def test_count_g_a_change():
"""
"""
in_file = "data_c_t_change.fasta"
ref_seq = get_ref(in_file)
cg_posits = get_cg_posits_in_ref(ref_seq)
num_c_t_change_in_reads = count_c_t_change(in_file, cg_posits)
num_g_a_change_in_reads = count_g_a_change(in_file, cg_posits)
assert num_c_t_change_in_reads == 4
assert num_g_a_change_in_reads == 0
in_file = "data_g_a_change.fasta"
ref_seq = get_ref(in_file)
cg_posits = get_cg_posits_in_ref(ref_seq)
num_c_t_change_in_reads = count_c_t_change(in_file, cg_posits)
num_g_a_change_in_reads = count_g_a_change(in_file, cg_posits)
assert num_c_t_change_in_reads == 0
assert num_g_a_change_in_reads == 4
in_file = "data_cg_ta_change.fasta"
ref_seq = get_ref(in_file)
cg_posits = get_cg_posits_in_ref(ref_seq)
num_c_t_change_in_reads = count_c_t_change(in_file, cg_posits)
num_g_a_change_in_reads = count_g_a_change(in_file, cg_posits)
assert num_c_t_change_in_reads == 4
assert num_g_a_change_in_reads == 4
def test_count_total_c_and_g_in_reads():
"""
"""
in_file = "data_c_pos.fasta"
ref_seq = get_ref(in_file)
ref_name = get_ref_name(in_file)
cg_posits = get_cg_posits_in_ref(ref_seq)
num_reads_in_file = get_num_of_reads_in_file(in_file)
num_c_in_ref, num_g_in_ref = count_num_of_c_and_g_in_ref(cg_posits)
total_num_c_in_reads, total_num_g_in_reads = count_total_c_and_g_in_reads(
ref_name, cg_posits, in_file)
assert total_num_c_in_reads == 12
assert total_num_g_in_reads == 0
in_file = "data_g_pos.fasta"
ref_seq = get_ref(in_file)
ref_name = get_ref_name(in_file)
cg_posits = get_cg_posits_in_ref(ref_seq)
num_reads_in_file = get_num_of_reads_in_file(in_file)
num_c_in_ref, num_g_in_ref = count_num_of_c_and_g_in_ref(cg_posits)
total_num_c_in_reads, total_num_g_in_reads = count_total_c_and_g_in_reads(
ref_name, cg_posits, in_file)
assert total_num_c_in_reads == 0
assert total_num_g_in_reads == 12
in_file = "data_cg_pos.fasta"
ref_seq = get_ref(in_file)
ref_name = get_ref_name(in_file)
cg_posits = get_cg_posits_in_ref(ref_seq)
num_reads_in_file = get_num_of_reads_in_file(in_file)
num_c_in_ref, num_g_in_ref = count_num_of_c_and_g_in_ref(cg_posits)
total_num_c_in_reads, total_num_g_in_reads = count_total_c_and_g_in_reads(
ref_name, cg_posits, in_file)
assert total_num_c_in_reads == 12
assert total_num_g_in_reads == 12
def test_get_cg_positions():
"""
"""
ref_seq = get_ref("data_cg_pos.fasta")
d = get_cg_posits_in_ref(ref_seq)
assert d["C_pos"][0] == 0
assert d["C_pos"][1] == 2
assert d["C_pos"][2] == 4
assert d["C_pos"][3] == 6
assert d["G_pos"][0] == 1
assert d["G_pos"][1] == 3
assert d["G_pos"][2] == 5
assert d["G_pos"][3] == 7
def test_calculate_total_percent_c_t_g_a_change_10_15_15():
"""
"""
test_percent_files = [
"data_ct_10_ga_10.fasta", "data_ct_20_ga_10.fasta",
"data_ct_10_ga_20.fasta", "data_ct_1_ga_10.fasta"
]
results = [10, 15, 15, 5.5]
counter = 0
for file in test_percent_files:
in_file = file #
ref_seq = get_ref(in_file)
ref_name = get_ref_name(in_file)
cg_posits = get_cg_posits_in_ref(ref_seq)
num_reads_in_file = get_num_of_reads_in_file(in_file)
num_c_in_ref, num_g_in_ref = count_num_of_c_and_g_in_ref(cg_posits)
total_num_c_in_reads, total_num_g_in_reads = count_total_c_and_g_in_reads(
ref_name, cg_posits, in_file)
num_c_t_change_in_reads = count_c_t_change(in_file, cg_posits)
num_g_a_change_in_reads = count_g_a_change(in_file, cg_posits)
percent_c_t_change = calculate_percent_c_t_change(
num_c_t_change_in_reads, total_num_c_in_reads, num_c_in_ref)
percent_g_a_change = calculate_percent_g_a_change(
num_g_a_change_in_reads, total_num_g_in_reads, num_g_in_ref)
c_t_and_g_a_change_percent = calculate_c_t_and_g_a_change_percent(
total_num_c_in_reads, total_num_g_in_reads,
num_c_t_change_in_reads, num_g_a_change_in_reads)
assert c_t_and_g_a_change_percent == results[counter]
counter += 1
def test_calculate_percent_c_t_change():
"""
"""
in_file = "data_c_t_10_percent_change.fasta" #
ref_seq = get_ref(in_file)
ref_name = get_ref_name(in_file)
cg_posits = get_cg_posits_in_ref(ref_seq)
num_reads_in_file = get_num_of_reads_in_file(in_file)
num_c_in_ref, num_g_in_ref = count_num_of_c_and_g_in_ref(cg_posits)
total_num_c_in_reads, total_num_g_in_reads = count_total_c_and_g_in_reads(
ref_name, cg_posits, in_file)
num_c_t_change_in_reads = count_c_t_change(in_file, cg_posits)
num_g_a_change_in_reads = count_g_a_change(in_file, cg_posits)
percent_c_t_change = calculate_percent_c_t_change(num_c_t_change_in_reads,
total_num_c_in_reads,
num_c_in_ref)
percent_g_a_change = calculate_percent_g_a_change(num_g_a_change_in_reads,
total_num_g_in_reads,
num_g_in_ref)
assert percent_c_t_change == 10
assert percent_g_a_change == "no G in reference"
def test_count_num_of_c_and_g_in_ref():
"""
"""
in_file = "data_c_pos.fasta"
ref_seq = get_ref(in_file)
cg_posits = get_cg_posits_in_ref(ref_seq)
num_c_in_ref, num_g_in_ref = count_num_of_c_and_g_in_ref(cg_posits)
assert num_c_in_ref == 4
assert num_g_in_ref == 0
in_file = "data_g_pos.fasta"
ref_seq = get_ref(in_file)
cg_posits = get_cg_posits_in_ref(ref_seq)
num_c_in_ref, num_g_in_ref = count_num_of_c_and_g_in_ref(cg_posits)
assert num_c_in_ref == 0
assert num_g_in_ref == 4
in_file = "data_cg_pos.fasta"
ref_seq = get_ref(in_file)
cg_posits = get_cg_posits_in_ref(ref_seq)
num_c_in_ref, num_g_in_ref = count_num_of_c_and_g_in_ref(cg_posits)
assert num_c_in_ref == 4
assert num_g_in_ref == 4