[BioRuby] Blast Problem

[Toshiaki Katayama]

To be precisely, the error message you got is not returned
from the remote server but raised from

>>   serv = Bio::Blast.new(program, database, options)

this line, which execute local blast search.

The meaning of the message is that your 'blastall' command
couldn't find index files for your 'SwissProt' database.

If you want to run BLAST locally, you need to run 'formatdb'
command, bundled with the blast package, on your 'SwissProt' file.

Toshiaki

On 2007/04/11, at 22:51, Toshiaki Katayama wrote:

> 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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>