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

Brian Osborne bosborne11 at verizon.net
Sun Feb 22 23:02:24 EST 2009


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/ 

   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');

   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

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