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合作者在一个 word 文档中给了我一些 DNA 序列，我想将其转换为一个文件中的一系列 fasta 序列。

我已经把它变成了一个文本文件，我想用正则表达式来提取基因名称和序列：

use warnings;
use strict;

die "usage: make_fasta.pl <sequence file>" unless (@ARGV == 1);

my $seq_filename    = shift;
my $fasta_db_name   = $seq_filename . "_db.fa";

open(my $seq_file, '<', $seq_filename) 
          or die "can't open file $seq_filename, $!";
open(my $fasta_file, '>', $fasta_db_name) 
          or die "can't open file $fasta_db_name, $!";

while (my $line = <$seq_file>) {
    chomp $line;
    if ($line =~ /^[ATCG]+$/) { # if the line is entirely DNA seqence
       print $fasta_file "$line\n";            

    } elsif ($line =~ /Full-length (\w+) cDNA/) { # if the line has gene info
        print $fasta_file ">$1\n";

    } else {
        next;

    } 
}

但这只是给了我第一个基因的名字。很明显，我在 DNA 正则表达式上做错了，但我终其一生都无法解决。在我看来，这与我在本网站和其他网站上发现的其他建议的 DNA 测试完全相同。

我试图解析的文件配置如下：

Collaborators name

title of gene set

Full-length clock cDNA coding sequence 

ATGGTAGGATGTGTAATGCGTACGTGATCGT

Full-length per cDNA coding sequence

ATGCTAGCTACGTACGTAGCTACGTAGTACG

我希望输出是一个fasta文件，所以：

>clock
ATGGTAGGATGTGTAATGCGTACGTGATCGT
>per
ATGCTAGCTACGTACGTAGCTACGTAGTACG

实际输入文件的前几行是：

Dr Lin Zhang (Leicester University 10/2012) 

Canonical clock genes 

Full-length per cDNA coding seq (3693bp) 

ATGGACACAGGAACACCCCATGAAGATGTGCCCTCAGAGGACCACACCTTGGAAGAAGGGGACAGCAAGAACCCCTCGTGCCAGCAAGAGTCAGCCTACGGCTCCCTCGAGTCATCCTCCAATGGACAGTCTCAGAAAAGTTTCGGAGGAAGTGGAAGCAAAAGCTTAAATAGTGGTTCGAGTCACAGCAGCGGCTTTGGGGACCAAAATGATTTCAAGGGTATCCATCTTCACGAAGCGAAACACATAGCGTTGAAGAAGAAGAAAACTGGGAAAGGAGGTGAAAAGGTAGCAGAAATCCCCTTTCAAACTGCCTCTGAGGCAGAACTGTCCTCCAAAGGAAACGAAACAGAAAAGGAGAAAGAAACAAGCCTCGAGGAGTCTCCTGCTGCAAAAGAGGAAGCAATTATCGAAAAGGAGTCTCGTTACATCCACCCGAGGAACT
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2 回答 2

1

Kind of hard to answer this question without seeing part of the actual input file.

There is a mis-match between your example input and your REGEX:

# looking for verbatim('Full-length') then <space> then one WORD_WITH_ALPHNUMERICS  then <space> and then verbatim 'cDNA'
$line =~ /Full-length (\w+) cDNA/;

Your example input line has 'Full length' without a dash, multiple words for the gene name not just one and no 'cDNA' at the end.

If your input line has 'Full-length gene name with multiple words cDNA', your REGEX can be: 

$line=~/Full-length\s+(.*?)\s+cDNA/;
于 2013-05-28T08:58:05.970 回答
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问题显然出在您的输入数据上。我修改了您发布的代码以生成以下程序：

#!/usr/bin/env perl    

use warnings;
use strict;

while (my $line = <DATA>) {
    chomp $line;
    if ($line =~ /^[ATCG]+$/) { # if the line is entirely DNA seqence
       print "$line\n";            
    } elsif ($line =~ /Full-length (\w+) cDNA/) { # if the line has gene info
        print ">$1\n";
    } 
}


__DATA__
Collaborators name

title of gene set

Full-length clock cDNA coding sequence 

ATGGTAGGATGTGTAATGCGTACGTGATCGT

Full-length per cDNA coding sequence

ATGCTAGCTACGTACGTAGCTACGTAGTACG

它会产生您指定的输出：

~$ src/tmp/cdna 
>clock
ATGGTAGGATGTGTAATGCGTACGTGATCGT
>per
ATGCTAGCTACGTACGTAGCTACGTAGTACG

我的修改只是为了让它自成一体，并没有改变任何流程控制或逻辑，除了删除无用的else { next }子句。

你能找到并发布几行对你来说失败的实际数据，因为提供的虚拟数据似乎工作正常吗？

于 2013-05-28T09:27:46.380 回答