Bio::Search::HSP::WABAHSP - HSP object suitable for describing WABA alignments

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Search::HSP::WABAHSP - HSP object suitable for describing WABA alignments

SYNOPSIS

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# use this object as you would a GenericHSP # a few other methods have been added including state

DESCRIPTION

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This object implements a few of the extra methods such as hmmstate_string which returns the HMM state representation for the WABA alignment. We also must implement a method to calculate homology_string since it is not returned by the algorithm in the machine readable format.

FEEDBACK

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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 - Jason Stajich

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Email jason@bioperl.org

APPENDIX

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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::Search::HSP::WABAHSP->new();
 Function: Builds a new Bio::Search::HSP::WABAHSP object 
 Returns : Bio::Search::HSP::WABAHSP
 Args    : -hmmstate_seq => the string representing the state output from WABA

hmmstate_string

 Title   : hmmstate_string
 Usage   : my $hmmseq = $wabahsp->hmmstate_string();
 Function: Get/Set the WABA HMM stateseq
 Returns : string
 Args    : [optional] string

homology_string

 Title   : homolgy_string
 Usage   : my $homology_str = $hsp->homology_string();
 Function: Homology string must be calculated for a WABA HSP so we can do
           so here and cache the result so it is only done once
 Returns : string
 Args    : none
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Search::HSP::WABAHSP
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code


# Let the code begin...


package Bio::Search::HSP::WABAHSP;
use strict;
use Bio::Root::RootI;

use base qw(Bio::Search::HSP::GenericHSP);


sub new {
  my($class,@args) = @_;

  # gotta do some preprocessing before we send the arguments to the superclass
  my ($len,$qs,$hs) = Bio::Root::RootI->_rearrange([qw(HSP_LENGTH
						       QUERY_SEQ 
						       HIT_SEQ)],@args);  
  if( $len != length($qs) ) {
    Bio::Root::RootI->warn("HSP_LENGTH must equal length of query_seq string, using value from QUERY_SEQ\n");
      $len = length($qs);
  }
  my( $homol_seq,$gapct,$identical) = ('',0,0);
  
  for(my $i=0;$i<$len;$i++) {
      my $q = substr($qs,$i,1);
      my $h = substr($hs,$i,1);
      if( $q eq '-' || $h eq '-' ) {
	  $homol_seq .= ' ';
	  $gapct ++;
      } elsif( $q eq $h ) { 
	  $homol_seq .= '|';
	  $identical++;
      } else { 
	  $homol_seq .= ' ';
      }
  }
  my $self = $class->SUPER::new('-conserved' => $identical,
				'-identical' => $identical,
				'-gaps'      => $gapct,
				'-homology_seq' => $homol_seq,
				@args);
    
  my ($hmmst) = $self->_rearrange([qw(HMMSTATE_SEQ)],@args);
  defined $hmmst && $self->hmmstate_string($hmmst);
  
  $self->add_tag_value('Target' , join(" ","Sequence:".$self->hit->seq_id, 
				       $self->hit->start, $self->hit->end));

  return $self;
}


sub hmmstate_string{
   my ($self,$val) = @_;
   if( defined $val ) { 
       $self->{'_hmmstate_string'} = $val;
   }
   return $self->{'_hmmstate_string'};
}


sub homology_string{
   my ($self) = @_;
   return '';
}


1;