#!/usr/bin/env perl
use strict;
use warnings;

my $filename = 'file';
open my $fh, "<", $filename or die $!;
local $/ = "//\n";
while(defined(my $line = <$fh>)) {
    chomp $line;
    my ($seq_length, $ID, $top, $seq);
    foreach my $part (split /\n/, $line) {
        if($part =~ /^(\d+)\s+(.*)$/) {
            $seq_length = $1;
            $ID = $2;
            next;
        }
        if($part =~ /^([S\.]+)$/) {
            $top .= $1;
            next;
        }
        $seq .= $part;
    }
    print ">$ID\n$seq\n$top\n";
}
close $fh;