|
0
|
1 # $Id: Mutation.pm,v 1.6 2002/10/22 07:38:34 lapp Exp $
|
|
|
2 #
|
|
|
3 # BioPerl module for Bio::LiveSeq::Mutation
|
|
|
4 #
|
|
|
5 # Cared for by Heikki Lehvaslaiho <heikki@ebi.ac.uk>
|
|
|
6 #
|
|
|
7 # Copyright Heikki Lehvaslaiho
|
|
|
8 #
|
|
|
9 # You may distribute this module under the same terms as perl itself
|
|
|
10
|
|
|
11 # POD documentation - main docs before the code
|
|
|
12
|
|
|
13 =head1 NAME
|
|
|
14
|
|
|
15 Bio::LiveSeq::Mutation - Mutation event descriptor class
|
|
|
16
|
|
|
17 =head1 SYNOPSIS
|
|
|
18
|
|
|
19 # full descrition of a point mutation
|
|
|
20 $mutation1a = Bio::LiveSeq::Mutation->new ( -seq => 'A',
|
|
|
21 -seqori => 'T',
|
|
|
22 -pos => 100,
|
|
|
23 -len => 1 # optional, defaults to length(seq)
|
|
|
24 );
|
|
|
25
|
|
|
26 # minimal information for a point mutation
|
|
|
27 $mutation1b = Bio::LiveSeq::Mutation->new ( -seq => 'A',
|
|
|
28 -pos => 100
|
|
|
29 );
|
|
|
30 # insertion
|
|
|
31 $mutation2 = Bio::LiveSeq::Mutation->new ( -seq => 'ATT',
|
|
|
32 -pos => 100,
|
|
|
33 -len => 0
|
|
|
34 );
|
|
|
35 # deletion
|
|
|
36 $mutation3 = Bio::LiveSeq::Mutation->new ( -seq => '', # optional
|
|
|
37 -seqori => 'TTG', # optional
|
|
|
38 -pos => 100
|
|
|
39 -len => 3
|
|
|
40 );
|
|
|
41 # complex
|
|
|
42 $mutation4 = Bio::LiveSeq::Mutation->new ( -seq => 'CC',
|
|
|
43 -seqori => 'TTG', # optional
|
|
|
44 -pos => 100
|
|
|
45 -len => 3
|
|
|
46 );
|
|
|
47
|
|
|
48
|
|
|
49 =head1 DESCRIPTION
|
|
|
50
|
|
|
51 This class describes a local mutation event using minimalistic
|
|
|
52 description. It is not necessary to know anything about the original
|
|
|
53 sequence. You need to give the changed sequence, the position of the
|
|
|
54 mutation in the (unidentified) reference sequence, and the length of
|
|
|
55 the affected subsequence in the reference sequence. If the original
|
|
|
56 allele sequence is given, the objects applying the mutation into the
|
|
|
57 reference sequence (e.g. L<Bio::LiveSeq::Mutator>) might check for its
|
|
|
58 validity.
|
|
|
59
|
|
|
60 =head1 FEEDBACK
|
|
|
61
|
|
|
62 =head2 Mailing Lists
|
|
|
63
|
|
|
64 User feedback is an integral part of the evolution of this and other
|
|
|
65 Bioperl modules. Send your comments and suggestions preferably to the
|
|
|
66 Bioperl mailing lists Your participation is much appreciated.
|
|
|
67
|
|
|
68 bioperl-l@bioperl.org - General discussion
|
|
|
69 http://bio.perl.org/MailList.html - About the mailing lists
|
|
|
70
|
|
|
71 =head2 Reporting Bugs
|
|
|
72
|
|
|
73 report bugs to the Bioperl bug tracking system to help us keep track
|
|
|
74 the bugs and their resolution. Bug reports can be submitted via
|
|
|
75 email or the web:
|
|
|
76
|
|
|
77 bioperl-bugs@bio.perl.org
|
|
|
78 http://bugzilla.bioperl.org/
|
|
|
79
|
|
|
80 =head1 AUTHOR - Heikki Lehvaslaiho
|
|
|
81
|
|
|
82 Email: heikki@ebi.ac.uk
|
|
|
83 Address:
|
|
|
84
|
|
|
85 EMBL Outstation, European Bioinformatics Institute
|
|
|
86 Wellcome Trust Genome Campus, Hinxton
|
|
|
87 Cambs. CB10 1SD, United Kingdom
|
|
|
88
|
|
|
89 =head1 APPENDIX
|
|
|
90
|
|
|
91 The rest of the documentation details each of the object
|
|
|
92 methods. Internal methods are usually preceded with a _
|
|
|
93
|
|
|
94 =cut
|
|
|
95
|
|
|
96
|
|
|
97 # Let the code begin...
|
|
|
98
|
|
|
99 package Bio::LiveSeq::Mutation;
|
|
|
100 use vars qw(@ISA);
|
|
|
101 use strict;
|
|
|
102
|
|
|
103 # Object preamble - inheritance
|
|
|
104
|
|
|
105 use Bio::Root::Root;
|
|
|
106
|
|
|
107 @ISA = qw( Bio::Root::Root );
|
|
|
108
|
|
|
109 sub new {
|
|
|
110 my($class,@args) = @_;
|
|
|
111 my $self;
|
|
|
112 $self = {};
|
|
|
113 bless $self, $class;
|
|
|
114
|
|
|
115 my ($seq, $seqori, $pos, $len, $label) =
|
|
|
116 $self->_rearrange([qw(SEQ
|
|
|
117 SEQORI
|
|
|
118 POS
|
|
|
119 LEN
|
|
|
120 )],
|
|
|
121 @args);
|
|
|
122
|
|
|
123 $seq && $self->seq($seq);
|
|
|
124 $seqori && $self->seqori($seqori);
|
|
|
125 $pos && $self->pos($pos);
|
|
|
126 defined($len) && $self->len($len); # defined() added otherwise won't work for len==0
|
|
|
127
|
|
|
128 return $self; # success - we hope!
|
|
|
129 }
|
|
|
130
|
|
|
131
|
|
|
132 =head2 seq
|
|
|
133
|
|
|
134 Title : seq
|
|
|
135 Usage : $obj->seq();
|
|
|
136 Function:
|
|
|
137
|
|
|
138 Sets and returns the mutated sequence. No checking is done
|
|
|
139 to validate the symbols.
|
|
|
140
|
|
|
141 Example :
|
|
|
142 Returns : string
|
|
|
143 Args : integer
|
|
|
144
|
|
|
145 =cut
|
|
|
146
|
|
|
147
|
|
|
148 sub seq {
|
|
|
149 my ($self,$value) = @_;
|
|
|
150 if( defined $value) {
|
|
|
151 $self->{'seq'} = $value;
|
|
|
152 }
|
|
|
153 return $self->{'seq'};
|
|
|
154 }
|
|
|
155
|
|
|
156
|
|
|
157 =head2 seqori
|
|
|
158
|
|
|
159 Title : seqori
|
|
|
160 Usage : $obj->seqori();
|
|
|
161 Function:
|
|
|
162
|
|
|
163 Sets and returns the original subsequence in the reference
|
|
|
164 sequence. No checking is done to validate the symbols.
|
|
|
165 Optional value.
|
|
|
166
|
|
|
167 Example :
|
|
|
168 Returns : string
|
|
|
169 Args : string
|
|
|
170
|
|
|
171 =cut
|
|
|
172
|
|
|
173
|
|
|
174 sub seqori {
|
|
|
175 my ($self,$value) = @_;
|
|
|
176 if( defined $value) {
|
|
|
177 $self->{'seqori'} = $value;
|
|
|
178 }
|
|
|
179 return $self->{'seqori'};
|
|
|
180 }
|
|
|
181
|
|
|
182
|
|
|
183 =head2 pos
|
|
|
184
|
|
|
185 Title : pos
|
|
|
186 Usage : $obj->pos();
|
|
|
187 Function:
|
|
|
188
|
|
|
189 Sets and returns the position of the first element in the
|
|
|
190 sequence.
|
|
|
191
|
|
|
192 Example :
|
|
|
193 Returns : string
|
|
|
194 Args : integer
|
|
|
195
|
|
|
196 =cut
|
|
|
197
|
|
|
198
|
|
|
199 sub pos {
|
|
|
200 my ($self,$value) = @_;
|
|
|
201 if( defined $value) {
|
|
|
202 if ( $value !~ /^([+-])?\d+$/ ) {
|
|
|
203 $self->throw("[$value] for pos has to be an integer\n");
|
|
|
204 } else {
|
|
|
205 $self->{'pos'} = $value;
|
|
|
206 }
|
|
|
207 }
|
|
|
208 return $self->{'pos'};
|
|
|
209 }
|
|
|
210
|
|
|
211 =head2 len
|
|
|
212
|
|
|
213 Title : len
|
|
|
214 Usage : $obj->len();
|
|
|
215 Function:
|
|
|
216
|
|
|
217 Sets and returns the len of the affected original allele
|
|
|
218 sequence. If value is not set, defaults to the lenght of
|
|
|
219 the mutated sequence (seq).
|
|
|
220
|
|
|
221 Example :
|
|
|
222 Returns : string
|
|
|
223 Args : string
|
|
|
224
|
|
|
225 =cut
|
|
|
226
|
|
|
227 sub len {
|
|
|
228 my ($self,$value) = @_;
|
|
|
229 if ( defined $value) {
|
|
|
230 $self->{'len'} = $value;
|
|
|
231 }
|
|
|
232 if ( ! exists $self->{'len'} ) {
|
|
|
233 return length $self->{'seq'};
|
|
|
234 }
|
|
|
235 return $self->{'len'};
|
|
|
236 }
|
|
|
237
|
|
|
238 =head2 label
|
|
|
239
|
|
|
240 Title : label
|
|
|
241 Usage : $obj->label();
|
|
|
242 Function:
|
|
|
243
|
|
|
244 Sets and returns the label of the affected original allele
|
|
|
245 location. Label is a stable identifier whereas location
|
|
|
246 can be changed by mutations. Label comes from
|
|
|
247 l<Bio::LiveSeq::Gene>.
|
|
|
248
|
|
|
249 Example :
|
|
|
250 Returns : string
|
|
|
251 Args : string
|
|
|
252
|
|
|
253 =cut
|
|
|
254
|
|
|
255 sub label {
|
|
|
256 my ($self,$value) = @_;
|
|
|
257 if ( defined $value) {
|
|
|
258 $self->{'label'} = $value;
|
|
|
259 }
|
|
|
260 if ( ! exists $self->{'label'} ) {
|
|
|
261 return undef;
|
|
|
262 }
|
|
|
263 return $self->{'label'};
|
|
|
264 }
|
|
|
265
|
|
|
266
|
|
|
267 =head2 transpos
|
|
|
268
|
|
|
269 Title : transpos
|
|
|
270 Usage : $obj->transpos();
|
|
|
271 Function:
|
|
|
272
|
|
|
273 Sets and returns the transcript position of the mutation.
|
|
|
274 Set when associated with a reference sequence. Value
|
|
|
275 depends on reference molecule and the co-ordinate system
|
|
|
276 used.
|
|
|
277
|
|
|
278 Example :
|
|
|
279 Returns : string
|
|
|
280 Args : integer
|
|
|
281
|
|
|
282 =cut
|
|
|
283
|
|
|
284
|
|
|
285 sub transpos {
|
|
|
286 my ($self,$value) = @_;
|
|
|
287 if( defined $value) {
|
|
|
288 if ( $value !~ /^([+-])?\d+$/ ) {
|
|
|
289 $self->throw("[$value] for transpos has to be an integer\n");
|
|
|
290 } else {
|
|
|
291 $self->{'transpos'} = $value;
|
|
|
292 }
|
|
|
293 }
|
|
|
294 return $self->{'transpos'};
|
|
|
295 }
|
|
|
296
|
|
|
297
|
|
|
298 =head2 issue
|
|
|
299
|
|
|
300 Title : issue
|
|
|
301 Usage : $obj->issue();
|
|
|
302 Function:
|
|
|
303
|
|
|
304 Sets and returns the position of the mutation in an array
|
|
|
305 of mutations to be issued. Set after the validity of the
|
|
|
306 mutation has been confirmed.
|
|
|
307
|
|
|
308 Example :
|
|
|
309 Returns : string
|
|
|
310 Args : integer
|
|
|
311
|
|
|
312 =cut
|
|
|
313
|
|
|
314
|
|
|
315 sub issue {
|
|
|
316 my ($self,$value) = @_;
|
|
|
317 if( defined $value) {
|
|
|
318 if ( $value !~ /^([+-])?\d+$/ ) {
|
|
|
319 $self->throw("[$value] for issue has to be an integer\n");
|
|
|
320 } else {
|
|
|
321 $self->{'issue'} = $value;
|
|
|
322 }
|
|
|
323 }
|
|
|
324 return $self->{'issue'};
|
|
|
325 }
|
|
|
326
|
|
|
327
|
|
|
328 =head2 prelabel
|
|
|
329
|
|
|
330 Title : prelabel
|
|
|
331 Usage : $obj->prelabel();
|
|
|
332 Function:
|
|
|
333
|
|
|
334 Sets and returns the prelabel of the affected original allele
|
|
|
335 location. Prelabel is a stable identifier whereas location
|
|
|
336 can be changed by mutations. Prelabel comes from
|
|
|
337 l<Bio::LiveSeq::Gene>.
|
|
|
338
|
|
|
339 Example :
|
|
|
340 Returns : string
|
|
|
341 Args : string
|
|
|
342
|
|
|
343 =cut
|
|
|
344
|
|
|
345 sub prelabel {
|
|
|
346 my ($self,$value) = @_;
|
|
|
347 if ( defined $value) {
|
|
|
348 $self->{'prelabel'} = $value;
|
|
|
349 }
|
|
|
350 if ( ! exists $self->{'prelabel'} ) {
|
|
|
351 return undef;
|
|
|
352 }
|
|
|
353 return $self->{'prelabel'};
|
|
|
354 }
|
|
|
355
|
|
|
356
|
|
|
357 =head2 postlabel
|
|
|
358
|
|
|
359 Title : postlabel
|
|
|
360 Usage : $obj->postlabel();
|
|
|
361 Function:
|
|
|
362
|
|
|
363 Sets and returns the postlabel of the affected original allele
|
|
|
364 location. Postlabel is a stable identifier whereas location
|
|
|
365 can be changed by mutations. Postlabel comes from
|
|
|
366 l<Bio::LiveSeq::Gene>.
|
|
|
367
|
|
|
368 Example :
|
|
|
369 Returns : string
|
|
|
370 Args : string
|
|
|
371
|
|
|
372 =cut
|
|
|
373
|
|
|
374 sub postlabel {
|
|
|
375 my ($self,$value) = @_;
|
|
|
376 if ( defined $value) {
|
|
|
377 $self->{'postlabel'} = $value;
|
|
|
378 }
|
|
|
379 if ( ! exists $self->{'postlabel'} ) {
|
|
|
380 return undef;
|
|
|
381 }
|
|
|
382 return $self->{'postlabel'};
|
|
|
383 }
|
|
|
384
|
|
|
385
|
|
|
386 =head2 lastlabel
|
|
|
387
|
|
|
388 Title : lastlabel
|
|
|
389 Usage : $obj->lastlabel();
|
|
|
390 Function:
|
|
|
391
|
|
|
392 Sets and returns the lastlabel of the affected original allele
|
|
|
393 location. Lastlabel is a stable identifier whereas location
|
|
|
394 can be changed by mutations. Lastlabel comes from
|
|
|
395 l<Bio::LiveSeq::Gene>.
|
|
|
396
|
|
|
397 Example :
|
|
|
398 Returns : string
|
|
|
399 Args : string
|
|
|
400
|
|
|
401 =cut
|
|
|
402
|
|
|
403 sub lastlabel {
|
|
|
404 my ($self,$value) = @_;
|
|
|
405 if ( defined $value) {
|
|
|
406 $self->{'lastlabel'} = $value;
|
|
|
407 }
|
|
|
408 if ( ! exists $self->{'lastlabel'} ) {
|
|
|
409 return undef;
|
|
|
410 }
|
|
|
411 return $self->{'lastlabel'};
|
|
|
412 }
|
|
|
413
|
|
|
414 1;
|
