Well, I do't know Bio::SeqIO, but at first sight this: 
  while($fh != -1)
  {
   $sequence = stream->next_seq
   @sequences = $sequence;
  }

[download]
looks strange, for
  1. both the name of $fh, and the way it is created suggest that it is a filehandle and thus 
    while(<$fh>)

    [download]
    would be the typical way to iterate over it;
  2. none of the statements in the block seem to modify $fh, so that whatever the correct test is, it is unlikely to ever succeed;
  3. stream->next_seq may well be correct, but it is more likely that there's a missing $ sigil;
  4. further, there's a missing semicolon. This code wouldn't even compile. It is recommended to post real code. It is recommended to paste rather than retype.

In reply to Re: Not sure about Bio::SeqIO by blazar
in thread Not sure about Bio::SeqIO by MonkPaul

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