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

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

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

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  http://bugzilla.open-bio.org/

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 _

new

 Title   : new
 Usage   : my $obj = new Bio::Tools::Promoterwise();
 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