从fasta文件中批量提取特定序列

如题，目的是从fasta文件中批量提取特定的基因序列.
实现办法有几种：

1. perl脚本：
   CSDN博主「little^raccoon」的原创文章perl实现根据序列ID从提取fasta文件序列
   原文链接：https://blog.csdn.net/weixin_40099163/article/details/109635328

   usage: perl thisScript.pl query.fa gene.lst outfile

query.fa 基因组或其他需要从中提取的fasta格式文件
gene.lst 需要提取的基因或染色体名字，有无>均可
outfile 输出文件

#!/bin/perl
#unless(@ARGV==3){
#   die "usage: $0   \n";
#}
$file=shift;
$lst=shift;
$out=shift;

open FILE,$file;
open LST,$lst;
open OUT,">".$out;

while(){
    chomp;
    my $line=$_;
    if($line=~/^>/){
        my @line=split /[ |\t]/,$line;
        our $name=$line[0];
        #print "$name\n";
    }
    else{
        $seq_hash{$name}.=$line;
    }
}
while(){
    chomp;
    my $line=$_;
    if($line=~/^>/){
        $ID=$line;
        if(exists $seq_hash{$ID}){
            print OUT "$ID\n$seq_hash{$ID}\n";
        }
        else{
            print OUT "error1: ".$ID." no found.\n";
        }
    }
    else{
        my $ID=">".$line;
        if(exists $seq_hash{$ID}){
            print OUT "$ID\n$seq_hash{$ID}\n";
        }
        else{
            print OUT "error2: ".$ID." no found.\n";
        }
    }
}

2. python
   采用click模块添加命令行参数。**
   CSDN博主「冷月、无声」的原创文章：根据ID从FASTA文件中批量提取序列【Python脚本】
   原文链接：https://blog.csdn.net/weixin_42358077/article/details/87985833

# -*- coding: utf-8 -*-
"""
@author: gyw
@Date:  Wed Feb 27 09:19:54 2019
@E-mail: [email protected]
@Description: This program can extract sequences 
              from a fasta file, according to a 
              given id list.
"""

import click

@click.command()
@click.option('-f', '--fastafile', help='Input a fasta file', required=True)
@click.option('-i', '--idfile', help='Input an idlist', required=True)
@click.option('-o', '--outfile', help='Input the name of result file', default='result.fa')


def main(fastafile, idfile, outfile):
    """ 
    Extract seqences from a fasta file 
    according to a id list.
    """
    idfile = open(idfile, 'r')
    resultfile = open(outfile, 'w')
    for id in idfile:
        qid = id.strip()
        flag = 0 
        with open(fastafile,'r') as ffile:
            for line in ffile:
                line = line.strip()
                if line.startswith('>'):
                    name = line.replace('>','').split()[0]
                    if name == qid:
                        flag = 1
                        resultfile.write(line + '\n')
                    else:
                        flag = 0
                else:
                    if flag == 0:
                        pass
                    else:
                        resultfile.write(line + '\n')
    resultfile.close()

if __name__ == '__main__':
    main()

3. TBtool software^[1]
   这个小工具诞生之初就是为了解决最基本的序列提取等操作，随着作者的不断完善，现在已经是一个小有名气的多功能生信软件，兼具绘图等功能，各类教程可以看作者发布的使用说明。

4. 在线云平台
   以联川生物的云平台为例，https://www.omicstudio.cn/tool/77，可以参看微信公众号推文使用说明，免费在线小工具：fasta序列提取

只要思想不滑坡，办法总比困难多。

---

1. Chen C , Chen H , Y Zhang, et al. TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data[J]. Molecular Plant, 2020, 13(8). ↩