#!/usr/bin/perl 
#use warnings;
#use strict;
use Bio::AlignIO;

my $usage = "homstrad2multifasta.pl infile outfile\n";

my $infile  = shift or die $usage;
my $outfile = shift or die $usage;


# note: we quote -format to keep older perl's from complaining.
open INFILE, "<".$infile or die $!;
open OUTFILE, ">".$outfile or die $!;
while ( <INFILE> ) {
    if ($_ =~ /^C;/ || 
	$_ =~ /^structure[XN]*:/){
    } else {
	print OUTFILE $_;
    }
}
close INFILE;
close OUTFILE;
