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 listsSupport
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/issuesAUTHOR
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 tosubmit_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 toheader
Title : header
Usage : my $header = $self->header
Function: Get HTTP header for blast query
Returns : string
Args : nonereadmethod
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 protocolsubmit_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 sequencesretrieve_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 : Noneget_rtoe
Title : get_rtoe
Usage : my $url = $self->rtoe
Function: Retrieve the retrieval time (defined after submit_blast())
Returns : number
Args : None