[Bioperl-l] formatdb with the nr database

Hubert Prielinger hubert.prielinger at gmx.at
Mon Jan 23 18:08:51 EST 2006


Hi,
thank you very much for the help, another questions that raises up, do I 
have to write the path to the database files as well, I guess so, but 
how I do that, the same way I write the path to teh blast bin files?
Does anybody know how to set the Composition based statistics parameter?
there is my code:

#!/usr/bin/perl -w

use Bio::Tools::Run::StandAloneBlast;
use Bio::Seq;
use Bio::SeqIO;
use strict;

BEGIN
{
    $ENV{PATH}=":/home/Hubert/blast/blast-2.2.13/bin/:";
}


# parameters
my $expect_value = 20000;
#my $filter_query_sequence = 'F';
my $one_line_description = 1000;
my $alignments = 1000;
# my $strands = 1;
my $count = 1;

my @params = ('program' => 'blastp', 'database' => 'nr');
#my $progress_interval = 100;


my $seqio_obj = Bio::SeqIO->new(
  -file   => "Perm.txt",
  -format => "raw",
);

# create factory object and set parameters
my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);

$factory->e($expect_value);
#$factory->F($filter_query_sequence);
$factory->v($one_line_description);
$factory->b($alignments);
#$factory->S($strands);


# get query

while ( my $query = $seqio_obj->next_seq ) {
      my $blast_report = $factory->blastall($query);
      my $filename = "comp_$count.txt";
      my $factory->outfile($filename);
      print $query->seq;
      print "\n";
 
  $count++;
}

thank you very much in advance
Hubert



Nagesh Chakka wrote:

> Hi Hubert,
> I downloaded the nr.00.tar.gz file a week ago. I was able to get the 
> following files
> .phr, .pin, .pnd, .pni, .ppd, .ppi, .psd, .psi, .psq, .pal files. I 
> have no trouble in running standalone blast. You are not required to 
> run formardb on the downloaded blast databases and that may be the 
> reason why the sequences are not included as it will also reduce the 
> size of the file.
> Did you try to run a blast search, if so is it giving you any errors?
> Nagesh
>
>
>
> Hubert Prielinger wrote:
>
>> Hi,
>> I have downloaded the nr database for doing a blast search locally, 
>> now I'm supposed to index the database with formatdb, but it doesn't 
>> work...
>> The online help says that you need a fasta file that is indexed to 
>> use for searching the database, but when I uncompressed the zip file, 
>> there were only .phr, .pnd, .pin, .pni, .ppd file....
>> Is there anybody who can tell me, how to use formatdb with the nr 
>> database...
>>
>> Help is very appreciated
>> Thank you very much in advance
>>
>> Hubert
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>



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