[Bioperl-l] Bioperl adds utility to msaexcise script

[Stephen Gordon Lenk]

I adopted Heikki Lehvaslaiho's ideas. The script now reads/writes multiple formats based on users request on 
command line. Thanks Bioperl developers! Snippet below shows use of AlignIO. I'll work on better/more flexible 
data mining for CD regions next. I'd like to be able to use multiple types of protein id's as are in user's 
alignment and get CD for it.

eval {

	##############
	# input stream
	##############
	
	use Bio::AlignIO;
	my $in = Bio::AlignIO->new( -fh        => \*STDIN,
	                                             -format => $informat ) -> next_aln();
	
	########## 
	# excision
	##########
	
	my $out = _excise( $max_e_value, 
					   $use_all_cds,
					   $full_excise,
					   \@excise_cd,
					   $in );
	
	
	###############
	# output stream
	###############
	
	Bio::AlignIO->new( -format => $outformat,
                                      -fh         => \*STDOUT ) -> write_aln($out);
};

Thanks,
Steve Lenk
slenk at emich.edu