如何在一个文件中提取fasta序列，该文件的头部行与另一个文件中的列表相匹配？

Question

我是一个新手，Perl的。我试图从一个与另一个文件中的行匹配的文件中提取fasta序列。两个示例文件如下：

File1.fasta：

> gene_44 | 105_nt | + | 47540 | 47644 GTGCGCCGGCGCGTCGCGATCGCGAACCGGCCCGTGCGAATCCTGCCGCATGCGCGCCGCATCTCGCCACGCCGCGCATTTCATTTCGACATCCATAACGTCTGA

> gene_69 | 111_nt | + | 75846 | 75956 ATGCCGTTGCCGTCGCGCATCGCGGCGGCCGTGCGCGGCGCGCATGCATACGCCGGCACGGCCGATGCGCGCGCGACGCGCAAACTGCACGCGGCGCGGGATTTGTGTTGA

> gene_88 | 177_nt | - | 97993 | 98169
ATGCGCCAGCCGACGCACGCCCATTCCGGGCGAAACGTTCCCCTTATCCATTCGATCATCCGTGCCGCACTGCGCGAAGCGGCCACCGCCGACACGTACCAAACCGCGCTCGATGCGACCGGCGCGGCACTCGTCGCCATCGCGGCGCTCGTGCGCGCGGAGGTGCGGCATGGCTGA

> gene_90 | 141_nt | - | 99016 | 99156
TTGGAAGGGCGCTTTCCGCGTGCGAGTCGTCTGACGCAGCGTTGCACGGTCTGGTCGAATCGCGAGCTTCATCGCTGGATGGCCGATCCGTTGAACTATCGCGCTGTCGACGCGGCGAACCAGACGACGGAGGGCGCGTAA

File2.list：

somewordsinfront，> gene_44 | somewordsattheback

blablabla，> gene_88 | blablablablabla

，我期望是如下输出：

> gene_44 | 105_nt | + | 47540 | 47644 GTGCGCCGGCGCGTCGCGATCGCGAACCGGCCCGTGCGAATCCTGCCGCATGCGCGCCGCATCTCGCCACGCCGCGCATTTCATTTCGACATCCATAACGTCTGA

> gene_88 | 177_nt | - | 97993 | 98169
ATGCGCCAGCCGACGCACGCCCATTCCGGGCGAAACGTTCCCCTTATCCATTCGATCATCCGTGCCGCACTGCGCGAAG CGGCCACCGCCGACACGTACCAAACCGCGCTCGATGCGACCGGCGCGGCACTCGTCGCCATCGCGGCGCTCGTGCGCGCGGAGGTGCGGCATGGCTGA

我怎样才能做到这一点？提前致谢！ :)

Answer 1

当你问的问题下一次，请您出示的代码，例如

use strict; 
use warnings; 

my @genes; 

open my $list, '<file2.list'; 
while (my $line = <$list>) { 
    push (@genes, $1) if $line =~ /[^>]+>([^|]+)/; 

} 
my $input; 
close $list; 
{ 
    local $/ = undef; 
    open my $fasta, '<file1.fasta'; 
    $input = <$fasta>; 
    close $fasta; 
} 
my @lines = split(/>/,$input); 
foreach my $l (@lines) { 
    foreach my $reg (@genes) { 
     print ">$l" if $l =~ /$reg/ 
    } 
}