[Bioperl-l] Sim4 output parsing using Bioperl
jason at cgt.duhs.duke.edu
Wed Jul 2 16:27:22 EDT 2003
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
1550 . : . : . : . : . :
1542 TGCTTTG CTCAAGAGTGAAAGTGCTGTCCTCAAGTCTACCG
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.
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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> Bioperl-l at portal.open-bio.org
jason at cgt.mc.duke.edu
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