[BioRuby] RPS Blast using Bioruby...
Sharvari Gujja
sgujja at broad.mit.edu
Fri Apr 11 15:20:17 EDT 2008
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
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