It is difficult to know quite what data structure and form you want from the description (See I know what I mean. Why don't you?). I've assumed you want an array formed with the even lines appended to the odd lines with a space between. Here's an SSCCE to demonstrate one technique for this.

use strict;
use warnings;

use Test::More tests => 1;

my @seq;
my @want = (
    '>NM_001 Homo sapiens ADA2 (CECR1) GATCCAA',
    '>NM_002 Homo sapiens IKBKG GGAGGTCTTTAGCTTTAGGGAAACCC',
);

while (<DATA>) {
    chomp;
    if (/^>/) {
        push @seq, "$_ ";
    } else {
        $seq[-1] .= $_;
    }
}

is_deeply \@seq, \@want;

__DATA__
>NM_001 Homo sapiens ADA2 (CECR1)
GATCCAA
>NM_002 Homo sapiens IKBKG
GGAGGTCTTTAGCTTTAGGGAAACCC

[download]

See also How to ask better questions using Test::More and sample data. HTH.

In reply to Re: Size of sequences in fastafile by hippo
in thread Size of sequences in fastafile by Sofie

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