[Bioperl-l] TBLAST Parsing

jasonraymond jasonraymond" <jasonraymond@asu.edu
Sat, 20 Oct 2001 19:56:17 -0700

Ahh this should have been my first suspicion... I'd been using the blast
module for parsing (not sure why now; must have been cutting code out of one
of the other example parsers which happened to use this module).  I'm using
v.91, so I'll rework this code using BPlite and see how this tackles the
problem.  thanks for the pointers -- jason

----- Original Message -----
From: "Jason Eric Stajich" <jason@cgt.mc.duke.edu>
To: "Jason Raymond" <jasonraymond@asu.edu>
Cc: <bioperl-l@bioperl.org>
Sent: Saturday, October 20, 2001 9:26 AM
Subject: Re: [Bioperl-l] TBLAST Parsing

> Jason -
> What version of bioperl are you using  and which module are you using for
> blast parsing -
> BPlite was fixed recently (after 0.7.1) to handle this problem, I would
> suggest using the CVS Head code for this to really work around the
> problem.
> -jason s
> On Fri, 19 Oct 2001, Jason Raymond wrote:
> > This is a pretty basic problem I seem to have hit, so I'm sure it's on
> > the mail list somewhere but I haven't been able to dig it up.  I've
> > been parsing BLASTP files without a problem with several example
> > scripts and a few I've written.  However on switching to TBLASTN
> > parsing, the programs halt and I get an ugly screen dump.  I've found
> > that this is due to the exclusion of "Identities = #, Positives = #,
> > Gaps = #" from the TBLASTN file, so that when I copy/paste this line
> > in from a BLASTP output (or delete this line from a BLASTP output), I
> > get these error messages.  I'm sure people haven't just been parsing
> > BLASTP files, so there must be some easy workaround I've overlooked??
> > Thanks!
> >
> >
> --
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu