[Bioperl-l] Historical cruft in module documentation

[Kris Boulez]

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()


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.