First ten hits, blast scripts

nb175

hi, I need help with my blast script. I need to specify that i need only the first ten hits, any idea how i could go about that?Thanks. here;s the script

Expand|Select|Wrap|Line Numbers

 
#! /usr/bin/perl

use warnings;

use strict;
 
use Bio::SeqIO;

use Bio::Seq;

use Bio::Tools::Run::StandAloneBlast;
 
my $seqio_obj;

my $seq_obj;

my @params;

my $blast_obj;

my $result_obj;

my $report_obj;
 
$seqio_obj = Bio::SeqIO->new(-file => 'seq.fasta',

-format => 'fasta' );

# to wrtie the sequence to afasta file

$seq_obj = $seqio_obj->next_seq;

#print $seq_obj->seq,"\n";

@params = (program => 'blastp',

database => 'pdbaa',

outfile => 'blast1.out');

$blast_obj = Bio::Tools::Run::StandAloneBlast->new(@params);

$report_obj = $blast_obj->blastall($seq_obj);

$result_obj = $report_obj->next_result;

print $result_obj->num_hits;

numberwhun

First, please use code tags. They are required around any and all code that you post in the forums.

Second, I don't really know all that much about BioPerl, but if you only want the first 10 of something, cycle through it and use a counter, exiting once it is greater than 10. Just a thought.

Regards,

Jeff

First ten hits, blast scripts

re: First ten hits, blast scripts

Similar Perl bytes

/bytes/development

/bytes/it

/bytes/about