[BioRuby] RPS Blast using Bioruby...

[Sharvari Gujja]

Sharvari Gujja wrote:
> Hi all,
>
> This is in reference to my earlier email on how to fetch CDD output 
> from NCBI.
>
> Like I said I am also trying to do RPS Blast on CDD database using 
> Bio::Blast.
>
> This is what I am trying to do:
>
> #!/usr/bin/env ruby
> require 'bio'
> program = 'blastp'
> db = 'nr-aa'
> fasta = File.open("input1" , "r+")
> blast = Bio::Blast.remote(program,db,'-e 1e-10')
> report = blast.query(fasta.read)
> report.each do |hit|
> puts hit.target_id
> end
>
> How can I do rps blast on cdd?
>
> Thanks
> S
>
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> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


Hi,

I have tried a bunch of things to run RPS Blast using Bioruby.Alas, no 
success yet!

I know that this can be done in Bioperl ( from a friend of mine) and 
this is the first time I could not do something in BioRuby.Can someone 
please tell me if this can be done in Bioruby.

Please help.

Thanks
Sharvari