[Bioperl-l] Sim4

Chris Mungall cjm@fruitfly.bdgp.berkeley.edu
Mon, 31 Jul 2000 14:51:33 -0700 (PDT)

Hi Hilmar

Your rewrite of the bioperl sim4 parser looks a lot cleaner. however, I
notice that you still seem to be ignoring the -> <- == -- symbols at the
end of each exon. I would have thought that you would want to start a new
exonset if the direction changed halway through - or record the exon
direction so that some post-parsing filtering could be done? Maybe I'm
misunderstanding your code, or sim4 - I'm sure George will correct me if
I'm speaking rubbish.

I imported the bioperl sim4 parsing code into our own namespace some time
ago to do this - you can see the code at
[with some horrible project-specific harcoded stuff that needs to go]

George Hartzell wrote an excellent perl sim4 parser (which I would have
used had I known about it - doh!), I'm sure he wouldn't mind if I sent you
the code to compare it.

On Mon, 31 Jul 2000, Hilmar Lapp wrote:

> Dear all,
> the Sim4 parser is functional again, and - hopefully - relatively clean. The
> module can now deal with either order of sequences (EST first and genomic
> first), and with all sim4 output formats except A=2.
> The basic methods for getting the results are
>    @exons = $sim4_result->parse_next_alignment();
> returning an array of Bio::Tools::Sim4::Exon objects, and, more convenient
>    $exonset = $sim_result->next_exonset();
> returning a container as a Bio::SeqFeature::Generic object holding individual
> exons as sub seqFeatures. Since the only capabilities of
> Bio::Tools::Sim4::ExonSet, as far as I understood the code, were to serve as a
> container and to provide an easy interface to getting start and end of the
> whole region the exons comprise, and as Bio::SeqFeature::Generic already
> provides both, I dismissed the dependency on ExonSet.pm (which may now be
> deleted from the repository).
> Documentations updated, but still not be perfect.
> 	Hilmar
> -- 
> -----------------------------------------------------------------------
> Hilmar Lapp                                      email: hlapp@gmx.net
> NFI Vienna, IFD/Bioinformatics                   phone: +43 1 86634 631
> A-1235 Vienna                                      fax: +43 1 86634 727
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