File: GAMEHandler.pm

package info (click to toggle)
libchado-perl 1.23-2
  • links: PTS, VCS
  • area: main
  • in suites: jessie, jessie-kfreebsd
  • size: 23,976 kB
  • ctags: 10,378
  • sloc: xml: 192,540; sql: 165,945; perl: 28,339; sh: 101; python: 73; makefile: 46
file content (423 lines) | stat: -rw-r--r-- 11,739 bytes parent folder | download | duplicates (5)
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
package SOI::GAMEHandler;

=head1 NAME

SOI::GAMEHandler

=head1 SYNOPSIS

perlSAX handler to parse GAME xml

(WARNING: very alpha software!)

=head1 USAGE

=begin

my $handler = SOI::SOIHandler->new([qw(your feature type list here)]);
my $parser = XML::Parser::PerlSAX->new(Handler=>$handler);
$parser->parse(Source => { SystemId =>$soixml_file});
my $feature = $handler->feature; #get SOI::Feature obj (feature tree) from soi xml

=end

=cut

=head1 FEEDBACK

Email sshu@fruitfly.org

=cut

use strict;
use SOI::Feature;
use FileHandle;
use Carp;

=head1 FUNCTIONS

=cut

sub new {
    my $class = shift;
    my $self = {};
    bless $self, $class;

    #element tag becomes feature type, but overwritten by its type attr if any
    my $types = shift || [qw(game map_position seq annotation feature_set feature_span result_set result_span computational_analysis)];

    #alias: synonym and output is also property, aspect is ontology
    my $mv_types = shift || [qw(property output dbxref ontology aspect comment)];
    my $single2prop = shift || [qw(synonym)];
    $types = [$types] unless (ref($types) eq 'ARRAY');
    $mv_types = [$mv_types] unless (ref($mv_types) eq 'ARRAY');
    $single2prop = [$single2prop] unless (ref($single2prop) eq 'ARRAY');
    $self->{feature_types} = $types;
    $self->{multi_types} = $mv_types;
    $self->{single_types} = $single2prop;
    return $self;
}

=head2 start_element

Called directly by SAX Parser.
Do NOT call this directly.

Adds element name string to stack.

=cut

sub start_element {
    my ($self, $element) = @_;

    my $name = $element->{Name};
    my $feature = $self->_curr_feature;
    my $attrs = $element->{Attributes};
    if (grep{$name eq $_}@{$self->{feature_types} || []}) {
        $feature = SOI::Feature->new({type=>$element->{Name}});
        map{
            my $m = $self->_field($_);
            $m = 'seqtype' if ($feature->type eq 'seq' && $_ eq 'type');
            $m = 'seqlen' if ($feature->type eq 'seq' && $_ eq 'length');
            $feature->$m($attrs->{$_});
        }keys %{$attrs || {}};

        $feature->depth(scalar(@{$self->{feature_stack} || []}));
        push @{$self->{feature_stack}}, $feature;
        push @{$self->{level_stack}}, "feature";
    }
    elsif (grep{$name eq $_}@{$self->{multi_types} || []}) {
        push @{$self->{level_stack}}, $name;
        $self->start_multi($element);
        map{
            $self->{hash}->{$_} = $attrs->{$_};
        }keys %{$attrs || {}}
    }
    elsif (grep{$name eq $_}@{$self->{single_types} || []}) {
        push @{$self->{level_stack}}, $name;
        $self->start_single($element);
    }
    elsif (grep{$name eq $_}qw(seq_relationship span)) {
        #special handling
        if ($name eq 'span') { #simply contain start/end

        } else {
            my $type = $attrs->{type};
            $feature = SOI::Feature->new();
            push @{$self->{feature_stack}}, $feature;
            push @{$self->{level_stack}}, "feature";
            $feature->src_seq($attrs->{seq});
            $feature->hash->{seq_relationship} = $type;
        }
    }
    elsif (grep{$name eq $_}qw(gene)) {

    }
    else {
        undef $self->{cur_e_char};
        if (keys %{$attrs || {}}) {
            my $level = $self->{level_stack}->[-1];
            if ($level eq 'feature') {
                my $f = $self->_curr_feature;
                map{
                    my $m = $self->_field($_);
                    $f->$m($attrs->{$_});
                }keys %{$attrs || {}}
            }
            elsif (grep{$level eq $_}@{$self->{multi_types} || []}) {
                map{
                    $self->{hash}->{$_} = $attrs->{$_};
                }keys %{$attrs || {}}
            }
        }
    }

    return 1;
}

=head2 end_element

Called directly by SAX Parser.
Do NOT call this directly.

Removes element name string from stack.

=cut

sub end_element {
    my ($self, $element) = @_;

    my $name = $element->{Name};
    my $feature = $self->_curr_feature;

    my $level = $self->{level_stack}->[-1];
    if (grep{$name eq $_}@{$self->{feature_types} || []}) {
        pop @{$self->{level_stack}};
        unless (@{$self->{feature_stack}} == 1) {
            my $child = pop @{$self->{feature_stack}};
            my $parent = $self->_curr_feature;
            if ($child->type eq 'seq') {
                $self->{seq_hash}->{$child->uniquename || $child->name} = $child;
            } else {
                $parent->add_node($child);
            }
        }
    }
    elsif (grep{$name eq $_}@{$self->{multi_types} || []}) {
        pop @{$self->{level_stack}};
        my $el_name = "end_multi";
        $self->$el_name($element);
    }
    elsif (grep{$name eq $_}@{$self->{single_types} || []}) {
        pop @{$self->{level_stack}};
        $self->end_single($element);
    }
    elsif (grep{$name eq $_}qw(seq_relationship span)) {
        #special handling
        if ($name eq 'span') { #simply contain start/end

        } else {
            pop @{$self->{level_stack}};
            $feature = pop @{$self->{feature_stack}};
            my $main_f = $self->_curr_feature;
            if ($feature->hash->{seq_relationship} eq 'subject') {
                $main_f->add_secondary_node($feature);
                delete $feature->hash->{seq_relationship};
            } else { #query
                #$feature->_setup_coord;
                map{
                    my $m = $_;
                    $main_f->$m($feature->$m)
                }keys %{$feature->hash};
                delete $main_f->hash->{seq_relationship};
            }
        }
    }
    elsif (grep{$name eq $_}qw(gene)) {

    }
    else {
        my $e_val = $self->{cur_e_char};
        if ($e_val) {
            $e_val =~ s/^\s*//g;
            $e_val =~ s/\s*$//g;
        }
        if ($level eq 'feature') {
            my $m = $self->_field($name);
            $feature->$m($e_val);
        }
        else {
            $self->{hash}->{$name} = $e_val;
        }
    }
    return 1;
}

#multi to auxillary: property dbxref ontology comment
sub start_multi {
    my ($self, $element) = @_;
    $self->{hash} = {};
}

sub end_multi {
    my ($self, $element) = @_;

    my $name = $element->{Name};
    $name =~ tr/A-Z/a-z/;
    my $feature = $self->_curr_feature;
    #alias tags!!!
    if ($name eq 'aspect') {
        $name = 'ontology';
    }
    elsif ($name eq 'output') {
        $name = 'property';
    }
    my $method = "add_$name";
    confess("unsupported auxillary: $name") unless ($feature->can($method));
    my $hs = $self->{hash};
    #turn array of hash into one hash
    my $h;
    map{
        my $k = $self->_field($_);
        $h->{$k}=$hs->{$_};
    }keys %{$hs || {}};
    $feature->$method($h);
}
#single to property (tag=type, val=val)
sub start_single {
    my ($self, $element) = @_;
    undef $self->{cur_e_char};
    #$self->{hash} = {};
}
sub end_single {
    my ($self, $element) = @_;
    my $name = $element->{Name};
    my $e_val = $self->{cur_e_char} || "";
    $e_val =~ s/^\s*//g;
    $e_val =~ s/\s*$//g;
    $self->_curr_feature->add_property({type=>$name, value=>$e_val});
}

sub start_document {
    my $self = shift;
    undef $self->{feature_stack};
    undef $self->{level_stack};
}

=head2 end_element

Called directly by SAX Parser.
Do NOT call this directly.

The last method called by the
Sax Parser.  This returns the
data in $self->data.

=cut


sub end_document {
  my $self = shift;

}

=head2 characters

Called directly by SAX Parser.
Do NOT call this directly.

Calls method with the name of the
current element with text as the 
first argument.

=cut

sub characters {
  my ($self, $characters) = @_;

  my $data = $characters->{Data};
  return $self->{cur_e_char} .= $data;
}

=head2 feature

 usage:  my $feature = $self->feature;

 returns: top node feature/apollo mini view feature

=cut


sub feature {
    my $self = shift;
    return unless (@{$self->{feature_stack} || []});
    my $feature = $self->_curr_feature;
    $feature->type('chromosome_arm');
    delete $feature->hash->{version};
    my (@all, $contig);

    foreach my $sf (@{$feature->nodes || []}) {
        if ($sf->type eq 'tile') {
            $sf->type('contig');
            $contig = $sf;
        }
        elsif ($sf->type eq 'gene') {
            $sf->_rsetup_coord;
            #do we have translation/polypeptide?
            foreach my $tr (@{$sf->nodes || []}) {
                my $seq = $self->{seq_hash}->{$tr->produces_seq};
                delete $tr->hash->{produces_seq};
                if ($seq) {
                    my $res = $seq->residues;
                    $res =~ s/\n//g;
                    $res =~ s/\s+//g;
                    $tr->residues($res);
                    $tr->seqlen($seq->seqlen);
                    $tr->md5checksum($seq->md5checksum);
                }
                my @prots = grep{$_->type eq 'translate offset'}@{$tr->nodes || []}; #only one
                foreach my $p (@prots) {
                    my $seq = $self->{seq_hash}->{$p->produces_seq};
                    $p->uniquename($p->produces_seq);
                    $p->type('protein');
                    delete $p->hash->{produces_seq};
                    if ($seq) {
                        my $res = $seq->residues;
                        my $res = $seq->residues;
                        $res =~ s/\n//g;
                        $res =~ s/\s+//g;
                        $p->residues($res);
                        $p->seqlen($seq->seqlen);
                        $p->md5checksum($seq->md5checksum);
                    }
                    #$p->to_soi_xml;
                }
            }
            push @all, $sf;
            #$sf->to_soi_xml;
        }
        elsif ($sf->type eq 'computational_analysis') {
            $sf->_rsetup_coord;
            foreach my $rset (@{$sf->nodes || []}) {
                foreach my $span (@{$rset->nodes || []}) {
                    my $seq = $span->secondary_node?$self->{seq_hash}->{$span->secondary_node->src_seq}:"";
                    if ($seq) {
                        my $res = $seq->residues;
                        $res =~ s/\n//g;
                        $res =~ s/\s+//g;
                        $seq->residues($res);
                        $span->secondary_node->sseq($seq);
                    }
                }
            }
            push @all, $sf;
            #$sf->to_soi_xml;
        }
    }
    unless ($contig) {
        #fishing for contig (arm dump)
        my ($arm) = grep{$_->hash->{focus} eq 'true'}values %{$self->{seq_hash} || {}};
        if ($arm) {
            $contig = SOI::Feature->new({type=>'contig'});
            $contig->name($arm->name);
            $contig->src_seq($arm->name);
            $contig->seqlen($arm->seqlen);
            map{$contig->$_($arm->$_)}qw(length version md5checksum);
        }
    }
    my $seq = $self->{seq_hash}->{$contig->hash->{seq}};
    if ($seq) {
        my $res = $seq->residues;
        $res =~ s/\n//g;
        $res =~ s/\s+//g;
        $contig->residues($res);
        $contig->name($seq->name);
        $contig->length($seq->length);
    }
    $feature->name($contig->src_seq);
    delete $contig->hash->{seq};

    $feature->nodes([$contig, @all]);
    return $feature;
}

sub _curr_feature {
    my $self = shift;
    return unless (@{$self->{feature_stack} || []});
    return $self->{feature_stack}->[-1];
}

#field transform
sub _field {
    my ($self, $field) = @_;
    my %map_h =
      (id        => 'uniquename',
       arm       => 'src_seq',
       alignment => 'residue_info',
       xref_db   => 'dbname',
       db_xref_id => 'accession',
      );
    return $map_h{$field} || $field;
}

1;