[Bioperl-l] Getting description of BLAST hits

[Marc Logghe]

It is only a typo:
$hit->accession(), "\t", hit->description(),"\t";

And perl barfs with Can't locate object method "description" via package
"hit"
And that makes sense because it should be:
$hit->accession(), "\t", $hit->description(),"\t";
                         ~~~~

HTH,
ML


> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org 
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of 
> Peter.Robinson at t-online.de
> Sent: Wednesday, April 06, 2005 7:48 AM
> To: bioperl-l at portal.open-bio.org
> Subject: Re: [Bioperl-l] Getting description of BLAST hits
> 
> On Tue, Apr 05, 2005 at 10:18:35PM -0400, Jason Stajich wrote:
> > what does
> > print ref($hit), "\n";
> > say?
> 
> ref($hit)= Bio::Search::Hit::BlastHit
> I am using Bioperl 1.4, perl 5.8, Debian linux (sarge, 2.6)
> 
> Thanks,
> Peter
> 
> 
> > 
> > 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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> > >Bioperl-l at portal.open-bio.org
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> > 
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