[Bioperl-l] Difference between Bio::SimpleAlign Object and Bio::Align::AlignI Object

[Brian Osborne]

Warren,

We can't tell what %nucseq_hash is from your message, so this is hard  
to diagnose. If you want to see functional code take a look at t/Align/ 
AlignUtil.t:

   my $in = Bio::AlignIO->new(-format => 'clustalw',
									-file   => test_input_file('pep-266.aln'));
   my $aln = $in->next_aln();
   isa_ok($aln, 'Bio::Align::AlignI');
   $in->close();

   my $seqin = Bio::SeqIO->new(-format => 'fasta',
									 -file   => test_input_file('cds-266.fas'));

   # get the cds sequences

   my %cds_seq;

   while( my $seq = $seqin->next_seq ) {
      $cds_seq{$seq->display_id} = $seq;
   }

   my $cds_aln = &aa_to_dna_aln($aln,\%cds_seq);


Brian O.



On Feb 21, 2009, at 5:59 PM, Warren Gallin wrote:

> aa_to_dna_aln