#!/usr/bin/perl
use warnings;
use strict;
use feature qw{ say };

say my $search_for_species = 'O4';

while (<>) {
    my %counts;
    my @species = split;
    my @numbers = split ' ', <>;
    warn "Different number of columns at line $.!" if @species != @num
+bers;
    for my $i (0 .. $#species) {
        $counts{ $species[$i] } = $numbers[$i];
    }
    say $counts{$search_for_species} // 0;
}
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To output to a file, use redirection:

perl script_from_choroba.pl > new_file
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($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
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