python处理fasta文件，ID和序列放在一行

Posted 2020-10-17 爬行的乌龟

#!/usr/bin/python
#-*- coding:utf-8 -*-
"处理fasta文件，将ID号和序列放在一行"
import sys
with open(sys.argv[1]) as f:
    fw=open(‘out.fasta‘, ‘w‘)
    line=f.read()
    line=line.replace(‘\n‘, ‘‘).replace(‘>‘, ‘\n>‘)
    for aa in line:
        fw.write(aa)
    fw.close()
"""
>chr1|hos107.1#gene1
ACACTCCCGGGCCCCCCCCCCCC
ACCTTTCAAAAAAAAAAAAAAA
AATTTTCCCCCCAAAGGGG
>chr1|hos107.2#gene2
ACACTCCCGGGCCCCCCCCCCCC
ACCTTTCAAAAAAAAAAAAAAA
AATTTTC
>chr1|hos107.4#gene3
ACACTCCCGGGCCCCCCCCCCCC
ACCTTTCAAAAAAAAAAAAAAA
AATTTTC
>chr1|hos107.5#gene4
ACACTCCCGGGCCCCCCCCCCCC
ACCTTTCAAAAAAAAAAAAAAA
AATTTTC
"""
"""
>chr1|hos107.1#gene1ACACTCCCGGGCCCCCCCCCCCCACCTTTCAAAAAAAAAAAAAAAAATTTTCCCCCCAAAGGGG
>chr1|hos107.2#gene2ACACTCCCGGGCCCCCCCCCCCCACCTTTCAAAAAAAAAAAAAAAAATTTTC
>chr1|hos107.4#gene3ACACTCCCGGGCCCCCCCCCCCCACCTTTCAAAAAAAAAAAAAAAAATTTTC
>chr1|hos107.5#gene4ACACTCCCGGGCCCCCCCCCCCCACCTTTCAAAAAAAAAAAAAAAAATTTTC
"""

#提取目标序列
f=open(‘./out.fasta‘, ‘r‘)
fw=open(‘target.fasta‘, ‘w‘) 
for line in f.readlines():
    if line.startswith(‘>chr1|hos107.1‘):
        fw.write(line)
f.close()
fw.close()


"""可以从上述处理好的单行文件out.fasta中提取指定目标ID的文件，并将其
写入到target.fasta文件中"""

#整体思路：
#先统一fasta文件格式从test.fasta----out.fasta
#取出目标ID序列：out.fasta----target.fasta