[Bioperl-l] RemoteBlast problem

[Thomas J Keller]

Jason 1.5.1 rocks!!
.. and solved my particular problem

Thanks for the responses.

Tom Keller, Ph.D.
http://www.ohsu.edu/research/core
kellert at ohsu.edu
503-494-2442

On Oct 28, 2005, at 1:22 PM, Jason Stajich wrote:

> Fixes to handle both changes in BLAST report format and CGI-server  
> at NCBI.  All this and more in bioperl 1.5.1
>
> You can install it locally without messing with your fink (leave  
> 1.4 installed)
>
> Just download bioperl 1.5.1 from bioperl - uncompress and move to  
> somewhere ( like $HOME/src/bioperl-1.5.1 or whatever you want) and  
> updated your PERL5LIB variable and prepend this path to it:
>
> So add this in your .bash_profile or .bashrc depending on how you  
> are setup
>
> export PERL5LIB=$HOME/src/bioperl-1.5.1:$PERL5LIB
>
> (after the test -r /sw/bin/init.sh && . /sw/bin/init.sh line)
>
> When fink supports 1.5.1 you can just remove this line and you'll  
> be back to normal.
>
> -jason
>
> On Oct 28, 2005, at 3:55 PM, Thomas J Keller wrote:
>
>
>> 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
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
>
>
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