Christopher Fields > BioPerl-1.6.921 > Bio::Tools::Promoterwise



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Module Version: 1.006921   Source   Latest Release: BioPerl-1.6.924


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


  use Bio::Tools::Promoterwise;

  my $pw = Bio::Tools::Promoterwise->new(-file=>"out",
  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";


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

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


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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   : 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


 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
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