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

Hilmar Lapp lapp@gnf.org
Wed, 25 Apr 2001 09:55:58 -0700

Ann Loraine wrote:
> The trick I think is to distinguish between two possibilities:
> 1. bl2seq ran but exited prematurely due to some kind of error.
> (no_alignment.1)
> 2. bl2seq ran without error but couldn't align the two sequences because
> they aren't homologous (no_alignment.2)

The problem with case 2 is that the cause is an interpretation. There
is no evidence in the output file that clearly suggests this, let
alone a standard string like 'Sequences did not produce an alignment'
you can check for, and most importantly, expect to be a constant over
blast revisions. That's why I like the idea of an interpretation layer
that's kept separate. Same power, but much higher maintainability and

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