#
# BioPerl module for Bio::Tools::Run::RemoteBlast
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# FORMERLY Cared for by Jason Stajich, Mat Wiepert
#
# Somewhat cared for by Roger Hall, Chris Fields (when they have time)
#
# Copyright Jason Stajich, Bioperl
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::RemoteBlast - Object for remote execution of the NCBI Blast
via HTTP
=head1 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' );
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'};
=head1 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.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR
Please do NOT contact Jason directly about this module. Please post to
the bioperl mailing list (L<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.
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Tools::Run::RemoteBlast;
use strict;
use warnings;
use Bio::SeqIO;
use IO::String;
use Bio::SearchIO;
use LWP;
use HTTP::Request::Common;
use constant {
NOT_FINISHED => 0,
ERR_QBSTATUS => 1,
ERR_NOCONTENT => 2,
ERR_HTTPFAIL => 4,
ERR_QBNONSPEC => 8
};
# Bio::Root::IO is-a Bio::Root::Roo
use base qw(Bio::Root::IO Exporter);
our @EXPORT = qw( NOT_FINISHED ERR_QBSTATUS ERR_NOCONTENT ERR_HTTPFAIL ERR_QBNONSPEC );
our $MODVERSION = $Bio::Root::Version::VERSION;
our $URLBASE = 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi';
# In GET/PUTPARAMS the values are regexes which validate the input.
our %PUTPARAMS = (
'AUTO_FORMAT' => '(Off|(Semi|Full)auto)', # Off, Semiauto, Fullauto
'COMPOSITION_BASED_STATISTICS' => '(0|1)', # yes, no on NCBI's site, but actually binary 0/1
'DATABASE' => '.*',
'DB_GENETIC_CODE' => '([1-9]|1[1-6]|2(1|2))', # 1..16,21,22
'DISPLAY_SORT' => '\d',
'ENDPOINTS' => '(yes|no)', # yes,no
'ENTREZ_QUERY' => '.*',
'EXPECT' => '\d+(\.\d+)?([eE]-\d+)?', # Positive double
'FILTER' => '[LRm]', # L or R or m
'GAPCOSTS' => '-?\d+(\.\d+)\s+-?\d+(\.\d+)',
# Two space separated float values
'GENETIC_CODE' => '([1-9]|1[1-6]|2(1|2))', # 1..16,21,22
'HITLIST_SIZE' => '\d+', # Positive integer
'I_THRESH' => '-?\d+(\.\d+)([eE]-\d+)?', # float
'LAYOUT' => '(One|Two)Windows?', # onewindow, twowindows
'LCASE_MASK' => '(yes|no)', # yes, no
'MATRIX_NAME' => '.*',
'NUCL_PENALTY' => '-\d+', # Negative integer
'NUCL_REWARD' => '-?\d+', # Integer
'OTHER_ADVANCED' => '.*',
'PERC_IDENT' => '\d\d+', # Integer, 0-99 inclusive
'PHI_PATTERN' => '.*',
'PROGRAM' => 't?blast[pnx]',
# tblastp, tblastn, tblastx, blastp, blastn, blastx
'QUERY' => '.*',
'QUERY_FILE' => '.*',
'QUERY_BELIEVE_DEFLINE' => '(yes|no)', # yes, no
'QUERY_FROM' => '\d+', # Positive integer
'QUERY_TO' => '\d+', # Positive integer
'SEARCHSP_EFF' => '\d+', # Positive integer
'SERVICE' => '(plain|p[sh]i|(rps|mega)blast)',
# plain,psi,phi,rpsblast,megablast
'SHORT_QUERY_ADJUST' => '(true|false)',
'THRESHOLD' => '-?\d+', # Integer
'UNGAPPED_ALIGNMENT' => '(yes|no)', # yes, no
'WORD_SIZE' => '\d+' # Positive integer
);
our %GETPARAMS = (
'ALIGNMENTS' => '\d+', # Positive integer
'ALIGNMENT_VIEW' =>
'(Pairwise|(Flat)?QueryAnchored(NoIdentities)?|Tabular)',
# Pairwise, QueryAnchored, QueryAnchoredNoIdentities,
# FlatQueryAnchored, FlatQueryAnchoredNoIdentities, Tabular
'DATABASE_SORT' => '\d',
'DESCRIPTIONS' => '\d+', # Positive integer
'ENTREZ_LINKS_NEW_WINDOW' => '(yes|no)', # yes, no
'EXPECT_LOW' => '\d+(\.\d+)?([eE]-\d+)?', # Positive double
'EXPECT_HIGH' => '\d+(\.\d+)?([eE]-\d+)?', # Positive double
'FORMAT_ENTREZ_QUERY' => '',
'FORMAT_OBJECT' =>
'(Alignment|Neighbors|PSSM|SearchInfo|TaxBlast(Parent|MultiFrame)?)',
# Alignment, Neighbors, PSSM, SearchInfo
# TaxBlast, TaxblastParent, TaxBlastMultiFrame
'FORMAT_TYPE' => '((HT|X)ML|ASN\.1|Text)',
# HTML, Text, ASN.1, XML
'NCBI_GI' => '(yes|no)', # yes, no
'NEW_VIEW' => '(true|false)',
'RID' => '.*',
'RESULTS_FILE' => '(yes|no)', # yes, no
'SERVICE' => '(plain|p[sh]i|(rps|mega)blast)',
# plain,psi,phi,rpsblast,megablast
'SHOW_OVERVIEW' => '(yes|no)' # yes, no
);
# Default values go in here for PUT
our %HEADER = (
'CMD' => 'Put',
'FORMAT_OBJECT' => 'Alignment',
'COMPOSITION_BASED_STATISTICS' => 'off',
'DATABASE' => 'nr',
'EXPECT' => '1e-3',
'FILTER' => 'L',
'PROGRAM' => 'blastp',
'SERVICE' => 'plain'
);
# Default values go in here for GET
our %RETRIEVALHEADER = (
'CMD' => 'Get',
'ALIGNMENTS' => '50',
'ALIGNMENT_VIEW' => 'Pairwise',
'DESCRIPTIONS' => '100',
'FORMAT_TYPE' => 'Text',
);
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, $readmethod, $url_base) =
$self->_rearrange([qw(PROG DATA READMETHOD URL_BASE)],
@args);
# Use these two parameters for backward-compatibility.
# Overridden by PROGRAM and DATABASE if supplied.
$self->submit_parameter('PROGRAM',$prog) if $prog;
$self->submit_parameter('DATABASE',$data) if $data;
$readmethod = 'SearchIO' unless defined $readmethod;
$self->readmethod($readmethod);
# Now read the rest of the parameters and set them all
# PUT parameters first
my @putValues = $self->_rearrange([keys %PUTPARAMS],@args);
my %putNames;
@putNames{keys %PUTPARAMS} = @putValues;
foreach my $putName (keys %putNames) {
$self->submit_parameter($putName,$putNames{$putName});
}
# GET parameters second
my @getValues = $self->_rearrange([keys %GETPARAMS],@args);
my %getNames;
@getNames{keys %GETPARAMS} = @getValues;
foreach my $getName (keys %getNames) {
$self->retrieve_parameter($getName,$getNames{$getName});
}
# private variable to keep track of total rids
$self->{'_total_rids'} = 0;
$url_base ||= $URLBASE; # default to regular NCBI BLAST URL
$self->set_url_base($url_base);
return $self;
}
=head2 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
$val : optional value to set the parameter to
=cut
sub retrieve_parameter {
my ($self, $name, $val) = @_;
$name = uc($name);
$self->throw($name." is not a valid GET parameter.") unless
exists $GETPARAMS{$name};
if (defined $val) {
my $regex = $GETPARAMS{$name};
$val =~ m/^$regex$/i or
$self->throw("Value ".$val." for GET parameter ".$name." does not match expression ".$regex.". Rejecting.");
$RETRIEVALHEADER{$name} = $val;
}
return $RETRIEVALHEADER{$name};
}
=head2 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
$val : optional value to set the parameter to
=cut
sub submit_parameter {
my ($self, $name, $val) = @_;
$name = uc($name);
$self->throw($name." is not a valid PUT parameter.") unless
exists $PUTPARAMS{$name};
if (defined $val) {
my $regex = $PUTPARAMS{$name};
$val =~ m/^$regex$/i or
$self->throw("Value ".$val." for PUT parameter ".$name." does not match expression ".$regex.". Rejecting.");
$HEADER{$name} = $val;
}
return $HEADER{$name};
}
=head2 header
Title : header
Usage : my $header = $self->header
Function: Get HTTP header for blast query
Returns : string
Args : none
=cut
sub header {
my ($self) = @_;
return %HEADER;
}
=head2 readmethod
Title : readmethod
Usage : my $readmethod = $self->readmethod
Function: Get/Set the method to read the blast report
Returns : string
Args : string [ blast, blasttable, xml ]
=cut
sub readmethod {
my ($self, $val) = @_;
if( defined $val ) {
if ($val =~ /bplite/i) {
$self->throw("Use of Bio::Tools::BPlite is deprecated; use Bio::SearchIO modules instead");
}
$self->{'_readmethod'} = $val;
}
return $self->{'_readmethod'};
}
=head2 program
Title : program
Usage : my $prog = $self->program
Function: Get/Set the program to run. Retained for backwards-compatibility.
Returns : string
Args : string [ blastp, blastn, blastx, tblastn, tblastx ]
=cut
sub program {
my ($self, $val) = @_;
return $self->submit_parameter('PROGRAM',$val);
}
=head2 database
Title : database
Usage : my $db = $self->database
Function: Get/Set the database to search. Retained for backwards-compatibility.
Returns : string
Args : string [ swissprot, nr, nt, etc... ]
=cut
sub database {
my ($self, $val) = @_;
return $self->submit_parameter('DATABASE',$val);
}
=head2 expect
Title : expect
Usage : my $expect = $self->expect
Function: Get/Set the E value cutoff. Retained for backwards-compatibility.
Returns : string
Args : string [ '1e-4' ]
=cut
sub expect {
my ($self, $val) = @_;
return $self->submit_parameter('EXPECT',$val);
}
=head2 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.
=cut
sub ua {
my ($self, $value) = @_;
if( ! defined $self->{'_ua'} ) {
$self->{'_ua'} = LWP::UserAgent->new(env_proxy => 1, parse_head => 0);
my $nm = ref($self);
$nm =~ s/::/_/g;
$self->{'_ua'}->agent("bioperl-$nm/$MODVERSION");
}
return $self->{'_ua'};
}
=head2 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
$proxyurl : url of the proxy to use for the specified protocol
=cut
sub proxy {
my ($self,$protocol,$proxy) = @_;
return if ( !defined $self->ua || !defined $protocol
|| !defined $proxy );
return $self->ua->proxy($protocol,$proxy);
}
sub add_rid {
my ($self, @vals) = @_;
foreach ( @vals ) {
$self->{'_rids'}->{$_} = $self->{'_total_rids'};
$self->{'_total_rids'}++;
}
return scalar keys %{$self->{'_rids'}};
}
sub remove_rid {
my ($self, @vals) = @_;
foreach ( @vals ) {
delete $self->{'_rids'}->{$_};
}
return scalar keys %{$self->{'_rids'}};
}
sub each_rid {
my ($self) = @_;
# sort on key value, a little tricky...
my @sort_rids = sort {$self->{'_rids'}->{$a} <=> $self->{'_rids'}->{$b}} keys %{$self->{'_rids'}};
return @sort_rids;
}
=head2 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 $self->readmethod
Args : input can be:
* sequence object
* array ref of sequence objects
* filename of file containing fasta formatted sequences
=cut
sub submit_blast {
my ($self, $input) = @_;
my @seqs = $self->_load_input($input);
my $url_base = $self->get_url_base;
return 0 unless ( @seqs );
my $tcount = 0;
my %header = $self->header;
$header{$_} ||= $RETRIEVALHEADER{$_} foreach (keys %RETRIEVALHEADER);
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 $url_base, [%header];
$self->debug($request->as_string) if ( $self->verbose > 1);
my $response = $self->ua->request( $request);
if( $response->is_success ) {
my @subdata = split(/\n/, $response->content );
my $count = 0;
foreach ( @subdata ) {
if( /^\s+RID\s+=\s+(\S+)/ ) {
$count++;
#$self->debug("RID: $1\n");
$self->add_rid($1);
} elsif (/^\s+RTOE\s+=\s+(.*$)/) {
$self->{rtoe} = $1;
$count++;
}
last if $count >= 2;
}
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;
}
=head2 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)
=cut
sub retrieve_blast {
my($self, $rid) = @_;
my $url_base = $self->get_url_base;
my %hdr = %RETRIEVALHEADER;
$hdr{'RID'} = $rid;
my $req = HTTP::Request->new(
GET => $url_base."?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=$rid",
);
#$self->debug("SearchInfo request is " . $req->as_string());
my $response = $self->ua->request($req);
if( $response->is_success ) {
my $status;
if($response->content =~ /Status=(WAITING|ERROR|FAILED|UNKNOWN|READY)/i ) {
$status = $1;
if( $status eq 'ERROR' ) {
$self->warn("Server Error");
return ERR_QBSTATUS;
} elsif( $status eq 'FAILED' ) {
$self->warn("Request Failed");
return ERR_QBSTATUS;
}
} else {
$self->warn("Error: No status reported\n");
}
if ( $status ne 'READY' ) {
return 0;
} else {
my ($fh,$tempfile) = $self->tempfile();
close $fh;
my $req = POST $url_base, [%hdr];
$self->debug("retrieve request is " . $req->as_string());
my $response = $self->ua->request($req, $tempfile);
my $blastobj;
my $mthd = $self->readmethod;
$mthd = ($mthd =~ /blasttable/i) ? 'blasttable' :
($mthd =~ /xml/i) ? 'blastxml' :
($mthd =~ /pull/i) ? 'blast_pull' :
'blast';
$blastobj = Bio::SearchIO->new(
-file => $tempfile,
-format => $mthd);
## store filename in object ##
$self->file($tempfile);
return $blastobj;
}
} else {
$self->warn($response->error_as_HTML);
return ERR_HTTPFAIL;
}
}
=head2 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]
=cut
sub save_output {
my ($self, $filename) = @_;
if( ! defined $filename ) {
$self->throw("Can't save blast output. You must specify a filename to save to.");
}
my $blastfile = $self->file;
#open temp file and output file, have to filter out some HTML
open(my $TMP, $blastfile) or $self->throw("cannot open $blastfile");
open(my $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 ||
/<\?xml\sversion=/ ||
/^#\s+(?:[T]?BLAST[NPX])\s*.+$/) {
$seentop=1;
}
next if !$seentop;
if( $seentop ) {
print $SAVEOUT $_;
}
}
return 1;
}
sub _load_input {
my ($self, $input) = @_;
if( ! defined $input ) {
$self->throw("Calling remote blast with no input");
}
my @seqs;
if( ! ref $input ) {
if( -e $input ) {
my $seqio = Bio::SeqIO->new(-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;
}
=head2 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
=cut
sub set_url_base {
my $self = shift;
$self->{'_urlbase'} = shift if @_;
}
=head2 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
=cut
sub get_url_base {
my $self = shift;
return $self->{'_urlbase'};
}
=head2 get_rtoe
Title : get_rtoe
Usage : my $url = $self->rtoe
Function: Retrieve the retrieval time (defined after submit_blast())
Returns : number
Args : None
=cut
sub get_rtoe {
my $self = shift;
return $self->{rtoe};
}
1;
__END__