[Bioperl-l] Simplealign question

Luba Pardo lubapardo at gmail.com
Thu Mar 8 09:56:06 EST 2007


Hello all,
I am trying to understand the objects of the Bio::SimpleAlign module. I read
in the doc of the module that you get an array of Seq objects if you use the
each_seq method.
So, can you get back the sequences used in the alignment from the align
object using the each_seq method? For example:

# Extract sequences and check values for the alignment column $pos (this is
part of the doc. example)
 foreach $seq ($aln->each_seq) {

  }
what the $seq is? I printed and is a locatableseq object, but if it is a Seq
object, should I be able to get the actual seq string? I tried something
like
...
my $seq_obj= Bio::Seq->new();

 my $x = $seq_obj->seq;
but it does not print anything.
Does someone know if this makes sense?

Regards,
L. Pardo


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