---
name: "Bio::Tools::Promoterwise"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Tools::Promoterwise"
---

# Bio::Tools::Promoterwise(3pm)

parser for Promoterwise tab format output

## 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
```

### 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 of the bugs and their resolution. Bug reports can be submitted via the web:

```
  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 \_

### 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
```