Christopher Fields > BioPerl-Run > Bio::Tools::Run::StandAloneBlastPlus::BlastMethods

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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:

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
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