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




         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";


       Wrapper for Exonerate alignment program. You can get exonerate at  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.


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


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AUTHOR - Shawn Hoon



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

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

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

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

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

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

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

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

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

        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    :