NAME

       Bio::Tools::Run::Promoterwise - Wrapper for aligning two sequences using promoterwise

SYNOPSIS

         # Build a Promoterwise alignment factory
         my @params = ('-s'=>1,'-query_start'=>10,'-dymem'=>1);
         my  $factory = Bio::Tools::Run::Promoterwise->new(@params);

         my (@fp)= $factory->run($seq1,$seq2);

         # each feature pair is a group of hsps
         foreach my $fp(@fp){
           print "Hit Length: ".$fp->feature1->length."\n";
           print "Hit Start: ".$fp->feature1->start."\n";
           print "Hit End: ".$fp->feature1->end."\n";
           print "Hsps: \n";
           my @first_hsp = $fp->feature1->sub_SeqFeature;
           my @second_hsp = $fp->feature2->sub_SeqFeature;
           for ($i..$#first_hsp){
             print $first_hsp[$i]->seq." ".$second_hsp[$i]->seq."\n";
           }
         }
         print "end: ". $fp->feature2->start."\t".$fp->feature2->end."\n";

         #Available parameters include:
         #( S T U V QUERY_START QUERY_END TARGET_START
         #TARGET_END LHWINDOW LHSEED LHALN LHSCORE LHREJECT
         #LHREJECT LHMAX DYMEM KBYTE DYCACHE)
         #For an explanation of these parameters, please see documentation
         #from the Wise package.

DESCRIPTION

       Promoterwise is an alignment algorithm that relaxes the constraint that local alignments
       have to be co-linear. Otherwise it provides a similar model to DBA, which is designed for
       promoter sequence alignments by Ewan Birney.  It is part of the wise2 package available
       at: http://www.sanger.ac.uk/software/wise2.

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    :

   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   : 2 sequence objects
                  @fp = $factory->run($seq1, $seq2);
        Function: run
        Returns : An array of <Bio::SeqFeature::FeaturePair>
        Args    : Name of a file containing a set of 2 fasta sequences
                  or else 2  Bio::Seq objects.

       Throws an exception if argument is not either a string (eg a filename) or 2 Bio::Seq
       objects.  If arguments are strings, throws exception if file corresponding to string name
       can not be found.

   _run
        Title   :  _run
        Usage   :  Internal function, not to be called directly
        Function:   makes actual system call to a promoterwise program
        Example :
        Returns : L<Bio::SeqFeature::FeaturePair>
        Args    : Name of a files containing 2 sequences in the order of peptide and genomic

   _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    :

   _query_pep_seq
        Title   :  _query_pep_seq
        Usage   :  Internal function, not to be called directly
        Function:  get/set for the query sequence
        Example :
        Returns :
        Args    :

   _subject_dna_seq
        Title   :  _subject_dna_seq
        Usage   :  Internal function, not to be called directly
        Function:  get/set for the subject sequence
        Example :
        Returns :

        Args    :