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die "some usage error msg" if (@ARGV !=2);
my ($domFile,$csafile)= @ARGV; 
...
    my ($pdb,$chain,$res) = (split(/,/, $_))[0,3,4];
    push (@{$csa_hash{"$pdb;$chain"}},$res}); 
}

while ((my $key, my $value) = each(%csa_hash))
{....}

if("$domchain" eq "$pdbchain"){....}