[Bioperl-l] XML output from RemoteBlast

Chris Fields cjfields at uiuc.edu
Thu Jan 19 15:55:23 EST 2006


...and I tried an XML-formatted BLASTP file (from blastcl3 output) to test
SearchIO directly; it's not SearchIO or blastxml.  They parsed accessions,
hits, etc very well.  So at least I can use a system call to blastcl3 with
parameters as a workaround for now.

I'm pretty sure it is the retrieve_blast() or save_output() method in
RemoteBlast.pm.  I'm busy trying to finish up a write-up for bioperl-db
(among the experiments going on in the lab), but I'll try to figure it out.

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

> -----Original Message-----
> From: Jason Stajich [mailto:jason.stajich at duke.edu]
> Sent: Wednesday, January 18, 2006 10:23 PM
> To: Chris Fields
> Subject: Re: [Bioperl-l] XML output from RemoteBlast
> 
> This doesn't work for you?
> http://bioperl.open-bio.org/news/2005/11/06/getting-blastxml-using-
> remoteblast/
> On Jan 18, 2006, at 11:04 PM, Chris Fields wrote:
> 
> > Is there any known way to save XML-formatted BLAST queries from
> > RemoteBlast?  Changing the FORMAT_TYPE in the retrieval header to
> > anything other than 'Text' gives a blank output file.
> >
> > Christopher Fields
> > Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Dept of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12




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