Пример #1
0
 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')
Пример #2
0
 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')
Пример #3
0
 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')
Пример #4
0
 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')