|
0
|
1 # $Id: FeaturePair.pm,v 1.17 2002/10/08 08:38:31 lapp Exp $
|
|
|
2 #
|
|
|
3 # BioPerl module for Bio::SeqFeature::FeaturePair
|
|
|
4 #
|
|
|
5 # Cared for by Ewan Birney <birney@sanger.ac.uk>
|
|
|
6 #
|
|
|
7 # Copyright Ewan Birney
|
|
|
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::SeqFeature::FeaturePair - hold pair feature information e.g. blast hits
|
|
|
16
|
|
|
17 =head1 SYNOPSIS
|
|
|
18
|
|
|
19 my $feat = new Bio::SeqFeature::FeaturePair(-feature1 => $f1,
|
|
|
20 -feature2 => $f2,
|
|
|
21 );
|
|
|
22
|
|
|
23 # Bio::SeqFeatureI methods can be used
|
|
|
24
|
|
|
25 my $start = $feat->start;
|
|
|
26 my $end = $feat->end;
|
|
|
27
|
|
|
28 # Bio::FeaturePair methods can be used
|
|
|
29 my $hstart = $feat->hstart;
|
|
|
30 my $hend = $feat->hend;
|
|
|
31
|
|
|
32 my $feature1 = $feat->feature1; # returns feature1 object
|
|
|
33
|
|
|
34 =head1 DESCRIPTION
|
|
|
35
|
|
|
36 A sequence feature object where the feature is itself a feature on
|
|
|
37 another sequence - e.g. a blast hit where residues 1-40 of a protein
|
|
|
38 sequence SW:HBA_HUMAN has hit to bases 100 - 220 on a genomic sequence
|
|
|
39 HS120G22. The genomic sequence coordinates are used to create one
|
|
|
40 sequence feature $f1 and the protein coordinates are used to create
|
|
|
41 feature $f2. A FeaturePair object can then be made
|
|
|
42
|
|
|
43 my $fp = new Bio::SeqFeature::FeaturePair(-feature1 => $f1, # genomic
|
|
|
44 -feature2 => $f2, # protein
|
|
|
45 );
|
|
|
46
|
|
|
47 This object can be used as a standard Bio::SeqFeatureI in which case
|
|
|
48
|
|
|
49 my $gstart = $fp->start # returns start coord on feature1 - genomic seq.
|
|
|
50 my $gend = $fp->end # returns end coord on feature1.
|
|
|
51
|
|
|
52 In general standard Bio::SeqFeatureI method calls return information
|
|
|
53 in feature1.
|
|
|
54
|
|
|
55 Data in the feature 2 object are generally obtained using the standard
|
|
|
56 methods prefixed by h (for hit!)
|
|
|
57
|
|
|
58 my $pstart = $fp->hstart # returns start coord on feature2 = protein seq.
|
|
|
59 my $pend = $fp->hend # returns end coord on feature2.
|
|
|
60
|
|
|
61 If you wish to swap feature1 and feature2 around :
|
|
|
62
|
|
|
63 $feat->invert
|
|
|
64
|
|
|
65 so...
|
|
|
66
|
|
|
67 $feat->start # etc. returns data in $feature2 object
|
|
|
68
|
|
|
69
|
|
|
70 No sub_SeqFeatures or tags can be stored in this object directly. Any
|
|
|
71 features or tags are expected to be stored in the contained objects
|
|
|
72 feature1, and feature2.
|
|
|
73
|
|
|
74 =head1 CONTACT
|
|
|
75
|
|
|
76 Ewan Birney E<lt>birney@sanger.ac.ukE<gt>
|
|
|
77
|
|
|
78 =head1 APPENDIX
|
|
|
79
|
|
|
80 The rest of the documentation details each of the object
|
|
|
81 methods. Internal methods are usually preceded with a _
|
|
|
82
|
|
|
83 =cut
|
|
|
84
|
|
|
85
|
|
|
86 # Let the code begin...
|
|
|
87
|
|
|
88
|
|
|
89 package Bio::SeqFeature::FeaturePair;
|
|
|
90 use vars qw(@ISA);
|
|
|
91 use strict;
|
|
|
92
|
|
|
93 use Bio::SeqFeatureI;
|
|
|
94 use Bio::SeqFeature::Generic;
|
|
|
95
|
|
|
96 @ISA = qw(Bio::SeqFeature::Generic);
|
|
|
97
|
|
|
98 sub new {
|
|
|
99 my ($class, @args) = @_;
|
|
|
100 my $self = $class->SUPER::new(@args);
|
|
|
101
|
|
|
102 my ($feature1,$feature2) =
|
|
|
103 $self->_rearrange([qw(FEATURE1
|
|
|
104 FEATURE2
|
|
|
105 )],@args);
|
|
|
106
|
|
|
107 # Store the features in the object
|
|
|
108 $feature1 && $self->feature1($feature1);
|
|
|
109 $feature2 && $self->feature2($feature2);
|
|
|
110 return $self;
|
|
|
111 }
|
|
|
112
|
|
|
113 =head2 feature1
|
|
|
114
|
|
|
115 Title : feature1
|
|
|
116 Usage : $f = $featpair->feature1
|
|
|
117 $featpair->feature1($feature)
|
|
|
118 Function: Get/set for the query feature
|
|
|
119 Returns : Bio::SeqFeatureI
|
|
|
120 Args : Bio::SeqFeatureI
|
|
|
121
|
|
|
122
|
|
|
123 =cut
|
|
|
124
|
|
|
125 sub feature1 {
|
|
|
126 my ($self,$arg) = @_;
|
|
|
127 if ( defined($arg) || !defined $self->{'feature1'} ) {
|
|
|
128 $arg = new Bio::SeqFeature::Generic() unless( defined $arg);
|
|
|
129 $self->throw("Argument [$arg] must be a Bio::SeqFeatureI")
|
|
|
130 unless (ref($arg) && $arg->isa("Bio::SeqFeatureI"));
|
|
|
131 $self->{'feature1'} = $arg;
|
|
|
132 }
|
|
|
133 return $self->{'feature1'};
|
|
|
134 }
|
|
|
135
|
|
|
136 =head2 feature2
|
|
|
137
|
|
|
138 Title : feature2
|
|
|
139 Usage : $f = $featpair->feature2
|
|
|
140 $featpair->feature2($feature)
|
|
|
141 Function: Get/set for the hit feature
|
|
|
142 Returns : Bio::SeqFeatureI
|
|
|
143 Args : Bio::SeqFeatureI
|
|
|
144
|
|
|
145
|
|
|
146 =cut
|
|
|
147
|
|
|
148 sub feature2 {
|
|
|
149 my ($self,$arg) = @_;
|
|
|
150
|
|
|
151 if ( defined($arg) || ! defined $self->{'feature2'}) {
|
|
|
152 $arg = new Bio::SeqFeature::Generic unless( defined $arg);
|
|
|
153 $self->throw("Argument [$arg] must be a Bio::SeqFeatureI")
|
|
|
154 unless (ref($arg) && $arg->isa("Bio::SeqFeatureI"));
|
|
|
155 $self->{'feature2'} = $arg;
|
|
|
156 }
|
|
|
157 return $self->{'feature2'};
|
|
|
158 }
|
|
|
159
|
|
|
160 =head2 start
|
|
|
161
|
|
|
162 Title : start
|
|
|
163 Usage : $start = $featpair->start
|
|
|
164 $featpair->start(20)
|
|
|
165 Function: Get/set on the start coordinate of feature1
|
|
|
166 Returns : integer
|
|
|
167 Args : [optional] beginning of feature
|
|
|
168
|
|
|
169 =cut
|
|
|
170
|
|
|
171 sub start {
|
|
|
172 my ($self,$value) = @_;
|
|
|
173 return $self->feature1->start($value);
|
|
|
174 }
|
|
|
175
|
|
|
176 =head2 end
|
|
|
177
|
|
|
178 Title : end
|
|
|
179 Usage : $end = $featpair->end
|
|
|
180 $featpair->end($end)
|
|
|
181 Function: get/set on the end coordinate of feature1
|
|
|
182 Returns : integer
|
|
|
183 Args : [optional] ending point of feature
|
|
|
184
|
|
|
185
|
|
|
186 =cut
|
|
|
187
|
|
|
188 sub end{
|
|
|
189 my ($self,$value) = @_;
|
|
|
190 return $self->feature1->end($value);
|
|
|
191 }
|
|
|
192
|
|
|
193 =head2 strand
|
|
|
194
|
|
|
195 Title : strand
|
|
|
196 Usage : $strand = $feat->strand()
|
|
|
197 $feat->strand($strand)
|
|
|
198 Function: get/set on strand information, being 1,-1 or 0
|
|
|
199 Returns : -1,1 or 0
|
|
|
200 Args : [optional] strand information to set
|
|
|
201
|
|
|
202
|
|
|
203 =cut
|
|
|
204
|
|
|
205 sub strand{
|
|
|
206 my ($self,$arg) = @_;
|
|
|
207 return $self->feature1->strand($arg);
|
|
|
208 }
|
|
|
209
|
|
|
210 =head2 location
|
|
|
211
|
|
|
212 Title : location
|
|
|
213 Usage : $location = $featpair->location
|
|
|
214 $featpair->location($location)
|
|
|
215 Function: Get/set location object (using feature1)
|
|
|
216 Returns : Bio::LocationI object
|
|
|
217 Args : [optional] LocationI to store
|
|
|
218
|
|
|
219 =cut
|
|
|
220
|
|
|
221 sub location {
|
|
|
222 my ($self,$value) = @_;
|
|
|
223 return $self->feature1->location($value);
|
|
|
224 }
|
|
|
225
|
|
|
226 =head2 score
|
|
|
227
|
|
|
228 Title : score
|
|
|
229 Usage : $score = $feat->score()
|
|
|
230 $feat->score($score)
|
|
|
231 Function: get/set on score information
|
|
|
232 Returns : float
|
|
|
233 Args : none if get, the new value if set
|
|
|
234
|
|
|
235
|
|
|
236 =cut
|
|
|
237
|
|
|
238 sub score {
|
|
|
239 my ($self,$arg) = @_;
|
|
|
240 return $self->feature1->score($arg);
|
|
|
241 }
|
|
|
242
|
|
|
243 =head2 frame
|
|
|
244
|
|
|
245 Title : frame
|
|
|
246 Usage : $frame = $feat->frame()
|
|
|
247 $feat->frame($frame)
|
|
|
248 Function: get/set on frame information
|
|
|
249 Returns : 0,1,2
|
|
|
250 Args : none if get, the new value if set
|
|
|
251
|
|
|
252
|
|
|
253 =cut
|
|
|
254
|
|
|
255 sub frame {
|
|
|
256 my ($self,$arg) = @_;
|
|
|
257 return $self->feature1->frame($arg);
|
|
|
258 }
|
|
|
259
|
|
|
260 =head2 primary_tag
|
|
|
261
|
|
|
262 Title : primary_tag
|
|
|
263 Usage : $ptag = $featpair->primary_tag
|
|
|
264 Function: get/set on the primary_tag of feature1
|
|
|
265 Returns : 0,1,2
|
|
|
266 Args : none if get, the new value if set
|
|
|
267
|
|
|
268
|
|
|
269 =cut
|
|
|
270
|
|
|
271 sub primary_tag{
|
|
|
272 my ($self,$arg) = @_;
|
|
|
273 return $self->feature1->primary_tag($arg);
|
|
|
274 }
|
|
|
275
|
|
|
276 =head2 source_tag
|
|
|
277
|
|
|
278 Title : source_tag
|
|
|
279 Usage : $tag = $feat->source_tag()
|
|
|
280 $feat->source_tag('genscan');
|
|
|
281 Function: Returns the source tag for a feature,
|
|
|
282 eg, 'genscan'
|
|
|
283 Returns : a string
|
|
|
284 Args : none
|
|
|
285
|
|
|
286
|
|
|
287 =cut
|
|
|
288
|
|
|
289 sub source_tag{
|
|
|
290 my ($self,$arg) = @_;
|
|
|
291 return $self->feature1->source_tag($arg);
|
|
|
292 }
|
|
|
293
|
|
|
294 =head2 seqname
|
|
|
295
|
|
|
296 Title : seqname
|
|
|
297 Usage : $obj->seq_id($newval)
|
|
|
298 Function: There are many cases when you make a feature that you
|
|
|
299 do know the sequence name, but do not know its actual
|
|
|
300 sequence. This is an attribute such that you can store
|
|
|
301 the seqname.
|
|
|
302
|
|
|
303 This attribute should *not* be used in GFF dumping, as
|
|
|
304 that should come from the collection in which the seq
|
|
|
305 feature was found.
|
|
|
306 Returns : value of seqname
|
|
|
307 Args : newvalue (optional)
|
|
|
308
|
|
|
309
|
|
|
310 =cut
|
|
|
311
|
|
|
312 sub seqname{
|
|
|
313 my ($self,$arg) = @_;
|
|
|
314 return $self->feature1->seq_id($arg);
|
|
|
315 }
|
|
|
316
|
|
|
317 =head2 hseqname
|
|
|
318
|
|
|
319 Title : hseqname
|
|
|
320 Usage : $featpair->hseqname($newval)
|
|
|
321 Function: Get/set method for the name of
|
|
|
322 feature2.
|
|
|
323 Returns : value of $feature2->seq_id
|
|
|
324 Args : newvalue (optional)
|
|
|
325
|
|
|
326
|
|
|
327 =cut
|
|
|
328
|
|
|
329 sub hseqname {
|
|
|
330 my ($self,$arg) = @_;
|
|
|
331 return $self->feature2->seq_id($arg);
|
|
|
332 }
|
|
|
333
|
|
|
334
|
|
|
335 =head2 hstart
|
|
|
336
|
|
|
337 Title : hstart
|
|
|
338 Usage : $start = $featpair->hstart
|
|
|
339 $featpair->hstart(20)
|
|
|
340 Function: Get/set on the start coordinate of feature2
|
|
|
341 Returns : integer
|
|
|
342 Args : none
|
|
|
343
|
|
|
344 =cut
|
|
|
345
|
|
|
346 sub hstart {
|
|
|
347 my ($self,$value) = @_;
|
|
|
348 return $self->feature2->start($value);
|
|
|
349 }
|
|
|
350
|
|
|
351 =head2 hend
|
|
|
352
|
|
|
353 Title : hend
|
|
|
354 Usage : $end = $featpair->hend
|
|
|
355 $featpair->hend($end)
|
|
|
356 Function: get/set on the end coordinate of feature2
|
|
|
357 Returns : integer
|
|
|
358 Args : none
|
|
|
359
|
|
|
360
|
|
|
361 =cut
|
|
|
362
|
|
|
363 sub hend{
|
|
|
364 my ($self,$value) = @_;
|
|
|
365 return $self->feature2->end($value);
|
|
|
366 }
|
|
|
367
|
|
|
368
|
|
|
369 =head2 hstrand
|
|
|
370
|
|
|
371 Title : hstrand
|
|
|
372 Usage : $strand = $feat->strand()
|
|
|
373 $feat->strand($strand)
|
|
|
374 Function: get/set on strand information, being 1,-1 or 0
|
|
|
375 Returns : -1,1 or 0
|
|
|
376 Args : none
|
|
|
377
|
|
|
378
|
|
|
379 =cut
|
|
|
380
|
|
|
381 sub hstrand{
|
|
|
382 my ($self,$arg) = @_;
|
|
|
383 return $self->feature2->strand($arg);
|
|
|
384 }
|
|
|
385
|
|
|
386 =head2 hscore
|
|
|
387
|
|
|
388 Title : hscore
|
|
|
389 Usage : $score = $feat->score()
|
|
|
390 $feat->score($score)
|
|
|
391 Function: get/set on score information
|
|
|
392 Returns : float
|
|
|
393 Args : none if get, the new value if set
|
|
|
394
|
|
|
395
|
|
|
396 =cut
|
|
|
397
|
|
|
398 sub hscore {
|
|
|
399 my ($self,$arg) = @_;
|
|
|
400 return $self->feature2->score($arg);
|
|
|
401 }
|
|
|
402
|
|
|
403 =head2 hframe
|
|
|
404
|
|
|
405 Title : hframe
|
|
|
406 Usage : $frame = $feat->frame()
|
|
|
407 $feat->frame($frame)
|
|
|
408 Function: get/set on frame information
|
|
|
409 Returns : 0,1,2
|
|
|
410 Args : none if get, the new value if set
|
|
|
411
|
|
|
412
|
|
|
413 =cut
|
|
|
414
|
|
|
415 sub hframe {
|
|
|
416 my ($self,$arg) = @_;
|
|
|
417 return $self->feature2->frame($arg);
|
|
|
418 }
|
|
|
419
|
|
|
420 =head2 hprimary_tag
|
|
|
421
|
|
|
422 Title : hprimary_tag
|
|
|
423 Usage : $ptag = $featpair->hprimary_tag
|
|
|
424 Function: Get/set on the primary_tag of feature2
|
|
|
425 Returns : 0,1,2
|
|
|
426 Args : none if get, the new value if set
|
|
|
427
|
|
|
428
|
|
|
429 =cut
|
|
|
430
|
|
|
431 sub hprimary_tag{
|
|
|
432 my ($self,$arg) = @_;
|
|
|
433 return $self->feature2->primary_tag($arg);
|
|
|
434 }
|
|
|
435
|
|
|
436 =head2 hsource_tag
|
|
|
437
|
|
|
438 Title : hsource_tag
|
|
|
439 Usage : $tag = $feat->hsource_tag()
|
|
|
440 $feat->source_tag('genscan');
|
|
|
441 Function: Returns the source tag for a feature,
|
|
|
442 eg, 'genscan'
|
|
|
443 Returns : a string
|
|
|
444 Args : none
|
|
|
445
|
|
|
446
|
|
|
447 =cut
|
|
|
448
|
|
|
449 sub hsource_tag{
|
|
|
450 my ($self,$arg) = @_;
|
|
|
451 return $self->feature2->source_tag($arg);
|
|
|
452 }
|
|
|
453
|
|
|
454 =head2 invert
|
|
|
455
|
|
|
456 Title : invert
|
|
|
457 Usage : $tag = $feat->invert
|
|
|
458 Function: Swaps feature1 and feature2 around
|
|
|
459 Returns : Nothing
|
|
|
460 Args : none
|
|
|
461
|
|
|
462
|
|
|
463 =cut
|
|
|
464
|
|
|
465 sub invert {
|
|
|
466 my ($self) = @_;
|
|
|
467
|
|
|
468 my $tmp = $self->feature1;
|
|
|
469
|
|
|
470 $self->feature1($self->feature2);
|
|
|
471 $self->feature2($tmp);
|
|
|
472 return undef;
|
|
|
473 }
|
|
|
474
|
|
|
475 1;
|
