Bio::Tools::Run::RemoteBlast - Object for remote execution of the NCBI Blast via HTTP #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'}; 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.

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/ Email jason@bioperl.org 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]