| Subject: | small fix |
| Date: | Fri, 11 Apr 2008 16:46:52 +0200 |
| To: | bug-Bio-NEXUS [...] rt.cpan.org |
| From: | guignon <valentin.guignon [...] lirmm.fr> |
Hi!
I was looking into the source code of Bio::NEXUS to understand how to
use a string data as input and not a filename since the documentation is
not really clear about it and I noticed a small bug easy to fix.
At line 88 in NEXUS.pm in "sub new" I saw:
$filename =~ s/.nex$//;
which I guess should be:
$filename =~ s/\.nex$//;
otherwise the regexp would replace file names like "kleenex" into
"klee"! It's not a big deal but it's easy to fix. ;-)
The version I got is:
# $Id: NEXUS.pm,v 1.89 2006/09/11 23:03:42 thladish Exp $
# $Revision: 1.89 $
By the way, the documentation for Bio::NEXUS::read is not really clear:
Usage : Bio::NEXUS->read({format => 'string', 'param' => $filename,
'verbose' => $verbose});
You should provide the 2 ways of using the method and not a mix of the
2! Something like this:
Usage : Bio::NEXUS->read({format => 'string', 'param' => $raw_data,
'verbose' => $verbose});
Usage : Bio::NEXUS->read({format => 'file', 'param' => $filename,
'verbose' => $verbose});
Cheers,
Valentin Guignon