Bio/Search/HSP/WABAHSP.pm

   1 #
   2 # BioPerl module for Bio::Search::HSP::WABAHSP
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Jason Stajich <jason@bioperl.org>
   7 #
   8 # Copyright Jason Stajich
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::Search::HSP::WABAHSP - HSP object suitable for describing WABA alignments
  17
  18 =head1 SYNOPSIS
  19
  20 # use this object as you would a GenericHSP
  21 # a few other methods have been added including state
  22
  23 =head1 DESCRIPTION
  24
  25 This object implements a few of the extra methods such as
  26 hmmstate_string which returns the HMM state representation for the
  27 WABA alignment.  We also must implement a method to calculate
  28 homology_string since it is not returned by the algorithm in the
  29 machine readable format.
  30
  31 =head1 FEEDBACK
  32
  33 =head2 Mailing Lists
  34
  35 User feedback is an integral part of the evolution of this and other
  36 Bioperl modules. Send your comments and suggestions preferably to
  37 the Bioperl mailing list.  Your participation is much appreciated.
  38
  39   bioperl-l@bioperl.org                  - General discussion
  40   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  41
  42 =head2 Support
  43
  44 Please direct usage questions or support issues to the mailing list:
  45
  46 I<bioperl-l@bioperl.org>
  47
  48 rather than to the module maintainer directly. Many experienced and
  49 reponsive experts will be able look at the problem and quickly
  50 address it. Please include a thorough description of the problem
  51 with code and data examples if at all possible.
  52
  53 =head2 Reporting Bugs
  54
  55 Report bugs to the Bioperl bug tracking system to help us keep track
  56 of the bugs and their resolution. Bug reports can be submitted via the
  57 web:
  58
  59   https://github.com/bioperl/bioperl-live/issues
  60
  61 =head1 AUTHOR - Jason Stajich
  62
  63 Email jason@bioperl.org
  64
  65 =head1 APPENDIX
  66
  67 The rest of the documentation details each of the object methods.
  68 Internal methods are usually preceded with a _
  69
  70 =cut
  71
  72 # Let the code begin...
  73
  74
  75 package Bio::Search::HSP::WABAHSP;
  76 use strict;
  77 use Bio::Root::RootI;
  78
  79 use base qw(Bio::Search::HSP::GenericHSP);
  80
  81 =head2 new
  82
  83  Title   : new
  84  Usage   : my $obj = Bio::Search::HSP::WABAHSP->new();
  85  Function: Builds a new Bio::Search::HSP::WABAHSP object
  86  Returns : Bio::Search::HSP::WABAHSP
  87  Args    : -hmmstate_seq => the string representing the state output from WABA
  88
  89 =cut
  90
  91 sub new {
  92   my($class,@args) = @_;
  93
  94   # gotta do some preprocessing before we send the arguments to the superclass
  95   my ($len,$qs,$hs) = Bio::Root::RootI->_rearrange([qw(HSP_LENGTH
  96                                                        QUERY_SEQ
  97                                                        HIT_SEQ)],@args);
  98   if( $len != length($qs) ) {
  99     Bio::Root::RootI->warn("HSP_LENGTH must equal length of query_seq string, using value from QUERY_SEQ\n");
 100       $len = length($qs);
 101   }
 102   my( $homol_seq,$gapct,$identical) = ('',0,0);
 103
 104   for(my $i=0;$i<$len;$i++) {
 105       my $q = substr($qs,$i,1);
 106       my $h = substr($hs,$i,1);
 107       if( $q eq '-' || $h eq '-' ) {
 108           $homol_seq .= ' ';
 109           $gapct ++;
 110       } elsif( $q eq $h ) {
 111           $homol_seq .= '|';
 112           $identical++;
 113       } else {
 114           $homol_seq .= ' ';
 115       }
 116   }
 117   my $self = $class->SUPER::new('-conserved' => $identical,
 118                                 '-identical' => $identical,
 119                                 '-gaps'      => $gapct,
 120                                 '-homology_seq' => $homol_seq,
 121                                 @args);
 122
 123   my ($hmmst) = $self->_rearrange([qw(HMMSTATE_SEQ)],@args);
 124   defined $hmmst && $self->hmmstate_string($hmmst);
 125
 126   $self->add_tag_value('Target' , join(" ","Sequence:".$self->hit->seq_id,
 127                                        $self->hit->start, $self->hit->end));
 128
 129   return $self;
 130 }
 131
 132 =head2 hmmstate_string
 133
 134  Title   : hmmstate_string
 135  Usage   : my $hmmseq = $wabahsp->hmmstate_string();
 136  Function: Get/Set the WABA HMM stateseq
 137  Returns : string
 138  Args    : [optional] string
 139
 140
 141 =cut
 142
 143 sub hmmstate_string{
 144    my ($self,$val) = @_;
 145    if( defined $val ) {
 146        $self->{'_hmmstate_string'} = $val;
 147    }
 148    return $self->{'_hmmstate_string'};
 149 }
 150
 151 =head2 homology_string
 152
 153  Title   : homolgy_string
 154  Usage   : my $homology_str = $hsp->homology_string();
 155  Function: Homology string must be calculated for a WABA HSP so we can do
 156            so here and cache the result so it is only done once
 157  Returns : string
 158  Args    : none
 159
 160
 161 =cut
 162
 163 sub homology_string{
 164    my ($self) = @_;
 165    return '';
 166 }
 167
 168
 169 1;