NAME¶

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

SYNOPSIS¶

  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";
    }
  }

DESCRIPTION¶

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.

FEEDBACK¶

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  https://github.com/bioperl/bioperl-live/issues

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 _

 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