Bio::Tools::Promoterwise - parser for Promoterwise tab format output

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

   new
        Title   : new
        Usage   : my $obj = Bio::Tools::Promoterwise->new();
        Function: Builds a new Bio::Tools::Promoterwise object
        Returns : L<Bio::Tools::Promoterwise>
        Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO

   next_result
        Title   : next_result
        Usage   : my $r = $rpt_masker->next_result
        Function: Get the next result set from parser data
        Returns : an  L<Bio::SeqFeature::FeaturePair>
        Args    : none

perl v5.32.1                                       2021-08-15                      Bio::Tools::Promoterwise(3pm)

       Email shawnh@fugu-sg.org

       Promoteriwise 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.
       Promoterwise is written by Ewan Birney.  It is part of the wise2 package available at
       <ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/>

       This module is the parser for the Promoterwise output in tab format.

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       Bio::Tools::Promoterwise - parser for Promoterwise tab format output

         use Bio::Tools::Promoterwise;

         my $pw = Bio::Tools::Promoterwise->new(-file=>"out",
                                                -query1_seq=>$seq1,
                                                -query2_seq=>$seq2);
         while (my $fp = $pw->next_result){
           print "Hit Length: ".$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;
           foreach my $i (0..$#first_hsp){
             print $first_hsp[$i]->start. " ".$first_hsp[$i]->end." ".
                   $second_hsp[$i]->start. " ".$second_hsp[$i]->end."\n";
           }
         }