[Bioperl-l] Re: Sim4

Ewan Birney birney@ebi.ac.uk
Fri, 28 Jul 2000 16:42:41 +0100 (GMT)

On Fri, 28 Jul 2000 hilmar.lapp@pharma.Novartis.com wrote:

> Dear all,
> we need to parse Sim4 results, and there appears to be a Sim4 parser
> available in BioPerl. However, the documentation refers to objects that do
> not exist my BioPerl version (which I checked out yesterday night with
> using cvs update -d, so I was able to get the new Variation stuff), like
> Bio::Tools::Sim4 (can you call new() on a directory?),
> Bio::SeqFeature::Homol, and Bio::Tools::Sim4::ExonSet. After looking at the
> code in Bio/Tools/Sim4/Result.pm, only ExonSet seems to be really required
> from those, and it is not there. Consequently, the module fails loading. (I
> wonder whether there's a functional test script for this module.)
> Can anyone tell me whether or not the Sim4 parser ought to be functional,
> and if so, how I can manage to get the modules I obviously miss. If the
> Sim4 module is not functional yet, can anyone tell me where it could make
> sense to take on, because I need one within the next days.


This is my fault hilmar. Let me see if I can figure out where this went ;)

Hmmmmmmmmmmm. Ok. I deleted it and removed in from teh repository. I
assume I did this for a good reason. I wonder why?

It is also using the outdated Bio::SeqFeature::Homol. I'll change that to
the newer Bio::SeqFeature::FeaturePair.


Everything now compiles at least.

I would not expect this to work cleanly - this was a very rushed job in
janurary whilst I was writing up. Apologies Hilmar - it is probably a

Of course, if you debug it/rewrite it that would be great. A test suite
would also be nice ;)

I have committed. Apologies again ...

Checking in Bio/Tools/Sim4/Exon.pm;
/home/repository/bioperl/bioperl-live/Bio/Tools/Sim4/Exon.pm,v  <--
new revision: 1.5; previous revision: 1.4

>      Hilmar

Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420