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1 | 1 | 1 | 2.87ms | 16.6ms | BEGIN@152 | Bio::Tools::GFF::
1 | 1 | 1 | 2.28ms | 31.9ms | BEGIN@151 | Bio::Tools::GFF::
1 | 1 | 1 | 389µs | 37.5ms | BEGIN@150 | Bio::Tools::GFF::
1 | 1 | 1 | 29µs | 78µs | BEGIN@147 | Bio::Tools::GFF::
1 | 1 | 1 | 17µs | 46µs | BEGIN@148 | Bio::Tools::GFF::
1 | 1 | 1 | 12µs | 601µs | BEGIN@154 | Bio::Tools::GFF::
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0 | 0 | 0 | 0s | 0s | READLINE | Bio::Tools::GFF::
0 | 0 | 0 | 0s | 0s | TIEHANDLE | Bio::Tools::GFF::
0 | 0 | 0 | 0s | 0s | _feature_idx_by_seq_id | Bio::Tools::GFF::
0 | 0 | 0 | 0s | 0s | _from_gff1_string | Bio::Tools::GFF::
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0 | 0 | 0 | 0s | 0s | _parse_header | Bio::Tools::GFF::
0 | 0 | 0 | 0s | 0s | _parse_sequence | Bio::Tools::GFF::
0 | 0 | 0 | 0s | 0s | _seq_by_id_h | Bio::Tools::GFF::
0 | 0 | 0 | 0s | 0s | features_attached_to_seqs | Bio::Tools::GFF::
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0 | 0 | 0 | 0s | 0s | get_seqs | Bio::Tools::GFF::
0 | 0 | 0 | 0s | 0s | gff_string | Bio::Tools::GFF::
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1 | # | ||||
2 | # BioPerl module for Bio::Tools::GFF | ||||
3 | # | ||||
4 | # Please direct questions and support issues to <bioperl-l@bioperl.org> | ||||
5 | # | ||||
6 | # Cared for by the Bioperl core team | ||||
7 | # | ||||
8 | # Copyright Matthew Pocock | ||||
9 | # | ||||
10 | # You may distribute this module under the same terms as perl itself | ||||
11 | |||||
12 | # POD documentation - main docs before the code | ||||
13 | |||||
14 | =head1 NAME | ||||
15 | |||||
16 | Bio::Tools::GFF - A Bio::SeqAnalysisParserI compliant GFF format parser | ||||
17 | |||||
18 | =head1 SYNOPSIS | ||||
19 | |||||
20 | use Bio::Tools::GFF; | ||||
21 | |||||
22 | # specify input via -fh or -file | ||||
23 | my $gffio = Bio::Tools::GFF->new(-fh => \*STDIN, -gff_version => 2); | ||||
24 | my $feature; | ||||
25 | # loop over the input stream | ||||
26 | while($feature = $gffio->next_feature()) { | ||||
27 | # do something with feature | ||||
28 | } | ||||
29 | $gffio->close(); | ||||
30 | |||||
31 | # you can also obtain a GFF parser as a SeqAnalasisParserI in | ||||
32 | # HT analysis pipelines (see Bio::SeqAnalysisParserI and | ||||
33 | # Bio::Factory::SeqAnalysisParserFactory) | ||||
34 | my $factory = Bio::Factory::SeqAnalysisParserFactory->new(); | ||||
35 | my $parser = $factory->get_parser(-input => \*STDIN, -method => "gff"); | ||||
36 | while($feature = $parser->next_feature()) { | ||||
37 | # do something with feature | ||||
38 | } | ||||
39 | |||||
40 | =head1 DESCRIPTION | ||||
41 | |||||
42 | This class provides a simple GFF parser and writer. In the sense of a | ||||
43 | SeqAnalysisParser, it parses an input file or stream into SeqFeatureI | ||||
44 | objects, but is not in any way specific to a particular analysis | ||||
45 | program and the output that program produces. | ||||
46 | |||||
47 | That is, if you can get your analysis program spit out GFF, here is | ||||
48 | your result parser. | ||||
49 | |||||
50 | =head1 GFF3 AND SEQUENCE DATA | ||||
51 | |||||
52 | GFF3 supports sequence data; see | ||||
53 | |||||
54 | http://www.sequenceontology.org/gff3.shtml | ||||
55 | |||||
56 | There are a number of ways to deal with this - | ||||
57 | |||||
58 | If you call | ||||
59 | |||||
60 | $gffio->ignore_sequence(1) | ||||
61 | |||||
62 | prior to parsing the sequence data is ignored; this is useful if you | ||||
63 | just want the features. It avoids the memory overhead in building and | ||||
64 | caching sequences | ||||
65 | |||||
66 | Alternatively, you can call either | ||||
67 | |||||
68 | $gffio->get_seqs() | ||||
69 | |||||
70 | Or | ||||
71 | |||||
72 | $gffio->seq_id_by_h() | ||||
73 | |||||
74 | At the B<end> of parsing to get either a list or hashref of Bio::Seq | ||||
75 | objects (see the documentation for each of these methods) | ||||
76 | |||||
77 | Note that these objects will not have the features attached - you have | ||||
78 | to do this yourself, OR call | ||||
79 | |||||
80 | $gffio->features_attached_to_seqs(1) | ||||
81 | |||||
82 | PRIOR to parsing; this will ensure that the Seqs have the features | ||||
83 | attached; ie you will then be able to call | ||||
84 | |||||
85 | $seq->get_SeqFeatures(); | ||||
86 | |||||
87 | And use Bio::SeqIO methods | ||||
88 | |||||
89 | Note that auto-attaching the features to seqs will incur a higher | ||||
90 | memory overhead as the features must be cached until the sequence data | ||||
91 | is found | ||||
92 | |||||
93 | =head1 TODO | ||||
94 | |||||
95 | Make a Bio::SeqIO class specifically for GFF3 with sequence data | ||||
96 | |||||
97 | =head1 FEEDBACK | ||||
98 | |||||
99 | =head2 Mailing Lists | ||||
100 | |||||
101 | User feedback is an integral part of the evolution of this and other | ||||
102 | Bioperl modules. Send your comments and suggestions preferably to one | ||||
103 | of the Bioperl mailing lists. Your participation is much appreciated. | ||||
104 | |||||
105 | bioperl-l@bioperl.org - General discussion | ||||
106 | http://bioperl.org/wiki/Mailing_lists - About the mailing lists | ||||
107 | |||||
108 | =head2 Support | ||||
109 | |||||
110 | Please direct usage questions or support issues to the mailing list: | ||||
111 | |||||
112 | I<bioperl-l@bioperl.org> | ||||
113 | |||||
114 | rather than to the module maintainer directly. Many experienced and | ||||
115 | reponsive experts will be able look at the problem and quickly | ||||
116 | address it. Please include a thorough description of the problem | ||||
117 | with code and data examples if at all possible. | ||||
118 | |||||
119 | =head2 Reporting Bugs | ||||
120 | |||||
121 | Report bugs to the Bioperl bug tracking system to help us keep track | ||||
122 | the bugs and their resolution. Bug reports can be submitted the web: | ||||
123 | |||||
124 | https://github.com/bioperl/bioperl-live/issues | ||||
125 | |||||
126 | =head1 AUTHOR - Matthew Pocock | ||||
127 | |||||
128 | Email mrp-at-sanger.ac.uk | ||||
129 | |||||
130 | =head1 CONTRIBUTORS | ||||
131 | |||||
132 | Jason Stajich, jason-at-biperl-dot-org | ||||
133 | Chris Mungall, cjm-at-fruitfly-dot-org | ||||
134 | Steffen Grossmann [SG], grossman at molgen.mpg.de | ||||
135 | Malcolm Cook, mec-at-stowers-institute.org | ||||
136 | |||||
137 | =head1 APPENDIX | ||||
138 | |||||
139 | The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ | ||||
140 | |||||
141 | =cut | ||||
142 | |||||
143 | # Let the code begin... | ||||
144 | |||||
145 | package Bio::Tools::GFF; | ||||
146 | |||||
147 | 2 | 56µs | 2 | 127µs | # spent 78µs (29+49) within Bio::Tools::GFF::BEGIN@147 which was called:
# once (29µs+49µs) by Bio::Roary::GeneNamesFromGFF::BEGIN@19 at line 147 # spent 78µs making 1 call to Bio::Tools::GFF::BEGIN@147
# spent 49µs making 1 call to vars::import |
148 | 2 | 44µs | 2 | 75µs | # spent 46µs (17+29) within Bio::Tools::GFF::BEGIN@148 which was called:
# once (17µs+29µs) by Bio::Roary::GeneNamesFromGFF::BEGIN@19 at line 148 # spent 46µs making 1 call to Bio::Tools::GFF::BEGIN@148
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149 | |||||
150 | 2 | 180µs | 1 | 37.5ms | # spent 37.5ms (389µs+37.1) within Bio::Tools::GFF::BEGIN@150 which was called:
# once (389µs+37.1ms) by Bio::Roary::GeneNamesFromGFF::BEGIN@19 at line 150 # spent 37.5ms making 1 call to Bio::Tools::GFF::BEGIN@150 |
151 | 2 | 147µs | 1 | 31.9ms | # spent 31.9ms (2.28+29.6) within Bio::Tools::GFF::BEGIN@151 which was called:
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152 | 2 | 202µs | 1 | 16.6ms | # spent 16.6ms (2.87+13.7) within Bio::Tools::GFF::BEGIN@152 which was called:
# once (2.87ms+13.7ms) by Bio::Roary::GeneNamesFromGFF::BEGIN@19 at line 152 # spent 16.6ms making 1 call to Bio::Tools::GFF::BEGIN@152 |
153 | |||||
154 | 2 | 4.01ms | 2 | 1.19ms | # spent 601µs (12+589) within Bio::Tools::GFF::BEGIN@154 which was called:
# once (12µs+589µs) by Bio::Roary::GeneNamesFromGFF::BEGIN@19 at line 154 # spent 601µs making 1 call to Bio::Tools::GFF::BEGIN@154
# spent 589µs making 1 call to base::import |
155 | |||||
156 | 1 | 500ns | my $i = 0; | ||
157 | 1 | 6µs | my %GFF3_ID_Tags = map { $_ => $i++ } qw(ID Parent Target); | ||
158 | |||||
159 | # for skipping data that may be represented elsewhere; currently, this is | ||||
160 | # only the score | ||||
161 | 1 | 1µs | my %SKIPPED_TAGS = map { $_ => 1 } qw(score); | ||
162 | |||||
163 | |||||
164 | =head2 new | ||||
165 | |||||
166 | Title : new | ||||
167 | Usage : my $parser = Bio::Tools::GFF->new(-gff_version => 2, | ||||
168 | -file => "filename.gff"); | ||||
169 | or | ||||
170 | my $writer = Bio::Tools::GFF->new(-gff_version => 3, | ||||
171 | -file => ">filename.gff3"); | ||||
172 | Function: Creates a new instance. Recognized named parameters are -file, -fh, | ||||
173 | and -gff_version. | ||||
174 | Returns : a new object | ||||
175 | Args : named parameters | ||||
176 | -gff_version => [1,2,3] | ||||
177 | |||||
178 | =cut | ||||
179 | |||||
180 | { # make a class variable such that we can generate unique ID's over | ||||
181 | # a session, no matter how many instances of GFF.pm we make | ||||
182 | # since these have to be unique within the scope of a GFF file. | ||||
183 | |||||
184 | 2 | 800ns | my $gff3_featureID = 0; | ||
185 | |||||
186 | sub _incrementGFF3ID { | ||||
187 | my ($self) = @_; | ||||
188 | return ++ $gff3_featureID; | ||||
189 | } | ||||
190 | } | ||||
191 | |||||
192 | |||||
193 | sub new { | ||||
194 | my ($class, @args) = @_; | ||||
195 | my $self = $class->SUPER::new(@args); | ||||
196 | |||||
197 | my ($gff_version, $noparse) = $self->_rearrange([qw(GFF_VERSION NOPARSE)],@args); | ||||
198 | |||||
199 | # initialize IO | ||||
200 | $self->_initialize_io(@args); | ||||
201 | $self->_parse_header() unless $noparse; | ||||
202 | |||||
203 | $gff_version ||= 2; | ||||
204 | if( ! $self->gff_version($gff_version) ) { | ||||
205 | $self->throw("Can't build a GFF object with the unknown version ". | ||||
206 | $gff_version); | ||||
207 | } | ||||
208 | $self->{'_first'} = 1; | ||||
209 | return $self; | ||||
210 | } | ||||
211 | |||||
212 | |||||
213 | =head2 _parse_header | ||||
214 | |||||
215 | Title : _parse_header | ||||
216 | Usage : $gffio->_parse_header() | ||||
217 | Function: used to turn parse GFF header lines. currently | ||||
218 | produces Bio::LocatableSeq objects from ##sequence-region | ||||
219 | lines | ||||
220 | Returns : 1 on success | ||||
221 | Args : none | ||||
222 | |||||
223 | |||||
224 | =cut | ||||
225 | |||||
226 | sub _parse_header{ | ||||
227 | my ($self) = @_; | ||||
228 | |||||
229 | my @unhandled; | ||||
230 | local $^W = 0; # hide warnings when we try and parse from a file opened | ||||
231 | # for writing - there isn't really a better way to do | ||||
232 | # AFAIK - cannot detech if a FH is read or write. | ||||
233 | while(my $line = $self->_readline()){ | ||||
234 | my $handled = 0; | ||||
235 | next if /^\s+$/; | ||||
236 | if($line =~ /^\#\#sequence-region\s+(\S+)\s+(\S+)\s+(\S+)\s*/){ | ||||
237 | my($seqid,$start,$end) = ($1,$2,$3); | ||||
238 | push @{ $self->{'segments'} }, Bio::LocatableSeq->new( | ||||
239 | -id => unescape($seqid), | ||||
240 | -start => $start, | ||||
241 | -end => $end, | ||||
242 | -length => ($end - $start + 1), ## make the length explicit | ||||
243 | ); | ||||
244 | $handled = 1; | ||||
245 | } elsif($line =~ /^(\#\#feature-ontology)/) { | ||||
246 | #to be implemented | ||||
247 | $self->warn("$1 header tag parsing unimplemented"); | ||||
248 | } elsif($line =~ /^(\#\#attribute-ontology)/) { | ||||
249 | #to be implemented | ||||
250 | $self->warn("$1 header tag parsing unimplemented"); | ||||
251 | } elsif($line =~ /^(\#\#source-ontology)/) { | ||||
252 | #to be implemented | ||||
253 | $self->warn("$1 header tag parsing unimplemented"); | ||||
254 | } elsif($line =~ /^(\#\#\#)/) { | ||||
255 | #to be implemented | ||||
256 | $self->warn("$1 header tag parsing unimplemented"); | ||||
257 | } elsif($line =~ /^(\#\#FASTA)/) { | ||||
258 | # initial ##FASTA is optional - artemis does not use it | ||||
259 | $line = $self->_readline(); | ||||
260 | if ($line !~ /^\>(\S+)/) { | ||||
261 | $self->throw("##FASTA directive must be followed by fasta header, not: $line"); | ||||
262 | } | ||||
263 | } | ||||
264 | |||||
265 | if ($line =~ /^\>(.*)/) { | ||||
266 | # seq data can be at header or footer | ||||
267 | my $seq = $self->_parse_sequence($line); | ||||
268 | if ($seq) { | ||||
269 | $self->_seq_by_id_h->{$seq->primary_id} = $seq; | ||||
270 | } | ||||
271 | } | ||||
272 | |||||
273 | |||||
274 | if(!$handled){ | ||||
275 | push @unhandled, $line; | ||||
276 | } | ||||
277 | |||||
278 | #looks like the header is over! | ||||
279 | last unless $line =~ /^\#/; | ||||
280 | } | ||||
281 | |||||
282 | foreach my $line (@unhandled){ | ||||
283 | $self->_pushback($line); | ||||
284 | } | ||||
285 | |||||
286 | return 1; | ||||
287 | } | ||||
288 | |||||
289 | sub _parse_sequence { | ||||
290 | my ($self, $line) = @_; | ||||
291 | |||||
292 | if ($line =~ /^\>(.*)/) { | ||||
293 | |||||
294 | my $seqid = $1; | ||||
295 | $seqid =~ s/\s+$//; | ||||
296 | my $desc = ''; | ||||
297 | if ($seqid =~ /(\S+)\s+(.*)/) { | ||||
298 | ($seqid, $desc) = ($1,$2); | ||||
299 | } | ||||
300 | my $res = ''; | ||||
301 | while (my $line = $self->_readline) { | ||||
302 | if ($line =~ /^\#/) { | ||||
303 | last; | ||||
304 | } | ||||
305 | if ($line =~ /^\>/) { | ||||
306 | $self->_pushback($line); | ||||
307 | last; | ||||
308 | } | ||||
309 | $line =~ s/\s//g; | ||||
310 | $res .= $line; | ||||
311 | } | ||||
312 | return if $self->ignore_sequence; | ||||
313 | |||||
314 | my $seqfactory = Bio::Seq::SeqFactory->new('Bio::Seq'); | ||||
315 | my $seq = $seqfactory->create(-seq=>$res, | ||||
316 | -id=>$seqid, | ||||
317 | -desc=>$desc); | ||||
318 | $seq->accession_number($seqid); | ||||
319 | if ($self->features_attached_to_seqs) { | ||||
320 | my @feats = | ||||
321 | @{$self->_feature_idx_by_seq_id->{$seqid}}; | ||||
322 | $seq->add_SeqFeature($_) foreach @feats; | ||||
323 | @{$self->_feature_idx_by_seq_id->{$seqid}} = (); | ||||
324 | } | ||||
325 | return $seq; | ||||
326 | } | ||||
327 | else { | ||||
328 | $self->throw("expected fasta header, not: $line"); | ||||
329 | } | ||||
330 | } | ||||
331 | |||||
332 | |||||
333 | =head2 next_segment | ||||
334 | |||||
335 | Title : next_segment | ||||
336 | Usage : my $seq = $gffio->next_segment; | ||||
337 | Function: Returns a Bio::LocatableSeq object corresponding to a | ||||
338 | GFF "##sequence-region" header line. | ||||
339 | Example : | ||||
340 | Returns : A Bio::LocatableSeq object, or undef if | ||||
341 | there are no more sequences. | ||||
342 | Args : none | ||||
343 | |||||
344 | |||||
345 | =cut | ||||
346 | |||||
347 | sub next_segment{ | ||||
348 | my ($self,@args) = @_; | ||||
349 | return shift @{ $self->{'segments'} } if defined $self->{'segments'}; | ||||
350 | return; | ||||
351 | } | ||||
352 | |||||
353 | |||||
354 | =head2 next_feature | ||||
355 | |||||
356 | Title : next_feature | ||||
357 | Usage : $seqfeature = $gffio->next_feature(); | ||||
358 | Function: Returns the next feature available in the input file or stream, or | ||||
359 | undef if there are no more features. | ||||
360 | Example : | ||||
361 | Returns : A Bio::SeqFeatureI implementing object, or undef if there are no | ||||
362 | more features. | ||||
363 | Args : none | ||||
364 | |||||
365 | =cut | ||||
366 | |||||
367 | sub next_feature { | ||||
368 | my ($self) = @_; | ||||
369 | |||||
370 | my $gff_string; | ||||
371 | |||||
372 | # be graceful about empty lines or comments, and make sure we return undef | ||||
373 | # if the input's consumed | ||||
374 | while(($gff_string = $self->_readline()) && defined($gff_string)) { | ||||
375 | if ($gff_string =~ /^\#\#\#/) { | ||||
376 | # all forward refs have been seen; TODO | ||||
377 | } | ||||
378 | next if($gff_string =~ /^\#/ || $gff_string =~ /^\s*$/ || | ||||
379 | $gff_string =~ m{^//}); | ||||
380 | |||||
381 | while ($gff_string =~ /^\>(.+)/) { | ||||
382 | # fasta can be in header or footer | ||||
383 | my $seq = $self->_parse_sequence($gff_string); | ||||
384 | if ($seq) { | ||||
385 | $self->_seq_by_id_h->{$seq->primary_id} = $seq; | ||||
386 | $gff_string = $self->_readline; | ||||
387 | last unless $gff_string; | ||||
388 | } | ||||
389 | } | ||||
390 | last; | ||||
391 | } | ||||
392 | return unless $gff_string; | ||||
393 | |||||
394 | my $feat = Bio::SeqFeature::Generic->new(); | ||||
395 | $self->from_gff_string($feat, $gff_string); | ||||
396 | |||||
397 | if ($self->features_attached_to_seqs) { | ||||
398 | push(@{$self->_feature_idx_by_seq_id->{$feat->seq_id}}, | ||||
399 | $feat); | ||||
400 | } | ||||
401 | |||||
402 | return $feat; | ||||
403 | } | ||||
404 | |||||
405 | sub _feature_idx_by_seq_id { | ||||
406 | my $self = shift; | ||||
407 | $self->{__feature_idx_by_seq_id} = shift if @_; | ||||
408 | $self->{__feature_idx_by_seq_id} = {} | ||||
409 | unless $self->{__feature_idx_by_seq_id}; | ||||
410 | return $self->{__feature_idx_by_seq_id}; | ||||
411 | } | ||||
412 | |||||
413 | |||||
414 | =head2 from_gff_string | ||||
415 | |||||
416 | Title : from_gff_string | ||||
417 | Usage : $gff->from_gff_string($feature, $gff_string); | ||||
418 | Function: Sets properties of a SeqFeatureI object from a GFF-formatted | ||||
419 | string. Interpretation of the string depends on the version | ||||
420 | that has been specified at initialization. | ||||
421 | |||||
422 | This method is used by next_feature(). It actually dispatches to | ||||
423 | one of the version-specific (private) methods. | ||||
424 | Example : | ||||
425 | Returns : void | ||||
426 | Args : A Bio::SeqFeatureI implementing object to be initialized | ||||
427 | The GFF-formatted string to initialize it from | ||||
428 | |||||
429 | =cut | ||||
430 | |||||
431 | sub from_gff_string { | ||||
432 | my ($self, $feat, $gff_string) = @_; | ||||
433 | |||||
434 | if($self->gff_version() == 1) { | ||||
435 | return $self->_from_gff1_string($feat, $gff_string); | ||||
436 | } elsif( $self->gff_version() == 3 ) { | ||||
437 | return $self->_from_gff3_string($feat, $gff_string); | ||||
438 | } else { | ||||
439 | return $self->_from_gff2_string($feat, $gff_string); | ||||
440 | } | ||||
441 | } | ||||
442 | |||||
443 | |||||
444 | =head2 _from_gff1_string | ||||
445 | |||||
446 | Title : _from_gff1_string | ||||
447 | Usage : | ||||
448 | Function: | ||||
449 | Example : | ||||
450 | Returns : void | ||||
451 | Args : A Bio::SeqFeatureI implementing object to be initialized | ||||
452 | The GFF-formatted string to initialize it from | ||||
453 | |||||
454 | =cut | ||||
455 | |||||
456 | sub _from_gff1_string { | ||||
457 | my ($gff, $feat, $string) = @_; | ||||
458 | chomp $string; | ||||
459 | my ($seqname, $source, $primary, $start, $end, $score, | ||||
460 | $strand, $frame, @group) = split(/\t/, $string); | ||||
461 | |||||
462 | if ( !defined $frame ) { | ||||
463 | $feat->throw("[$string] does not look like GFF to me"); | ||||
464 | } | ||||
465 | $frame = 0 unless( $frame =~ /^\d+$/); | ||||
466 | $feat->seq_id($seqname); | ||||
467 | $feat->source_tag($source); | ||||
468 | $feat->primary_tag($primary); | ||||
469 | $feat->start($start); | ||||
470 | $feat->end($end); | ||||
471 | $feat->frame($frame); | ||||
472 | if ( $score eq '.' ) { | ||||
473 | #$feat->score(undef); | ||||
474 | } else { | ||||
475 | $feat->score($score); | ||||
476 | } | ||||
477 | if ( $strand eq '-' ) { $feat->strand(-1); } | ||||
478 | if ( $strand eq '+' ) { $feat->strand(1); } | ||||
479 | if ( $strand eq '.' ) { $feat->strand(0); } | ||||
480 | foreach my $g ( @group ) { | ||||
481 | if ( $g =~ /(\S+)=(\S+)/ ) { | ||||
482 | my $tag = $1; | ||||
483 | my $value = $2; | ||||
484 | $feat->add_tag_value($1, $2); | ||||
485 | } else { | ||||
486 | $feat->add_tag_value('group', $g); | ||||
487 | } | ||||
488 | } | ||||
489 | } | ||||
490 | |||||
491 | |||||
492 | =head2 _from_gff2_string | ||||
493 | |||||
494 | Title : _from_gff2_string | ||||
495 | Usage : | ||||
496 | Function: | ||||
497 | Example : | ||||
498 | Returns : void | ||||
499 | Args : A Bio::SeqFeatureI implementing object to be initialized | ||||
500 | The GFF2-formatted string to initialize it from | ||||
501 | |||||
502 | |||||
503 | =cut | ||||
504 | |||||
505 | sub _from_gff2_string { | ||||
506 | my ($gff, $feat, $string) = @_; | ||||
507 | chomp($string); | ||||
508 | |||||
509 | # according to the Sanger website, GFF2 should be single-tab | ||||
510 | # separated elements, and the free-text at the end should contain | ||||
511 | # text-translated tab symbols but no "real" tabs, so splitting on | ||||
512 | # \t is safe, and $attribs gets the entire attributes field to be | ||||
513 | # parsed later | ||||
514 | |||||
515 | # sendu: but the tag value pair can (should?) be separated by a tab. The | ||||
516 | # 'no tabs' thing seems to apply only to the free text that is allowed for | ||||
517 | # the value | ||||
518 | |||||
519 | my ($seqname, $source, $primary, $start, | ||||
520 | $end, $score, $strand, $frame, @attribs) = split(/\t+/, $string); | ||||
521 | my $attribs = join ' ', @attribs; | ||||
522 | |||||
523 | if ( !defined $frame ) { | ||||
524 | $feat->throw("[$string] does not look like GFF2 to me"); | ||||
525 | } | ||||
526 | $feat->seq_id($seqname); | ||||
527 | $feat->source_tag($source); | ||||
528 | $feat->primary_tag($primary); | ||||
529 | $feat->start($start); | ||||
530 | $feat->end($end); | ||||
531 | $feat->frame($frame); | ||||
532 | if ( $score eq '.' ) { | ||||
533 | # $feat->score(undef); | ||||
534 | } else { | ||||
535 | $feat->score($score); | ||||
536 | } | ||||
537 | if ( $strand eq '-' ) { $feat->strand(-1); } | ||||
538 | if ( $strand eq '+' ) { $feat->strand(1); } | ||||
539 | if ( $strand eq '.' ) { $feat->strand(0); } | ||||
540 | |||||
541 | |||||
542 | # <Begin Inefficient Code from Mark Wilkinson> | ||||
543 | # this routine is necessay to allow the presence of semicolons in | ||||
544 | # quoted text Semicolons are the delimiting character for new | ||||
545 | # tag/value attributes. it is more or less a "state" machine, with | ||||
546 | # the "quoted" flag going up and down as we pass thorugh quotes to | ||||
547 | # distinguish free-text semicolon and hash symbols from GFF control | ||||
548 | # characters | ||||
549 | |||||
550 | my $flag = 0; # this could be changed to a bit and just be twiddled | ||||
551 | my @parsed; | ||||
552 | |||||
553 | # run through each character one at a time and check it | ||||
554 | # NOTE: changed to foreach loop which is more efficient in perl | ||||
555 | # --jasons | ||||
556 | for my $a ( split //, $attribs ) { | ||||
557 | # flag up on entering quoted text, down on leaving it | ||||
558 | if( $a eq '"') { $flag = ( $flag == 0 ) ? 1:0 } | ||||
559 | elsif( $a eq ';' && $flag ) { $a = "INSERT_SEMICOLON_HERE"} | ||||
560 | elsif( $a eq '#' && ! $flag ) { last } | ||||
561 | push @parsed, $a; | ||||
562 | } | ||||
563 | $attribs = join "", @parsed; # rejoin into a single string | ||||
564 | |||||
565 | # <End Inefficient Code> | ||||
566 | # Please feel free to fix this and make it more "perlish" | ||||
567 | |||||
568 | my @key_vals = split /;/, $attribs; # attributes are semicolon-delimited | ||||
569 | |||||
570 | foreach my $pair ( @key_vals ) { | ||||
571 | # replace semicolons that were removed from free-text above. | ||||
572 | $pair =~ s/INSERT_SEMICOLON_HERE/;/g; | ||||
573 | |||||
574 | # separate the key from the value | ||||
575 | my ($blank, $key, $values) = split /^\s*([\w\d]+)\s/, $pair; | ||||
576 | |||||
577 | if( defined $values ) { | ||||
578 | my @values; | ||||
579 | # free text is quoted, so match each free-text block | ||||
580 | # and remove it from the $values string | ||||
581 | while ($values =~ s/"(.*?)"//){ | ||||
582 | # and push it on to the list of values (tags may have | ||||
583 | # more than one value... and the value may be undef) | ||||
584 | push @values, $1; | ||||
585 | } | ||||
586 | |||||
587 | # and what is left over should be space-separated | ||||
588 | # non-free-text values | ||||
589 | |||||
590 | my @othervals = split /\s+/, $values; | ||||
591 | foreach my $othervalue(@othervals){ | ||||
592 | # get rid of any empty strings which might | ||||
593 | # result from the split | ||||
594 | if (CORE::length($othervalue) > 0) {push @values, $othervalue} | ||||
595 | } | ||||
596 | |||||
597 | foreach my $value(@values){ | ||||
598 | $feat->add_tag_value($key, $value); | ||||
599 | } | ||||
600 | } | ||||
601 | } | ||||
602 | } | ||||
603 | |||||
604 | |||||
605 | sub _from_gff3_string { | ||||
606 | my ($gff, $feat, $string) = @_; | ||||
607 | chomp($string); | ||||
608 | |||||
609 | # according to the now nearly final GFF3 spec, columns should | ||||
610 | # be tab separated, allowing unescaped spaces to occur in | ||||
611 | # column 9 | ||||
612 | |||||
613 | my ($seqname, $source, $primary, $start, $end, | ||||
614 | $score, $strand, $frame, $groups) = split(/\t/, $string); | ||||
615 | |||||
616 | if ( ! defined $frame ) { | ||||
617 | $feat->throw("[$string] does not look like GFF3 to me"); | ||||
618 | } | ||||
619 | $feat->seq_id($seqname); | ||||
620 | $feat->source_tag($source); | ||||
621 | $feat->primary_tag($primary); | ||||
622 | $feat->start($start); | ||||
623 | $feat->end($end); | ||||
624 | $feat->frame($frame); | ||||
625 | if ( $score eq '.' ) { | ||||
626 | #$feat->score(undef); | ||||
627 | } else { | ||||
628 | $feat->score($score); | ||||
629 | } | ||||
630 | if ( $strand eq '-' ) { $feat->strand(-1); } | ||||
631 | if ( $strand eq '+' ) { $feat->strand(1); } | ||||
632 | if ( $strand eq '.' ) { $feat->strand(0); } | ||||
633 | my @groups = split(/\s*;\s*/, $groups); | ||||
634 | |||||
635 | for my $group (@groups) { | ||||
636 | my ($tag,$value) = split /=/,$group; | ||||
637 | $tag = unescape($tag); | ||||
638 | my @values = map {unescape($_)} split /,/,$value; | ||||
639 | for my $v ( @values ) { $feat->add_tag_value($tag,$v); } | ||||
640 | } | ||||
641 | } | ||||
642 | |||||
643 | # taken from Bio::DB::GFF | ||||
644 | sub unescape { | ||||
645 | my $v = shift; | ||||
646 | $v =~ tr/+/ /; | ||||
647 | $v =~ s/%([0-9a-fA-F]{2})/chr hex($1)/ge; | ||||
648 | return $v; | ||||
649 | } | ||||
650 | |||||
651 | |||||
652 | =head2 write_feature | ||||
653 | |||||
654 | Title : write_feature | ||||
655 | Usage : $gffio->write_feature($feature); | ||||
656 | Function: Writes the specified SeqFeatureI object in GFF format to the stream | ||||
657 | associated with this instance. | ||||
658 | Returns : none | ||||
659 | Args : An array of Bio::SeqFeatureI implementing objects to be serialized | ||||
660 | |||||
661 | =cut | ||||
662 | |||||
663 | sub write_feature { | ||||
664 | my ($self, @features) = @_; | ||||
665 | return unless @features; | ||||
666 | if( $self->{'_first'} && $self->gff_version() == 3 ) { | ||||
667 | $self->_print("##gff-version 3\n"); | ||||
668 | } | ||||
669 | $self->{'_first'} = 0; | ||||
670 | foreach my $feature ( @features ) { | ||||
671 | $self->_print($self->gff_string($feature)."\n"); | ||||
672 | } | ||||
673 | } | ||||
674 | |||||
675 | |||||
676 | =head2 gff_string | ||||
677 | |||||
678 | Title : gff_string | ||||
679 | Usage : $gffstr = $gffio->gff_string($feature); | ||||
680 | Function: Obtain the GFF-formatted representation of a SeqFeatureI object. | ||||
681 | The formatting depends on the version specified at initialization. | ||||
682 | |||||
683 | This method is used by write_feature(). It actually dispatches to | ||||
684 | one of the version-specific (private) methods. | ||||
685 | Example : | ||||
686 | Returns : A GFF-formatted string representation of the SeqFeature | ||||
687 | Args : A Bio::SeqFeatureI implementing object to be GFF-stringified | ||||
688 | |||||
689 | =cut | ||||
690 | |||||
691 | sub gff_string{ | ||||
692 | my ($self, $feature) = @_; | ||||
693 | |||||
694 | if($self->gff_version() == 1) { | ||||
695 | return $self->_gff1_string($feature); | ||||
696 | } elsif( $self->gff_version() == 3 ) { | ||||
697 | return $self->_gff3_string($feature); | ||||
698 | } elsif( $self->gff_version() == 2.5 ) { | ||||
699 | return $self->_gff25_string($feature); | ||||
700 | } else { | ||||
701 | return $self->_gff2_string($feature); | ||||
702 | } | ||||
703 | } | ||||
704 | |||||
705 | |||||
706 | =head2 _gff1_string | ||||
707 | |||||
708 | Title : _gff1_string | ||||
709 | Usage : $gffstr = $gffio->_gff1_string | ||||
710 | Function: | ||||
711 | Example : | ||||
712 | Returns : A GFF1-formatted string representation of the SeqFeature | ||||
713 | Args : A Bio::SeqFeatureI implementing object to be GFF-stringified | ||||
714 | |||||
715 | =cut | ||||
716 | |||||
717 | sub _gff1_string{ | ||||
718 | my ($gff, $feat) = @_; | ||||
719 | my ($str,$score,$frame,$name,$strand); | ||||
720 | |||||
721 | if( $feat->can('score') ) { | ||||
722 | $score = $feat->score(); | ||||
723 | } | ||||
724 | $score = '.' unless defined $score; | ||||
725 | |||||
726 | if( $feat->can('frame') ) { | ||||
727 | $frame = $feat->frame(); | ||||
728 | } | ||||
729 | $frame = '.' unless defined $frame; | ||||
730 | |||||
731 | $strand = $feat->strand(); | ||||
732 | if(! $strand) { | ||||
733 | $strand = "."; | ||||
734 | } elsif( $strand == 1 ) { | ||||
735 | $strand = '+'; | ||||
736 | } elsif ( $feat->strand == -1 ) { | ||||
737 | $strand = '-'; | ||||
738 | } | ||||
739 | |||||
740 | if( $feat->can('seqname') ) { | ||||
741 | $name = $feat->seq_id(); | ||||
742 | $name ||= 'SEQ'; | ||||
743 | } else { | ||||
744 | $name = 'SEQ'; | ||||
745 | } | ||||
746 | |||||
747 | $str = join("\t", | ||||
748 | $name, | ||||
749 | $feat->source_tag, | ||||
750 | $feat->primary_tag, | ||||
751 | $feat->start, | ||||
752 | $feat->end, | ||||
753 | $score, | ||||
754 | $strand, | ||||
755 | $frame); | ||||
756 | |||||
757 | foreach my $tag ( $feat->get_all_tags ) { | ||||
758 | next if exists $SKIPPED_TAGS{$tag}; | ||||
759 | foreach my $value ( $feat->get_tag_values($tag) ) { | ||||
760 | $str .= " $tag=$value" if $value; | ||||
761 | } | ||||
762 | } | ||||
763 | |||||
764 | return $str; | ||||
765 | } | ||||
766 | |||||
767 | |||||
768 | =head2 _gff2_string | ||||
769 | |||||
770 | Title : _gff2_string | ||||
771 | Usage : $gffstr = $gffio->_gff2_string | ||||
772 | Function: | ||||
773 | Example : | ||||
774 | Returns : A GFF2-formatted string representation of the SeqFeature | ||||
775 | Args : A Bio::SeqFeatureI implementing object to be GFF2-stringified | ||||
776 | |||||
777 | =cut | ||||
778 | |||||
779 | sub _gff2_string{ | ||||
780 | my ($gff, $origfeat) = @_; | ||||
781 | my $feat; | ||||
782 | if ($origfeat->isa('Bio::SeqFeature::FeaturePair')){ | ||||
783 | $feat = $origfeat->feature2; | ||||
784 | } else { | ||||
785 | $feat = $origfeat; | ||||
786 | } | ||||
787 | my ($str1, $str2,$score,$frame,$name,$strand); | ||||
788 | |||||
789 | if( $feat->can('score') ) { | ||||
790 | $score = $feat->score(); | ||||
791 | } | ||||
792 | $score = '.' unless defined $score; | ||||
793 | |||||
794 | if( $feat->can('frame') ) { | ||||
795 | $frame = $feat->frame(); | ||||
796 | } | ||||
797 | $frame = '.' unless defined $frame; | ||||
798 | |||||
799 | $strand = $feat->strand(); | ||||
800 | if(! $strand) { | ||||
801 | $strand = "."; | ||||
802 | } elsif( $strand == 1 ) { | ||||
803 | $strand = '+'; | ||||
804 | } elsif ( $feat->strand == -1 ) { | ||||
805 | $strand = '-'; | ||||
806 | } | ||||
807 | |||||
808 | if( $feat->can('seqname') ) { | ||||
809 | $name = $feat->seq_id(); | ||||
810 | } | ||||
811 | $name ||= 'SEQ'; | ||||
812 | |||||
813 | $str1 = join("\t", | ||||
814 | $name, | ||||
815 | $feat->source_tag(), | ||||
816 | $feat->primary_tag(), | ||||
817 | $feat->start(), | ||||
818 | $feat->end(), | ||||
819 | $score, | ||||
820 | $strand, | ||||
821 | $frame); | ||||
822 | # the routine below is the only modification I made to the original | ||||
823 | # ->gff_string routine (above) as on November 17th, 2000, the | ||||
824 | # Sanger webpage describing GFF2 format reads: "From version 2 | ||||
825 | # onwards, the attribute field must have a tag value structure | ||||
826 | # following the syntax used within objects in a .ace file, | ||||
827 | # flattened onto one line by semicolon separators. Tags must be | ||||
828 | # standard identifiers ([A-Za-z][A-Za-z0-9_]*). Free text values | ||||
829 | # must be quoted with double quotes". | ||||
830 | # MW | ||||
831 | |||||
832 | my @group; | ||||
833 | |||||
834 | foreach my $tag ( $feat->get_all_tags ) { | ||||
835 | next if exists $SKIPPED_TAGS{$tag}; | ||||
836 | my @v; | ||||
837 | foreach my $value ( $feat->get_tag_values($tag) ) { | ||||
838 | unless( defined $value && length($value) ) { | ||||
839 | # quote anything other than valid tag/value characters | ||||
840 | $value = '""'; | ||||
841 | } elsif ($value =~ /[^A-Za-z0-9_]/){ | ||||
842 | # substitute tab and newline chars by their UNIX equivalent | ||||
843 | $value =~ s/\t/\\t/g; | ||||
844 | $value =~ s/\n/\\n/g; | ||||
845 | $value = '"' . $value . '" '; | ||||
846 | } | ||||
847 | push @v, $value; | ||||
848 | # for this tag (allowed in GFF2 and .ace format) | ||||
849 | } | ||||
850 | push @group, "$tag ".join(" ", @v); | ||||
851 | } | ||||
852 | |||||
853 | $str2 .= join(' ; ', @group); | ||||
854 | # Add Target information for Feature Pairs | ||||
855 | if( ! $feat->has_tag('Target') && # This is a bad hack IMHO | ||||
856 | ! $feat->has_tag('Group') && | ||||
857 | $origfeat->isa('Bio::SeqFeature::FeaturePair') ) { | ||||
858 | $str2 = sprintf("Target %s %d %d", $origfeat->feature1->seq_id, | ||||
859 | ( $origfeat->feature1->strand < 0 ? | ||||
860 | ( $origfeat->feature1->end, | ||||
861 | $origfeat->feature1->start) : | ||||
862 | ( $origfeat->feature1->start, | ||||
863 | $origfeat->feature1->end) | ||||
864 | )) . ($str2?" ; ".$str2:""); # need to put Target information before other tag/value pairs - mw | ||||
865 | } | ||||
866 | return $str1."\t".$str2; | ||||
867 | } | ||||
868 | |||||
869 | |||||
870 | =head2 _gff25_string | ||||
871 | |||||
872 | Title : _gff25_string | ||||
873 | Usage : $gffstr = $gffio->_gff2_string | ||||
874 | Function: To get a format of GFF that is peculiar to Gbrowse/Bio::DB::GFF | ||||
875 | Example : | ||||
876 | Returns : A GFF2.5-formatted string representation of the SeqFeature | ||||
877 | Args : A Bio::SeqFeatureI implementing object to be GFF2.5-stringified | ||||
878 | |||||
879 | =cut | ||||
880 | |||||
881 | sub _gff25_string { | ||||
882 | my ($gff, $origfeat) = @_; | ||||
883 | my $feat; | ||||
884 | if ($origfeat->isa('Bio::SeqFeature::FeaturePair')){ | ||||
885 | $feat = $origfeat->feature2; | ||||
886 | } else { | ||||
887 | $feat = $origfeat; | ||||
888 | } | ||||
889 | my ($str1, $str2,$score,$frame,$name,$strand); | ||||
890 | |||||
891 | if( $feat->can('score') ) { | ||||
892 | $score = $feat->score(); | ||||
893 | } | ||||
894 | $score = '.' unless defined $score; | ||||
895 | |||||
896 | if( $feat->can('frame') ) { | ||||
897 | $frame = $feat->frame(); | ||||
898 | } | ||||
899 | $frame = '.' unless defined $frame; | ||||
900 | |||||
901 | $strand = $feat->strand(); | ||||
902 | if(! $strand) { | ||||
903 | $strand = "."; | ||||
904 | } elsif( $strand == 1 ) { | ||||
905 | $strand = '+'; | ||||
906 | } elsif ( $feat->strand == -1 ) { | ||||
907 | $strand = '-'; | ||||
908 | } | ||||
909 | |||||
910 | if( $feat->can('seqname') ) { | ||||
911 | $name = $feat->seq_id(); | ||||
912 | $name ||= 'SEQ'; | ||||
913 | } else { | ||||
914 | $name = 'SEQ'; | ||||
915 | } | ||||
916 | $str1 = join("\t", | ||||
917 | $name, | ||||
918 | $feat->source_tag(), | ||||
919 | $feat->primary_tag(), | ||||
920 | $feat->start(), | ||||
921 | $feat->end(), | ||||
922 | $score, | ||||
923 | $strand, | ||||
924 | $frame); | ||||
925 | |||||
926 | my @all_tags = $feat->all_tags; | ||||
927 | my @group; my @firstgroup; | ||||
928 | if (@all_tags) { # only play this game if it is worth playing... | ||||
929 | foreach my $tag ( @all_tags ) { | ||||
930 | my @v; | ||||
931 | foreach my $value ( $feat->get_tag_values($tag) ) { | ||||
932 | next if exists $SKIPPED_TAGS{$tag}; | ||||
933 | unless( defined $value && length($value) ) { | ||||
934 | $value = '""'; | ||||
935 | } elsif ($value =~ /[^A-Za-z0-9_]/){ | ||||
936 | $value =~ s/\t/\\t/g; # substitute tab and newline | ||||
937 | # characters | ||||
938 | $value =~ s/\n/\\n/g; # to their UNIX equivalents | ||||
939 | $value = '"' . $value . '" '; | ||||
940 | } # if the value contains | ||||
941 | # anything other than valid | ||||
942 | # tag/value characters, then | ||||
943 | # quote it | ||||
944 | push @v, $value; | ||||
945 | # for this tag (allowed in GFF2 and .ace format) | ||||
946 | } | ||||
947 | if (($tag eq 'Group') || ($tag eq 'Target')){ # hopefully we wont get both... | ||||
948 | push @firstgroup, "$tag ".join(" ", @v); | ||||
949 | } else { | ||||
950 | push @group, "$tag ".join(" ", @v); | ||||
951 | } | ||||
952 | } | ||||
953 | } | ||||
954 | $str2 = join(' ; ', (@firstgroup, @group)); | ||||
955 | # Add Target information for Feature Pairs | ||||
956 | if( ! $feat->has_tag('Target') && # This is a bad hack IMHO | ||||
957 | ! $feat->has_tag('Group') && | ||||
958 | $origfeat->isa('Bio::SeqFeature::FeaturePair') ) { | ||||
959 | $str2 = sprintf("Target %s ; tstart %d ; tend %d", $origfeat->feature1->seq_id, | ||||
960 | ( $origfeat->feature1->strand < 0 ? | ||||
961 | ( $origfeat->feature1->end, | ||||
962 | $origfeat->feature1->start) : | ||||
963 | ( $origfeat->feature1->start, | ||||
964 | $origfeat->feature1->end) | ||||
965 | )) . ($str2?" ; ".$str2:""); # need to put the target info before other tag/value pairs - mw | ||||
966 | } | ||||
967 | return $str1 . "\t". $str2; | ||||
968 | } | ||||
969 | |||||
970 | |||||
971 | =head2 _gff3_string | ||||
972 | |||||
973 | Title : _gff3_string | ||||
974 | Usage : $gffstr = $gffio->_gff3_string | ||||
975 | Function: | ||||
976 | Example : | ||||
977 | Returns : A GFF3-formatted string representation of the SeqFeature | ||||
978 | Args : A Bio::SeqFeatureI implementing object to be GFF3-stringified | ||||
979 | |||||
980 | =cut | ||||
981 | |||||
982 | sub _gff3_string { | ||||
983 | my ($gff, $origfeat) = @_; | ||||
984 | my $feat; | ||||
985 | if ($origfeat->isa('Bio::SeqFeature::FeaturePair')){ | ||||
986 | $feat = $origfeat->feature2; | ||||
987 | } else { | ||||
988 | $feat = $origfeat; | ||||
989 | } | ||||
990 | |||||
991 | my $ID = $gff->_incrementGFF3ID(); | ||||
992 | |||||
993 | my ($score,$frame,$name,$strand); | ||||
994 | |||||
995 | if( $feat->can('score') ) { | ||||
996 | $score = $feat->score(); | ||||
997 | } | ||||
998 | $score = '.' unless defined $score; | ||||
999 | |||||
1000 | if( $feat->can('frame') ) { | ||||
1001 | $frame = $feat->frame(); | ||||
1002 | } | ||||
1003 | $frame = '1' unless defined $frame; | ||||
1004 | |||||
1005 | $strand = $feat->strand(); | ||||
1006 | |||||
1007 | if(! $strand) { | ||||
1008 | $strand = "."; | ||||
1009 | } elsif( $strand == 1 ) { | ||||
1010 | $strand = '+'; | ||||
1011 | } elsif ( $feat->strand == -1 ) { | ||||
1012 | $strand = '-'; | ||||
1013 | } | ||||
1014 | |||||
1015 | if( $feat->can('seqname') ) { | ||||
1016 | $name = $feat->seq_id(); | ||||
1017 | $name ||= 'SEQ'; | ||||
1018 | } else { | ||||
1019 | $name = 'SEQ'; | ||||
1020 | } | ||||
1021 | |||||
1022 | my @groups; | ||||
1023 | |||||
1024 | # force leading ID and Parent tags | ||||
1025 | my @all_tags = grep { ! exists $GFF3_ID_Tags{$_} } $feat->all_tags; | ||||
1026 | for my $t ( sort { $GFF3_ID_Tags{$b} <=> $GFF3_ID_Tags{$a} } | ||||
1027 | keys %GFF3_ID_Tags ) { | ||||
1028 | unshift @all_tags, $t if $feat->has_tag($t); | ||||
1029 | } | ||||
1030 | |||||
1031 | for my $tag ( @all_tags ) { | ||||
1032 | next if exists $SKIPPED_TAGS{$tag}; | ||||
1033 | # next if $tag eq 'Target'; | ||||
1034 | if ($tag eq 'Target' && ! $origfeat->isa('Bio::SeqFeature::FeaturePair')){ | ||||
1035 | # simple Target,start,stop | ||||
1036 | my($target_id, $b,$e,$strand) = $feat->get_tag_values($tag); | ||||
1037 | next unless(defined($e) && defined($b) && $target_id); | ||||
1038 | ($b,$e)= ($e,$b) if(defined $strand && $strand<0); | ||||
1039 | $target_id =~ s/([\t\n\r%&\=;,])/sprintf("%%%X",ord($1))/ge; | ||||
1040 | push @groups, sprintf("Target=%s %d %d", $target_id,$b,$e); | ||||
1041 | next; | ||||
1042 | } | ||||
1043 | |||||
1044 | my $valuestr; | ||||
1045 | # a string which will hold one or more values | ||||
1046 | # for this tag, with quoted free text and | ||||
1047 | # space-separated individual values. | ||||
1048 | my @v; | ||||
1049 | for my $value ( $feat->get_tag_values($tag) ) { | ||||
1050 | if( defined $value && length($value) ) { | ||||
1051 | #$value =~ tr/ /+/; #spaces are allowed now | ||||
1052 | if ( ref $value eq 'Bio::Annotation::Comment') { | ||||
1053 | $value = $value->text; | ||||
1054 | } | ||||
1055 | |||||
1056 | if ($value =~ /[^a-zA-Z0-9\,\;\=\.:\%\^\*\$\@\!\+\_\?\-]/) { | ||||
1057 | $value =~ s/\t/\\t/g; # substitute tab and newline | ||||
1058 | # characters | ||||
1059 | $value =~ s/\n/\\n/g; # to their UNIX equivalents | ||||
1060 | |||||
1061 | # Unescaped quotes are not allowed in GFF3 | ||||
1062 | # $value = '"' . $value . '"'; | ||||
1063 | } | ||||
1064 | $value =~ s/([\t\n\r%&\=;,])/sprintf("%%%X",ord($1))/ge; | ||||
1065 | } else { | ||||
1066 | # if it is completely empty, then just make empty double quotes | ||||
1067 | $value = '""'; | ||||
1068 | } | ||||
1069 | push @v, $value; | ||||
1070 | } | ||||
1071 | # can we figure out how to improve this? | ||||
1072 | $tag = lcfirst($tag) unless ( $tag =~ | ||||
1073 | /^(ID|Name|Alias|Parent|Gap|Target|Derives_from|Note|Dbxref|Ontology_term)$/); | ||||
1074 | |||||
1075 | push @groups, "$tag=".join(",",@v); | ||||
1076 | } | ||||
1077 | # Add Target information for Feature Pairs | ||||
1078 | if( $feat->has_tag('Target') && | ||||
1079 | ! $feat->has_tag('Group') && | ||||
1080 | $origfeat->isa('Bio::SeqFeature::FeaturePair') ) { | ||||
1081 | |||||
1082 | my $target_id = $origfeat->feature1->seq_id; | ||||
1083 | $target_id =~ s/([\t\n\r%&\=;,])/sprintf("%%%X",ord($1))/ge; | ||||
1084 | |||||
1085 | push @groups, sprintf("Target=%s %d %d", | ||||
1086 | $target_id, | ||||
1087 | ( $origfeat->feature1->strand < 0 ? | ||||
1088 | ( $origfeat->feature1->end, | ||||
1089 | $origfeat->feature1->start) : | ||||
1090 | ( $origfeat->feature1->start, | ||||
1091 | $origfeat->feature1->end) | ||||
1092 | )); | ||||
1093 | } | ||||
1094 | |||||
1095 | # unshift @groups, "ID=autogenerated$ID" unless ($feat->has_tag('ID')); | ||||
1096 | if ( $feat->can('name') && defined($feat->name) ) { | ||||
1097 | # such as might be for Bio::DB::SeqFeature | ||||
1098 | unshift @groups, 'Name=' . $feat->name; | ||||
1099 | } | ||||
1100 | |||||
1101 | my $gff_string = ""; | ||||
1102 | if ($feat->location->isa("Bio::Location::SplitLocationI")) { | ||||
1103 | my @locs = $feat->location->each_Location; | ||||
1104 | foreach my $loc (@locs) { | ||||
1105 | $gff_string .= join("\t", | ||||
1106 | $name, | ||||
1107 | $feat->source_tag() || '.', | ||||
1108 | $feat->primary_tag(), | ||||
1109 | $loc->start(), | ||||
1110 | $loc->end(), | ||||
1111 | $score, | ||||
1112 | $strand, | ||||
1113 | $frame, | ||||
1114 | join(';', @groups)) . "\n"; | ||||
1115 | } | ||||
1116 | chop $gff_string; | ||||
1117 | return $gff_string; | ||||
1118 | } else { | ||||
1119 | $gff_string = join("\t", | ||||
1120 | $name, | ||||
1121 | $feat->source_tag() || '.', | ||||
1122 | $feat->primary_tag(), | ||||
1123 | $feat->start(), | ||||
1124 | $feat->end(), | ||||
1125 | $score, | ||||
1126 | $strand, | ||||
1127 | $frame, | ||||
1128 | join(';', @groups)); | ||||
1129 | } | ||||
1130 | return $gff_string; | ||||
1131 | } | ||||
1132 | |||||
1133 | |||||
1134 | =head2 gff_version | ||||
1135 | |||||
1136 | Title : _gff_version | ||||
1137 | Usage : $gffversion = $gffio->gff_version | ||||
1138 | Function: | ||||
1139 | Example : | ||||
1140 | Returns : The GFF version this parser will accept and emit. | ||||
1141 | Args : none | ||||
1142 | |||||
1143 | =cut | ||||
1144 | |||||
1145 | sub gff_version { | ||||
1146 | my ($self, $value) = @_; | ||||
1147 | if(defined $value && grep {$value == $_ } ( 1, 2, 2.5, 3)) { | ||||
1148 | $self->{'GFF_VERSION'} = $value; | ||||
1149 | } | ||||
1150 | return $self->{'GFF_VERSION'}; | ||||
1151 | } | ||||
1152 | |||||
1153 | |||||
1154 | # Make filehandles | ||||
1155 | |||||
1156 | =head2 newFh | ||||
1157 | |||||
1158 | Title : newFh | ||||
1159 | Usage : $fh = Bio::Tools::GFF->newFh(-file=>$filename,-format=>'Format') | ||||
1160 | Function: does a new() followed by an fh() | ||||
1161 | Example : $fh = Bio::Tools::GFF->newFh(-file=>$filename,-format=>'Format') | ||||
1162 | $feature = <$fh>; # read a feature object | ||||
1163 | print $fh $feature; # write a feature object | ||||
1164 | Returns : filehandle tied to the Bio::Tools::GFF class | ||||
1165 | Args : | ||||
1166 | |||||
1167 | =cut | ||||
1168 | |||||
1169 | sub newFh { | ||||
1170 | my $class = shift; | ||||
1171 | return unless my $self = $class->new(@_); | ||||
1172 | return $self->fh; | ||||
1173 | } | ||||
1174 | |||||
1175 | |||||
1176 | =head2 fh | ||||
1177 | |||||
1178 | Title : fh | ||||
1179 | Usage : $obj->fh | ||||
1180 | Function: | ||||
1181 | Example : $fh = $obj->fh; # make a tied filehandle | ||||
1182 | $feature = <$fh>; # read a feature object | ||||
1183 | print $fh $feature; # write a feature object | ||||
1184 | Returns : filehandle tied to Bio::Tools::GFF class | ||||
1185 | Args : none | ||||
1186 | |||||
1187 | =cut | ||||
1188 | |||||
1189 | |||||
1190 | sub fh { | ||||
1191 | my $self = shift; | ||||
1192 | my $class = ref($self) || $self; | ||||
1193 | my $s = Symbol::gensym; | ||||
1194 | tie $$s,$class,$self; | ||||
1195 | return $s; | ||||
1196 | } | ||||
1197 | |||||
1198 | # This accessor is used for accessing the Bio::Seq objects from a GFF3 | ||||
1199 | # file; if the file you are using has no sequence data you can ignore | ||||
1200 | # this accessor | ||||
1201 | |||||
1202 | # This accessor returns a hash reference containing Bio::Seq objects, | ||||
1203 | # indexed by Bio::Seq->primary_id | ||||
1204 | |||||
1205 | sub _seq_by_id_h { | ||||
1206 | my $self = shift; | ||||
1207 | |||||
1208 | return $self->{'_seq_by_id_h'} = shift if @_; | ||||
1209 | $self->{'_seq_by_id_h'} = {} | ||||
1210 | unless $self->{'_seq_by_id_h'}; | ||||
1211 | return $self->{'_seq_by_id_h'}; | ||||
1212 | } | ||||
1213 | |||||
1214 | |||||
1215 | =head2 get_seqs | ||||
1216 | |||||
1217 | Title : get_seqs | ||||
1218 | Usage : | ||||
1219 | Function: Returns all Bio::Seq objects populated by GFF3 file | ||||
1220 | Example : | ||||
1221 | Returns : | ||||
1222 | Args : | ||||
1223 | |||||
1224 | =cut | ||||
1225 | |||||
1226 | sub get_seqs { | ||||
1227 | my ($self,@args) = @_; | ||||
1228 | return values %{$self->_seq_by_id_h}; | ||||
1229 | } | ||||
1230 | |||||
1231 | |||||
1232 | =head2 features_attached_to_seqs | ||||
1233 | |||||
1234 | Title : features_attached_to_seqs | ||||
1235 | Usage : $obj->features_attached_to_seqs(1); | ||||
1236 | Function: For use with GFF3 containg sequence only | ||||
1237 | |||||
1238 | Setting this B<before> parsing ensures that all Bio::Seq object | ||||
1239 | created will have the appropriate features added to them | ||||
1240 | |||||
1241 | defaults to false (off) | ||||
1242 | |||||
1243 | Note that this mode will incur higher memory usage because features | ||||
1244 | will have to be cached until the relevant feature comes along | ||||
1245 | |||||
1246 | Example : | ||||
1247 | Returns : value of features_attached_to_seqs (a boolean) | ||||
1248 | Args : on set, new value (a boolean, optional) | ||||
1249 | |||||
1250 | |||||
1251 | =cut | ||||
1252 | |||||
1253 | sub features_attached_to_seqs{ | ||||
1254 | my $self = shift; | ||||
1255 | |||||
1256 | return $self->{'_features_attached_to_seqs'} = shift if @_; | ||||
1257 | return $self->{'_features_attached_to_seqs'}; | ||||
1258 | } | ||||
1259 | |||||
1260 | |||||
1261 | =head2 ignore_sequence | ||||
1262 | |||||
1263 | Title : ignore_sequence | ||||
1264 | Usage : $obj->ignore_sequence(1); | ||||
1265 | Function: For use with GFF3 containg sequence only | ||||
1266 | |||||
1267 | Setting this B<before> parsing means that all sequence data will be | ||||
1268 | ignored | ||||
1269 | |||||
1270 | Example : | ||||
1271 | Returns : value of ignore_sequence (a boolean) | ||||
1272 | Args : on set, new value (a boolean, optional) | ||||
1273 | |||||
1274 | =cut | ||||
1275 | |||||
1276 | sub ignore_sequence{ | ||||
1277 | my $self = shift; | ||||
1278 | |||||
1279 | return $self->{'_ignore_sequence'} = shift if @_; | ||||
1280 | return $self->{'_ignore_sequence'}; | ||||
1281 | } | ||||
1282 | |||||
1283 | |||||
1284 | sub DESTROY { | ||||
1285 | my $self = shift; | ||||
1286 | $self->close(); | ||||
1287 | } | ||||
1288 | |||||
1289 | sub TIEHANDLE { | ||||
1290 | my ($class,$val) = @_; | ||||
1291 | return bless {'gffio' => $val}, $class; | ||||
1292 | } | ||||
1293 | |||||
1294 | sub READLINE { | ||||
1295 | my $self = shift; | ||||
1296 | return $self->{'gffio'}->next_feature() || undef unless wantarray; | ||||
1297 | my (@list, $obj); | ||||
1298 | push @list, $obj while $obj = $self->{'gffio'}->next_feature(); | ||||
1299 | return @list; | ||||
1300 | } | ||||
1301 | |||||
1302 | sub PRINT { | ||||
1303 | my $self = shift; | ||||
1304 | $self->{'gffio'}->write_feature(@_); | ||||
1305 | } | ||||
1306 | |||||
1307 | 1 | 10µs | 1; | ||
1308 |