NAME

Bio::Tools::Run::RemoteBlast - Object for remote execution of the NCBI Blast via HTTP

SYNOPSIS

  #Remote-blast "factory object" creation and blast-parameter initialization

  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 $v = 1;
  #$v is just to turn on and off the messages

  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";
            }
          }
        }
      }
    }
  }

  # This example shows how to change a CGI parameter:
  $Bio::Tools::Run::RemoteBlast::HEADER{'MATRIX_NAME'} = 'BLOSUM25';

  # And this is how to delete a CGI parameter:
  delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};

DESCRIPTION

Class for remote execution of the NCBI Blast via HTTP.

For a description of the many CGI parameters see: http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html

Various additional options and input formats are available.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org               - General discussion
  http://bio.perl.org/MailList.html   - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHOR - Jason Stajich

Email jason@bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

header

 Title   : header
 Usage   : my $header = $self->header
 Function: Get/Set HTTP header for blast query
 Returns : string
 Args    : none

readmethod

 Title   : readmethod
 Usage   : my $readmethod = $self->readmethod
 Function: Get/Set the method to read the blast report
 Returns : string
 Args    : string [ Blast, BPlite ]

program

 Title   : program
 Usage   : my $prog = $self->program
 Function: Get/Set the program to run
 Returns : string
 Args    : string [ blastp, blastn, blastx, tblastn, tblastx ]

database

 Title   : database
 Usage   : my $db = $self->database
 Function: Get/Set the database to search
 Returns : string
 Args    : string [ swissprot, nr, nt, etc... ]

expect

 Title   : expect
 Usage   : my $expect = $self->expect
 Function: Get/Set the E value cutoff
 Returns : string
 Args    : string [ '1e-4' ]

ua

 Title   : ua
 Usage   : my $ua = $self->ua or
           $self->ua($ua)
 Function: Get/Set a LWP::UserAgent for use
 Returns : reference to LWP::UserAgent Object
 Args    : none
 Comments: Will create a UserAgent if none has been requested before.

proxy

 Title   : proxy
 Usage   : $httpproxy = $db->proxy('http')  or
           $db->proxy(['http','ftp'], 'http://myproxy' )
 Function: Get/Set a proxy for use of proxy
 Returns : a string indicating the proxy
 Args    : $protocol : an array ref of the protocol(s) to set/get
           $proxyurl : url of the proxy to use for the specified protocol

submit_blast

 Title   : submit_blast
 Usage   : $self->submit_blast([$seq1,$seq2]);
 Function: Submit blast jobs to ncbi blast queue on sequence(s)
 Returns : Blast report object as defined by $self->readmethod
 Args    : input can be:
           * sequence object
           * array ref of sequence objects
           * filename of file containing fasta formatted sequences

retrieve_blast

 Title   : retrieve_blast
 Usage   : my $blastreport = $blastfactory->retrieve_blast($rid);
 Function: Attempts to retrieve a blast report from remote blast queue
 Returns : -1 on error,
           0 on 'job not finished',
           Bio::Tools::BPlite or Bio::Tools::Blast object
           (depending on how object was initialized) on success
 Args    : Remote Blast ID (RID)

save_output

 Title   : saveoutput
 Usage   : my $saveoutput = $self->save_output($filename)
 Function: Method to save the blast report
 Returns : 1 (throws error otherwise)
 Args    : string [rid, filename]

cpanm LocalConfig

perl -MCPAN -e shell
install LocalConfig