[Bioperl-l] Re: bioperl Registry

[Heikki Lehvaslaiho]

On Friday 21 Nov 2003 TT:01, Lincoln Stein wrote:
> 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).

Great stuff! Thanks a million.

> 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.

That was my recent modification. I thought that would make sense. end() 
returns undef. If there is no sequence and start() has not been set, why is 
it necessary to assume that start equals 1?

I happy to accept this but would like to understand why before I change the 
t/Locatable.t.

	-Heikki

> 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

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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
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