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

my @output = (
        { file => "chr1.gens", pattern => qr/^0/ },
        { file => "chr2.gens", pattern => qr/^1/ },
        { file => "chr3.gens", pattern => qr/^2/ },
);

my $file = "test.txt";
open(IN,'<'.$file) || die "Can not open file $file: $!";

# open the output handles
foreach my $o (@output) {
        my $file = $o->{file};
        open(my $handle, "> $file") or die "Can't open $file: $!";
        $o->{handle} = $handle;
}

while (my $line = <IN>) {
                
        foreach my $o (@output) {
        
                my $pattern = $o->{pattern};
                if($line =~ $pattern) {
                        print $o->{handle} $line;
                        # oder eben print $o->{handle} "$line\n";
                        # falls das zusätzlich \n erwünscht ist
                }
        }
                
}

# close the output handles
foreach my $o (@output) { close $o->{handle}; }

close IN;