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+<?php
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+namespace Tests\tripal_chado\api;
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+
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+use StatonLab\TripalTestSuite\DBTransaction;
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+use StatonLab\TripalTestSuite\TripalTestCase;
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+
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+class TripalChadoFeatureAPITest extends TripalTestCase {
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+ // Uncomment to auto start and rollback db transactions per test method.
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+ use DBTransaction;
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+
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+ /**
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+ * Tests chado_get_feature_sequences().
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+ *
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+ * @group tripal_chado_api
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+ * @group feature-module
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+ */
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+ public function testChadoGetFeatureSeqs() {
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+
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+ // Preparation... Create the features.
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+ $base_seq = 'GGG' . str_repeat('A', 25) . str_repeat('G', 10) . str_repeat('C', 50) . 'GGG';
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+ $base_feature = factory('chado.feature')->create([
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+ 'residues' => $base_seq,
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+ ]);
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+ // Create two derived features matching the region of AAA's.
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+ $mRNA_feature = factory('chado.feature')->create([
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+ 'residues' => '',
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+ ]);
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+ chado_insert_record('featureloc', [
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+ 'feature_id' => $mRNA_feature->feature_id,
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+ 'srcfeature_id' => $base_feature->feature_id,
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+ 'fmin' => 3,
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+ 'fmax' => (3 + 25),
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+ 'strand' => 1,
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+ 'rank' => 0,
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+ ]);
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+ chado_insert_record('featureloc', [
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+ 'feature_id' => $mRNA_feature->feature_id,
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+ 'srcfeature_id' => $base_feature->feature_id,
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+ 'fmin' => (3 + 25 + 10),
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+ 'fmax' => (3 + 25 + 10 + 50),
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+ 'strand' => 1,
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+ 'rank' => 1,
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+ ]);
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+
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+ // Make sure we can retrieve the correct sequence for the base feature.
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+ $returned_seq_results = chado_get_feature_sequences([
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+ 'feature_id' => $base_feature->feature_id
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+ ], ['is_html' => FALSE, 'width' => 100]);
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+
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+ $this->assertCount(1, $returned_seq_results, "There should only be the base sequence returned.");
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+
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+ $returned_seq = $returned_seq_results[0]['residues'];
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+ $this->assertEquals($base_seq, $returned_seq, "The returned sequence did not match the base sequence we created the feature with.");
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+
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+ // Now check we can get the derived sequence based using the mRNA.
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+ $returned_seq_results = chado_get_feature_sequences([
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+ 'feature_id' => $mRNA_feature->feature_id
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+ ], ['is_html' => FALSE, 'width' => 100, 'derive_from_parent' => 1]);
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+ $this->assertCount(2, $returned_seq_results, 'We added two locations therefore we should have two returned sequences.');
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+ $this->assertEquals(
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+ str_repeat('A', 25),
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+ $returned_seq_results[0]['residues'],
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+ 'The first region located on the base was not returned correctly.'
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+ );
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+ $this->assertEquals(
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+ str_repeat('C', 50),
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+ $returned_seq_results[1]['residues'],
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+ 'The second region located on the base was not returned correctly.'
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+ );
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+
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+ // Now change our featurelocs to be on the negative strand.
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+ // Note: fmin/fmax do not change because they are always the leftmost not
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+ // necessarily the start or 5' end.
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+ chado_delete_record('featureloc',
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+ ['srcfeature_id' => $base_feature->feature_id]);
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+ chado_insert_record('featureloc', [
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+ 'feature_id' => $mRNA_feature->feature_id,
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+ 'srcfeature_id' => $base_feature->feature_id,
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+ 'fmin' => 3,
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+ 'fmax' => (3 + 25),
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+ 'strand' => -1,
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+ 'rank' => 0,
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+ ]);
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+ chado_insert_record('featureloc', [
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+ 'feature_id' => $mRNA_feature->feature_id,
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+ 'srcfeature_id' => $base_feature->feature_id,
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+ 'fmin' => (3 + 25 + 10),
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+ 'fmax' => (3 + 25 + 10 + 50),
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+ 'strand' => -1,
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+ 'rank' => 1,
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+ ]);
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+
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+ // Now check we can get the derived sequence based using the negative mRNA.
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+ $returned_seq_results = chado_get_feature_sequences([
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+ 'feature_id' => $mRNA_feature->feature_id
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+ ], ['is_html' => FALSE, 'width' => 100, 'derive_from_parent' => 1]);
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+ $this->assertCount(2, $returned_seq_results, 'We added two locations therefore we should have two returned sequences.');
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+ $this->assertEquals(
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+ str_repeat('G', 50),
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+ $returned_seq_results[0]['residues'],
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+ 'The first region located on the base was not returned correctly.'
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+ );
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+ $this->assertEquals(
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+ str_repeat('T', 25),
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+ $returned_seq_results[1]['residues'],
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+ 'The second region located on the base was not returned correctly.'
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+ );
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+ }
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+}
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Lacey Sanderson