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

Jeffrey Chang jchang@SMI.Stanford.EDU
Tue, 24 Apr 2001 22:42:52 -0700 (PDT)

On Tue, 24 Apr 2001, Brad Chapman wrote:

> Anyways, it is kind of ugly, since it is not guaranteed that Blast
> will continue to produce similar junk in different revisions, but it's 
> better than nothing. It also introduces a little extra overhead since we
> save each BLAST report before parsing it, but I couldn't see a way
> around that without messing with Jeff's pretty parsing code (and he
> didn't want that :-).

Nah, I don't mind you working with the code in general.  However, I
believe parsing code should be separate from code that diagnoses
unspecified faults in the input file.  One of the reasons is because there
is only one interpretation of a correct file, but possibly many
interpretations of ambiguously incorrect ones.  This allows people to use
different interpretations.

Keeping things separate does impose some overhead than if it were tightly
coupled.  But, you always have the option of not using the extra code if
you're not worried about faults in the output.  If the diagnostic code
were integrated, you wouldn't have that option.