debian man page for bio::tools::promoterwise

Bio::Tools::Promoterwise(3pm)				User Contributed Perl Documentation			     Bio::Tools::Promoterwise(3pm)

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."
";
	   print "Hit Start: ".$fp->feature1->start."
";
	   print "Hit End: ".$fp->feature1->end."
";
	   print "Hsps: 
";
	   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."
";
	   }
	 }

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://redmine.open-bio.org/projects/bioperl/

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

perl v5.14.2							    2012-03-02					     Bio::Tools::Promoterwise(3pm)