die "some usage error msg" if (@ARGV !=2);
my ($domFile,$csafile)= @ARGV; 

open(CSAFILE, "$csafile") or die "unable to open $csafile: $!";

my %csa_hash;
my %dom_hash;
my $domain_dir = "<my directory>";

while(<CSAFILE>)
{
    chomp;
    s/\s+//g;  #keep things simple, delete spaces
    my ($pdb,$chain,$res) = (split(/,/, $_))[0,3,4];
    push (@{$csa_hash{"$pdb;$chain"}},$res}); 
}