Convert Stockholm sequence format to Fasta

The original stockholm2fasta.pl didn't preserve the order of sequences. I fixed it to preserve the order:

	#!/usr/bin/perl -w
	my $columns = 50;
	my $gapped = 0;
	my $progname = $0;
	$progname =~ s/^.*?([^\/]+)$/$1/;
	my $usage = "Usage: $progname [<Stockholm file(s)>]\n";
	$usage .= " [-h] print this help message\n";
	$usage .= " [-g] write gapped FASTA output\n";
	$usage .= " [-s] sort sequences by name\n";
	$usage .= " [-c <cols>] number of columns for FASTA output (default is $columns)\n";
	# parse cmd-line opts
	my @argv;
	while (@ARGV) {
	my $arg = shift;
	if ($arg eq "-h") {
	die $usage;
	} elsif ($arg eq "-g") {
	$gapped = 1;
	} elsif ($arg eq "-s"){
	$sorted = 1;
	} elsif ($arg eq "-c") {
	defined ($columns = shift) or die $usage;
	} else {
	push @argv, $arg;
	}
	}
	@ARGV = @argv;
	my @seqorder = ();
	my %seq;
	while (<>) {
	next unless /\S/;
	next if /^\s*\#/;
	if (/^\s*\/\//) { printseq() }
	else {
	chomp;
	my ($name, $seq) = split;
	$seq =~ s/[\.\-]//g unless $gapped;
	push @seqorder, $name unless exists $seq{$name};
	$seq{$name} .= $seq;
	}
	}
	printseq();
	sub printseq {
	@seqorder = sort @seqorder if $sorted;
	foreach $key (@seqorder) {
	print ">$key\n";
	for (my $i = 0; $i < length $seq{$key}; $i += $columns){
	print substr($seq{$key}, $i, $columns), "\n";
	}
	}
	%seq = ();
	@seqorder = ();
	}

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