Provided by: libbio-perl-perl_1.7.2-3_all bug

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.

         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:

         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