[Bioperl-l] BPbl2seq problem

[Debashis Rana]

Hi,

I want to use the BPbl2seq module. But I am getting some errors. The 
next_feature method is not working with BPbl2seq object. I will 
appreciate if someone please point out what I am doing wrong.  I am 
using perl 5.6.1, bioperl 1.2 and installed the NCBI blast.

Here is part of the code I am using:


use Bio::SeqIO;
use Bio::Tools::BPbl2seq;
use Bio::Tools::Run::StandAloneBlast;


my $usage="pairwise_blast.pl file |n";
my $file=shift or die $usage;


my $inseq = Bio::SeqIO->new('-file' => "<$file",
                '-format' =>'Fasta');

my $seq1=$inseq->next_seq();
my $seq2=$inseq->next_seq();


$factory=Bio::Tools::Run::StandAloneBlast->new ('program'=>'blastn', 
'file'=>'bl2seq.out');

my $bl2seq_report=$factory->bl2seq($seq2, $seq1);
 
 
$hsp=$bl2seq_report->next_feature;


The _*error message*_ I am getting is as follows:
Can't locate object method "next_feature" via package 
"Bio::Tools::BPbl2seq" (perhaps you forgot to load 
"Bio::Tools::BPbl2seq"?) at pairwise_blast line 31, <GEN1> line 179.


Will greatly appreciate your help.

Sincerely,
Debashis

Dept of Genetics,
University of Cambridge
UK