Bio::Tools::Run::RemoteBlast.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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 paramter
   $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' );
 
   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: 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://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

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

bioperl-l@bioperl.org

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:
   http://bugzilla.bioperl.org
 
 

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 : -1 on error,
            0 on 'job not finished',
            Bio::SearchIO object
  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 NCBI BLAST database
  Returns : None
  Args    : string (database url like
  NOTE    : This is highly experimental; we cannot maintain support on
            databases other than the default NCBI database at this time
 
 

get_url_base

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