-
Notifications
You must be signed in to change notification settings - Fork 182
/
Factory.pm
787 lines (628 loc) · 25.7 KB
/
Factory.pm
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
# $Id: Util.pm 15875 2009-07-21 19:20:00Z chmille4 $
#
# BioPerl module for Bio::Nexml::Factory
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chase Miller <chmille4@gmail.com>
#
# Copyright Chase Miller
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Nexml::Factory - A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents
=head1 SYNOPSIS
Do not use this module directly. It shoulde be used through
Bio::NexmlIO, Bio::SeqIO::nexml, Bio::AlignIO::nexml, or
Bio::TreeIO::nexml
=head1 DESCRIPTION
This is a factory/utility module in the Nexml namespace. It contains
methods that are needed by multiple modules.
This module handles the creation of BioPerl objects from Bio::Phylo
objects and vice versa, which is used to read and write nexml
documents to and from BioPerl objects.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Chase Miller
Email chmille4@gmail.com
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
#Let the code begin
package Bio::Nexml::Factory;
use strict;
BEGIN {
use Bio::Root::Root;
unless (eval "require Bio::Phylo; 1") {
Bio::Root::Root->throw("Bio::Phylo package required; see http://www.nexml.org for download details");
}
}
use Bio::Phylo::Factory;
use Bio::Phylo::Matrices;
use Bio::Phylo::Matrices::Matrix;
use Bio::Phylo::Matrices::Datum;
use Bio::Phylo::Forest::Tree;
use Bio::Phylo::Matrices;
use Bio::Phylo::IO;
use Bio::SeqFeature::Generic;
use base qw(Bio::Root::Root);
my $fac = Bio::Phylo::Factory->new();
=head2 new
Title : new
Usage : my $obj = Bio::Nexml::Factory->new();
Function: Builds a new L<Bio::Nexml::Factory> object
Returns : L<Bio::Nexml::Factory> object
Args : none
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
}
#should all these creates be private methods?
# naah./maj
=head2 create_bperl_aln
Title : create_bperl_aln
Usage : my @alns = $factory->create_bperl_aln($objIO);
Function: Converts Bio::Phylo::Matrices::Matrix objects into L<Bio::SimpleAlign> objects
Returns : an array of L<Bio::SimpleAlign> objects
Args : Bio::NexmlIO, Bio::SeqIO, Bio::AlignIO, or Bio::TreeIO
see [http://search.cpan.org/~rvosa/Bio-Phylo/lib/Bio/Phylo/Project.pm Bio::Phylo::Project]
=cut
sub create_bperl_aln {
my ($self, $caller) = @_;
my ($start, $end, $seq, $desc);
my $matrices = $caller->doc->get_matrices();
my @alns;
foreach my $matrix (@$matrices)
{
#check if mol_type is something that makes sense to be an aln
my $mol_type = lc($matrix->get_type());
unless ($mol_type eq 'dna' || $mol_type eq 'rna' || $mol_type eq 'protein')
{
next;
# something for the back-burner: BioPerl has objects
# to handle arbitrary genotypes; might be cool to
# be able to create something besides alignments
# here .../maj
}
#continue creating an aln
my $aln = Bio::SimpleAlign->new();
my $taxa = $matrix->get_taxa();
# TODO: should $caller->{_ID} always be defined?
# ATM, this is a Bio::AlignIO::nexml stream...
$aln->{_Nexml_ID} = $caller->{_ID}? $caller->{_ID} . $taxa->get_xml_id : $taxa->get_xml_id;
my $aln_feats = Bio::SeqFeature::Generic->new();
$aln_feats->add_tag_value('NexmlIO_ID', $caller->{_ID});
#check if there is a taxa associated with this alignment
if ($taxa) {
$aln_feats->add_tag_value('taxa_id', $taxa->get_xml_id());
$aln_feats->add_tag_value('taxa_label', $taxa->get_name()) if $taxa->get_name();
my $taxon = $taxa->first;
while ($taxon) {
$aln_feats->add_tag_value('taxon', $taxon->get_name);
$taxon = $taxa->next;
}
}
$aln->add_SeqFeature($aln_feats);
my $basename = $matrix->get_name();
$aln->id($basename);
my $seqNum = 0;
my$row = $matrix->first;
while ($row)
{
my $newSeq = $row->get_char();
my $rowlabel;
$seqNum++;
#constuct seqID based on matrix label and row id
my $seqID = "$basename.row_$seqNum";
#Check if theres a row label and if not default to seqID
if( !defined($rowlabel = $row->get_name())) {$rowlabel = $seqID;}
$seq = Bio::LocatableSeq->new(
-seq => $newSeq,
-display_id => "$rowlabel",
#-description => $desc,
-alphabet => $mol_type,
);
my $seq_feats;
#check if there is a taxa associated w/ this alignment
if($taxa)
{
if (my $taxon = $taxa->get_by_name($row->get_taxon->get_name())) {
#attach taxon to each sequence by using the sequenceID because
#LocatableSeq does not support features
my $taxon_name = $taxon->get_name();
$seq_feats = Bio::SeqFeature::Generic->new();
$seq_feats->add_tag_value('taxon', "$taxon_name");
$seq_feats->add_tag_value('id', "$rowlabel");
}
}
$aln->add_seq($seq);
$aln->add_SeqFeature($seq_feats);
$self->debug("Reading r$rowlabel\n");
$row = $matrix->next();
}
push (@alns, $aln);
}
return \@alns;
}
=head2 create_bperl_tree
Title : create_bperl_tree
Usage : my @trees = $factory->create_bperl_seq($objIO);
Function: Converts Bio::Phylo::Forest::Tree objects into L<Bio::Tree::Tree> objects
Returns : an array of L<Bio::Tree::Tree> objects
Args : Bio::NexmlIO, Bio::SeqIO, Bio::AlignIO, or Bio::TreeIO
see [http://search.cpan.org/~rvosa/Bio-Phylo/lib/Bio/Phylo/Project.pm Bio::Phylo::Project]
=cut
sub create_bperl_tree {
my($self, $caller) = @_;
my @trees;
my $forests = $caller->doc->get_forests();
foreach my $forest (@$forests)
{
my $basename = $forest->get_name() || '';
my $taxa = $forest->get_taxa();
my $taxa_label = $taxa->get_name();
my $taxa_id = $taxa->get_xml_id();
my $t = $forest->first();
while ($t)
{
my %created_nodes;
my $tree_id = $t->get_name();
my $tree = Bio::Tree::Tree->new(-id => "$basename.$tree_id");
#set the taxa info of the tree
$tree->add_tag_value('taxa_label', $taxa_label) if defined($taxa_label);
$tree->add_tag_value('taxa_id', $taxa_id) if defined($taxa_id);
# TODO: should $caller->{_ID} always be defined?
# ATM, this is a Bio::TreeIO::nexml stream...
$tree->add_tag_value('_NexmlIO_ID', $caller->{_ID}) if $caller->{_ID};
my $taxon = $taxa->first;
while($taxon) {
$tree->add_tag_value('taxon', $taxon->get_name()) if defined($taxon->get_name);
$taxon = $taxa->next;
}
#process terminals only, removing terminals as they get processed
#which inturn creates new terminals to process until the entire tree has been processed
my $terminals = $t->get_terminals();
# for(my $i=0; $i<@$terminals; $i++)
while (my $terminal = shift @$terminals)
{
# my $terminal = $$terminals[$i];
my $new_node_id = $terminal->get_name();
my $newNode;
if(exists $created_nodes{$new_node_id})
{
$newNode = $created_nodes{$new_node_id};
}
else
{
$newNode = Bio::Tree::Node->new();
$new_node_id ||= 'internal_'.$newNode->_creation_id;
$newNode->id($new_node_id);
$created_nodes{$new_node_id} = $newNode;
}
#check if taxa data exists for the current node ($terminal)
if($taxa) {
my $taxon = $terminal->get_taxon();
$newNode->add_tag_value("taxon", $taxon->get_name()) if $taxon && $taxon->get_name;
}
#check if you've reached the root of the tree and if so, stop.
if($terminal->is_root()) {
$tree->set_root_node($newNode);
last;
}
#transfer attributes that apply to non-root only nodes
$newNode->branch_length($terminal->get_branch_length());
my $parent = $terminal->get_parent();
my $parentID = $parent->get_name();
if(exists $created_nodes{$parentID})
{
$created_nodes{$parentID}->add_Descendent($newNode);
}
else
{
my $parent_node = Bio::Tree::Node->new();
$parentID ||= 'internal_'.$parent_node->_creation_id;
$parent_node->id($parentID);
$parent_node->add_Descendent($newNode);
$created_nodes{$parentID} = $parent_node;
}
#remove processed node from tree
$parent->prune_child($terminal);
#check if the parent of the removed node is now a terminal node and should be added for processing
if($parent->is_terminal())
{
push(@$terminals, $terminal->get_parent()) if $terminal->get_parent;
}
}
push @trees, $tree;
$t = $forest->next();
}
}
return \@trees;
}
=head2 create_bperl_seq
Title : create_bperl_seq
Usage : my @seqs = $factory->create_bperl_seq($objIO);
Function: Converts Bio::Phylo::Matrices::Datum objects into L<Bio::Seq> objects
Returns : an array of L<Bio::Seq> objects
Args : Bio::NexmlIO, Bio::SeqIO, Bio::AlignIO, or Bio::TreeIO
see [http://search.cpan.org/~rvosa/Bio-Phylo/lib/Bio/Phylo/Project.pm Bio::Phylo::Project]
=cut
sub create_bperl_seq {
my($self, $caller) = @_;
my $matrices = $caller->doc->get_matrices();
my @seqs;
foreach my $matrix (@$matrices)
{
#check if mol_type is something that makes sense to be a seq
my $mol_type = lc($matrix->get_type());
unless ($mol_type eq 'dna' || $mol_type eq 'rna' || $mol_type eq 'protein')
{
next;
}
my $taxa = $matrix->get_taxa();
my $seqnum = 0;
my $taxa_id = $taxa->get_xml_id();
my $taxa_label = $taxa->get_name();
my $basename = $matrix->get_name();
my $row = $matrix->first;
while ($row)
{
my $newSeq = $row->get_char();
my $feat = Bio::SeqFeature::Generic->new();
$feat->add_tag_value('matrix_label', $matrix->get_name()) if defined($matrix->get_name);
$feat->add_tag_value('matrix_id', $matrix->get_xml_id());
$feat->add_tag_value('NexmlIO_ID', $caller->{_ID});
$feat->add_tag_value('taxa_id', $taxa_id) if defined($taxa_id);
$feat->add_tag_value('taxa_label', $taxa_label) if defined($taxa_label);
$seqnum++;
#construct full sequence id by using bio::phylo "matrix label" and "row id"
my $seqID = "$basename.seq_$seqnum";
my $rowlabel;
#check if there is a label for the row, if not default to seqID
if (!defined ($rowlabel = $row->get_name())) {$rowlabel = $seqID;}
else {$seqID = $rowlabel;}
#build the seq object using the factory create method
my $seqbuilder = Bio::Seq::SeqFactory->new('-type' => 'Bio::Seq');
my $seq = $seqbuilder->create(
-seq => $newSeq,
-id => $rowlabel,
-primary_id => $seqID,
#-desc => $fulldesc,
-alphabet => $mol_type,
-direct => 1,
);
# TODO: should $caller->{_ID} always be defined?
# ATM, this is a Bio::SeqIO::nexml stream...
$seq->{_Nexml_ID} = $caller->{_ID} ? $caller->{_ID} . $taxa_id : $taxa_id;
$seq->{_Nexml_matrix_ID} = $caller->{_ID} ? $caller->{_ID} . $matrix->get_xml_id() : $matrix->get_xml_id();
#check if taxon linked to sequence if so create feature to attach to alignment
if ($taxa) {
my $taxon = $taxa->first;
while ($taxon) {
$feat->add_tag_value('taxon', $taxon->get_name) if defined($taxon->get_name);
if($taxon eq $row->get_taxon) {
my $taxon_name = $taxon->get_name();
$feat->add_tag_value('my_taxon', "$taxon_name") if defined($taxon_name);
$feat->add_tag_value('id', $rowlabel);
}
$taxon = $taxa->next;
}
}
$seq->add_SeqFeature($feat);
push (@seqs, $seq);
$row = $matrix->next;
}
}
return \@seqs;
}
=head2 create_bphylo_tree
Title : create_bphylo_tree
Usage : my $bphylo_tree = $factory->create_bphylo_tree($bperl_tree);
Function: Converts a L<Bio::Tree::Tree> object into Bio::Phylo::Forest::Tree object
Returns : a Bio::Phylo::Forest::Tree object
Args : Bio::Tree::Tree object
=cut
sub create_bphylo_tree {
my ($self, $bptree, $taxa) = @_;
#most of the code below ripped form Bio::Phylo::Forest::Tree::new_from_bioperl()d
my $tree = $fac->create_tree;
my $class = 'Bio::Phylo::Forest::Tree';
if ( ref $bptree && $bptree->isa('Bio::Tree::TreeI') ) {
bless $tree, $class;
($tree) = _copy_tree( $tree, $bptree->get_root_node, "", $taxa);
# copy name
my $name = $bptree->id;
$tree->set_name( $name ) if defined $name;
# copy score
my $score = $bptree->score;
$tree->set_score( $score ) if defined $score;
}
else {
$self->throw('Not a bioperl tree!');
}
return $tree;
}
sub _copy_tree {
my ( $tree, $bpnode, $parent, $taxa ) = @_;
my $node = create_bphylo_node($bpnode);
my $taxon;
if ($parent) {
$parent->set_child($node);
}
if (my $bptaxon_name = $bpnode->get_tag_values('taxon'))
{
$node->set_taxon($taxa->get_by_name($bptaxon_name));
}
$tree->insert($node);
foreach my $bpchild ( $bpnode->each_Descendent ) {
_copy_tree( $tree, $bpchild, $node, $taxa );
}
return $tree;
}
=head2 create_bphylo_node
Title : create_bphylo_node
Usage : my $bphylo_node = $factory->create_bphylo_node($bperl_node);
Function: Converts a L<Bio::Tree::Node> object into Bio::Phylo::Forest::Node object
Returns : a Bio::Phylo::Forest::Node object
Args : L<Bio::Tree::Node> object
=cut
sub create_bphylo_node {
my ($bpnode) = @_;
my $node = Bio::Phylo::Forest::Node->new();
#mostly ripped from Bio::Phylo::Forest::Node->new_from_bioperl()
# copy name
my $name = $bpnode->id;
$node->set_name( $name ) if defined $name;
# copy branch length
my $branch_length = $bpnode->branch_length;
$node->set_branch_length( $branch_length ) if defined $branch_length;
# copy description
my $desc = $bpnode->description;
$node->set_desc( $desc ) if defined $desc;
# copy bootstrap
my $bootstrap = $bpnode->bootstrap;
$node->set_score( $bootstrap ) if defined $bootstrap and looks_like_number $bootstrap;
# copy other tags
for my $tag ( $bpnode->get_all_tags ) {
my @values = $bpnode->get_tag_values( $tag );
$node->set_generic( $tag => \@values );
}
return $node;
}
=head2 create_bphylo_aln
Title : create_bphylo_aln
Usage : my $bphylo_aln = $factory->create_bphylo_aln($bperl_aln);
Function: Converts a L<Bio::SimpleAlign> object into Bio::Phylo::Matrices::Matrix object
Returns : a Bio::Phylo::Matrices::Matrix object
Args : Bio::SimpleAlign object
=cut
sub create_bphylo_aln {
my ($self, $aln, $taxa, @args) = @_;
#most of the code below ripped from Bio::Phylo::Matrices::Matrix::new_from_bioperl()
if ( $aln->isa('Bio::Align::AlignI') ) {
$aln->unmatch;
$aln->map_chars('\.','-');
my @seqs = $aln->each_seq;
my ( $type, $missing, $gap, $matchchar );
if ( $seqs[0] ) {
$type = $seqs[0]->alphabet || $seqs[0]->_guess_alphabet || 'dna';
}
else {
$type = 'dna';
}
my $matrix = $fac->create_matrix(
'-type' => $type,
'-special_symbols' => {
'-missing' => $aln->missing_char || '?',
'-matchchar' => $aln->match_char || '.',
'-gap' => $aln->gap_char || '-',
},
@args
);
# XXX create raw getter/setter pairs for annotation, accession, consensus_meta source
for my $field ( qw(description accession id annotation consensus_meta score source) ) {
$matrix->$field( $aln->$field );
}
my $to = $matrix->get_type_object;
my @feats = $aln->get_all_SeqFeatures();
for my $seq ( @seqs ) {
#create datum linked to taxa
my $datum = create_bphylo_datum($seq, $taxa, \@feats, '-type_object' => $to);
$matrix->insert($datum);
}
return $matrix;
}
else {
$self->throw('Not a bioperl alignment!');
}
}
=head2 create_bphylo_seq
Title : create_bphylo_seq
Usage : my $bphylo_seq = $factory->create_bphylo_seq($bperl_seq);
Function: Converts a L<Bio::Seq> object into Bio::Phylo::Matrices::Matrix object
Returns : a Bio::Phylo::Matrices::Matrix object
Args : Bio::Seq object
=cut
sub create_bphylo_seq {
my ($self, $seq, $taxa, @args) = @_;
my $type = $seq->alphabet || $seq->_guess_alphabet || 'dna';
$type = uc($type);
my $dat = create_bphylo_datum($seq, $taxa, '-type' => $type);
# copy seq string
my $seqstring = $seq->seq;
if ( $seqstring and $seqstring =~ /\S/ ) {
eval { $dat->set_char( $seqstring ) };
if ( $@ and UNIVERSAL::isa($@,'Bio::Phylo::Util::Exceptions::InvalidData') ) {
$self->throw("\n\nThe BioPerl sequence object contains invalid data ($seqstring)\n");
}
}
# copy name
my $name = $seq->display_id;
#$dat->set_name( $name ) if defined $name;
# copy desc
my $desc = $seq->desc;
$dat->set_desc( $desc ) if defined $desc;
#get features from SeqFeatureI
for my $field ( qw(start end strand) ) {
$dat->$field( $seq->$field ) if $seq->can($field);
}
return $dat;
}
=head2 create_bphylo_taxa
Title : create_bphylo_seq
Usage : my $taxa = $factory->create_bphylo_taxa($bperl_obj);
Function: creates a taxa object from the data attached to a bioperl object
Returns : a Bio::Phylo::Taxa object
Args : L<Bio::Seq> object, or L<Bio::SimpleAlign> object, or L<Bio::Tree::Tree> object
=cut
sub create_bphylo_taxa {
my $self = shift @_;
my ($obj) = @_;
#check if tree or aln object
if ( UNIVERSAL::isa( $obj, 'Bio::Align::AlignI' ) || UNIVERSAL::isa( $obj, 'Bio::Seq')) {
return $self->_create_bphylo_matrix_taxa(@_);
}
elsif ( UNIVERSAL::isa( $obj, 'Bio::Tree::TreeI' ) ) {
return $self->_create_bphylo_tree_taxa(@_);
}
}
sub _create_bphylo_tree_taxa {
my ($self, $tree) = @_;
my $taxa = $fac->create_taxa();
my $taxon;
#check if taxa exists
unless ($tree->has_tag('taxa_id')) {
return 0;
}
#copy taxa details
$taxa->set_xml_id(($tree->get_tag_values('taxa_id'))[0]);
$taxa->set_name(($tree->get_tag_values('taxa_label'))[0]);
foreach my $taxon_name ($tree->get_tag_values('taxon')) {
$taxon = $fac->create_taxon(-name => $taxon_name);
$taxa->insert($taxon);
}
return $taxa;
}
sub _create_bphylo_matrix_taxa {
my ($self, $aln) = @_;
my $taxa = $fac->create_taxa();
my $taxon;
my @feats = $aln->get_all_SeqFeatures();
foreach my $feat (@feats) {
if (my $taxa_id = ($feat->get_tag_values('taxa_id'))[0]) {
my $taxa_label = ($feat->get_tag_values('taxa_label'))[0];
$taxa->set_name($taxa_label) if defined $taxa_label;
$taxa->set_xml_id($taxa_id) if defined $taxa_label;
my @taxa_bp = $feat->get_tag_values('taxon');
foreach my $taxon_name (@taxa_bp) {
$taxon = $fac->create_taxon(-name => $taxon_name);
$taxa->insert($taxon);
}
last;
}
}
return $taxa
}
=head2 create_bphylo_datum
Title : create_bphylo_datum
Usage : my $bphylo_datum = $factory->create_bphylo_datum($bperl_datum);
Function: Converts a L<Bio::Seq> object into Bio::Phylo::Matrices::datum object
Returns : a Bio::Phylo::Matrices::datum object
Args : Bio::Seq object, Bio::Phylo::Taxa object,
[optional] arrayref to SeqFeatures,
[optional] key => value pairs to pass to Bio::Phylo constructor
=cut
sub create_bphylo_datum {
#mostly ripped from Bio::Phylo::Matrices::Datum::new_from_bioperl()
my ( $seq, $taxa, @args ) = @_;
my $class = 'Bio::Phylo::Matrices::Datum';
my $feats;
# want $seq type-check here? Allowable: is-a Bio::PrimarySeq,
# Bio::LocatableSeq /maj
if (@args % 2) { # odd
$feats = shift @args;
unless (ref($feats) eq 'ARRAY') {
Bio::Root::Root->throw("Third argument must be array of SeqFeatures");
}
}
my $type = $seq->alphabet || $seq->_guess_alphabet || 'dna';
my $self = $class->new( '-type' => $type, @args );
# copy seq string
my $seqstring = $seq->seq;
if ( $seqstring and $seqstring =~ /\S/ ) {
eval { $self->set_char( $seqstring ) };
if ( $@ and UNIVERSAL::isa($@,'Bio::Phylo::Util::Exceptions::InvalidData') ) {
$self->throw("\n\nThe BioPerl sequence object contains invalid data ($seqstring)\n");
}
}
# copy name
my $name = $seq->display_id;
$self->set_name( $name ) if defined $name;
my $taxon;
my @feats = (defined $feats ? @$feats : $seq->get_all_SeqFeatures);
# convert taxa
foreach my $feat (@feats)
{
#get sequence id associated with taxa to compare
my $taxa_id = ($feat->get_tag_values('id'))[0] if $feat->has_tag('id');
if ($taxa_id && $name eq $taxa_id)
{
my $taxon_name;
if($feat->has_tag('my_taxon')) {
$taxon_name = ($feat->get_tag_values('my_taxon'))[0]
}
else {
$taxon_name = ($feat->get_tag_values('taxon'))[0];
}
$self->set_taxon($taxa->get_by_name($taxon_name));
}
}
# copy desc
my $desc = $seq->desc;
$self->set_desc( $desc ) if defined $desc;
# only Bio::LocatableSeq objs have these fields...
for my $field ( qw(start end strand) ) {
$self->$field( $seq->$field ) if $seq->can($field);
}
return $self;
}
=head2 CREATOR
=cut
=head1 bioperl_create
Title : bioperl_create
Usage : $bioperl_obj = $fac->bioperl_create($obj_type, $biophylo_proj);
Function: Create a specified bioperl object using a Bio::Phylo project
Args : scalar string ('aln', 'tree', 'seq') type designator
Bio::Phylo::Project object
Returns : Appropriate BioPerl object
=cut
sub bioperl_create {
my $self = shift;
my ($type, @args) = @_;
unless (grep /^type/,qw( seq aln tree )) {
$self->throw("Unrecognized type for argument 1");
}
my $call = 'create_bioperl_'.$type;
return $self->$call(@args);
}
1;