[Bioperl-l] Re: bl2seq reader chokes when no results (PR#927)

Hilmar Lapp lapp@gnf.org
Tue, 24 Apr 2001 17:16:33 -0700

Brad Chapman wrote:
> [Moving to bioperl-l from guts]
> Ann Loraine writes:
> > Attached please find two files (no_alignment.1 and no_alignment.2) which
> > contain output from bl2seq's failed attempt to align two different
> > sequence pairs.
> [description and examples of horribly truncated reports]
> [...]
> My rationale behind doing things like this was that I really don't
> want to parse these bogus reports, I just don't want them to mess up
> the rest of the parsing. Additionally, I also didn't want to muck
> around in a working parser just to make it happy about a bad report.

Hmm. Very true. I didn't expect them to be so crappy. So, this appears
to boil down to 1) recognize by a parsing error that the program
producing the file failed (crashed), and 2) start to interpret that
failure of the program. Sounds like fun to add this doesn't it.

Does this mean that your ErrorParser in fact does such an

Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757