[Bioperl-l] _READMETHOD default

[Torsten Seemann]

> I don¹t pay much attention to StandAloneBlast.pm but I was surprised to see
> this in the latest version:
>     $DEFAULTREADMETHOD = 'BLAST';
> Shouldn¹t that be ŒSearchIO¹?

My understanding of StandAloneBlast.pm is that

_READMETHOD =~ /BLAST/i     # uses SearchIO
_READMETHOD =~ /BPLite/i    # use BPlite / BPpsilite
_READMETHOD =~ ????????     # prints warning, then returns undef

ie. "blastxml" is NOT explicity handled and therefore a warning
     will be printed and an undef blast report returned

Considering the discussion recently about switching RemoteBlast to 'blastxml'
this should probably be changed.

I am very busy this week (still recovering from primary server death) but will 
get to it soon.

(Brian, i'm happy for you to patch it in, if you are willing, it's line 829)

-- 
Torsten Seemann
Victorian Bioinformatics Consortium, Monash University, Australia
http://www.vicbioinformatics.com/