Bio::Tools::Run::RemoteBlast(3pm)

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 query parameter
  $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens [ORGN]';
  #change a retrieval parameter
  $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'DESCRIPTIONS'} = 1000;
  #remove a parameter
  delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};
  #$v is just to turn on and off the messages
  my $v = 1;
  my $str = Bio::SeqIO->new(-file=>'amino.fa' , -format => 'fasta' );
  #optional: send BLAST request to a cloud service provider instead of NCBI
  #$factory->set_url_base("http://host.my.cloud.service.provider.com/cgi-bin/blast.cgi");
  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'} = 'BLOSUM45';
  $Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'} = '15 2';
  # 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: https://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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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 the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR

Please do NOT contact Jason directly about this module. Please post to the bioperl mailing list (FEEDBACK). If you would like to be the official maintainer of this module, please volunteer on the list and we will make it official in this POD.

First written by Jason Stajich, many others have helped keep it running.

APPENDIX

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

retrieve_parameter

 Title   : retrieve_parameter
 Usage   : my $db = $self->retrieve_parameter
 Function: Get/Set the named parameter for the retrieve_blast operation.
 Returns : string
 Args    : $name : name of GET parameter
         $val : optional value to set the parameter to

submit_parameter

 Title   : submit_parameter
 Usage   : my $db = $self->submit_parameter
 Function: Get/Set the named parameter for the submit_blast operation.
 Returns : string
 Args    : $name : name of PUT parameter
    $val : optional value to set the parameter to

header

 Title   : header
 Usage   : my $header = $self->header
 Function: Get 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, blasttable, xml ]

program

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

database

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

expect

 Title   : expect
 Usage   : my $expect = $self->expect
 Function: Get/Set the E value cutoff. Retained for backwards-compatibility.
 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 : scalar int (constant) or Bio::SearchIO object
           Constants:
            NOT_FINISHED (= 0)   : 'job not finished'
            code on error:
              ERR_QBSTATUS (= 1) : return line matches 'Status=ERROR'
              ERR_NOCONTENT (= 2): HTTP request successful, but no content
                                   returned
              ERR_HTTPFAIL (= 4) : HTTP request failed
              ERR_QBNONSPEC (= 8): return line matches 'ERROR' (not status line)
 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]

set_url_base

 Title   : set_url_base
 Usage   : $self->set_url_base($url)
 Function: Method to override the default URL to access the NCBI BLAST web service
 Returns : None
 Args    : string (URL used for remote BLAST searches)
 NOTE    : This is highly experimental; we cannot maintain support on
           web services other than the default NCBI BLAST web service at this
           time. Only some URL parameters may be supported by other BLAST
           web services.

get_url_base

 Title   : get_url_base
 Usage   : my $url = $self->set_url_base
 Function: Get the current URL for BLAST searching
 Returns : string (URL used for remote blast searches)
 Args    : None

get_rtoe

 Title   : get_rtoe
 Usage   : my $url = $self->rtoe
 Function: Retrieve the retrieval time (defined after submit_blast())
 Returns : number
 Args    : None