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:

       •   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 ]);

       •   HTML output can be created using this workaround:

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

       •   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;

   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 v5.36.0                              Bio::Tools::Run::StandAloneBlastPlus::BlastMethods(3pm)