[BioRuby] Remote blast not working?

[Michael Barton]

Hi,

I appear to be having a similar problem again using ruby 1.9.3 and bio 1.4.2.

blast = Bio::Blast.remote('blastp', 'nr-aa', '-e 0.001', 'genomenet')

/Users/mike/.gem/gems/bio-1.4.2/lib/bio/appl/blast/genomenet.rb:251:in
`exec_genomenet': cannot understand response (RuntimeError)
	from /Users/mike/.gem/gems/bio-1.4.2/lib/bio/appl/blast.rb:368:in `query'
	from bin/blast:17:in `<main>'

I've tried downloading the latest version of genomenet.rb but this did
not appear to solve the problem this time.

Thank you

Michael Barton



On 20 March 2011 16:56, Michael Barton <mail at michaelbarton.me.uk> wrote:
> Hi Toshiaki,
>
> Thank you for the patch. That worked perfectly. I sometimes get unusual parsing
> errors which I think are originating from raxml. Has anyone else experienced
> something similar?
>
> Cheers
>
> Mike
>
> On Thu, Mar 17, 2011 at 10:28:21AM +0900, Toshiaki Katayama wrote:
>> As for the GenomeNet part, it is already fixed but not yet released.
>>
>> https://github.com/bioruby/bioruby/blob/master/lib/bio/appl/blast/genomenet.rb#L241
>>
>> You can replace your installation with the above file for quick fix.
>>
>> Thanks,
>> Toshiaki
>>
>> On 2011/03/17, at 6:12, Michael Barton wrote:
>>
>> > Hi,
>> >
>> > I'm struggling to use the remote blast part of bioruby. I get errors using
>> > either the ddbj or genomenet versions. With genomenet I get an error about
>> > a nil response and with genomenet I get an error for 'cannot understand
>> > response'. I've tried different combinations of databases and options but keep
>> > getting the same problems.
>> >
>> > Bio::Blast::Remote.ddbj('blastp', 'nr-aa', '-e 0.001')
>> >
>> > Can anyone offer any suggestions?
>> >
>> > Cheers
>> >
>> > Mike
>> > _______________________________________________
>> > BioRuby Project - http://www.bioruby.org/
>> > BioRuby mailing list
>> > BioRuby at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioruby
>>