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  • python处理fasta文件,ID和序列放在一行

    #!/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('
    ', '').replace('>', '
    >')
        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
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  • 原文地址:https://www.cnblogs.com/lmt921108/p/8023209.html
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