[Bioperl-l] Re: bioperl Registry

[Lincoln Stein]

I've fixed issues in the Registry, SeqFeature and GFF modules.  The 
corresponding regression tests all pass with Perl 5.8.2 (built from source).

I've had to change Bio::Tools::GFF IO slightly.  The module used to default to 
reading from ARGV if no filehandle or filename was passed to it in new().  
However, this is no good when you don't want to read from a file but just 
write GFF output, and this was causing the SeqFeature regression test to 
hang.  So I removed this default.  

In LocatableSeq.pm, there was the following odd bit of code in the start() 
method:

	$self->seq ? (return $self->{'start'} || 1) : undef;

This is weird, because it means if there is no sequence attached to the 
LocatableSeq, it returns undef as the start coordinate.  This was causing the 
GFF regression tests to fail.  I replaced the line with a simple return 
$self->{'start'} || 1.

Lincoln

On Thursday 20 November 2003 09:16 pm, Lincoln Stein wrote:
> I've got perl 5.8.2 installed now and can partially reproduce the problem. 
> I am working on it now.
>
> Lincoln
>
> On Thursday 20 November 2003 08:19 am, Heikki Lehvaslaiho wrote:
> > Michele & Lincoln,
> >
> > Could I bother either of you two to have a look at the bioperl live
> > Registry/ Bio::DB::Flat modules. There is something wrong in the
> > BerkeleyDB version of flatdb and I can not get my head around it.
> >
> > Brian has been  working on it but everything works under his cygwin
> > system so he is stuck. I isolated the BDB tests from t/Registry.t into an
> > other file and put it into bugzilla:
> > http://bugzilla.bioperl.org/show_bug.cgi?id=1562
> >
> > The tests fail in both Mandrake Linux 9.2+cooker (Perl 5.8.2) and RedHat
> > Linux 9 (Perl 5.8.1), so it is definitely not just my system's problem.
> >
> > Cheers,
> > 		-Heikki

-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)