in reply to Not sure about Bio::SeqIO

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.

Replies are listed 'Best First'.
Re^2: Not sure about Bio::SeqIO
by MonkPaul (Friar) on May 10, 2005 at 16:21 UTC
    Thanks,
    I posted my real code not a copy, so i apologise for my lack of precision. Im pretty useless at the moment with perl.

    With respect to Bio::Seq, im still unsure if i have done things right, to me it seems like it should work, but again i am naff.

[reply]
      As I wrote, irrespectful of the fact that it may seem to you like it should work, it can't because, irregardless of Bio::SeqIO or whatever, it contains a syntax error that will simply prevent it from compiling. Why don't you try yourself?!? (Not to be intended as a personal offence - just a consideration!)
[reply]
        Hi,
        Im in the process of decoding my program as i have been sent a mail that it causing the server to lock up. I think it may be some loop that is still running even when results are retruned to the user .

        With this in mind i have had to comment out my new file code and wont be working on it until i have sorted the previous out.
        I will have to get back to you on the old syntax error if that is ok.

        Cheers, MonkPaul.

[reply]

In Section Seekers of Perl Wisdom