def test_check_fasta_seqs_with_barcodes_at_start(self):
""" Properly detects barcodes at the start of the sequences """
# Test against all data that should give some percent failures
sample_barcodes = set(['ACAAG', 'AGATTATAT'])
sample_primers = set(['AGATTTACCA', 'TTATTACCGAT'])
total_seq_count = 4
perc_invalid_chars, perc_barcodes_detected, perc_primers_detected,\
perc_bcs_seq_start =\
check_fasta_seqs(self.sample_fasta_invalid_fp, sample_barcodes,
sample_primers, total_seq_count)
expected_perc_invalid_chars = "%1.3f" % 0.50
expected_perc_barcodes_detected = "%1.3f" % 0.50
expected_perc_primers_detected = "%1.3f" % 0.25
expected_perc_bcs_seq_start = "%1.3f" % 0.25
self.assertEqual(perc_invalid_chars, expected_perc_invalid_chars)
self.assertEqual(perc_barcodes_detected,
expected_perc_barcodes_detected)
self.assertEqual(perc_primers_detected,
expected_perc_primers_detected)
self.assertEqual(perc_bcs_seq_start, expected_perc_bcs_seq_start)
def test_check_fasta_seqs_with_barcodes_at_start(self):
""" Properly detects barcodes at the start of the sequences """
# Test against all data that should give some percent failures
sample_barcodes = set(['ACAAG', 'AGATTATAT'])
sample_primers = set(['AGATTTACCA', 'TTATTACCGAT'])
total_seq_count = 4
perc_invalid_chars, perc_barcodes_detected, perc_primers_detected,\
perc_bcs_seq_start =\
check_fasta_seqs(self.sample_fasta_invalid_fp, sample_barcodes,
sample_primers, total_seq_count)
expected_perc_invalid_chars = "%1.3f" % 0.50
expected_perc_barcodes_detected = "%1.3f" % 0.50
expected_perc_primers_detected = "%1.3f" % 0.25
expected_perc_bcs_seq_start = "%1.3f" % 0.25
self.assertEqual(perc_invalid_chars, expected_perc_invalid_chars)
self.assertEqual(perc_barcodes_detected,
expected_perc_barcodes_detected)
self.assertEqual(perc_primers_detected,
expected_perc_primers_detected)
self.assertEqual(perc_bcs_seq_start, expected_perc_bcs_seq_start)
def test_check_fasta_seqs_all_valid(self):
""" Properly returns invalid chars, barcodes, primers detected """
# Test against all valid data
sample_barcodes = set(['ACCATACC', 'CCAGATTACG'])
sample_primers = set(['ACATTATTTT', 'TTATTACCGAT'])
total_seq_count = 3
perc_invalid_chars, perc_barcodes_detected, perc_primers_detected,\
perc_bcs_seq_start =\
check_fasta_seqs(self.sample_fasta_fp, sample_barcodes,
sample_primers, total_seq_count)
expected_perc_invalid_chars = "%1.3f" % 0
expected_perc_barcodes_detected = "%1.3f" % 0
expected_perc_primers_detected = "%1.3f" % 0
self.assertEqual(perc_invalid_chars, expected_perc_invalid_chars)
self.assertEqual(perc_barcodes_detected,
expected_perc_barcodes_detected)
self.assertEqual(perc_primers_detected, expected_perc_primers_detected)
def test_check_fasta_seqs_all_valid(self):
""" Properly returns invalid chars, barcodes, primers detected """
# Test against all valid data
sample_barcodes = set(['ACCATACC', 'CCAGATTACG'])
sample_primers = set(['ACATTATTTT', 'TTATTACCGAT'])
total_seq_count = 3
perc_invalid_chars, perc_barcodes_detected, perc_primers_detected,\
perc_bcs_seq_start =\
check_fasta_seqs(self.sample_fasta_fp, sample_barcodes,
sample_primers, total_seq_count)
expected_perc_invalid_chars = "%1.3f" % 0
expected_perc_barcodes_detected = "%1.3f" % 0
expected_perc_primers_detected = "%1.3f" % 0
self.assertEqual(perc_invalid_chars, expected_perc_invalid_chars)
self.assertEqual(perc_barcodes_detected,
expected_perc_barcodes_detected)
self.assertEqual(perc_primers_detected,
expected_perc_primers_detected)
