[BioRuby] Remote Blast
Anthony Underwood
email2ants at gmail.com
Fri Jul 4 12:13:45 UTC 2008
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
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