[Bioperl-l] Sim4 output parsing using Bioperl

[Jason Stajich]

Send me a file and your code.



On Tue, 1 Jul 2003, Arnaud Kerhornou wrote:

> Selon Jason Stajich <jason at cgt.duhs.duke.edu>:
> >
> > > --->
> > > 138736-138759  (192-218)   75%
> > > <---
> > >
> > > If this line is missing, it stops.
> > >
> > > Am I misusing the parser ?
> >
> > If the line is missing then there is no alignment so it can't build a
> > gene/exon for you.
>
> The sim4 output reports the (potential) alignments against an ESTs database. If
> the first EST doesn't align with the genomic sequence, it can't build an exon
> but the parsing should carry on and parse the information about the second EST
> and so on, until the all set of ESTs data have been processed.
>
> Arnaud
>
> > -jason
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> >
>
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu