[Bioperl-l] remoteblast result in text format

[Wiepert, Mathieu]

Hi,

Just saw this, sorry for the delay.  If you look at the synopsis for RemoteBlast, you can see how to save the output.  What I sent you earlier was not what I finally put in.  You have my alpha code ;-)  So parseBlastObject() is garbage.  I have cut and pasted the synopsis into a script, and it executed (assuming it can find the test amino.fa file, and I see there is a problem with the way I have the $result->query_name(), keeps returning me a reference not the string name, but you get the idea...)

This is what I just ran...

#!/usr/bin/perl -w
use Bio::Tools::Run::RemoteBlast;
use strict;
my $prog = 'blastp';
my $db   = 'swissprot';
my $e_val= '1e-10';
my @params = ( '-prog' => $prog,
       '-data' => $db,
       '-expect' => $e_val, 
       '-readmethod' => 'SearchIO' );

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

#change a paramter
$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens [ORGN]';

#remove a parameter
delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};

my $v = 1;
my $str = Bio::SeqIO->new(-file=>'amino.fa' , '-format' => 'fasta' );
 while (my $input = $str->next_seq()){
  #Blast a sequence against a database:
  
  #Alternatively, you could  pass in a file with many  
  #sequences rather than loop through sequence one at a time
  #Remove the loop starting 'while (my $input = $str->next_seq())'
  #and swap the two lines below for an example of that.
  my $r = $factory->submit_blast($input);
  #my $r = $factory->submit_blast('amino.fa');
  print STDERR "waiting..." if( $v > 0 );
  while ( my @rids = $factory->each_rid ) {
    foreach my $rid ( @rids ) {
      my $rc = $factory->retrieve_blast($rid);
      if( !ref($rc) ) {
        if( $rc < 0 ) {
          $factory->remove_rid($rid);
        }
        print STDERR "." if ( $v > 0 );
        sleep 5;
      } else { 
        my $result = $rc->next_result();
        #save the output
        my $filename = $result->query_name()."\.out";
        $factory->save_output($filename);
        $factory->remove_rid($rid);
        print "\nQuery Name: ", $result->query_name(), "\n";
        while ( my $hit = $result->next_hit ) {
          next unless ( $v > 0);
          print "\thit name is ", $hit->name, "\n";
          while( my $hsp = $hit->next_hsp ) {
            print "\t\tscore is ", $hsp->score, "\n";
          } 
        }
      }
    }
  }
}