[BioRuby] Blast Problem

george georgkam at gmail.com
Tue Apr 10 23:47:59 UTC 2007


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




More information about the BioRuby mailing list