NAME

       Bio::Tools::Run::Alignment::Exonerate

SYNOPSIS

         use Bio::Tools::Run::Alignment::Exonerate;
         use Bio::SeqIO;

         my $qio = Bio::SeqIO->new(-file=>$ARGV[0],-format=>'fasta');
         my $query = $qio->next_seq();
         my $tio = Bio::SeqIO->new(-file=>$ARGV[1],-format=>'fasta');
         my $target = $sio->next_seq();

         #exonerate parameters can all be passed via arguments parameter.
         #parameters passed are not checked for validity

         my $run = Bio::Tools::Run::Alignment::Exonerate->
             new(arguments=>'--model est2genome --bestn 10');
         my $searchio_obj = $run->run($query,$target);

         while(my $result = $searchio->next_result){
           while( my $hit = $result->next_hit ) {
             while( my $hsp = $hit->next_hsp ) {
               print $hsp->start."\t".$hsp->end."\n";
             }
           }
         }

DESCRIPTION

       Wrapper for Exonerate alignment program. You can get exonerate at
       http://www.ebi.ac.uk/~guy/exonerate/.  This wrapper is written without parameter checking.
       All parameters are passed via the arugment parameter that is passed in the constructor.
       See SYNOPSIS.  For exonerate parameters, run exonerate --help for more details.

PROGRAM VERSIONS

       The tests have been shown to pass with exonorate versions 2.0 - 2.2.

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-at-stanford.edu

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 $factory= Bio::Tools::Run::Phrap->new();
        Function: creates a new Phrap factory
        Returns:  Bio::Tools::Run::Phrap
        Args    :

   version
        Title   : version
        Usage   : exit if $prog->version() < 1.8
        Function: Determine the version number of the program
        Example :
        Returns : float or undef
        Args    : none

   run
        Title   :   run()
        Usage   :   my $feats = $factory->run($seq)
        Function:   Runs Phrap
        Returns :   An array of Bio::SeqFeature::Generic objects
        Args    :   A Bio::PrimarySeqI

   _input
        Title   :   _input
        Usage   :   $factory->_input($seqFile)
        Function:   get/set for input file
        Returns :
        Args    :

   _run
        Title   :   _run
        Usage   :   $factory->_run()
        Function:   Makes a system call and runs Phrap
        Returns :   An array of Bio::SeqFeature::Generic objects
        Args    :

   _writeInput
        Title   :   _writeInput
        Usage   :   $factory->_writeInput($query,$target)
        Function:   Creates a file from the given seq object
        Returns :   A string(filename)
        Args    :   Bio::PrimarySeqI

   _setparams
        Title   :  _setparams
        Usage   :  Internal function, not to be called directly
        Function:  creates a string of params to be used in the command string
        Example :
        Returns :  string of params
        Args    :