plucky (3) Bio::Tools::Promoterwise.3pm.gz

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