def test_visit_features_node_feature_ignored(self, embl_feature_mock):
converter = EMBLConverter(None)
feature_node = self.mock_feature_node(1, 'ignored_type', 1, 100, '', {'attr_k1': 'attr_v1'})
embl_feature_mock.return_value.format.return_value = None
converter.visit_feature_node(feature_node)
self.assertEqual(converter.contigs, {})
def test_visit_features_node_feature_included(self, embl_feature_mock):
converter = EMBLConverter(None)
feature_node = self.mock_feature_node(1, 'type_1', 1, 100, '', {'attr_k1': 'attr_v1'})
embl_feature_mock.return_value.format.return_value = 'Feature_string'
converter.visit_feature_node(feature_node)
self.assertEqual(converter.contigs.keys(), [1])
self.assertIsInstance(converter.contigs[1], EMBLContig)
def test_visit_features_node_feature_ignored(self, embl_feature_mock):
converter = EMBLConverter(None)
feature_node = self.mock_feature_node(1, 'ignored_type', 1, 100, '',
{'attr_k1': 'attr_v1'})
embl_feature_mock.return_value.format.return_value = None
converter.visit_feature_node(feature_node)
self.assertEqual(converter.contigs, {})
def test_visit_features_node_feature_included(self, embl_feature_mock):
converter = EMBLConverter(None)
feature_node = self.mock_feature_node(1, 'type_1', 1, 100, '',
{'attr_k1': 'attr_v1'})
embl_feature_mock.return_value.format.return_value = 'Feature_string'
converter.visit_feature_node(feature_node)
self.assertEqual(converter.contigs.keys(), [1])
self.assertIsInstance(converter.contigs[1], EMBLContig)
def test_visit_features_node_two_different_features(self, embl_feature_mock):
converter = EMBLConverter(None)
feature_node = self.mock_feature_node(1, 'type_1', 1, 100, '', {'attr_k1': 'attr_v1'})
embl_feature_mock.return_value.format.return_value = 'Feature_string'
converter.visit_feature_node(feature_node)
feature_node = self.mock_feature_node(2, 'type_2', 101, 200, '', {'attr_k1': 'attr_v1'})
embl_feature_mock.return_value.format.return_value = "Another_feature_string"
converter.visit_feature_node(feature_node)
self.assertEqual(converter.contigs.keys(), [1, 2])
self.assertIsInstance(converter.contigs[1], EMBLContig)
self.assertIsInstance(converter.contigs[2], EMBLContig)
def __init__(self,
gff3_file,
organism,
taxonid,
project,
description,
authors,
title,
publication,
genome_type,
classification,
output_filename,
locus_tag=None,
translation_table=11,
chromosome_list=None):
self.locus_tag = locus_tag
self.translation_table = translation_table
self.conv = EMBLConverter(locus_tag, translation_table)
self.gff3_file = gff3_file
self.organism = organism
self.taxonid = taxonid
self.project = project
self.authors = authors
self.title = title
self.publication = publication
self.genome_type = genome_type
self.classification = classification
self.output_filename = output_filename
self.chromosome_list = chromosome_list
self.fixed_gff_file = str(self.gff3_file) + "_fixed.gff"
def test_visit_features_node_two_different_features(
self, embl_feature_mock):
converter = EMBLConverter(None)
feature_node = self.mock_feature_node(1, 'type_1', 1, 100, '',
{'attr_k1': 'attr_v1'})
embl_feature_mock.return_value.format.return_value = 'Feature_string'
converter.visit_feature_node(feature_node)
feature_node = self.mock_feature_node(2, 'type_2', 101, 200, '',
{'attr_k1': 'attr_v1'})
embl_feature_mock.return_value.format.return_value = "Another_feature_string"
converter.visit_feature_node(feature_node)
self.assertEqual(converter.contigs.keys(), [1, 2])
self.assertIsInstance(converter.contigs[1], EMBLContig)
self.assertIsInstance(converter.contigs[2], EMBLContig)