[Bioperl-l] Sim4

[Hilmar Lapp]

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

-- 
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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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