def test_process_barcode_in_label(self):
""" Handles label barcodes from one or two fastq labels """
fastq1_data = ["HWI-ST830:ATCG","AAAATTTTCCCCGGGG", "1234567890ABCDEF"]
fastq2_data = ["HWI-ST830:GGGG","TCCCCGGGG", "ABCDEFGHI"]
bcs_out = FakeOutFile()
process_barcode_in_label(fastq1_data, fastq2_data, bcs_out,
bc1_len = 4, bc2_len = 3, rev_comp_bc1 = True, rev_comp_bc2 = True)
actual_bcs = bcs_out.data.split('\n')
expected_bcs = ['@HWI-ST830:ATCG', 'CGATCCC', '+', 'FFFFFFF', '']
self.assertEqual(actual_bcs, expected_bcs)
def test_process_barcode_in_label(self):
""" Handles label barcodes from one or two fastq labels """
fastq1_data = [
"HWI-ST830:ATCG",
"AAAATTTTCCCCGGGG",
np.arange(3, 19, dtype=np.int8)]
fastq2_data = ["HWI-ST830:GGGG", "TCCCCGGGG",
np.arange(3, 12, dtype=np.int8)]
bcs_out = FakeOutFile()
process_barcode_in_label(fastq1_data, fastq2_data, bcs_out,
bc1_len=4, bc2_len=3, rev_comp_bc1=True, rev_comp_bc2=True)
actual_bcs = bcs_out.data.split('\n')
expected_bcs = ['@HWI-ST830:ATCG', 'CGATCCC', '+', "'''''''", '']
self.assertEqual(actual_bcs, expected_bcs)
def test_process_barcode_in_label(self):
""" Handles label barcodes from one or two fastq labels """
fastq1_data = [
"HWI-ST830:ATCG", "AAAATTTTCCCCGGGG", "1234567890ABCDEF"
]
fastq2_data = ["HWI-ST830:GGGG", "TCCCCGGGG", "ABCDEFGHI"]
bcs_out = FakeOutFile()
process_barcode_in_label(fastq1_data,
fastq2_data,
bcs_out,
bc1_len=4,
bc2_len=3,
rev_comp_bc1=True,
rev_comp_bc2=True)
actual_bcs = bcs_out.data.split('\n')
expected_bcs = ['@HWI-ST830:ATCG', 'CGATCCC', '+', 'FFFFFFF', '']
self.assertEqual(actual_bcs, expected_bcs)