[Bioperl-l] Sim4 output parsing using Bioperl

[Jason Stajich]

I parse the alignment but I don't think the
query_string,hit_string,homology_string  matches up with start/end
properly because I don't know how long the gap is here without referring
back to the top part specifying start/end (which may not exist in some
formats).

 1550     .    :    .    :    .    :    .    :    .    :
   1542 TGCTTTG         CTCAAGAGTGAAAGTGCTGTCCTCAAGTCTACCG
        |||||||>>>...>>>||||||||||||||||||||||||||||||||||
 341396 TGCTTTGGTG...TAGCTCAAGAGTGAAAGTGCTGTCCTCAAGTCTACCG

Give it a whirl though with some data and let me know if you have ideas or
expectations that aren't met.  I wrote it in May and haven't tested it out
on a bunch of new data since I'm becoming partial to exonerate.

-jason

On Wed, 2 Jul 2003, Chris Mungall wrote:

>
>
> On Wed, 2 Jul 2003, Hilmar Lapp wrote:
>
> >
> > On Tuesday, July 1, 2003, at 01:53  PM, Jason Stajich wrote:
> >
> > > I have written SearchIO::sim4 which doesn't have this problem, but is
> > > only
> > > on the main trunk (checkout via CVS) but it returns Bio::Search objects
> > > not Exons.
> > >
> >
> > (Jason I didn't reply to all first)
> >
> > Would people be opposed to or have concerns with us desupporting
> > Bio::Tools::Sim4 in favor of SearchIO::sim4?
>
> does SearchIO::sim4 support the A=4 option?
>
> > 	-hilmar
> >
> >
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu