[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
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