[Bioperl-l] RemoteBlast problem

[Marc Logghe]

Hi Tom,
What a coincidence. I had exactly the same a few hours ago.
Did a few things with conditionals in the script, but in the end, I had
to change the size check in B::T::R::RemoteBlast::retrieve_blast()
In my case it worked when the size was set to 2000 instead of 1000

                ## if proper reply 
                my $size = -s $tempfile;
                if( $size > 2000 ) {


HTH,
Marc


> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org 
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of 
> Thomas J Keller
> Sent: Friday, October 28, 2005 9:55 PM
> To: bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] RemoteBlast problem
> 
> Greetings,
> I'm using perl 5.8.6 and the fink installation of bioperl 
> 1.4.5 on an Apple G5 running OS X 10.4.2 running my script 
> with a simple fasta dna sequence file:
> $ bp_remote_blast2.pl -p blastx -d nr -i test.fa
> 
> Here's the error:
> 
> ------------- EXCEPTION  -------------
> MSG: no data for midline Query  78    
> HRRPSFSACRCVLSASSVFPSRLGNNYITAAGAQVLAEGLRGNTSLQFLG  227 STACK 
> Bio::SearchIO::blast::next_result /sw/lib/perl5/5.8.6/Bio/
> SearchIO/blast.pm:1151
> STACK toplevel 
> /Users/kellert/Sandbox/Perlscripts/bp_remote_blast2.pl:90
> 
> 
> It looks like Bio::SearchIO::blast
> is choking on the result from Bio::Tools::Run::RemoteBlast
> 
> I lifted this from Jason's exampleL bp_remote_blast but modified it  
> to use SearchIO method instead of BPLite:
> 
> use warnings;
> use strict;
> use vars qw($USAGE);
> 
> use Bio::Tools::Run::RemoteBlast;
> use Bio::SeqIO;
> use Bio::SearchIO;
> use Getopt::Long;
> 
> $USAGE = "remote_blast.pl [-h] [-p prog] [-d db] [-e expect]  [-f  
> seqformat] -i seqfile\n";
> 
> my ($prog, $db, $expect );
> 
> my ($sequencefile,$sequenceformat,$help) = (undef, 'fasta',undef);
> 
> &GetOptions('prog|p=s'               => \$prog,
>          'db|d=s'                 => \$db,
>          'expect|e=s'             => \$expect,
>          'input|i=s'              => \$sequencefile,
>          'format|f=s'             => \$sequenceformat,
>          'help|h'                 => \$help,
>          );
> 
> if( $help ) {
>      exec('perldoc', $0);
>      die;
> }
> 
> if( !defined $prog ) {
>      die($USAGE . "\n\tMust specify a valid program name ([t]blast 
> [pxn])\n");
> }
> if( !defined $db ) {
>      die($USAGE . "\n\tMust specify a db (e.g. \'nr\') to search\n");
> }
> if( !defined $sequencefile ) {
>      die($USAGE . "\n\tMust specify a path to a sequence file.\n");
> }
> 
> my $factory = new Bio::Tools::Run::RemoteBlast ('-prog'      => $prog,
>                               '-data'      => $db,
>                               '-expect'    => $expect,
>                               'readmethod' => 'SearchIO',     
>    #use  
> SearchIO to parse
>                               );
> 
> # submit_blast can only currenly handle fasta format files so I'll
> # preprocess outside of the module but I'd rather be sure here
> 
> my $input;
> if( $sequenceformat !~ /fasta/ ) {
>      my @seqs;
>      my $seqio = new Bio::SeqIO('-format' => $sequenceformat,
>                     '-file'   => $sequencefile );
>      while( my $seq = $seqio->next_seq() ) {
>      push @seqs, $seq;
>      }
>      $input = \@seqs;
> } else {
>      $input = $sequencefile;
> }
> my $r = $factory->submit_blast($input);
> 
> my $v = 1;
> ## set to 0 to turn off Sanity check messages
> print STDERR  "retrieving blasts for $input ...\n" 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 = $rc->next_result();
>                  next unless ($result);
>                   print "\nQuery Name: ", $result->query_name(), "\n";
>                  #save the output
>                  my $filename = $result->query_name()."\.out";
>                  print STDERR  "Saving result to 
> $filename.\n" if( $v  
>  > 0);
>                  $factory->save_output($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";
>                                }
>                          }
>                    }
>              }
>            }
> 
> I'm guessing either NCBI has changed it blast format and bioperl 1.4  
> no longer works, or I'm missing something that should be obvious.
> 
> Help much apprecieated.
> 
> Tom K
> 
> 
> Thomas J. Keller, Ph.D.
> Director, MMI Core Facility
> Oregon Health & Science University
> 3181 SW Sam Jackson Park Rd.
> Portland, OR, USA,   97239
> 
> http://www.ohsu.edu/research/core
> 
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