def test_adjust_sff_cycles(self):
sff_data = parse_binary_sff(open(self.sff_fp))
sff_gz_data = parse_binary_sff(qiime_open(self.sff_gz_fp))
header, reads = adjust_sff_cycles(sff_data, 2)
header_gz, reads_gz = adjust_sff_cycles(sff_gz_data, 2)
expected_header = {
'header_length': 48,
'version': 1,
'index_length': 0,
'magic_number': 779314790,
'number_of_flows_per_read': 8,
'flowgram_format_code': 1,
'flow_chars': 'TACGTACG',
'index_offset': 0,
'key_sequence': 'TCAG',
'number_of_reads': 1,
'key_length': 4,
}
self.assertEqual(header, expected_header)
self.assertEqual(header_gz, expected_header)
expected_read = {
'name_length':
14,
'Name':
'FA6P1OK01CGMHQ',
'flowgram_values':
[1.04, 0.0, 1.01, 0.0, 0.0, 0.95999999999999996, 0.0, 1.02],
'clip_adapter_left':
0,
'read_header_length':
32,
'Bases':
'TCAG',
'number_of_bases':
4,
'flow_index_per_base': (1, 2, 3, 2),
'clip_qual_left':
4,
'clip_adapter_right':
0,
'clip_qual_right':
4,
'quality_scores': (32, 32, 32, 32),
}
reads = list(reads)
reads_gz = list(reads_gz)
self.assertEqual(len(reads), 1)
self.assertEqual(len(reads_gz), 1)
self.assertEqual(reads[0], expected_read)
self.assertEqual(reads_gz[0], expected_read)
def test_adjust_sff_cycles(self):
sff_data = parse_binary_sff(open(self.sff_fp))
header, reads = adjust_sff_cycles(sff_data, 2)
expected_header = {
'header_length': 48,
'version': 1,
'index_length': 0,
'magic_number': 779314790,
'number_of_flows_per_read': 8,
'flowgram_format_code': 1,
'flow_chars': 'TACGTACG',
'index_offset': 0,
'key_sequence': 'TCAG',
'number_of_reads': 1,
'key_length': 4,
}
self.assertEqual(header, expected_header)
expected_read = {
'name_length': 14,
'Name': 'FA6P1OK01CGMHQ',
'flowgram_values': [1.04, 0.0, 1.01, 0.0, 0.0, 0.95999999999999996, 0.0, 1.02],
'clip_adapter_left': 0,
'read_header_length': 32,
'Bases': 'TCAG',
'number_of_bases': 4,
'flow_index_per_base': (1, 2, 3, 2),
'clip_qual_left': 4,
'clip_adapter_right': 0,
'clip_qual_right': 4,
'quality_scores': (32, 32, 32, 32),
}
reads = list(reads)
self.assertEqual(len(reads), 1)
self.assertEqual(reads[0], expected_read)