[Bioperl-l] _READMETHOD default
torsten.seemann at infotech.monash.edu.au
Sat Mar 11 17:02:52 EST 2006
> 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)
Victorian Bioinformatics Consortium, Monash University, Australia
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