#!/usr/sbin/perl
if (!@ARGV) {
    print STDERR "usage: $0 alignment_file [threshold%]...\n";
    print_sets();
    exit 0;
}
my $FILE       = shift @ARGV;
my @THRESHOLD;
if (@ARGV) {
    @THRESHOLD = @ARGV;
} else {
    @THRESHOLD = (90, 80, 70, 60, 50);
}
my @ID;
my @ALIGNMENT;

read_alignment($FILE);
$n=@ID;
for ($i=0; $i<$n; $i++){
printf "%-15s %s\n", $ID[$i], join("", @{$ALIGNMENT{$ID[$i]}});
}
sub read_alignment {
    my ($file) = @_;
    my ($id, $line, %alignment);
    local (*TMP);

    open(TMP, "< $file") or die "can't open file '$file'\n";
    while ($line = <TMP>) {
        next    if $line =~ /^CLUSTAL/;

        if ($line =~ /^([^      ]+)\s+([-a-zA-Z*.]+) *$/) {
       
       if (! $alignment{$1}) {
                
               # new sequence identifier
                push (@ID, $1);
             
          }


            #strip spaces,tabs,newlines: extend alignment array
            $line = $2;
            $line =~ tr/ \t\n//d;
            push (@{$ALIGNMENT{$1}}, split("", $line));

        }

    }
   
close TMP;
}