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)