[Bioperl-l] Sim4

hilmar.lapp@pharma.Novartis.com hilmar.lapp@pharma.Novartis.com
Fri, 28 Jul 2000 17:51:08 +0100

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.