def test_process_barcode_single_end_data(self):
""" Handles fastq lines, parses barcodes """
fastq_data = [
"HWI-ST830", "AAAATTTTCCCCGGGG",
np.arange(3, 19, dtype=np.int8)
]
reads_out = FakeOutFile()
bcs_out = FakeOutFile()
process_barcode_single_end_data(fastq_data,
bcs_out,
reads_out,
bc1_len=5,
rev_comp_bc1=True)
actual_bcs = bcs_out.data.split('\n')
expected_bcs = ["@HWI-ST830", "ATTTT", "+", "('&%$", ""]
self.assertEqual(actual_bcs, expected_bcs)
actual_reads = reads_out.data.split('\n')
expected_reads = ['@HWI-ST830', 'TTTCCCCGGGG', '+', ')*+,-./0123', '']
self.assertEqual(actual_reads, expected_reads)
def test_process_barcode_single_end_data(self):
""" Handles fastq lines, parses barcodes """
fastq_data = ["HWI-ST830", "AAAATTTTCCCCGGGG", "1234567890ABCDEF"]
reads_out = FakeOutFile()
bcs_out = FakeOutFile()
process_barcode_single_end_data(fastq_data, bcs_out, reads_out,
bc1_len=5, rev_comp_bc1=True)
actual_bcs = bcs_out.data.split('\n')
expected_bcs = ["@HWI-ST830", "ATTTT", "+", "54321", ""]
self.assertEqual(actual_bcs, expected_bcs)
actual_reads = reads_out.data.split('\n')
expected_reads = ['@HWI-ST830', 'TTTCCCCGGGG', '+', '67890ABCDEF', '']
self.assertEqual(actual_reads, expected_reads)
def test_process_barcode_single_end_data(self):
""" Handles fastq lines, parses barcodes """
fastq_data = ["HWI-ST830", "AAAATTTTCCCCGGGG",
np.arange(3, 19, dtype=np.int8)]
reads_out = FakeOutFile()
bcs_out = FakeOutFile()
process_barcode_single_end_data(fastq_data, bcs_out, reads_out,
bc1_len=5, rev_comp_bc1=True)
actual_bcs = bcs_out.data.split('\n')
expected_bcs = ["@HWI-ST830", "ATTTT", "+", "('&%$", ""]
self.assertEqual(actual_bcs, expected_bcs)
actual_reads = reads_out.data.split('\n')
expected_reads = ['@HWI-ST830', 'TTTCCCCGGGG', '+', ')*+,-./0123', '']
self.assertEqual(actual_reads, expected_reads)
def test_process_barcode_single_end_data(self):
""" Handles fastq lines, parses barcodes """
fastq_data = ["HWI-ST830", "AAAATTTTCCCCGGGG", "1234567890ABCDEF"]
reads_out = FakeOutFile()
bcs_out = FakeOutFile()
process_barcode_single_end_data(fastq_data,
bcs_out,
reads_out,
bc1_len=5,
rev_comp_bc1=True)
actual_bcs = bcs_out.data.split('\n')
expected_bcs = ["@HWI-ST830", "ATTTT", "+", "54321", ""]
self.assertEqual(actual_bcs, expected_bcs)
actual_reads = reads_out.data.split('\n')
expected_reads = ['@HWI-ST830', 'TTTCCCCGGGG', '+', '67890ABCDEF', '']
self.assertEqual(actual_reads, expected_reads)
