Bio::Tools::Run StandAloneBlastPlus
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Summary
Bio::Tools::Run::StandAloneBlastPlus::BlastMethods - Provides BLAST methods to StandAloneBlastPlus
Package variables
No package variables defined.
Included modules
Bio::SearchIO
Bio::Tools::Run::BlastPlus
File::Copy
File::Spec
File::Temp
lib ' ../../../.. '
Synopsis
 # create a factory:
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-db_name => 'testdb'
);
# get your results
$result = $fac->blastn( -query => 'query_seqs.fas',
-outfile => 'query.bls',
-method_args => [ '-num_alignments' => 10 ] );
$result = $fac->tblastx( -query => $an_alignment_object, -outfile => 'query.bls', -outformat => 7 ); # do a bl2seq $fac->bl2seq( -method => 'blastp', -query => $seq_object_1, -subject => $seq_object_2 );
Description
This module provides the BLAST methods (blastn, blastp, psiblast,
etc.) to the Bio::Tools::Run::StandAloneBlastPlus object.
Methods
runDescriptionCode
bl2seqDescriptionCode
next_result()
No description
Code
rewind_resultsDescriptionCode
blast_outDescriptionCode
_demodernize
No description
Code
Methods description
run()code    nextTop
 Title   : run
Usage :
Function: Query the attached database using a specified blast
method
Returns : Bio::Search::Result::BlastResult object
Args : key => value:
-method => $method [blastp|blastn|blastx|tblastx|tblastn|
rpsblast|psiblast|rpstblastn]
-query => $query_sequences (a fasta file name or BioPerl sequence
object or sequence collection object)
-outfile => $blast_report_file (optional: default creates a tempfile)
-outformat => $format_code (integer in [0..10], see blast+ docs)
-method_args => [ -key1 => $value1, ... ] (additional arguments
for the given method)
bl2seq()(2)codeprevnextTop
 Title   : bl2seq
Usage :
Function: emulate bl2seq using blast+ programs
Returns : Bio::Search::Result::BlastResult object
Args : key => value
-method => $blast_method [blastn|blastp|blastx|
tblastn|tblastx]
-query => $query (fasta file or BioPerl sequence object
-subject => $subject (fasta file or BioPerl sequence object)
-outfile => $blast_report_file
-method_args => [ $key1 => $value1, ... ] (additional method
parameters)
rewind_results()codeprevnextTop
 Title   : rewind_results
Usage : $fac->rewind_results;
Function: rewind BLAST results
Returns : true on success
Args :
blast_out()codeprevnextTop
 Title   : blast_out
Usage : $file = $fac->blast_out
Function: get the filename of the blast report file
Returns : scalar string
Args : none
Methods code
rundescriptionprevnextTop
sub run {
    my $self = shift;
    my @args = @_;
    my ($method, $query, $outfile, $outformat, $method_args) = $self->_rearrange( [qw( 
                                         METHOD
                                         QUERY
                                         OUTFILE
                                         OUTFORMAT
                                         METHOD_ARGS
                                         )], @args);
    my $ret;
    my (%blast_args, %usr_args);
    
    unless ($method) {
	$self->throw("Blast run: method not specified, use -method");
    }
    unless ($query) {
	$self->throw("Blast run: query data required, use -query");
    }
    unless ($outfile) { # create a tempfile name
my $fh = File::Temp->new(TEMPLATE => 'BLOXXXXX', DIR => $self->db_dir, UNLINK => 0); $outfile = $fh->filename; $fh->close; $self->_register_temp_for_cleanup($outfile); } if ($outformat) { unless ($outformat =~ /^[0-9]{1,2}$/) { $self->throw("Blast run: output format code should be integer 0-10"); } $blast_args{'-outfmt'} = $outformat; } if ($method_args) { $self->throw("Blast run: method arguments must be name => value pairs") unless !(@$method_args % 2); %usr_args = @$method_args; } # make db if necessary
$self->make_db unless $self->check_db or $self->is_remote or $usr_args{'-subject'} or $usr_args{'-SUBJECT'}; # no db nec if this is bl2seq...
$self->{_factory} = Bio::Tools::Run::BlastPlus->new( -command => $method ); if (%usr_args) { my @avail_parms = $self->factory->available_parameters('all'); while ( my( $key, $value ) = each %usr_args ) { $key =~ s/^-//; unless (grep /^$key$/, @avail_parms) { $self->throw("Blast run: parameter '$key' is not available for method '$method'"); } } } # remove a leading ./ on remote databases. Something adds that in the
# factory, easier to remove here.
my $db = $self->db_path; if ($self->is_remote) { $db =~ s#^\./##; } $blast_args{-db} = $db; $blast_args{-query} = $self->_fastize($query); $blast_args{-out} = $outfile; # user arg override
if (%usr_args) { $blast_args{$_} = $usr_args{$_} for keys %usr_args; } # override for bl2seq;
if ($blast_args{'-db'} && $blast_args{'-subject'}) { delete $blast_args{'-db'}; } $self->factory->set_parameters( %blast_args ); $self->factory->no_throw_on_crash( $self->no_throw_on_crash ); my $status = $self->_run; return $status unless $status; # kludge to demodernize the bl2seq output
if ($blast_args{'-subject'}) { unless (_demodernize($outfile)) { $self->throw("Ack! demodernization failed!"); } } # if here, success
for ($method) { m/^(t|psi|rps|rpst)?blast[npx]?/ && do {
$ret = Bio::SearchIO->new(-file => $outfile);
$self->{_blastout} = $outfile; $self->{_results} = $ret; $ret = $ret->next_result; last; }; do { 1; # huh?
}; } return $ret;
}
bl2seqdescriptionprevnextTop
sub bl2seq {
    my $self = shift;
    my @args = @_;
    my ($method, $query, $subject, $outfile, $outformat, $method_args) = $self->_rearrange( [qw( 
                                         METHOD
                                         QUERY
                                         SUBJECT
                                         OUTFILE
                                         OUTFORMAT
                                         METHOD_ARGS
                                         )], @args);

    unless ($method) {
	$self->throw("bl2seq: blast method not specified, use -method");
    }
    unless ($query) {
	$self->throw("bl2seq: query data required, use -query");
    }
    unless ($subject) {
	$self->throw("bl2seq: subject data required, use -subject");
    }
    $subject = $self->_fastize($subject);

    my @run_args;
    if ($method_args) {
	@run_args = @$method_args;
    }
    return $self->run( -method => $method,
		       -query => $query,
		       -outfile => $outfile, 
		       -outformat => $outformat,
		       -method_args => [ @run_args, '-subject' => $subject ]
	);
}
next_result()descriptionprevnextTop
sub next_result() {
    my $self = shift;
    return unless $self->{_results};
    return $self->{_results}->next_result;
}
rewind_resultsdescriptionprevnextTop
sub rewind_results {
    my $self = shift;
    return unless $self->blast_out;
    $self->{_results} = Bio::SearchIO->new( -file => $self->blast_out );
    return 1;
}
blast_outdescriptionprevnextTop
sub blast_out {
 shift->{_blastout}
}
_demodernizedescriptionprevnextTop
sub _demodernize {
    my $file = shift;
    my $tf = File::Temp->new();
    open (my $f, $file);
    while (<$f>) {
	s/^Subject=\s+/>/;
	print $tf $_;
    }
    $tf->close;
    copy($tf->filename, $file);
}
1;
}
General documentation
USAGETop
This POD describes the use of BLAST methods against a
Bio::Tools::Run::StandAloneBlastPlus factory object. The object
itself has extensive facilities for creating, formatting, and masking
BLAST databases; please refer to
Bio::Tools::Run::StandAloneBlastPlus POD for these details.
Given a StandAloneBlastPlus factory, such as
 $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-db_name => 'testdb'
);
you can run the desired BLAST method directly from the factory object,
against the database currently attached to the factory (in the
example, testdb). -query is a required argument:
 $result = $fac->blastn( -query => 'query_seqs.fas' );
Here, $result is a Bio::Search::Result::BlastResult object.
Other details:
    * The blast output file can be named explicitly:
    
$result = $fac->blastn( -query => 'query_seqs.fas',
-outfile => 'query.bls' );

    * The output format can be specified:
    
$result = $fac->blastn( -query => 'query_seqs.fas',
-outfile => 'query.bls',
-outformat => 7 ); #tabular

    * Additional arguments to the method can be specified:
    
$result = $fac->blastn( -query => 'query_seqs.fas',
-outfile => 'query.bls',
-method_args => [ '-num_alignments' => 10 ,
'-evalue' => 100 ]);

    * To get the name of the blast output file, do
    
$file = $fac->blast_out;

    * To clean up the temp files (you must do this explicitly):
    
$fac->cleanup;

Return valuesTop
The return value is always a Bio::Search::Result::BlastResult
object on success, undef on failure.
SEE ALSOTop
Bio::Tools::Run::StandAloneBlastPlus, Bio::Tools::Run::BlastPlus
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
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
SupportTop
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 BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
  http://redmine.open-bio.org/projects/bioperl/
AUTHOR - Mark A. JensenTop
Email maj -at- fortinbras -dot- us
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
next_result()Top
 Title   : next_result
Usage : $result = $fac->next_result;
Function: get the next BLAST result
Returns : Bio::Search::Result::BlastResult object
Args : none