Help With Bioperl Remote Blast Script (Bio::Tools::Run::Remoteblast)

Question

[campbell.malachy]

Hi, I would like to run a blast search for a fasta file containing many (100+) seqences. I wrote a test script and ran it using a test query file (contains only one sequence; fh= diffexp1). If my code is right, the script should output the query name and the hit name in terminal. Although the script doesn't throw out any errors when I run it from command line, I don't get any output. I've let the program run for hours and still nothing. I'm using BioPerl-1.6.1 and Perl-5.16.1 on Ubuntu 12.04 LTS. Any help would be appreciated.

Here's the script:

#!/home/mack/bin/perl
use Bio::Tools::Run::RemoteBlast;
use Bio::SearchIO;


my $prog='blastn';
my $db='nr';
my $e_val='1e-10';
my $Input='diffexp1';
my @params = ('-prog' =>  $prog, '-data' =>  $db, '-expect' =>
$e_val, '-readmethod' => 'SearchIO');

my $factory = Bio::Tools::Run::RemoteBlast->new(@params);

$r =$factory->submit_blast($Input);
while (@rids =$factory->each_rid ){
    for $rid (@rids ){
      $rc =$factory->retrieve_blast($rid);
   }
}

my $report = Bio::SearchIO->new(-file =>$rc, -format =>'blast');
while (my $result = $report->next_result) {
    my $i=0;
    while (my $hit = $result->next_hit){
    print STDOUT $result->query_name, "\t";
    print STDOUT $hit->name, "\t";
    }
}
    if (i==0) {print STDOUT "No Hits \n"; }

Answer 1

[dfornika]

This is a really unsophisticated suggestion, but you can toss a few simple print statements at various spots in the script where you think it may be hanging. That will at least help you to zero in on the line(s) that are causing the problem.