[BioRuby] Blast Problem

[Toshiaki Katayama]

Hi,

To use GenomeNet server, you need to select the database name
which the server can accept (described in the bio/appl/blast.rb
or see the HTML source of http://blast.genome.jp/ form).

------------------------------------------------------------
program = 'blastp'
database = 'swissprot'     # <- here
options = '-e 0.0001'
server = 'genomenet'

serv = Bio::Blast.remote(program, database, options, server)
report = serv.query(sequence_text)

p report
------------------------------------------------------------

Toshiaki

On 2007/04/11, at 8:47, george wrote:

> Hi,
> am trying to run a remote blast job as follows:
>
> require 'bio'
> sequence_text='MRKLYCVLLLSAFEFTYMINFGRGQNYWEHPYQNSDVYRPINEHREHPKEYEYPLHQEHT
> YQQEDSGEDENTLQHAYPIDHEGAEPAPQEQNLFSSIEIVERSNYMGNPWTEYMAKYDIE
> EVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSNTTFLTPVATGNQYLKDGG
> FAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAGNMIPDNDKNSNYKYPAVY
> DDKDKKCHILYIAAQENNGPRYCNKDESKRNSMFCFRPAKDISFQNYTYLSKNVVDNWEK
> VCPRKNLQNAKFGLWVDGNCEDIPHVNEFPAIDLFECNKLVFELSASDQPKQYEQHLTDY
> EKIKEGFKNKNASMIKSAFLPTGAFKADRYKSHGKGYNWGNYNTETQKCEIFNVKPTCLI
> NNSSYIATTALSHPIEVENNFPCSLYKDEIMKEIERESKRIKLNDNDDEGNKKIIAPRIF
> ISDDKDSLKCPCDPEMVSNSTCRFFVCKCVERRAEVTSNNEVVVKEEYKDEYADIPEHKP
> TYDKMKIIIASSAAVAVLATILMVYLYKRKGNAEKYDKMDEPQDYGKSNSRNDEMLDPEA
> SFWGEEKRASHTTPVLMEKPYY'
>
>
> program = 'blastp'
>   database = 'SwissProt'
>   options = '-e 0.0001'
>   serv = Bio::Blast.new(program, database, options)
>
>   server = 'genomenet'
>   genomenet = Bio::Blast.remote(program, database, options, server)
>
>   report = serv.query(sequence_text)
>
> But i get this:
>
>> ruby blast.rb
> [NULL_Caption] WARNING: Could not find index files for database SwissProt
> [NULL_Caption] WARNING: Could not find index files for database SwissProt
> [NULL_Caption] WARNING: Could not find index files for database SwissProt
> c:/ruby/lib/ruby/gems/1.8/gems/bio-1.0.0/lib/bio/appl/blast/format8.rb:77:in 
> `tab_parse_hsp': undefined method `strip' for nil:NilClass (NoMethodError)
>     from 
> c:/ruby/lib/ruby/gems/1.8/gems/bio-1.0.0/lib/bio/appl/blast/format8.rb:40:in 
> `tab_parse'
>     from 
> c:/ruby/lib/ruby/gems/1.8/gems/bio-1.0.0/lib/bio/appl/blast/format8.rb:38:in 
> `each'
>     from 
> c:/ruby/lib/ruby/gems/1.8/gems/bio-1.0.0/lib/bio/appl/blast/format8.rb:38:in 
> `tab_parse'
>     from 
> c:/ruby/lib/ruby/gems/1.8/gems/bio-1.0.0/lib/bio/appl/blast/report.rb:54:in 
> `auto_parse'
>     from 
> c:/ruby/lib/ruby/gems/1.8/gems/bio-1.0.0/lib/bio/appl/blast/report.rb:70:in 
> `initialize'
>     from 
> c:/ruby/lib/ruby/gems/1.8/gems/bio-1.0.0/lib/bio/appl/blast.rb:202:in `new'
>     from 
> c:/ruby/lib/ruby/gems/1.8/gems/bio-1.0.0/lib/bio/appl/blast.rb:202:in 
> `parse_result'
>     from 
> c:/ruby/lib/ruby/gems/1.8/gems/bio-1.0.0/lib/bio/appl/blast.rb:216:in 
> `exec_local'
>     from 
> c:/ruby/lib/ruby/gems/1.8/gems/bio-1.0.0/lib/bio/appl/blast.rb:182:in `send'
>     from 
> c:/ruby/lib/ruby/gems/1.8/gems/bio-1.0.0/lib/bio/appl/blast.rb:182:in 
> `query'
>     from blast.rb:23
>> Exit code: 1
>
>
> What could be the reason?
>
> Thanks
>
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