[Bioperl-l] RemoteBlast.pm and Bio::SearchIO::blast.pm - partially resolved

[Chris Fields]

I submitted two bugs on Bugzilla to describe recent problems with
RemoteBlast.pm and SearchIO::blast.pm

http://bugzilla.bioperl.org/show_bug.cgi?id=1934
http://bugzilla.bioperl.org/show_bug.cgi?id=1935

Today I submitted a patched version of Bio::SearchIO::blast.pm which should
fix the text parsing issue for old (2.2.12) and new (2.2.13) versions of
NCBI's BLAST; the bug link above describes the problem and the fix.  Problem
is, I know it will likely break again b/c NCBI will probably change text
output in a future BLAST version.  I also agree with Jason about changing
the default for SearchIO to XML.  So, does text output parsing through
blast.pm need to be deprecated in favor of XML, or should both be available?

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign