NAME

       Bio::Tools::Run::Primate - wrapper for Primate,  Guy Slater's near exact match finder for
       short sequence tags.

SYNOPSIS

         use Bio::Tools::Run::Primate;
         use Bio::SeqIO;

         my $query = "primer.fa";
         my $target = "contig.fa";

         my @params = ("query" => $query,"target" => $target,"m"=>0);
         my $fact = Bio::Tools::Run::Primate->new(@params);

         my @feat = $fact->run;
         foreach my $feat(@feat) {
             print $feat->seqname."\t".$feat->primary_tag."\t".$feat->start.
             "\t".$feat->end."\t".$feat->strand."\t".$feat->seq->seq."\n";
         }

DESCRIPTION

       Primate is available under to ensembl-nci package at
       http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/ensembl-nci/?cvsroot=Ensembl

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 one of the Bioperl mailing lists.  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 the bugs and their
       resolution.  Bug reports can be submitted via the web:

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

AUTHOR - Shawn Hoon

       Email shawnh@fugu-sg.org

APPENDIX

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

   program_name
        Title   : program_name
        Usage   : $factory>program_name()
        Function: holds the program name
        Returns:  string
        Args    : None

   program_dir
        Title   : program_dir
        Usage   : $factory->program_dir(@params)
        Function: returns the program directory, obtained from ENV variable.
        Returns:  string
        Args    :

   new
        Title   : new
        Usage   : my $obj = Bio::Tools::Run::Primate->new()
        Function: Builds a new Bio::Tools::Run::Primate objet
        Returns : Bio::Tools::Run::Primate
        Args    : query => the L<Bio::PrimarySeqI> object or a file path
                  target => the L<Bio::PrimarySeqI> object or a file path
                  m  => the number of mismatches allowed, default 1(integer)
                  b  => [TRUE|FALSE] find best match, default FALSE
                  executable=>where the program sits

   version
        Title   : version
        Usage   : $primate->version
        Function: Determine the version number of the program
        Returns : float or undef
        Args    : none

   search
        Title   : search
        Usage   : DEPRECATED. Use $factory->run() instead
        Function: Perform a primate search
        Returns : Array of L<Bio::SeqFeature::Generic>
        Args    :

   run
        Title   : run
        Usage   : @feat = $factory->run();
        Function: Perform a primate search
        Returns : Array of L<Bio::SeqFeature::Generic>
        Args    :

   _run
        Title   :  _run
        Usage   : Internal function, not to be called directly
        Function: makes actual system call to dba program
        Returns : array of L<Bio::SeqFeature::Generic>
        Args    : path to query and target file and parameter string

   _parse_results
        Title   :  _parse_results
        Usage   :  Internal function, not to be called directly
        Function:  Passes primate output
        Returns : array of L<Bio::SeqFeature::Generic>
        Args    : the name of the output file

   _setinput()
        Title   : _setinput
        Usage   : Internal function, not to be called directly
        Function: Create input files for primate
        Returns : name of file containing query and target
        Args    : query and target (either a filename or a L<Bio::PrimarySeqI>

   _setparams()
        Title   : _setparams
        Usage   : Internal function, not to be called directly
        Function: Create parameter inputs for primate program
        Returns : parameter string to be passed to primate
        Args    : the param array

   _query_seq()
        Title   :  _query_seq
        Usage   :  Internal function, not to be called directly
        Function:  get/set for the query sequence
        Returns :  a hash of seq with key the query tag
        Args    :  optional

   _target_seq()
        Title   : _target_seq
        Usage   : Internal function, not to be called directly
        Function: get/set for the target sequence
        Returns : L<Bio::PrimarySeqI>
        Args    : optional