[Bioperl-l] Historical cruft in module documentation

[Jason Stajich]

Thanks Kris.

On Tue, 6 Feb 2001, Kris Boulez wrote:

> In checking for the correctnes of every modules SYNOPSIS portion of the
> documentation, I found the following modules which contain example code
> which isn't OK and look like historical cruft.
> 
> Bio::DB::GDB
> ------------
>  $gb = new Bio::DB::GDB;
>  $primers = $gb->get_primers_for_marker('D1S243'); # Marker name
> 
> I can't find any reference (in the whole of BioPerl) to the method
> get_primers_for_marker()
> 
Cruft it was.  Fixed.

> 
> Bio::Index::GenBank
> -------------------
>         print $seq->layout('GCG');
> 
> I think this is now ('-format => "GCG" ') on the $seqio handle
> 
> 
> Bio::Index::SwissPfam
> ---------------------
>         my $seq = $inx->fetch($id); # Returns stream
>         while( <$seq> ) {
>             /^>/ && last;
>             print;
>         }
> 
> This code is correct (apart from the closing curly brace which is
> missing), but doesn't produce any output (first line from <$seq> starts
> with a ">"). What are we trying to show here ?
> 
> 
> Still 120 more modules to check. Stay tuned.
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/