[BioRuby] Help with Bio::Blast

Greg Traub gtraub at flmnh.ufl.edu
Tue Aug 12 18:09:56 UTC 2008


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.


#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 }

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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