[Bioperl-l] TBLAST Parsing

Jason Eric Stajich jason@cgt.mc.duke.edu
Sat, 20 Oct 2001 12:26:04 -0400 (EDT)

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

-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