From looking at the source, I think this is equivalent:

use Bio::LocatableSeq ();
use Bio::SimpleAlign  ();
    
my $aln = Bio::SimpleAlign->new();

foreach (qw/ AAAAAAAAAAAAAAA AAAAAAAGGAAACCA /) {
   $aln->add_seq(
      Bio::LocatableSeq->new(
         '-seq'   => $_,
         '-start' => 1,
         '-end'   => length($_),
      )
   );
}

print("IDENTITY : ", $aln->percentage_identity, "\n");
print("CONSENSUS: ", $aln->consensus_string(28), "\n");

[download]

You can optionally add
'-display_id'  => 'Seq'.++$seq_id,
as an argument to the Bio::LocatableSeq constructor.

Warning: This is untested code written using unfamiliar modules.

In reply to Re: Converting Filehandle to Array call in Object Creation by ikegami
in thread Converting Filehandle to Array call in Object Creation by monkfan

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