def test_parse_fastq_no_newlines(self):
parsed_record = self.parser.parse_fastq(
"@SRR959238.1 HWI-ST897:104:C015GACXX:6:1101:1337:2122/1",
"AATTGAGTCG", "+", "===+=AA=AD")
self.assertEqual(
parsed_record,
ParsedFastqRecord(
"AATTGAGTCG",
np.array([28, 28, 28, 10, 28, 32, 32, 28, 32, 35])))
def test_parse_fastq_newlines(self):
# TODO: do we want to do validations on the FastQ?
parsed_record = self.parser.parse_fastq(
"@SRR959238.1 HWI-ST897:104:C015GACXX:6:1101:1337:2122/1\n",
"AATTGAGTCG\n", "+\n", "===+=AA=AD\n")
self.assertEqual(
parsed_record,
ParsedFastqRecord(
"AATTGAGTCG",
np.array([28, 28, 28, 10, 28, 32, 32, 28, 32, 35])))
def test_reverse_sequence_palindrome(self):
sequence = ParsedFastqRecord("ATGCAT", [10, 11, 12, 13, 14, 15])
reverse_sequence = self.reverser.reverse_sequence(sequence)
expected_reverse_sequence = ParsedFastqRecord("ATGCAT",
[15, 14, 13, 12, 11, 10])
self.assertEqual(reverse_sequence, expected_reverse_sequence)
def test_reverse_sequence_empty(self):
sequence = ParsedFastqRecord("", [])
reverse_sequence = self.reverser.reverse_sequence(sequence)
expected_reverse_sequence = ParsedFastqRecord("", [])
self.assertEqual(reverse_sequence, expected_reverse_sequence)
def parse_fastq(self, id, sequence, optional_id, quality_string):
filtered_sequence = super()._strip_terminal_newline(sequence)
filtered_quality = super()._strip_terminal_newline(quality_string)
phred_quality = self.base_quality_convert.convert_quality_to_phred(
filtered_quality)
return ParsedFastqRecord(filtered_sequence, phred_quality)
def reverse_sequence(self, parsed_fastq):
reverse_complement = self.reverse_complement(parsed_fastq.sequence)
reverse_quality = parsed_fastq.phred_quality[::-1]
return ParsedFastqRecord(reverse_complement, reverse_quality)