Question

我试图在多个fasta文件中获得RNA的反向补体

输入：

>cel-mir-39 MI0010 C elegans miR-39
UAUACCGAGAGCCCAGCUGAUUUCGUCUUGGUAAUAAGCUCGUCAUUGAGAUUAUCACCGGGUGUAAAUCAGCUUGGCUCAAAAAAAA

>cel-let-7 MI0001 C elegans let-7
UACACUGUGGAUCCGGUGAGGUAGUAGGUUGUAUAGUUUGGAAUAUUACCACCGGUGAACUAUGCAAUUUUCUACCUUACCGGAGGGGGGG

输出：

>cel-mir-39 MI0010 C elegans miR-39
UUUUUUUUGAGCCAAGCUGAUUUACACCCGGUGAUAAUCUCAAUGACGAGCUUAUUACCAAGACGAAAUCAGCUGGGCUCUCGGUAUA

>cel-let-7 MI0001 C elegans let-7
CCCCCCCUCCGGUAAGGUAGAAAAUUGCAUAGUUCACCGGUGGUAAUAUUCCAAACUAUACAACCUACUACCUCACCGGAUCCACAGUGUA

但是我得到了这个：

UUUUUUUUGAGCCAAGCUGAUUUACACCCGGUGAUAAUCUCAAUGACGAGCUUAUUACCAAGACGAAAUCAGCUGGGCUCUCGGUAUA
93-Rim snucele G 0100IM 93-rim-leg 
CCCCCCCUCCGGUAAGGUAGAAAAUUGCAUAGUUCACCGGUGGUAAUAUUCCAAACUAUACAACCUACUACCUCACCGGAUCCACAGUGUA
7-tel snucele G 1000IM 7-tel-leg

我的代码：

#!/usr/bin/perl
use strict;
use warnings;

print "type in the path of the file\n";
my $file_name = <>;
chomp($file_name); 

open (FASTA, $file_name) or die "error #!"; 

$/ = ">";
<FASTA>;    
while (my $entry = <FASTA>){
    $entry = reverse $entry;
    $entry =~ tr/ACGUacgu/UGCAugca/;
    print "$entry \n";
}

close(FASTA);

如何只反转序列而不是标题？感谢

Answer 1

读取由>分隔的记录是一个不错的主意，因为它一次为您提供整个块。但是，在这里您要处理和合并行而不是标题，从而区分行。逐行阅读更清楚。

序列行是特定的：全部大写，没有别的。空行将记录分隔为处理。剩下的可能性是标题。序列是通过连接与其图案匹配的线来组装的，一旦我们点击空行，就会对其进行处理和打印。

open (FASTA, $file_name) or die "error $!";

# sequence, built by joining lines =~ /^[A-Z]+$/
my $sequence = '';

while (my $entry = <FASTA>)
{
    if ($entry =~ m/^[A-Z]+$/) {
        # Assemble the sequence from separate lines
        chomp($entry);
        $sequence .= $entry;
    }
    elsif ($entry =~ m/^\s*$/) { 
        # process and print the sequence and blank line, reset for next
        $sequence = reverse $sequence;
        $sequence =~ tr/ACGUacgu/UGCAugca/;
        print "$sequence\n";
        print "\n";
        $sequence = '';
    }
    else { # header
        print $entry;
    }
}

# Print the last sequence if the file didn't end with blank line    
if (length $sequence) {
    $sequence = reverse $sequence;
    $sequence =~ tr/ACGUacgu/UGCAugca/;
    print "$sequence\n";
}

^和$是锚点，用于字符串的开头和结尾。因此匹配序列的正则表达式要求整行严格限制。另一个正则表达式只允许可选空格\s*，指定一个空行。

从问题中复制序列处理。

Answer 2

TXR解决方案：

@(bind compl @(hash-from-pairs (zip "ACGUacgu" "UGCAugca")))
@(repeat)
>@header
@  (collect)
@rna
@  (until)

@  (end)
@  (output)
>@header
@(mapcar compl (reverse (cat-str rna)))

@  (end)
@(end)

执行命令

$ txr revcomp.txr data
>cel-mir-39 MI0010 C elegans miR-39
UUUUUUUUGAGCCAAGCUGAUUUACACCCGGUGAUAAUCUCAAUGACGAGCUUAUUACCAAGACGAAAUCAGCUGGGCUCUCGGUAUA

>cel-let-7 MI0001 C elegans let-7
CCCCCCCUCCGGUAAGGUAGAAAAUUGCAUAGUUCACCGGUGGUAAUAUUCCAAACUAUACAACCUACUACCUCACCGGAUCCACAGUGUA

此变体将输出格式化为46列，与原始格式相同：

@(bind compl @(hash-from-pairs (zip "ACGUacgu" "UGCAugca")))
@(repeat)
>@header
@  (collect)
@rna
@  (until)

@  (end)
@  (output)
>@header
@  (repeat :vars ((crna (tuples 46 (mapcar compl (reverse (cat-str rna)))))))
@crna
@  (end)

@  (end)
@(end)

执行命令

$ txr revcomp.txr data
>cel-mir-39 MI0010 C elegans miR-39
UUUUUUUUGAGCCAAGCUGAUUUACACCCGGUGAUAAUCUCAAUGA
CGAGCUUAUUACCAAGACGAAAUCAGCUGGGCUCUCGGUAUA

>cel-let-7 MI0001 C elegans let-7
CCCCCCCUCCGGUAAGGUAGAAAAUUGCAUAGUUCACCGGUGGUAA
UAUUCCAAACUAUACAACCUACUACCUCACCGGAUCCACAGUGUA

Answer 3

尝试以下内容

首先，我按换行符分割数据。并将标题存储到$header和@ar中的其余数据中。

然后通过换行符加入数组并存储到$entry。然后执行替换以从RNA序列中删除\n>\r\s个字符。

然后像往常一样反转字符串并执行翻译。最后通过print语句获取输出。

open my $fh,"<","filename.text" or die"error opening $!";

$/ = ">";

<$fh>;

while (<$fh>)
{
    my ($header,@ar) = split("\n",$_);

    my $entry =join("\n",@ar);

    $entry=~s/\n|\r|>|\s//g;

    $entry = reverse $entry;

    $entry =~ tr/ACGUacgu/UGCAugca/;

    print ">$header\n$entry\n\n";
}

fasta文件的反向补充

3 个答案: