Bio/Matrix/PSM/InstanceSiteI.pm

   1
   2 =head1 NAME
   3
   4 Bio::Matrix::PSM::InstanceSiteI - InstanceSite interface, holds an instance of a PSM
   5
   6 =head1 SYNOPSIS
   7
   8   use Bio::Matrix::PSM::InstanceSite;
   9   #Y ou can get an InstanceSite object either from a file:
  10   my ($instances,$matrix)=$SomePSMFile->parse_next;
  11   #or from memory
  12   my %params=(seq       => 'TATAAT',
  13               id        => "TATAbox1",
  14               accession => 'ENSG00000122304',
  15               mid       => 'TB1',
  16               desc      => 'TATA box, experimentally verified in PRM1 gene',
  17               relpos    => -35);
  18
  19 =head1 DESCRIPTION
  20
  21 Abstract interface to PSM site occurrence (PSM sequence
  22 match). InstanceSite objects may be used to describe a PSM (See
  23 Bio::Matrix::PSM::SiteMatrix) sequence matches.  The usual
  24 characteristic of such a match is sequence coordinates, score,
  25 sequence and sequence (gene) identifier- accession number or other
  26 id. This object inherits from Bio::LocatableSeq (which defines the
  27 real sequence) and might hold a SiteMatrix object, used to detect the
  28 CRE (cis-regulatory element), or created from this CRE.  While the
  29 documentation states that the motif id and gene id (accession)
  30 combination should be unique, this is not entirely true- there might
  31 be more than one occurrence of the same cis-regulatory element in the
  32 upstream region of the same gene.  Therefore relpos would be the third
  33 element to create a really unique combination.
  34
  35 =head1 FEEDBACK
  36
  37 =head2 Mailing Lists
  38
  39 User feedback is an integral part of the evolution of this and other
  40 Bioperl modules. Send your comments and suggestions preferably to one
  41 of the Bioperl mailing lists.  Your participation is much appreciated.
  42
  43   bioperl-l@bioperl.org                  - General discussion
  44   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  45
  46 =head2 Support
  47
  48 Please direct usage questions or support issues to the mailing list:
  49
  50 I<bioperl-l@bioperl.org>
  51
  52 rather than to the module maintainer directly. Many experienced and
  53 reponsive experts will be able look at the problem and quickly
  54 address it. Please include a thorough description of the problem
  55 with code and data examples if at all possible.
  56
  57 =head2 Reporting Bugs
  58
  59 Report bugs to the Bioperl bug tracking system to help us keep track
  60 the bugs and their resolution.  Bug reports can be submitted via the
  61 web:
  62
  63   https://github.com/bioperl/bioperl-live/issues
  64
  65 =head1 AUTHOR - Stefan Kirov
  66
  67 Email skirov@utk.edu
  68
  69 =head1 SEE ALSO
  70
  71 L<Bio::Matrix::PSM::SiteMatrix>, L<Bio::Matrix::PSM::Psm>, L<Bio::Matrix::PSM::IO>
  72
  73 =head1 APPENDIX
  74
  75 =cut
  76
  77
  78 # Let the code begin...
  79 package Bio::Matrix::PSM::InstanceSiteI;
  80 use strict;
  81
  82 use base qw(Bio::Root::RootI);
  83
  84 =head2 mid
  85
  86  Title   : mid
  87  Usage   : my $mid=$instance->mid;
  88  Function: Get/Set the motif id
  89  Throws  :
  90  Returns : scalar
  91  Args    : scalar
  92
  93
  94 =cut
  95
  96 sub mid {
  97     my $self = shift;
  98     $self->throw_not_implemented();
  99 }
 100
 101 =head2 score
 102
 103  Title   : score
 104  Usage   : my $score=$instance->score;
 105  Function: Get/Set the score (mismatches) between the instance and the attached (or
 106             initial) PSM
 107  Throws  :
 108  Returns : real number
 109  Args    : real number
 110
 111 =cut
 112
 113 sub score {
 114     my $self = shift;
 115     $self->throw_not_implemented();
 116 }
 117
 118 =head2 start
 119
 120  Title   : start
 121  Usage   : my $start=$instance->start;
 122  Function: Get/Set the position of the instance on the sequence used
 123  Throws  :
 124  Returns : integer
 125  Args    : integer
 126
 127 =cut
 128
 129 sub start {
 130     my $self = shift;
 131     $self->throw_not_implemented();
 132 }
 133
 134 =head2 relpos
 135
 136  Title   : relpos
 137  Usage   : my $seqpos=$instance->relpos;
 138  Function: Get/Set the relative position of the instance with respect to the transcription start
 139             site (if known). Can and usually is negative.
 140  Throws  :
 141  Returns : integer
 142  Args    : integer
 143
 144 =cut
 145
 146 sub relpos {
 147     my $self = shift;
 148     $self->throw_not_implemented();
 149 }
 150
 151
 152 =head2 minstance
 153
 154  Title   : minstance
 155  Usage   : my $minstance=$misntance->score;
 156  Function: Get/Set the unique identifier- sequence id/motif id, for example PRM1_TATAbox.
 157           Not necessarily human readable.
 158  Throws  :
 159  Returns : string
 160  Args    : string
 161
 162 =cut
 163
 164 sub minstance {
 165     my $self = shift;
 166     $self->throw_not_implemented();
 167 }
 168
 169
 170 1;