[Bioperl-l] AlignIO and SimpleAlign

[Jason Stajich]

Nope - it's different. It removes every column which has a gap in any 
sequence - so it effectively removes all indels.

If you want the original sequence

  for my $seq ( $aln->each_seq ) {
   my $str = $seq->seq;
  $str =~ s/\-//g;
  $seq->seq($str);
  }

-jason


--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/

On Feb 16, 2005, at 3:09 AM, michael watson ((IAH-C)) wrote:

> Hi
>
> Is it safe to say that if I read in alignment using AlignIO, then call
> remove_gaps on the SimpleAlign object, then access each sequence using
> each_seq, and print each sequence out as fasta using SeqIO, that I will
> have the original sequences that went to make up the alignment 
> (exactly,
> with gaps removed etc)?
>
> Thanks
> Mick
>
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