[BioRuby] basic remote query and plans for NCBI Bio:Blast hook?

[Matt]

Hi all,

As far as I can tell there is yet no straightforward way to use
Bio:Blast with the NCBI portal? I've seen this on the wiki: "Add
remote BLAST search sites", and understand the basic concept, but
don't have time at present to work on this.  Is anyone actively
working on this? (just FYI see
http://github.com/kwicher/ruby-blast-at-ncbi).

I ask in part because I'm struggling to get a basic remote blast working:

seq = Bio::Sequence::NA.new('GTCACAAAATCATGGTTTTGCGGTTAATGCTAATGATTTGCCAGCTGATTGGGAACCATTATTTACAAATGCGAACGACAATACAAATGAAGGAATTGTACACAAAACACATCCATTCTTTAGTGTACAATTTCATCCCGAACACACAGCCGGTCCAGAAGATTTAGAAATCTTATTTGATGTCTTTCTGGATGGAGTAAAAGCATTTAAAAATAAGGAAAAGTTCAYCATGAARGATAAATTGATCGAAAAATTGACTTACACGCCGGATGTACCCGTTTGCACTGAAAAACCTAAAAAGATATTGATTTTAGGTTCAGGCGGTTTATCCATAGGYCAAGCAGGCGAATTTGATTATTCCGGATCTCAGGCTATCAAGGCTCTTAAAGAAGAAAAAATACAAACGGTGYTAATAAATCCAAATATTGCAACGGTTCARACATCAAAAGGCCTTGCGGACAAAGTTTACTTCCTACCCATTACACCGGATTACGTTGAACAGGTTATAAAAGCCGAGCGACCTGATGGTGTGCTTTTAACTTTTGGCGGACAAACAGCTTTGAATTGTGGAATTGAATTAGAAAAAACTAAAGTGTTTCAACGATTCGGTGTTAAAGTGTTGGGTACRCCGATACAATCAATTATTGAAACTGAAGATAGAAAAATATTTTCGGATCGAGTACACGAAATCGGAGAAAAAGTAGCGCCGTCTGCCGCAGTTTATTCGGTGCAAGAAGCTCTAGATGCCGCTGAAATTCTTGGTTATCCCGTTATGGCTCGAGCTGCATTTTCATTAGGTGGACTAGGTTCTGGTTTTGCAAATAATATTGATGAATTAAAACATCTTGCACAACAGGCTCTTGCGCATTCCAACCAGTTAATCATTGATAAATCGCTTAAAGGTTGGAAGGAAGTTGAATACGAGGTCGTTCGTGATGCATATGACAATTGTATTACAGTTTGTAATATGGAAAATGTAGATCCACTAGGAATTCATACAGGGGAGAGTATAGTAGTGGCACCGTCACAAACTCTCTCCAACAAGGAATATAATATGTTGCGTACTACAGCAATTAAAGTGATTCGGCATTTTGGCGTCGTCGGTGAATGTAATATACAATATGCCTTAAATCCACATTCYGAGCAATACTATATAATTGAAGTTAATGCTAGGTTATCGAGGAGTTCGGCACTAGCTAGTAAAGCGACAGGCTATCCATTAGCATACGTTGCGGCTAAACTAGCACTCGGTATCGCTTTACCTGATATTAAAAATTCGGTAACTGGAGTTACCACCGCCTGTTTTGAGCCAAGTTTAGATTACTGTGTGGTAAAAATTCCACGATGGGATTTAGCAAAATTTGTTCGCGTTTCAAAAAATATTGGAAGCTCTATGAAAAGTGTAGGTGAGGTCATGGCAATCGGCCGCCGATTTGAAGAAGCGTTCCAAAAA')

blast_factory = Bio::Blast.new('blastn','nr-nt', '', 'genomenet')
foo = blast_factory.query(seq)

... freezes, when I ctrl-C

from /Library/Ruby/Gems/1.8/gems/bio-1.3.1.5000/lib/bio/appl/blast/genomenet.rb:224:in
`call'
from /Library/Ruby/Gems/1.8/gems/bio-1.3.1.5000/lib/bio/appl/blast/genomenet.rb:224:in
`sleep'
from /Library/Ruby/Gems/1.8/gems/bio-1.3.1.5000/lib/bio/appl/blast/genomenet.rb:224:in
`exec_genomenet'
from /Library/Ruby/Gems/1.8/gems/bio-1.3.1.5000/lib/bio/appl/blast.rb:368:in
`__send__'
from /Library/Ruby/Gems/1.8/gems/bio-1.3.1.5000/lib/bio/appl/blast.rb:368:in
`query'
from (irb):25

any glaring problems with this? Is it just waiting for the results of
the remote query?   I noticed that the genomenet blasts are much
slower than NCBI in general (I'm in the US).

thanks,
Matt