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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Promoterwise 3pm"
.TH Bio::Tools::Promoterwise 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Tools::Promoterwise \- parser for Promoterwise tab format output
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  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."\en";
\&    print "Hit Start: ".$fp\->feature1\->start."\en";
\&    print "Hit End: ".$fp\->feature1\->end."\en";
\&    print "Hsps: \en";
\&    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."\en";
\&    }
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "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 \s-1DBA,\s0 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/>
.PP
This module is the parser for the Promoterwise output in tab format.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Shawn Hoon"
.IX Header "AUTHOR - Shawn Hoon"
Email shawnh@fugu\-sg.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 5
\& 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
.Ve
.SS "next_result"
.IX Subsection "next_result"
.Vb 5
\& 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
.Ve