def test_get_consensus_seqs_lookup(self):
fn_call_fwd_rev_read = read_fwd_rev_read(self.fwd_read_fh,
self.rev_read_fh,
self.bc_to_sid,
self.barcode_len,
self.barcode_correction_fn,
self.bc_to_fwd_primers,
self.bc_to_rev_primers,
self.max_barcode_errors,
self.fwd_length,
self.rev_length)
random_bc_lookup = fn_call_fwd_rev_read[0]
random_bc_reads = fn_call_fwd_rev_read[1]
random_bcs = fn_call_fwd_rev_read[2]
min_difference_bcs = self.min_difference_in_bcs
min_diff_clusters = self.min_difference_in_clusters
min_reads_rand_bc = self.min_reads_per_random_bc
max_cluster_ratio = self.max_cluster_ratio
output_dir = self.temp_dir
fn_call_get_consensus = get_consensus_seqs_lookup(random_bc_lookup,
random_bc_reads,
random_bcs,
min_difference_bcs,
min_reads_rand_bc,
output_dir,
min_diff_clusters,
max_cluster_ratio,
min_consensus)
actual = fn_call_get_consensus['Sample1']['AGCTACGAGCTATTGC']
expected = 'AAAAAAAAAAAAAAAAAAA^AAAAAAAAAAAAAAAAAA'
self.assertEqual(actual, expected)
def test_get_consensus_seqs_lookup(self):
fn_call_fwd_rev_read = read_fwd_rev_read(self.fwd_read_fh,
self.rev_read_fh,
self.bc_to_sid,
self.barcode_len,
self.barcode_correction_fn,
self.bc_to_fwd_primers,
self.bc_to_rev_primers,
self.max_barcode_errors,
self.fwd_length,
self.rev_length)
random_bc_lookup = fn_call_fwd_rev_read[0]
random_bc_reads = fn_call_fwd_rev_read[1]
random_bcs = fn_call_fwd_rev_read[2]
min_difference_bcs = self.min_difference_in_bcs
min_diff_clusters = self.min_difference_in_clusters
min_reads_rand_bc = self.min_reads_per_random_bc
max_cluster_ratio = self.max_cluster_ratio
output_dir = self.temp_dir
fn_call_get_consensus = get_consensus_seqs_lookup(random_bc_lookup,
random_bc_reads,
random_bcs,
min_difference_bcs,
min_reads_rand_bc,
output_dir,
min_diff_clusters,
max_cluster_ratio,
min_consensus)
actual = fn_call_get_consensus['Sample1']['AGCTACGAGCTATTGC']
expected = 'AAAAAAAAAAAAAAAAAAA^AAAAAAAAAAAAAAAAAA'
self.assertEqual(actual, expected)
def test_read_fwd_rev_read(self):
expected_seqs_kept = 4
function_call = read_fwd_rev_read(
self.fwd_read_fh, self.rev_read_fh, self.bc_to_sid,
self.barcode_len, self.barcode_correction_fn,
self.bc_to_fwd_primers, self.bc_to_rev_primers,
self.max_barcode_errors, self.fwd_length, self.rev_length)
actual_seqs_kept = function_call[-1]
self.assertEqual(actual_seqs_kept, expected_seqs_kept)
def test_read_fwd_rev_read(self):
expected_seqs_kept = 4
function_call = read_fwd_rev_read(self.fwd_read_fh,
self.rev_read_fh,
self.bc_to_sid,
self.barcode_len,
self.barcode_correction_fn,
self.bc_to_fwd_primers,
self.bc_to_rev_primers,
self.max_barcode_errors,
self.fwd_length,
self.rev_length)
actual_seqs_kept = function_call[-1]
self.assertEqual(actual_seqs_kept, expected_seqs_kept)
