[BioRuby] Blast Problem

[George Githinji]

On 4/10/07, george <georgkam at gmail.com> 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
>
>  Hi George,

I would guess that there is no SwissProt database to blast against on
the genomenet server.
therefore the method returns nil (it should probably die with an
Error instead to make it more clear).
Any Bio::Blast methods called on nil can't be resolved as they don't
exist (like nil.strip , nil.each , ....).

hope I am not completely wrong,

Michael


Hi Michael,

I checked the rdoc and sure swissprot is listed as one of the available
databases for blast. Unfortunately not even the example outlined in the rdoc
seems to work!
maybe am wrong but can someone help please please. i also guess the rdoc
could be out of date, since index files for the database are reported
missing ,.

Can someone out please show how to run blastp on genomenet?