[Bioperl-l] Sim4 output parsing using Bioperl

[Arnaud Kerhornou]

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
>