[BioRuby] Help with Bio::Blast

Ben Woodcroft donttrustben at gmail.com
Wed Aug 13 03:59:03 UTC 2008

I don't personally use the bioruby blast interface because I'm more
used to the plain old blast command line interface, but I can suggest
a workaround. What if you just put '-m 7' (ie blast output) in the

The only other problem is that the new version of blast XML isn't well
supported by bioruby. Read the bug report for more information:


2008/8/13 Greg Traub <gtraub at flmnh.ufl.edu>:
> Hello,
> I'm new to BioRuby but not new to Ruby. I've been trying to write code to
> submit a fasta formated sequence for BLAST search, however I never get back
> anything thats usable. After reading the documentation, I should be
> receiving xml formated responses to my search, but I dont receive anything.
> I altered the code in Bio::Blast class to print out whatever raw data was
> being sent back from my request and to my surprise, I keep receiving
> standard formated HTML page that tells me my request is either requesting
> the wrong program or the wrong database . I've been trying to use 'blastn'
> with 'nr' or 'nr-nt' ...documentation seems differ as to what the name of
> the databases are, so I've tried all of them with no luck. Now what really
> gets me is that i should be getting back XML. I would even an expect the
> error message to be in XML but instead its in a  HTML page  with javascript
> included.  This makes me think that the request is going to URL not intended
> for XML responses. Can anybody help me?  I've pasted some example code that
> I've tried below.
> Thanks,
> Greg
> #files is array of file locations
> #res is response
> #im just trying to get back any info i can from the request
> #in the example code below
> blast = Bio::Blast.remote('blastn','nr')
> files.each do |file|
>    Bio::FastaFormat.open(file).each_entry do |c|
>       reports = blast.query(c.seq)
>       reports.each { |report| res << report.query_seq }
>    end
> end
> --
> Database Programmer
> Florida Museum of Natural History
> University of Florida
> gtraub at flmnh.ufl.edu
> (352) 392-1721 ext. 514
> ----------------------------------
> Experience is what you get when
> you didn't get what you want.
> -National Vacuum sign
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