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

Jason Stajich jason.stajich at duke.edu
Tue Jan 24 12:15:47 EST 2006

Thanks Chris - I don't know when I'll have time to check in bugs so  
anyone else who has commit access feel free to give these a whirl and  
check in.

I would propose making the XML default but allowing the text version  
to still be supported in the event that someone has setup their own  
local NCBI BLAST Web interface which still supports the simple Text  


On Jan 24, 2006, at 12:09 PM, Chris Fields wrote:

> 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

Jason Stajich
Duke University

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