[BioRuby] RPS Blast using Bioruby...
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp
Tue Apr 15 13:59:06 UTC 2008
Hi,
RPS Blast output parser is now added into CVS HEAD.
0. Database preparation
You can download formatted databases from NCBI.
Be careful that formatted databases are architecture-dependent.
For little-endian machines, you can download from
ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian
For big-endian machines,
ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/big_endian
If you want to create database from scratch, please see
the document "Using RPS-BLAST with Biopython"
http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/python/rpsblast/
This is useful not only for Biopython users but also
for RPS-BLAST newbies.
1. Runs rpsblast command
% rpsblast -i test.fst -d Pfam -o test.rpsblast
2. Parses the result
The usage of Bio::Blast::RPSBlast::Report is almost the same
as Bio::Blast::Default::Report, except for multi-query output
supports and some methods (see RDoc in the class).
Below is a sample script.
require 'bio'
filename = 'test.rpsblast'
Bio::FlatFile.open(Bio::Blast::RPSBlast::Report, filename) do |ff|
ff.each do |e|
i = 0
e.each_iteration do |result|
i += 1
print "Query\##{i} = ", result.query_def, "\n"
j = 0
result.each do |hit|
j += 1
print "Query\##{i}/Hit\##{j} = ", hit.target_def, "\n"
k = 0
hit.each do |hsp|
k += 1
print "Query\##{i}/Hit\##{j}/Hsp\##{k} = ",
"evalue=#{hsp.evalue}, ",
"Positions #{hsp.query_from}..#{hsp.query_to}:",
"#{hsp.hit_from}..#{hsp.hit_to}\n"
print "Query : #{hsp.qseq}\n"
print " #{hsp.midline}\n"
print "Hit : #{hsp.hseq}\n"
end
end
end
end
end
3. References
Using RPS-BLAST with Biopython
http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/python/rpsblast/
Regards,
Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
On Mon, 14 Apr 2008 21:51:42 +0900
Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:
> Hi,
>
> Currently, RPS-Blast is not suppoted in BioRuby.
>
> In addition, currently, Bio::Blast in BioRuby does not support
> remote BLAST on NCBI. It supports GenomeNet or stand-alone BLAST.
>
> Thanks,
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>
> On Thu, 10 Apr 2008 15:34:29 -0400
> Sharvari Gujja <sgujja at broad.mit.edu> 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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