File Coverage

Bio/Matrix/PSM/InstanceSiteI.pm
Criterion Covered Total %
statement 6 16 37.5
branch n/a
condition n/a
subroutine 2 7 28.5
pod 5 5 100.0
total 13 28 46.4


line stmt bran cond sub pod time code
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
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, L, L
72              
73             =head1 APPENDIX
74              
75             =cut
76              
77              
78             # Let the code begin...
79             package Bio::Matrix::PSM::InstanceSiteI;
80 4     4   28 use strict;
  4         45  
  4         113  
81              
82 4     4   43 use base qw(Bio::Root::RootI);
  4         7  
  4         586  
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 0     0 1   my $self = shift;
98 0           $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 0     0 1   my $self = shift;
115 0           $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 0     0 1   my $self = shift;
131 0           $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 0     0 1   my $self = shift;
148 0           $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 0     0 1   my $self = shift;
166 0           $self->throw_not_implemented();
167             }
168              
169              
170             1;