif kind1.extension == 'gz':
outfile = gzip.open(args.outfile, 'wb')
if kind2 is None:
with open(args.idlist, 'r') as idfile:
for line in idfile:
readsid = line.strip()
for key in fastqdict.keys():
if readsid == key:
res = '@' + key + '\n' + fastqdict[key]
if kind1 is None:
outfile.write(res)
elif kind1.extension == 'gz':
outfile.write(res.encode())
elif kind2.extension == 'gz':
with gzip.open(args.idlist, 'rb') as idfile:
for line in idfile:
readsid = line.decode().strip()
for key in fastqdict.keys():
if readsid == key:
res = '@' + key + '\n' + fastqdict[key]
if kind1 is None:
outfile.write(res)
elif kind1.extension == 'gz':
outfile.write(res.encode())
outfile.close()
如有错误,欢迎大家指正。