[Bioperl-l] Getting description of BLAST hits

[Jason Stajich]

what does
print ref($hit), "\n";
say?

What version of Bioperl?

On Apr 5, 2005, at 6:09 PM, Peter.Robinson at t-online.de wrote:

> Dear list,
>
> I am trying to get a list of all BLAST hits to various sequences using 
> code adapted from the bioperl website. In essence, I would like to get 
> the descriptions
> from lines such as
>
>
> gb|BC021898.1| Homo sapiens adaptor-related protein complex 1, s...  
> 2956   0.0
>
>
>
> Using the following code:
>
> 	while ( my $hit = $result->next_hit ) {
> 	  next unless ( $v > 0);
> 	  print "\thit name is ", $hit->name, "\t",
> 	    $hit->accession(), "\t", hit->description(),"\t";
>
>
> leads to the error:
>
> Can't locate object method "description" via package "hit" (perhaps 
> you forgot to load "hit"?) at blast2SpeciesList.pl line 60.
>
>
> However, the documentation for Bio::Search::Hit indicates that Hit 
> objects should have a description() method.
>
> What am I misunderstanding?
>
> Thanks in advance for any tips. Just in case, I am pasting the 
> complete code snippet at the bottom of this mail.
>
> Peter
>
>
> #!/usr/bin/perl -w
> use strict;
>
>
> #Remote-blast "factory object" creation and blast-parameter 
> initialization
>
> use Bio::Tools::Run::RemoteBlast;
>
> my $prog = 'blastn';
> my $db   = 'nr';
> 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 $v = 1;
> #$v is just to turn on and off the messages
>
> my $str = Bio::SeqIO->new(-file=>'testSeqs.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(), "\t",
> 	  $result->query_accession(),"\n";
> 	while ( my $hit = $result->next_hit ) {
> 	  next unless ( $v > 0);
> 	  print "\thit name is ", $hit->name, "\t",
> 	    $hit->accession(), "\t", hit->description(),"\t";
> 	
> 	  while( my $hsp = $hit->next_hsp ) {
> 	    print "\te-val is ", $hsp->evalue, "\n";
> 	    last;
> 	  }
> 	}
>       }
>     }
>   }
> }
>
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