Provided by: libbio-perl-run-perl_1.7.1-3_all bug


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


        # 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 );


       This module provides the BLAST methods (blastn, blastp, psiblast, etc.) to the
       Bio::Tools::Run::StandAloneBlastPlus object.


       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):


       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


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


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       rather than to the module maintainer directly. Many experienced and reponsive experts will
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   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:

AUTHOR - Mark A. Jensen

       Email maj -at- fortinbras -dot- us

       Describe contact details here


       Additional contributors names and emails here


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

        Title   : run
        Usage   :
        Function: Query the attached database using a specified blast
        Returns : Bio::Search::Result::BlastResult object
        Args    : key => value:
                  -method => $method [blastp|blastn|blastx|tblastx|tblastn|
                  -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)

        Title   : bl2seq
        Usage   :
        Function: emulate bl2seq using blast+ programs
        Returns : Bio::Search::Result::BlastResult object
        Args    : key => value
                  -method => $blast_method [blastn|blastp|blastx|
                  -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

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

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

        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(3pm)