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Bio::Tools::PromoterwiUser)Contributed Perl DocumenBio::Tools::Promoterwise(3)

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

perl v5.32.1			  2019-12-07	   Bio::Tools::Promoterwise(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Shawn Hoon | APPENDIX

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