def test_single_feature_translation_table(self):
'''test that the script will convert from GFF3 to EMBL and change the locus tag'''
emblwriter = EMBLWriter(os.path.join(data_dir,'single_feature.gff'),
'Organism',
1234,
'My project',
'My description',
'John',
'Some title',
'Some journal',
'circular',
'PROK',
'single_feature.embl', None, 1, None )
emblwriter.parse_and_run()
self.compare_files('single_feature.embl', os.path.join(data_dir, 'expected_single_feature_translation_table.embl'))
os.remove('single_feature.embl')
def test_large_conversion(self):
'''test a large gff3 file converts to EMBL'''
emblwriter = EMBLWriter(os.path.join(data_dir,'large_annotation.gff'),
'Organism',
1234,
'My project',
'My description',
'John',
'Some title',
'Some journal',
'circular',
'PROK',
'large_annotation.embl', None, 11, None )
emblwriter.parse_and_run()
self.compare_files('large_annotation.embl', os.path.join(data_dir, 'expected_large_annotation.embl'))
os.remove('large_annotation.embl')
def test_remove_duplicate_tags(self):
'''test remove duplicate tags '''
emblwriter = EMBLWriter(os.path.join(data_dir,'duplicate_coords.gff'),
'Organism',
1234,
'ABC',
'My description',
'John',
'Some title',
'Some journal',
'circular',
'PROK',
'duplicate_coords.embl', None, 11, None )
emblwriter.parse_and_run()
self.compare_files('duplicate_coords.embl', os.path.join(data_dir, 'expected_duplicate_coords.embl'))
os.remove('duplicate_coords.embl')
def test_chromosome_list_conversion(self):
'''test chromosome list creation'''
emblwriter = EMBLWriter(os.path.join(data_dir,'chromosome_list.gff'),
'Organism',
1234,
'ABC',
'My description',
'John',
'Some title',
'Some journal',
'circular',
'PROK',
'chromosome_list.embl', None, 11, 'chromosome_list.txt' )
emblwriter.parse_and_run()
self.compare_files('chromosome_list.txt', os.path.join(data_dir, 'expected_chromosome_list.txt'))
os.remove('chromosome_list.embl')
os.remove('chromosome_list.txt')
