[Bioperl-l] Historical cruft in module documentation

Kris Boulez krbou@pgsgent.be
Tue, 6 Feb 2001 22:44:57 +0100

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.

 $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

        print $seq->layout('GCG');

I think this is now ('-format => "GCG" ') on the $seqio handle

        my $seq = $inx->fetch($id); # Returns stream
        while( <$seq> ) {
            /^>/ && last;

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.