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使用Perl和REGEX连接FASTA文件中的样本的多个序列

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我有超过200个多序列fasta文件，并且在每个fasta文件中，有一些序列可供选择基因的数百个样本（即样本输入fasta文件中的PF3D7_1467550） . fasta文件中的大多数样本（即样本303.1-样本输入文件中的第一个序列）具有一个序列，但是其他样本（即IGS-MLW-089sA和IGS-MWI-254sA）具有需要连接的基因的多个序列一起 .

示例输入fasta文件

>303.1_assembled_PF3D7_1475500.[1:126].sp.tr
MHHLLFIIWYIILNYYVSGQESATNFYKFIDSFASSTYISEESGSSAYDAKRAIQNNPNY
EEKKTYDEELKESKEKANDLNNKLSLLTSVNVNTLDSDILKLGILPGDSYNFPANDCAVI
KNVQ

>IGS-MLW-089sA_assembled_PF3D7_1475500.[1:61].sp.tr
MHHLLFIIWYIILNYYVSGQESATNFYKFIDSFASSTYISEESGSSAYDAKRAIQNNPNY
>IGS-MLW-089sA_assembled_PF3D7_1475500.[65:126].sp.tr
TYDEELKESKEKANDLNNKLSLLTSVNVNTLDSDILKLGILPGDSYNFPANDCAVIKNVQ

>IGS-MWI-254sA_assembled_PF3D7_1475500.[1:61].sp.tr
MHHLLFIIWYIILNYYVSGQESATNFYKFIDSFASSTYISEESGSSAYDAKRAIQNNPNY
>IGS-MWI-254sA_assembled_PF3D7_1475500.[65:119].sp.tr
TYDEELKESKEKANDLNNKLSLLTSVNVNTLDSDILKLGILPGDSYNFPANDC

期望的输出：

>303.1_assembled_PF3D7_1475500.[1:126].sp.tr
 MHHLLFIIWYIILNYYVSGQESATNFYKFIDSFASSTYISEESGSSAYDAKRAIQNNPNY
 EEKKTYDEELKESKEKANDLNNKLSLLTSVNVNTLDSDILKLGILPGDSYNFPANDCAVI
 KNVQ

 >IGS-MLW-089sA_assembled_PF3D7_1475500.[1:61][65:126].sp.tr
 MHHLLFIIWYIILNYYVSGQESATNFYKFIDSFASSTYISEESGSSAYDAKRAIQNNPNY
 TYDEELKESKEKANDLNNKLSLLTSVNVNTLDSDILKLGILPGDSYNFPANDCAVIKNVQ

 >IGS-MWI-254sA_assembled_PF3D7_1475500.[1:61][65:119].sp.tr
 MHHLLFIIWYIILNYYVSGQESATNFYKFIDSFASSTYISEESGSSAYDAKRAIQNNPNY
 TYDEELKESKEKANDLNNKLSLLTSVNVNTLDSDILKLGILPGDSYNFPANDC

我相信来自另一张票的代码可能很有用 .

%hash;
 while (<DATA>) {
    if (/^>(miRNA\d+)/) {
            $hash{$1}[0] = $_;
            chomp($n = <DATA>);
            unshift @{$hash{$1}[1]}, $n;
    }
}

for $k (sort keys %hash) {
    print $hash{$k}[0], join(',', @{$hash{$k}[1]}), "\n";
 }

这是上一张票的链接：

I need search a pattern in a header line of my file and concatenates the next line with Perl

我正在寻找帮助来修改以下部分代码来处理选择sampleID或替代建议 .

/^>(miRNA\d+)/

谢谢

regex perl pattern-matching concatenation fasta

2 回答

  • 3

    如果要连接的样本是相邻的，则可以只收集范围（例如 [1:61] ）和要在两个数组中打印的行 .

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

sub without_ranges {
    my ($header) = @_;
    ( my $without = $header ) =~ s/\[[^\]]+\]//g;
    return $without
}

sub output {
    my ($header, $ranges, $buffer) = @_;
    my $header_with_ranges = $header;
    $header_with_ranges =~ s/(.*\])/$1\[$_]/ for @$ranges;
    print $header_with_ranges, @$buffer;
}


my (@buffer, @ranges);
my $header = "";

while (<>) {
    if (/^>/) {
        my $new_header = $_;
        if (without_ranges($new_header) eq without_ranges($header)) {
            push @ranges, $new_header =~ /\[([^\]]+)\]/;

        } else {
            output($header, \@ranges, \@buffer) if $header;
            $header = $new_header;
            @buffer = @ranges = ();
        }
        last if eof;

    } else {
        push @buffer, $_;
    }
}
output($header, \@ranges, \@buffer);
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  • -1

    来自另一张票的代码没有那么有用，而且有点......不够理想，坦率地说 .
    这是一个可能的解决方案，假设您总是有范围 [x:y] .

    use strict; use warnings;

my (%hash,$key,$start
    );
while(<DATA>) {
    chomp;
    if (m{^(>.*?)(?:\[(\d+):(\d+)\]\.sp\.tr)?$}) {
        ($key,$start)=($1,$2);
        next;
    }
    $hash{$key}{$start}.=$_;
}

for my $key (sort keys %hash) {
      my $keyref=$hash{$key};
      printf "%ssp.tr\n%s\n", $key, join (''
                                , map { $keyref->{$_}} sort {$a<=>$b} keys %$keyref
                                );
}

__DATA__
>303.1_assembled_PF3D7_1475500.[1:126].sp.tr
MHHLLFIIWYIILNYYVSGQESATNFYKFIDSFASSTYISEESGSSAYDAKRAIQNNPNY
EEKKTYDEELKESKEKANDLNNKLSLLTSVNVNTLDSDILKLGILPGDSYNFPANDCAVI
KNVQ

>IGS-MLW-089sA_assembled_PF3D7_1475500.[1:61].sp.tr
MHHLLFIIWYIILNYYVSGQESATNFYKFIDSFASSTYISEESGSSAYDAKRAIQNNPNY
>IGS-MLW-089sA_assembled_PF3D7_1475500.[65:126].sp.tr
TYDEELKESKEKANDLNNKLSLLTSVNVNTLDSDILKLGILPGDSYNFPANDCAVIKNVQ

>IGS-MWI-254sA_assembled_PF3D7_1475500.[1:61].sp.tr
MHHLLFIIWYIILNYYVSGQESATNFYKFIDSFASSTYISEESGSSAYDAKRAIQNNPNY
>IGS-MWI-254sA_assembled_PF3D7_1475500.[65:119].sp.tr
TYDEELKESKEKANDLNNKLSLLTSVNVNTLDSDILKLGILPGDSYNFPANDC

    >303.1_assembled_PF3D7_1475500.sp.tr
MHHLLFIIWYIILNYYVSGQESATNFYKFIDSFASSTYISEESGSSAYDAKRAIQNNPNYEEKKTYDEELKESKEKANDLNNKLSLLTSVNVNTLDSDILKLGILPGDSYNFPANDCAVIKNVQ
>IGS-MLW-089sA_assembled_PF3D7_1475500.sp.tr
MHHLLFIIWYIILNYYVSGQESATNFYKFIDSFASSTYISEESGSSAYDAKRAIQNNPNYTYDEELKESKEKANDLNNKLSLLTSVNVNTLDSDILKLGILPGDSYNFPANDCAVIKNVQ
>IGS-MWI-254sA_assembled_PF3D7_1475500.sp.tr
MHHLLFIIWYIILNYYVSGQESATNFYKFIDSFASSTYISEESGSSAYDAKRAIQNNPNYTYDEELKESKEKANDLNNKLSLLTSVNVNTLDSDILKLGILPGDSYNFPANDC
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