Bio::Tools::Run::StandAloneBlastPlus::BlastMethods(3pm) User Contributed Perl DocumentationBio::Tools::Run::StandAloneBlastPlus::BlastMethods(3pm)

NAME

       Bio::Tools::Run::StandAloneBlastPlus::BlastMethods - Provides BLAST methods to StandAloneBlastPlus

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.

USAGE

       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:

       o   The blast output file can be named explicitly:

	    $result = $fac->blastn( -query => 'query_seqs.fas',
				    -outfile => 'query.bls' );

       o   The output format can be specified:

	    $result = $fac->blastn( -query => 'query_seqs.fas',
				    -outfile => 'query.bls',
				    -outformat => 7 ); #tabular

       o   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 ]);

       o   To get the name of the blast output file, do

	    $file = $fac->blast_out;

       o   To clean up the temp files (you must do this explicitly):

	    $fac->cleanup;

   bl2seq()
       Running "bl2seq" is similar, but both "-query" and "-subject" are required, and the attached database is ignored. The blast method must be
       specified explicitly with the "-method" parameter:

	$fac->bl2seq( -method => 'blastp',
		      -query => $seq_object_1,
		      -subject => $seq_object_2 );

       Other parameters ( "-method_args", "-outfile", and "-outformat" ) are valid.

   Return values
       The return value is always a Bio::Search::Result::BlastResult object on success, undef on failure.

SEE ALSO

       Bio::Tools::Run::StandAloneBlastPlus, Bio::Tools::Run::BlastPlus

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 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

   Support
       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 of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Mark A. Jensen
       Email maj -at- fortinbras -dot- us

       Describe contact details here

CONTRIBUTORS

       Additional contributors names and emails here

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   run()
	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()
	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)

   next_result()
	Title	: next_result
	Usage	: $result = $fac->next_result;
	Function: get the next BLAST result
	Returns : Bio::Search::Result::BlastResult object
	Args	: none

   rewind_results()
	Title	: rewind_results
	Usage	: $fac->rewind_results;
	Function: rewind BLAST results
	Returns : true on success
	Args	:

   blast_out()
	Title	: blast_out
	Usage	: $file = $fac->blast_out
	Function: get the filename of the blast report file
	Returns : scalar string
	Args	: none

perl v5.12.3							    2011-06-18		   Bio::Tools::Run::StandAloneBlastPlus::BlastMethods(3pm)