File Coverage

Bio/Map/GenePosition.pm
Criterion Covered Total %
statement 47 52 90.3
branch 15 26 57.6
condition 5 9 55.5
subroutine 10 10 100.0
pod 6 6 100.0
total 83 103 80.5


line stmt bran cond sub pod time code
1             # $Id: GenePosition.pm,v 1.19 2006/09/20 10:20:01 sendu Exp $
2             #
3             # BioPerl module for Bio::Map::GenePosition
4             #
5             # Please direct questions and support issues to
6             #
7             # Cared for by Sendu Bala
8             #
9             # Copyright Sendu Bala
10             #
11             # You may distribute this module under the same terms as perl itself
12              
13             # POD documentation - main docs before the code
14              
15             =head1 NAME
16              
17             Bio::Map::GenePosition - A typed position, suitable for modelling the various
18             regions of a gene.
19              
20             =head1 SYNOPSIS
21              
22             use Bio::Map::GenePosition;
23             use Bio::Map::GeneMap;
24              
25             # say that the first transcript of a particular gene on a particular map
26             # (species) is 1000bp long
27             my $map = Bio::Map:GeneMap->get(-universal_name => 'BRCA2',
28             -species => 'human');
29             my $gene = $map->gene;
30             Bio::Map::GenePosition->new(-map => $map,
31             -element => $gene,
32             -start => 0,
33             -length => 1000,
34             -type => 'transcript');
35              
36             # say that the coding region of the gene starts 30bp into the first
37             # transcript
38             Bio::Map::GenePosition->new(-map => $map,
39             -element => $gene,
40             -start => 30,
41             -length => 600,
42             -type => 'coding');
43              
44             # A GenePosition isa PositionWithSequence, so can have sequence associated
45             # with it
46             my $exon = Bio::Map::GenePosition->new(-map => $map,
47             -element => $gene,
48             -start => 0,
49             -type => 'exon',
50             -seq => 'ATGGGGTGGG');
51             my $length = $exon->length; # $length is 10
52              
53             =head1 DESCRIPTION
54              
55             Define where various sub-regions (transcripts, exons, introns etc.) of a gene
56             are. Do this so that you can then go onto to model other mappable elements as
57             having positions 20bp upstream of transcript 2, or 10bp into intron 3 etc., all
58             without having to know the absolute position of anything.
59              
60             See Bio::Map::GeneRelative and t/Map/Map.t for more example usage.
61              
62             =head1 FEEDBACK
63              
64             =head2 Mailing Lists
65              
66             User feedback is an integral part of the evolution of this and other
67             Bioperl modules. Send your comments and suggestions preferably to
68             the Bioperl mailing list. Your participation is much appreciated.
69              
70             bioperl-l@bioperl.org - General discussion
71             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
72              
73             =head2 Support
74              
75             Please direct usage questions or support issues to the mailing list:
76              
77             I
78              
79             rather than to the module maintainer directly. Many experienced and
80             reponsive experts will be able look at the problem and quickly
81             address it. Please include a thorough description of the problem
82             with code and data examples if at all possible.
83              
84             =head2 Reporting Bugs
85              
86             Report bugs to the Bioperl bug tracking system to help us keep track
87             of the bugs and their resolution. Bug reports can be submitted via the
88             web:
89              
90             https://github.com/bioperl/bioperl-live/issues
91              
92             =head1 AUTHOR - Sendu Bala
93              
94             Email bix@sendu.me.uk
95              
96             =head1 APPENDIX
97              
98             The rest of the documentation details each of the object methods.
99             Internal methods are usually preceded with a _
100              
101             =cut
102              
103             # Let the code begin...
104              
105             package Bio::Map::GenePosition;
106 1     1   6 use strict;
  1         2  
  1         26  
107              
108 1     1   589 use Bio::Map::GeneRelative;
  1         2  
  1         30  
109              
110 1     1   6 use base qw(Bio::Map::PositionWithSequence);
  1         1  
  1         652  
111              
112             =head2 new
113              
114             Title : new
115             Usage : my $obj = Bio::Map::GenePosition->new();
116             Function: Builds a new Bio::Map::GenePosition object
117             Returns : Bio::Map::GenePosition
118             Args : -map => Bio::Map::GeneMap object
119             -element => Bio::Map::Gene object
120             -relative => Bio::Map::GeneRelative object
121             -type => 'transcript|coding|exon|intron', REQUIRED
122             -seq => string, length of this string will set the length
123             of this position's range
124              
125             * If this position has no range, or if a single value can describe
126             the range *
127             -value => scalar : something that describes the single
128             point position or range of this
129             Position, most likely an int
130              
131             * Or if this position has a range, at least two of *
132             -start => int : value of the start co-ordinate
133             -end => int : value of the end co-ordinate
134             -length => int : length of the range
135              
136             =cut
137              
138             sub new {
139 8     8 1 29 my ($class, @args) = @_;
140 8         37 my $self = $class->SUPER::new(@args);
141            
142 8         32 my ($type) = $self->_rearrange([qw( TYPE )], @args);
143 8 50       17 $type || $self->throw("type must be supplied");
144 8         19 $self->type($type);
145            
146 8         15 $self->{_relative_not_implicit} = 1;
147            
148 8         27 return $self;
149             }
150              
151             =head2 map
152              
153             Title : map
154             Usage : my $map = $position->map();
155             $position->map($map);
156             Function: Get/set the map the position is in.
157             Returns : L
158             Args : none to get
159             new L to set
160              
161             =cut
162              
163             sub map {
164 286     286 1 365 my ($self, $map) = @_;
165 286 100       381 if ($map) {
166 8 50       29 $map->isa('Bio::Map::GeneMap') || $self->throw("This is [$map], not a Bio::Map::GeneMap");
167             }
168 286         522 return $self->SUPER::map($map);
169             }
170              
171             =head2 element
172              
173             Title : element
174             Usage : my $element = $position->element();
175             $position->element($element);
176             Function: Get/set the element the position is for.
177             Returns : L
178             Args : none to get
179             new L to set
180              
181             =cut
182              
183             sub element {
184 1     1 1 3 my ($self, $element) = @_;
185 1 50       3 if ($element) {
186 0 0       0 $element->isa('Bio::Map::Gene') || $self->throw("This is [$element], not a Bio::Map::Gene");
187             }
188 1         12 return $self->SUPER::element($element);
189             }
190              
191             =head2 type
192              
193             Title : type
194             Usage : my $type = $position->type();
195             $position->type($type);
196             Function: Get/set the type of this position.
197             Returns : string
198             Args : none to get, OR
199             string transcript|coding|exon|intron to set
200              
201             =cut
202              
203             sub type {
204 2366     2366 1 2177 my $self = shift;
205 2366 100       2752 if (@_) {
206 16         22 my $type = shift;
207 16 50       80 if ($type !~ /transcript|coding|exon|intron/i) {
208 0         0 $self->throw("type must be supplied and be one of 'transcript', 'coding', 'exon', 'intron'");
209             }
210 16         30 $self->{type} = $type;
211             }
212 2366         3830 return $self->{type};
213             }
214              
215             =head2 relative
216              
217             Title : relative
218             Usage : my $relative = $position->relative();
219             $position->relative($relative);
220             Function: Get/set the thing this Position's coordinates (numerical(), start(),
221             end()) are relative to, as described by a RelativeI object.
222             Returns : Bio::Map::GeneRelative. The default GeneRelative returned has a
223             meaning that depends on the type() of GenePosition this is:
224             'transcript' : "relative to the start of the gene on the
225             Position's map"
226             'coding|exon|intron' : "relative to the start of the default
227             transcript of the gene on the Position's map"
228             Args : none to get, OR
229             Bio::Map::GeneRelative to set
230              
231             =cut
232              
233             sub relative {
234 717     717 1 830 my ($self, $relative) = @_;
235 717 50       945 if ($relative) {
236 0 0       0 $self->throw("Must supply an object") unless ref($relative);
237 0 0       0 $self->throw("This is [$relative], not a Bio::Map::GeneRelative") unless $relative->isa('Bio::Map::GeneRelative');
238 0         0 $self->{_relative} = $relative;
239             }
240 717   33     1439 return $self->{_relative} || $self->_default_relative;
241             }
242              
243             =head2 seq
244              
245             Title : seq
246             Usage : my $string = $position->seq();
247             Function: Get/set the sequence as a string of letters. If no sequence is
248             manually set by you, the position's map will be asked for the
249             sequence, and if available, that will be returned.
250             Returns : scalar
251             Args : Optionally on set the new value (a string). An optional second
252             argument presets the alphabet (otherwise it will be guessed).
253              
254             =cut
255              
256             sub seq {
257             # $shortcut is internal-use only by GeneMap
258 13     13 1 26 my ($self, $str, $alpha, $shortcut) = @_;
259            
260 13         31 my $seq = $self->SUPER::seq($str, $alpha);
261            
262 13 100 66     32 if ($seq) {
    100 66        
263 5         13 $self->length(CORE::length($seq));
264 5         50 return $seq;
265             }
266             elsif (! $shortcut && defined(my $map = $self->map) && ! defined $self->{_getting_seq}) {
267 1         3 $self->{_getting_seq} = 1;
268 1         5 $seq = $map->subseq($self);
269 1         3 delete $self->{_getting_seq};
270 1         13 return $seq;
271             }
272 7         13 return;
273             }
274              
275             # return a Relative that is suitable for the type
276             sub _default_relative {
277 717     717   880 my $self = shift;
278 717         867 my $type = $self->type;
279 717 100       1071 if ($type eq 'transcript') {
280 341         716 return Bio::Map::GeneRelative->new(-gene => 0, -description => 'start of gene');
281             }
282             else {
283 376         804 return Bio::Map::GeneRelative->new(-transcript => 0, -description => 'start of default transcript');
284             }
285             }
286              
287             1;