[BioRuby] Remote Blast

[Anthony Underwood]

Hi all, is remote blast broken for bioruby?

I have some code

fasta_sequences.each do |seq_obj|
   blast_report = remote_blast(seq_obj.seq, 'blastn', 'nr-nt')
  ..........
end

this calls the method

def remote_blast(seq_obj, program, db = 'nr-nt', options = '', server  
= 'genomenet')
   # create BLAST factory object
   factory = Bio::Blast.remote(program, db, '-m 8' + options, server)
   report = factory.query(seq_obj)
end

This fails to return anything - just times out

If I include the -V option to limit the number of hits returned

   blast_report = remote_blast(seq_obj.seq, 'blastn', 'nr-nt', "-V 10")

I get no hits , or a message "RuntimeError: cannot understand  
response" which I think is due to the "holding page" that occurs when  
a job is running


Does anybody know  a fix for this? Should I start to try and get a  
ncbi remote blast working. Is there anybody who would like to help  
with this?

Thanks

Anthony