Bio::Tools::Run RemoteBlast
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Summary
Bio::Tools::Run::RemoteBlast - Object for remote execution of the NCBI Blast
via HTTP
Package variables
No package variables defined.
Included modules
Bio::Root::IO
Bio::Root::Root
Bio::SearchIO
Bio::SeqIO
Bio::Tools::BPlite
HTTP::Request::Common
IO::String
LWP
Inherit
Bio::Root::IO Bio::Root::Root
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 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'};
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.
Methods
BEGIN Code
_load_input
No description
Code
add_rid
No description
Code
databaseDescriptionCode
each_rid
No description
Code
expectDescriptionCode
headerDescriptionCode
new
No description
Code
programDescriptionCode
proxyDescriptionCode
readmethodDescriptionCode
remove_rid
No description
Code
retrieve_blastDescriptionCode
save_outputDescriptionCode
submit_blastDescriptionCode
uaDescriptionCode
Methods description
databasecode    nextTop
 Title   : database
Usage : my $db = $self->database
Function: Get/Set the database to search
Returns : string
Args : string [ swissprot, nr, nt, etc... ]
expectcodeprevnextTop
 Title   : expect
Usage : my $expect = $self->expect
Function: Get/Set the E value cutoff
Returns : string
Args : string [ '1e-4' ]
headercodeprevnextTop
 Title   : header
Usage : my $header = $self->header
Function: Get/Set HTTP header for blast query
Returns : string
Args : none
programcodeprevnextTop
 Title   : program
Usage : my $prog = $self->program
Function: Get/Set the program to run
Returns : string
Args : string [ blastp, blastn, blastx, tblastn, tblastx ]
proxycodeprevnextTop
 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
readmethodcodeprevnextTop
 Title   : readmethod
Usage : my $readmethod = $self->readmethod
Function: Get/Set the method to read the blast report
Returns : string
Args : string [ Blast, BPlite ]
retrieve_blastcodeprevnextTop
 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_outputcodeprevnextTop
 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]
submit_blastcodeprevnextTop
 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
uacodeprevnextTop
 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.
Methods code
BEGINTop
BEGIN {
    $URLBASE = 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi';
    %HEADER = ('CMD'                          => 'Put',
	       'PROGRAM'                      => '',
	       'DATABASE'                     => '',
	       'FILTER'                       => 'L',
	       'EXPECT'                       => '',
	       'QUERY'                        =>  '',
	       'CDD_SEARCH'                   => 'off',
	       'COMPOSITION_BASED_STATISTICS' => 'off',
	       'FORMAT_OBJECT'                => 'Alignment',
	       'SERVICE'                      => 'plain',
	       );

    %RETRIEVALHEADER = ('CMD'            => 'Get',
			'RID'            => '',
			'ALIGNMENT_VIEW' => 'Pairwise',
			'DESCRIPTIONS'   => 100,
			'ALIGNMENTS'     => 50,
			'FORMAT_TYPE'    => 'Text',
			);

    $RIDLINE = 'RID\s+=\s+(\S+)';

    %BLAST_PARAMS = ( 'prog' => 'blastp',
		       'data' => 'nr',
		       'expect' => '1e-3',
		       'readmethod' => 'SearchIO'
		       );
}
_load_inputdescriptionprevnextTop
sub _load_input {
    my ($self, $input) = @_;

    if( ! defined $input ) {
	$self->throw("Calling remote blast with no input");	
    }
    my @seqs;
    if( ! ref $input ) {
	if( -e $input ) {
	    my $seqio = new Bio::SeqIO(-format => 'fasta', -file => $input);
	    while( my $seq = $seqio->next_seq ) {
		push @seqs, $seq;
	    }
	} else {
	    $self->throw("Input $input was not a valid filename");
	}	
    } elsif( ref($input) =~ /ARRAY/i ) {
	foreach ( @$input ) {
	    if( ref($_) && $_->isa('Bio::PrimarySeqI') ) {
		push @seqs, $_;
	    } else {
		$self->warn("Trying to add a " . ref($_) .
			    " but expected a Bio::PrimarySeqI");
	    }
	}
	if( ! @seqs) {
	    $self->throw("Did not pass in valid input -- no sequence objects found");
	}
    } elsif( $input->isa('Bio::PrimarySeqI') ) {
	push @seqs, $input;
    }
    return @seqs;
}
1;
__END__
}
add_riddescriptionprevnextTop
sub add_rid {
    my ($self, @vals) = @_;
    foreach ( @vals ) {
	$self->{'_rids'}->{$_} = 1;
    }
    return scalar keys %{$self->{'_rids'}};
}
databasedescriptionprevnextTop
sub database {
    my ($self, $val) = @_;
    if( defined $val ) {
#	$self->{'_database'} = $val;
$HEADER{'DATABASE'} = $val; } return $HEADER{'DATABASE'};
}
each_riddescriptionprevnextTop
sub each_rid {
    my ($self) = @_;
    return keys %{$self->{'_rids'}};
}
expectdescriptionprevnextTop
sub expect {
    my ($self, $val) = @_;
    if( defined $val ) {
#	$self->{'_expect'} = $val;
$HEADER{'EXPECT'} = $val; } return $HEADER{'EXPECT'};
}
headerdescriptionprevnextTop
sub header {
    my ($self) = @_;
    my %h = %HEADER;
    $h{'PROGRAM'} = $self->program;
    $h{'DATABASE'} = $self->database;
    $h{'EXPECT'}  = $self->expect;
    return %h;
}
newdescriptionprevnextTop
sub new {
    my ($caller, @args) = @_;
    # chained new
my $self = $caller->SUPER::new(@args); # so that tempfiles are cleaned up
$self->_initialize_io(); my ($prog, $data, $expect, $readmethod) = $self->_rearrange([qw(PROG DATA EXPECT READMETHOD)], @args); $readmethod = $BLAST_PARAMS{'readmethod'} unless defined $readmethod; $prog = $BLAST_PARAMS{'prog'} unless defined $prog; $data = $BLAST_PARAMS{'data'} unless defined $data; $expect = $BLAST_PARAMS{'expect'} unless defined $expect; $self->readmethod($readmethod); $self->program($prog); $self->database($data); $self->expect($expect); return $self;
}
programdescriptionprevnextTop
sub program {
    my ($self, $val) = @_;
    if( defined $val ) {
	$val = lc $val;
	if( $val !~ /t?blast[pnx]/ ) {
	    $self->warn("trying to set program to an invalid program name ($val) -- defaulting to blastp");
	    $val = 'blastp';
	}
#	$self->{'_program'} = $val;
$HEADER{'PROGRAM'} = $val; } return $HEADER{'PROGRAM'};
}
proxydescriptionprevnextTop
sub proxy {
    my ($self,$protocol,$proxy) = @_;
    return undef if ( !defined $self->ua || !defined $protocol
		      || !defined $proxy );
    return $self->ua->proxy($protocol,$proxy);
}
readmethoddescriptionprevnextTop
sub readmethod {
    my ($self, $val) = @_;
    if( defined $val ) {
	$self->{'_readmethod'} = $val;
    }
    return $self->{'_readmethod'};
}
remove_riddescriptionprevnextTop
sub remove_rid {
    my ($self, @vals) = @_;
    foreach ( @vals ) {
	delete $self->{'_rids'}->{$_};
    }
    return scalar keys %{$self->{'_rids'}};
}
retrieve_blastdescriptionprevnextTop
sub retrieve_blast {
    my($self, $rid) = @_;
    my (undef,$tempfile) = $self->tempfile();
    my %hdr = %RETRIEVALHEADER;
    $hdr{'RID'} = $rid;
    my $req = POST $URLBASE, [%hdr];
    if( $self->verbose > 0 ) {
	$self->warn("retrieve request is " . $req->as_string());
    }
    my $response = $self->ua->request($req, $tempfile);
    if( $self->verbose > 0 ) {
	open(TMP, $tempfile) or $self->throw("cannot open $tempfile");
	while(<TMP>) { print $_; }
	close TMP;
    }
    if( $response->is_success ) {	
	my $size = -s $tempfile;
	if( $size > 1000 ) {
	    my $blastobj;
	    if( $self->readmethod =~ /BPlite/ ) {
		$blastobj = new Bio::Tools::BPlite(-file => $tempfile);
	    } else {
		$blastobj = new Bio::SearchIO(-file => $tempfile,
					      -format => 'blast');
	    }
	    #save tempfile
$self->file($tempfile); return $blastobj; } elsif( $size < 500 ) { # search had a problem
open(ERR, "<$tempfile") or $self->throw("cannot open file $tempfile"); $self->warn(join("", <ERR>)); close ERR; return -1; } else { # still working
return 0; } } else { $self->warn($response->error_as_HTML); return -1; }
}
save_outputdescriptionprevnextTop
sub save_output {
    my ($self, $filename) = @_;
    if( ! defined $filename ) {
        	$self->throw("Can't save blast output.  You must specify a filename to save to.");
    }
    #should be set when retrieving blast
my $blastfile = $self->file; #open temp file and output file, have to filter out some HTML
open(TMP, $blastfile) or $self->throw("cannot open $blastfile"); open(SAVEOUT, ">$filename") or $self->throw("cannot open $filename"); my $seentop=0; while(<TMP>) { next if (/<pre>/); if( /^(?:[T]?BLAST[NPX])\s*.+$/i || /^RPS-BLAST\s*.+$/i ) { $seentop=1; } next if !$seentop; if( $seentop ) { print SAVEOUT; } } close SAVEOUT; close TMP; return 1;
}
submit_blastdescriptionprevnextTop
sub submit_blast {
    my ($self, $input) = @_;
    my @seqs = $self->_load_input($input);
    return 0 unless ( @seqs );
    my $tcount = 0;
    my %header = $self->header;
    foreach my $seq ( @seqs ) {
	#If query has a fasta header, the output has the query line.
$header{'QUERY'} = ">".(defined $seq->display_id() ? $seq->display_id() : ""). " ".(defined $seq->desc() ? $seq->desc() : "")."\n".$seq->seq(); my $request = POST $URLBASE, [%header]; $self->warn($request->as_string) if ( $self->verbose > 0); my $response = $self->ua->request( $request); if( $response->is_success ) { if( $self->verbose > 0 ) { my ($tempfh) = $self->tempfile(); # Hmm, what exactly are we trying to do here?
print $tempfh $response->content; close($tempfh); undef $tempfh; } my @subdata = split(/\n/, $response->content ); my $count = 0; foreach ( @subdata ) { if( /$RIDLINE/ ) { $count++; print STDERR $_ if( $self->verbose > 0); $self->add_rid($1); last; } } if( $count == 0 ) { $self->warn("req was ". $request->as_string() . "\n"); $self->warn(join('', @subdata)); } $tcount += $count; } else { # should try and be a little more verbose here
$self->warn("req was ". $request->as_string() . "\n" . $response->error_as_HTML); $tcount = -1; } } return $tcount;
}
uadescriptionprevnextTop
sub ua {
    my ($self, $value) = @_;
    if( ! defined $self->{'_ua'} ) {
	$self->{'_ua'} = new LWP::UserAgent;
    }
    return $self->{'_ua'};
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 BugsTop
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/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _