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Bio::Tools::Run::StandUseriContributeduPerltDocumentalastPlus::BlastMethods(3)

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 v5.24.1		 Bio::Tools::Run::StandAloneBlastPlus::BlastMethods(3)

NAME | SYNOPSIS | DESCRIPTION | USAGE | SEE ALSO | FEEDBACK | AUTHOR - Mark A. Jensen | CONTRIBUTORS | APPENDIX

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