use Data::Dumper;
my %hoa;

while ( my $line = <DATA> )
{
    chomp $line;
    my $fname;

    if ( $line =~ /^[a-z]/ )
    {
       $fname = $line;
    }
    elsif ($line =~ /^[0-9]+,/)
    {
        my $content = $line;
        push @{ $hoa{$fname} }, $content;
    }
}               # -----  end while  -----

print Dumper \%hoa;

#There are many datasets, here I just take 3 of them

__DATA__
>data set
dm01
>instances
0,-869,foofoofoofoofoofoofoofoo,28
0,-853,barbarbarbarbar,14
>data set
yst02
>instances
0,-1566,quxquxquxqux,9
0,-1545,bembembem,9
0,-1394,birbirbirbir,9
>data set
mus03
>instances
0,-1274,tingtingtingting,11
0,-1220,tongtongtong,11
0,-475,bubububu,11
0,-459,catcatcatcatcat,11

##</code><code>##

$HoA = {

         'yst02'=> [
                    '0,-1566,quxquxquxqux,9',
                    '0,-1545,bembembem,9',
                    '0,-1394,birbirbirbir,9'
                   ],
         'dm01'=> [
                    '0,-869,foofoofoofoofoofoofoofoo,28',
                    '0,-853,barbarbarbarbar,14'
                  ],
         'mus03'=> [
                    '0,-1274,tingtingtingting,11',
                    '0,-1220,tongtongtong,11',
                    '0,-475,bubububu,11',
                    '0,-459,catcatcatcatcat,11',
                  ],
}