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1 | # | ||||
2 | # BioPerl module for Bio::Location::Simple | ||||
3 | # Please direct questions and support issues to <bioperl-l@bioperl.org> | ||||
4 | # | ||||
5 | # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> | ||||
6 | # | ||||
7 | # Copyright Heikki Lehvaslaiho | ||||
8 | # | ||||
9 | # You may distribute this module under the same terms as perl itself | ||||
10 | # POD documentation - main docs before the code | ||||
11 | |||||
12 | =head1 NAME | ||||
13 | |||||
14 | Bio::Location::Simple - Implementation of a Simple Location on a Sequence | ||||
15 | |||||
16 | =head1 SYNOPSIS | ||||
17 | |||||
18 | use Bio::Location::Simple; | ||||
19 | |||||
20 | my $location = Bio::Location::Simple->new( | ||||
21 | -start => 1, | ||||
22 | -end => 100, | ||||
23 | -strand => 1, | ||||
24 | ); | ||||
25 | |||||
26 | if( $location->strand == -1 ) { | ||||
27 | printf "complement(%d..%d)\n", $location->start, $location->end; | ||||
28 | } else { | ||||
29 | printf "%d..%d\n", $location->start, $location->end; | ||||
30 | } | ||||
31 | |||||
32 | =head1 DESCRIPTION | ||||
33 | |||||
34 | This is an implementation of Bio::LocationI to manage exact location | ||||
35 | information on a Sequence: '22' or '12..15' or '16^17'. | ||||
36 | |||||
37 | You can test the type of the location using length() function () or | ||||
38 | directly location_type() which can one of two values: 'EXACT' or | ||||
39 | 'IN-BETWEEN'. | ||||
40 | |||||
41 | |||||
42 | =head1 FEEDBACK | ||||
43 | |||||
44 | User feedback is an integral part of the evolution of this and other | ||||
45 | Bioperl modules. Send your comments and suggestions preferably to one | ||||
46 | of the Bioperl mailing lists. Your participation is much appreciated. | ||||
47 | |||||
48 | bioperl-l@bioperl.org - General discussion | ||||
49 | http://bioperl.org/wiki/Mailing_lists - About the mailing lists | ||||
50 | |||||
51 | =head2 Support | ||||
52 | |||||
53 | Please direct usage questions or support issues to the mailing list: | ||||
54 | |||||
55 | I<bioperl-l@bioperl.org> | ||||
56 | |||||
57 | rather than to the module maintainer directly. Many experienced and | ||||
58 | reponsive experts will be able look at the problem and quickly | ||||
59 | address it. Please include a thorough description of the problem | ||||
60 | with code and data examples if at all possible. | ||||
61 | |||||
62 | =head2 Reporting Bugs | ||||
63 | |||||
64 | Report bugs to the Bioperl bug tracking system to help us keep track | ||||
65 | the bugs and their resolution. Bug reports can be submitted via the | ||||
66 | web: | ||||
67 | |||||
68 | https://github.com/bioperl/bioperl-live/issues | ||||
69 | |||||
70 | =head1 AUTHOR - Heikki Lehvaslaiho | ||||
71 | |||||
72 | Email heikki-at-bioperl-dot-org | ||||
73 | |||||
74 | =head1 APPENDIX | ||||
75 | |||||
76 | The rest of the documentation details each of the object | ||||
77 | methods. Internal methods are usually preceded with a _ | ||||
78 | |||||
79 | =cut | ||||
80 | |||||
81 | # Let the code begin... | ||||
82 | |||||
83 | |||||
84 | package Bio::Location::Simple; | ||||
85 | 2 | 28µs | 2 | 39µs | # spent 27µs (15+12) within Bio::Location::Simple::BEGIN@85 which was called:
# once (15µs+12µs) by Bio::LocatableSeq::BEGIN@105 at line 85 # spent 27µs making 1 call to Bio::Location::Simple::BEGIN@85
# spent 12µs making 1 call to strict::import |
86 | |||||
87 | 2 | 896µs | 2 | 12.4ms | # spent 6.21ms (9µs+6.21) within Bio::Location::Simple::BEGIN@87 which was called:
# once (9µs+6.21ms) by Bio::LocatableSeq::BEGIN@105 at line 87 # spent 6.21ms making 1 call to Bio::Location::Simple::BEGIN@87
# spent 6.21ms making 1 call to base::import |
88 | |||||
89 | 1 | 3µs | our %RANGEENCODE = ('\.\.' => 'EXACT', | ||
90 | '\^' => 'IN-BETWEEN' ); | ||||
91 | |||||
92 | 1 | 2µs | our %RANGEDECODE = ('EXACT' => '..', | ||
93 | 'IN-BETWEEN' => '^' ); | ||||
94 | |||||
95 | sub new { | ||||
96 | my ($class, @args) = @_; | ||||
97 | my $self = $class->SUPER::new(@args); | ||||
98 | |||||
99 | my ($locationtype) = $self->_rearrange([qw(LOCATION_TYPE)],@args); | ||||
100 | |||||
101 | $locationtype && $self->location_type($locationtype); | ||||
102 | |||||
103 | return $self; | ||||
104 | } | ||||
105 | |||||
106 | =head2 start | ||||
107 | |||||
108 | Title : start | ||||
109 | Usage : $start = $loc->start(); | ||||
110 | Function: get/set the start of this range | ||||
111 | Returns : the start of this range | ||||
112 | Args : optionaly allows the start to be set | ||||
113 | using $loc->start($start) | ||||
114 | |||||
115 | =cut | ||||
116 | |||||
117 | sub start { | ||||
118 | my ($self, $value) = @_; | ||||
119 | $self->{'_start'} = $value if defined $value ; | ||||
120 | |||||
121 | $self->throw("Only adjacent residues when location type ". | ||||
122 | "is IN-BETWEEN. Not [". $self->{'_start'}. "] and [". | ||||
123 | $self->{'_end'}. "]" ) | ||||
124 | if defined $self->{'_start'} && defined $self->{'_end'} && | ||||
125 | $self->location_type eq 'IN-BETWEEN' && | ||||
126 | ($self->{'_end'} - 1 != $self->{'_start'}); | ||||
127 | return $self->{'_start'}; | ||||
128 | } | ||||
129 | |||||
130 | |||||
131 | =head2 end | ||||
132 | |||||
133 | Title : end | ||||
134 | Usage : $end = $loc->end(); | ||||
135 | Function: get/set the end of this range | ||||
136 | Returns : the end of this range | ||||
137 | Args : optionaly allows the end to be set | ||||
138 | : using $loc->end($start) | ||||
139 | Note : If start is set but end is undefined, this now assumes that start | ||||
140 | is the same as end but throws a warning (i.e. it assumes this is | ||||
141 | a possible error). If start is undefined, this now throws an | ||||
142 | exception. | ||||
143 | |||||
144 | =cut | ||||
145 | |||||
146 | sub end { | ||||
147 | my ($self, $value) = @_; | ||||
148 | |||||
149 | $self->{'_end'} = $value if defined $value ; | ||||
150 | |||||
151 | # Assume end is the same as start if not defined | ||||
152 | if (!defined $self->{'_end'}) { | ||||
153 | if (!defined $self->{'_start'}) { | ||||
154 | $self->warn('Can not set Bio::Location::Simple::end() equal to start; start not set'); | ||||
155 | return; | ||||
156 | } | ||||
157 | $self->warn('Setting end to equal start['. $self->{'_start'}. ']'); | ||||
158 | $self->{'_end'} = $self->{'_start'}; | ||||
159 | } | ||||
160 | $self->throw("Only adjacent residues when location type ". | ||||
161 | "is IN-BETWEEN. Not [". $self->{'_start'}. "] and [". | ||||
162 | $self->{'_end'}. "]" ) | ||||
163 | if defined $self->{'_start'} && defined $self->{'_end'} && | ||||
164 | $self->location_type eq 'IN-BETWEEN' && | ||||
165 | ($self->{'_end'} - 1 != $self->{'_start'}); | ||||
166 | |||||
167 | return $self->{'_end'}; | ||||
168 | } | ||||
169 | |||||
170 | =head2 strand | ||||
171 | |||||
172 | Title : strand | ||||
173 | Usage : $strand = $loc->strand(); | ||||
174 | Function: get/set the strand of this range | ||||
175 | Returns : the strandedness (-1, 0, +1) | ||||
176 | Args : optionaly allows the strand to be set | ||||
177 | : using $loc->strand($strand) | ||||
178 | |||||
179 | =cut | ||||
180 | |||||
181 | =head2 length | ||||
182 | |||||
183 | Title : length | ||||
184 | Usage : $len = $loc->length(); | ||||
185 | Function: get the length in the coordinate space this location spans | ||||
186 | Example : | ||||
187 | Returns : an integer | ||||
188 | Args : none | ||||
189 | |||||
190 | =cut | ||||
191 | |||||
192 | sub length { | ||||
193 | my ($self) = @_; | ||||
194 | if ($self->location_type eq 'IN-BETWEEN' ) { | ||||
195 | return 0; | ||||
196 | } else { | ||||
197 | return abs($self->end - $self->start) + 1; | ||||
198 | } | ||||
199 | } | ||||
200 | |||||
201 | |||||
202 | =head2 min_start | ||||
203 | |||||
204 | Title : min_start | ||||
205 | Usage : my $minstart = $location->min_start(); | ||||
206 | Function: Get minimum starting location of feature startpoint | ||||
207 | Returns : integer or undef if no minimum starting point. | ||||
208 | Args : none | ||||
209 | |||||
210 | =cut | ||||
211 | |||||
212 | =head2 max_start | ||||
213 | |||||
214 | Title : max_start | ||||
215 | Usage : my $maxstart = $location->max_start(); | ||||
216 | Function: Get maximum starting location of feature startpoint. | ||||
217 | |||||
218 | In this implementation this is exactly the same as min_start(). | ||||
219 | |||||
220 | Returns : integer or undef if no maximum starting point. | ||||
221 | Args : none | ||||
222 | |||||
223 | =cut | ||||
224 | |||||
225 | =head2 start_pos_type | ||||
226 | |||||
227 | Title : start_pos_type | ||||
228 | Usage : my $start_pos_type = $location->start_pos_type(); | ||||
229 | Function: Get start position type (ie <,>, ^). | ||||
230 | |||||
231 | Returns : type of position coded as text | ||||
232 | ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') | ||||
233 | Args : none | ||||
234 | |||||
235 | =cut | ||||
236 | |||||
237 | =head2 min_end | ||||
238 | |||||
239 | Title : min_end | ||||
240 | Usage : my $minend = $location->min_end(); | ||||
241 | Function: Get minimum ending location of feature endpoint | ||||
242 | Returns : integer or undef if no minimum ending point. | ||||
243 | Args : none | ||||
244 | |||||
245 | =cut | ||||
246 | |||||
247 | |||||
248 | =head2 max_end | ||||
249 | |||||
250 | Title : max_end | ||||
251 | Usage : my $maxend = $location->max_end(); | ||||
252 | Function: Get maximum ending location of feature endpoint | ||||
253 | |||||
254 | In this implementation this is exactly the same as min_end(). | ||||
255 | |||||
256 | Returns : integer or undef if no maximum ending point. | ||||
257 | Args : none | ||||
258 | |||||
259 | =cut | ||||
260 | |||||
261 | =head2 end_pos_type | ||||
262 | |||||
263 | Title : end_pos_type | ||||
264 | Usage : my $end_pos_type = $location->end_pos_type(); | ||||
265 | Function: Get end position type (ie <,>, ^) | ||||
266 | |||||
267 | Returns : type of position coded as text | ||||
268 | ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') | ||||
269 | Args : none | ||||
270 | |||||
271 | =cut | ||||
272 | |||||
273 | =head2 location_type | ||||
274 | |||||
275 | Title : location_type | ||||
276 | Usage : my $location_type = $location->location_type(); | ||||
277 | Function: Get location type encoded as text | ||||
278 | Returns : string ('EXACT' or 'IN-BETWEEN') | ||||
279 | Args : 'EXACT' or '..' or 'IN-BETWEEN' or '^' | ||||
280 | |||||
281 | =cut | ||||
282 | |||||
283 | sub location_type { | ||||
284 | my ($self, $value) = @_; | ||||
285 | |||||
286 | if( defined $value || ! defined $self->{'_location_type'} ) { | ||||
287 | $value = 'EXACT' unless defined $value; | ||||
288 | $value = uc $value; | ||||
289 | if (! defined $RANGEDECODE{$value}) { | ||||
290 | $value = '\^' if $value eq '^'; | ||||
291 | $value = '\.\.' if $value eq '..'; | ||||
292 | $value = $RANGEENCODE{$value}; | ||||
293 | } | ||||
294 | $self->throw("Did not specify a valid location type. [$value] is no good") | ||||
295 | unless defined $value; | ||||
296 | $self->{'_location_type'} = $value; | ||||
297 | } | ||||
298 | $self->throw("Only adjacent residues when location type ". | ||||
299 | "is IN-BETWEEN. Not [". $self->{'_start'}. "] and [". | ||||
300 | $self->{'_end'}. "]" ) | ||||
301 | if $self->{'_location_type'} eq 'IN-BETWEEN' && | ||||
302 | defined $self->{'_start'} && | ||||
303 | defined $self->{'_end'} && | ||||
304 | ($self->{'_end'} - 1 != $self->{'_start'}); | ||||
305 | |||||
306 | return $self->{'_location_type'}; | ||||
307 | } | ||||
308 | |||||
309 | =head2 is_remote | ||||
310 | |||||
311 | Title : is_remote | ||||
312 | Usage : $is_remote_loc = $loc->is_remote() | ||||
313 | Function: Whether or not a location is a remote location. | ||||
314 | |||||
315 | A location is said to be remote if it is on a different | ||||
316 | 'object' than the object which 'has' this | ||||
317 | location. Typically, features on a sequence will sometimes | ||||
318 | have a remote location, which means that the location of | ||||
319 | the feature is on a different sequence than the one that is | ||||
320 | attached to the feature. In such a case, $loc->seq_id will | ||||
321 | be different from $feat->seq_id (usually they will be the | ||||
322 | same). | ||||
323 | |||||
324 | While this may sound weird, it reflects the location of the | ||||
325 | kind of AL445212.9:83662..166657 which can be found in GenBank/EMBL | ||||
326 | feature tables. | ||||
327 | |||||
328 | Example : | ||||
329 | Returns : TRUE if the location is a remote location, and FALSE otherwise | ||||
330 | Args : Value to set to | ||||
331 | |||||
332 | =cut | ||||
333 | |||||
334 | =head2 to_FTstring | ||||
335 | |||||
336 | Title : to_FTstring | ||||
337 | Usage : my $locstr = $location->to_FTstring() | ||||
338 | Function: returns the FeatureTable string of this location | ||||
339 | Returns : string | ||||
340 | Args : none | ||||
341 | |||||
342 | =cut | ||||
343 | |||||
344 | sub to_FTstring { | ||||
345 | my($self) = @_; | ||||
346 | |||||
347 | my $str; | ||||
348 | if( $self->start == $self->end ) { | ||||
349 | $str = $self->start; | ||||
350 | } else { | ||||
351 | $str = $self->start . $RANGEDECODE{$self->location_type} . $self->end; | ||||
352 | } | ||||
353 | if($self->is_remote() && $self->seq_id()) { | ||||
354 | $str = $self->seq_id() . ":" . $str; | ||||
355 | } | ||||
356 | if( defined $self->strand && | ||||
357 | $self->strand == -1 ) { | ||||
358 | $str = "complement(".$str.")"; | ||||
359 | } | ||||
360 | return $str; | ||||
361 | } | ||||
362 | |||||
363 | |||||
364 | =head2 valid_Location | ||||
365 | |||||
366 | Title : valid_Location | ||||
367 | Usage : if ($location->valid_location) {...}; | ||||
368 | Function: boolean method to determine whether location is considered valid | ||||
369 | (has minimum requirements for Simple implementation) | ||||
370 | Returns : Boolean value: true if location is valid, false otherwise | ||||
371 | Args : none | ||||
372 | |||||
373 | =cut | ||||
374 | |||||
375 | # comments, not function added by jason | ||||
376 | # | ||||
377 | # trunc is untested, and as of now unannounced method for truncating a | ||||
378 | # location. This is to eventually be part of the procedure to | ||||
379 | # truncate a sequence with annotation and properly remap the location | ||||
380 | # of all the features contained within the truncated segment. | ||||
381 | |||||
382 | # presumably this might do things a little differently for the case | ||||
383 | # where the truncation splits the location in half | ||||
384 | # | ||||
385 | # in short- you probably don't want to use this method. | ||||
386 | |||||
387 | sub trunc { | ||||
388 | my ($self,$start,$end,$relative_ori) = @_; | ||||
389 | my $newstart = $self->start - $start+1; | ||||
390 | my $newend = $self->end - $start+1; | ||||
391 | my $newstrand = $relative_ori * $self->strand; | ||||
392 | |||||
393 | my $out; | ||||
394 | if( $newstart < 1 || $newend > ($end-$start+1) ) { | ||||
395 | $out = Bio::Location::Simple->new(); | ||||
396 | $out->start($self->start); | ||||
397 | $out->end($self->end); | ||||
398 | $out->strand($self->strand); | ||||
399 | $out->seq_id($self->seqid); | ||||
400 | $out->is_remote(1); | ||||
401 | } else { | ||||
402 | $out = Bio::Location::Simple->new(); | ||||
403 | $out->start($newstart); | ||||
404 | $out->end($newend); | ||||
405 | $out->strand($newstrand); | ||||
406 | $out->seq_id(); | ||||
407 | } | ||||
408 | |||||
409 | return $out; | ||||
410 | } | ||||
411 | |||||
412 | 1 | 7µs | 1; | ||
413 |