#!/usr/bin/perl -w
use strict;
use Bio::AlignIO;
use Bio::Align::Utilities qw(aa_to_dna_aln);
use Bio::SeqIO;
my $dir = shift @ARGV || 'clusterfam';

opendir(DIR, $dir) || die "cannot open dir $dir: $!";
for my $file ( readdir(DIR) ) {
 if( $file =~ /(\S+)\.pep\.aln$/ ) {
  my $stem = $1;
  my $in = Bio::SeqIO->new(-format => 'fasta', 
			   -file  => "$dir/$stem.cds.fa");
  my %cds_map;
  while( my $seq = $in->next_seq ) {
    my $id = $seq->display_id;
    $cds_map{$id} = $seq;
  } 
  my $alnin = Bio::AlignIO->new(-format => 'fasta',
				-file   => "$dir/$file");
  if( my $pepaln = $alnin->next_aln ) {
   my $cds_aln = aa_to_dna_aln( $pepaln, \%cds_map);
   my $alnout = Bio::AlignIO->new(-format => 'phylip',
				  -file  => ">$dir/$stem.cds.phy");
   $alnout->write_aln($cds_aln); 
  } else { 
	die("there was something weird, I can't read alignment in $dir/$file");
  }
 }
}