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|
#!/usr/bin/perl
use strict;
use warnings;
use FindBin;
use lib "$FindBin::RealBin/../lib";
use Test::More tests => 37;
use Test::Exception;
use Test::Warn;
use Bio::Chado::Schema::Test;
my $schema = Bio::Chado::Schema::Test->init_schema();
my $sf = $schema->resultset('Sequence::Feature');
isa_ok( $sf, 'DBIx::Class::ResultSet' );
$schema->txn_do(sub{
# try a joined query through one of the longer has_many rels
lives_ok {
$sf->search_related('feature_relationship_objects')->count;
} 'join through a long has_many name does not die';
$schema->txn_rollback;
});
$schema->txn_do(sub{
# insert a feature with some sequence
my $cvterm = $schema->resultset('Cv::Cvterm')
->create_with({
name => 'tester',
cv => 'testing cv',
db => 'fake db',
dbxref => 'fake accession',
});
my $large_seq_type =
$schema->resultset('Cv::Cvterm')
->create_with({
name => 'large_residues',
cv => 'testing cv',
db => 'fake db',
dbxref => 'fake large_residues accession',
});
my $test_seq = 'ACTAGCATCATGCCGCTAGCTAATATGCTG';
my $grandpa = $schema->resultset('Sequence::Feature')
->find_or_create({
residues => $test_seq,
seqlen => length( $test_seq ),
name => 'BCS_grandpa',
uniquename => 'BCS_pappy',
type => $cvterm,
organism_id=> 4,
});
is( $grandpa->subseq( 3, 5 ), 'TAG', 'subseq on regular residues works' );
is( $grandpa->trunc( 3, 5 )->seq, 'TAG', 'trunc on regular residues works' );
my $parent = $schema->resultset('Sequence::Feature')
->find_or_create({
seqlen => length( $test_seq ),
name => 'BCS_stuff_parent',
uniquename => 'BCS_foo',
type => $cvterm,
organism_id=> 4,
});
$parent->find_or_create_related(
'featureprops',
{ type => $large_seq_type,
value => $test_seq,
},
);
is( $parent->alphabet, 'dna', 'got right alphabet' );
is( $parent->subseq( 3, 5 ), 'TAG', 'subseq on large_residues prop works' );
is( $parent->trunc( 3, 5 )->seq, 'TAG', 'subseq on large_residues prop works' );
is( $parent->trunc( 3, 5 )->id, $parent->name, 'subseq on large_residues has proper name' );
my $child = $schema->resultset('Sequence::Feature')
->find_or_create({
residues => $test_seq,
seqlen => length( $test_seq ),
name => 'BCS_stuff_child',
uniquename => 'BCS_foo2',
type => $cvterm,
organism_id=> 4,
});
my $stepchild = $schema->resultset('Sequence::Feature')
->find_or_create({
residues => $test_seq,
seqlen => length( $test_seq ),
name => 'BCS_stepchild',
uniquename => 'BCS_step',
type => $cvterm,
organism_id=> 4,
});
lives_ok(sub {
$parent->add_to_child_features( $stepchild, { type => $stepchild->type })
}, 'add_to_child_features');
lives_ok(sub {
$parent->add_to_parent_features( $grandpa, { type => $grandpa->type })
}, 'add_to_parent_features');
$parent->create_related( 'feature_relationship_subjects', {
object_id => $parent->feature_id,
subject_id => $child->feature_id,
type => $parent->type,
});
$schema->resultset('Organism::Organism')
->find_or_create({ genus => 'test', species => 'testus' })
->create_related( 'features', {
residues => $test_seq,
seqlen => length( $test_seq ),
name => 'BCS_test_seq_deleteme',
uniquename => 'BCS_test_seq_deleteme',
type => $cvterm,
});
# find a feature with some sequence. might be the one we just
# inserted.
my $feature = $sf->search({
'residues' => {'!=', undef},
'seqlen' => {'!=', undef},
'name' => {'!=', 'BSC_stuff'},
}, { 'rows' => 1 })->single;
# test some Bio::SeqI methods for it
for (
[qw[ length seqlen ]],
[qw[ id name ]],
[qw[ primary_id name ]],
[qw[ residues seq ]],
) {
my ($m1,$m2) = @$_;
is( $feature->$m1, $feature->$m2,
"$m1() returns same thing as $m2()" );
}
can_ok($feature,'child_features');
can_ok($feature,'parent_features');
can_ok($feature,'child_relationships');
can_ok($feature,'parent_relationships');
my (@children_rels) = $parent->child_relationships;
my (@parents_rels) = $parent->parent_relationships;
isa_ok($children_rels[0], 'Bio::Chado::Schema::Result::Sequence::FeatureRelationship');
isa_ok($parents_rels[0], 'Bio::Chado::Schema::Result::Sequence::FeatureRelationship');
isnt($parent->feature_id, $child->feature_id, 'child and parent are different');
my (@children) = $parent->child_features;
my (@parents) = $child->parent_features;
is(scalar @children, 2, "the parent feature has two child features");
is(scalar @parents, 1, "the child feature has one parent feature");
my (@grandparents) = $parent->parent_features;
my (@grandkids) = $child->child_features;
is(scalar @grandparents, 1, "the parent feature has one parent feature");
is(scalar @grandkids, 0, "the child feature has no child feature");
isa_ok($children[0], 'Bio::Chado::Schema::Result::Sequence::Feature');
isa_ok($parents[0], 'Bio::Chado::Schema::Result::Sequence::Feature');
is_deeply( [ map { $_->name } @children ], [ 'BCS_stepchild', 'BCS_stuff_child' ], 'child feature_id is correct' );
is_deeply( [ map { $_->name } @parents ], [ 'BCS_stuff_parent' ], 'parent feature_id is correct' );
#test some featureloc stuff
my $featureloc = $schema->resultset('Sequence::Featureloc')
->create({ srcfeature => $grandpa,
feature => $parent,
fmin => 20,
fmax => 28,
strand => 1,
});
is( $featureloc->length, 8, 'got right featureloc length' );
is( $featureloc->to_range->start, 21, 'featureloc to_range start' );
is( $featureloc->to_range->end, 28, 'featureloc to_range end' );
is( $featureloc->to_range->strand, 1, 'featureloc to_range strand' );
# test the synonyms many-to-many
is( scalar( $feature->synonyms ), 0, 'synonyms mm rel works' );
# insert a feature with no seqlen or residues
{ my $no_seq = $schema->resultset('Sequence::Feature')
->create({ name => 'mostly_blank',
uniquename => 'mostly_blank',
organism_id => 4,
type => $cvterm,
});
is( $no_seq->subseq(1,0), undef, 'undef for strange subseq on a feature with no residues' );
is( $no_seq->subseq(1,1), undef, 'slightly different subseq args' );
is( $no_seq->seqlen, undef, 'undef on seqlen for this also' );
}
$schema->txn_rollback;
});
|
