#!/usr/bin/perl -w

#
# Splits multi-contig-ace file into several single-contig-ace files
# 
# Author: Bernd Senf ( bsenf@fli-leibniz.de ), 2008
#
# Syntax: perl ace_split.pl < 454Contigs.ace
#

my $cnt=1;
my $in_contig=0;
my @lines;


sub print_contig {
	my $ace;
	my $rd=0;
	
	foreach ( @lines ) { 
		$rd++  if /^AF /; 
	}
	
	return if ( ! $rd );
	
	$ace=sprintf("contig_%5.5d.ace",$cnt);
	$lst=sprintf("contig_%5.5d.lst",$cnt);
	
	$cnt++;
	
	print STDERR "Write $ace and $lst with $rd traces ...\n";
	
	open(ACE,">$ace") || die "Can't create $ace : $!\n";	
	print ACE  "AS 1 $rd\n\n";
	print ACE  @lines;
	close(ACE);
		
	open(LST,">$lst") || die "Can't create $lst : $!\n";
	foreach (@lines) {
		if ( /^RD (\S+) / ) { 
			my @A=split(/\./,$1);
			print LST "$A[0]\n"; };
	}
	close(LST)
}


while (<>) {
	if (/^CO/) 
	{
		$in_contig=1;	
		print_contig();
		@lines=();
	}
	push (@lines,$_) if ( $in_contig);
}

print_contig();