def test_get_duplex_posits_C():
"""
FIRST and second position test
"""
ref_seq = "TCTTTCTTCT"
d = get_duplex_posits_with_ref_nuc_at_first_pos(ref_seq, "C")
assert d["start_pos"][0] == 1
assert d["stop_pos"][0] == 2
assert d["ref_duplex"][0] == "CT"
assert d["start_pos"][1] == 5
assert d["stop_pos"][1] == 6
assert d["ref_duplex"][1] == "CT"
assert d["start_pos"][2] == 8
assert d["stop_pos"][2] == 9
assert d["ref_duplex"][2] == "CT"
d = get_duplex_posits_with_ref_nuc_at_second_pos(ref_seq, "C")
assert d["start_pos"][0] == 0
assert d["stop_pos"][0] == 1
assert d["ref_duplex"][0] == "TC"
assert d["start_pos"][1] == 4
assert d["stop_pos"][1] == 5
assert d["ref_duplex"][1] == "TC"
assert d["start_pos"][2] == 7
assert d["stop_pos"][2] == 8
assert d["ref_duplex"][2] == "TC"
def test_get_duplex_posits_at_second_pos_at_the_start_and_at_the_end():
"""
"""
ref_seq = "TCTTTTTTTC"
d = get_duplex_posits_with_ref_nuc_at_second_pos(ref_seq, "C")
assert d["start_pos"][0] == 0
assert d["stop_pos"][0] == 1
assert d["ref_duplex"][0] == "TC"
assert d["start_pos"][1] == 8
assert d["stop_pos"][1] == 9
assert d["ref_duplex"][1] == "TC"
# nucs to find is at the start without duplexes: like false positives
ref_seq = "CTTTTTTTT"
d = get_duplex_posits_with_ref_nuc_at_second_pos(ref_seq, "C")
assert d["start_pos"] == []
assert d["stop_pos"] == []
assert d["ref_duplex"] == []
def test_get_duplex_posits_at_second_pos_with_gaps():
"""
"""
ref_seq = "T-CTTT---CTTT--C"
d = get_duplex_posits_with_ref_nuc_at_second_pos(ref_seq, "C")
assert d["start_pos"][0] == 0
assert d["stop_pos"][0] == 2
assert d["ref_duplex"][0] == "TC"
assert d["start_pos"][1] == 5
assert d["stop_pos"][1] == 9
assert d["ref_duplex"][1] == "TC"
assert d["start_pos"][2] == 12
assert d["stop_pos"][2] == 15
assert d["ref_duplex"][2] == "TC"
def test_create_pivot_df():
print(os.listdir("./input_data"))
input_files = get_input_files_names("./input_data")
#print("input_files: ", input_files)
ref_seq = get_ref("data_C_1.fasta")
input_file = "data_C_1.fasta"
#print(ref_seq)
nuc = "C"
snp_type = ["A", "T", "G"]
duplex_posits_at_first = get_duplex_posits_with_ref_nuc_at_first_pos(
ref_seq, nuc)
duplex_posits_at_second = get_duplex_posits_with_ref_nuc_at_second_pos(
ref_seq, nuc)
df_first_pos = create_df(duplex_posits_at_first, snp_type)
df_second_pos = create_df(duplex_posits_at_second, snp_type)
df_snp_first_pos, coverage_first_pos, record_id_first_pos = count_snp_with_ref_nuc_at_first_pos(
input_file, df_first_pos, nuc)
df_snp_second_pos, coverage_second_pos, record_id_second_pos = count_snp_with_ref_nuc_at_second_pos(
input_file, df_second_pos, nuc)
pivot_df_C_first_pos = create_pivot_df(df_snp_first_pos)
pivot_df_C_second_pos = create_pivot_df(df_snp_second_pos)
print(pivot_df_C_first_pos)
print(pivot_df_C_second_pos)
assert pivot_df_C_first_pos.loc["CT", "A"] == 4
assert pivot_df_C_first_pos.loc["CT", "G"] == 2
assert pivot_df_C_first_pos.loc["CT", "T"] == 3
assert pivot_df_C_second_pos.loc["TC", "A"] == 4
assert pivot_df_C_second_pos.loc["TC", "G"] == 2
assert pivot_df_C_second_pos.loc["TC", "T"] == 3
def test_snp_df_nuc_A():
#print(os.listdir("./input_data"))
input_files = get_input_files_names("./input_data")
#print("input_files: ", input_files)
ref_seq = get_ref("data_A.fasta")
input_file = "data_A.fasta"
#print(ref_seq)
nuc = "A"
snp_type = ["T", "G", "C"]
duplex_posits_at_first = get_duplex_posits_with_ref_nuc_at_first_pos(
ref_seq, nuc)
duplex_posits_at_second = get_duplex_posits_with_ref_nuc_at_second_pos(
ref_seq, nuc)
df_first_pos = create_df(duplex_posits_at_first, snp_type)
df_second_pos = create_df(duplex_posits_at_second, snp_type)
df_snp_first_pos, coverage_first_pos, record_id_first_pos = count_snp_with_ref_nuc_at_first_pos(
input_file, df_first_pos, nuc)
df_snp_second_pos, coverage_second_pos, record_id_second_pos = count_snp_with_ref_nuc_at_second_pos(
input_file, df_second_pos, nuc)
# uncomment to have a look at dataframes
#print(df_snp_first_pos)
#print(df_snp_second_pos)
#########################################################
# at first position
assert df_snp_first_pos.loc[0, "start_pos"] == 2
assert df_snp_first_pos.loc[0, "stop_pos"] == 3
assert df_snp_first_pos.loc[0, "ref_duplex"] == "AT"
assert df_snp_first_pos.loc[0, "G"] == 0
assert df_snp_first_pos.loc[0, "C"] == 0
assert df_snp_first_pos.loc[0, "T"] == 1
assert df_snp_first_pos.loc[1, "start_pos"] == 5
assert df_snp_first_pos.loc[1, "stop_pos"] == 6
assert df_snp_first_pos.loc[1, "ref_duplex"] == "AT"
assert df_snp_first_pos.loc[1, "G"] == 0
assert df_snp_first_pos.loc[1, "C"] == 2
assert df_snp_first_pos.loc[1, "T"] == 0
assert df_snp_first_pos.loc[2, "start_pos"] == 8
assert df_snp_first_pos.loc[2, "stop_pos"] == 9
assert df_snp_first_pos.loc[2, "ref_duplex"] == "AT"
assert df_snp_first_pos.loc[2, "G"] == 3
assert df_snp_first_pos.loc[2, "C"] == 0
assert df_snp_first_pos.loc[2, "T"] == 0
assert df_snp_first_pos.loc[3, "start_pos"] == 10
assert df_snp_first_pos.loc[3, "stop_pos"] == 11
assert df_snp_first_pos.loc[3, "ref_duplex"] == "AT"
assert df_snp_first_pos.loc[3, "G"] == 0
assert df_snp_first_pos.loc[3, "C"] == 0
assert df_snp_first_pos.loc[3, "T"] == 0
######################################################
# at second position
assert df_snp_second_pos.loc[0, "start_pos"] == 1
assert df_snp_second_pos.loc[0, "stop_pos"] == 2
assert df_snp_second_pos.loc[0, "ref_duplex"] == "TA"
assert df_snp_second_pos.loc[0, "G"] == 0
assert df_snp_second_pos.loc[0, "C"] == 0
assert df_snp_second_pos.loc[0, "T"] == 1
assert df_snp_second_pos.loc[1, "start_pos"] == 4
assert df_snp_second_pos.loc[1, "stop_pos"] == 5
assert df_snp_second_pos.loc[1, "ref_duplex"] == "TA"
assert df_snp_second_pos.loc[1, "G"] == 0
assert df_snp_second_pos.loc[1, "C"] == 2
assert df_snp_second_pos.loc[1, "T"] == 0
assert df_snp_second_pos.loc[2, "start_pos"] == 7
assert df_snp_second_pos.loc[2, "stop_pos"] == 8
assert df_snp_second_pos.loc[2, "ref_duplex"] == "TA"
assert df_snp_second_pos.loc[2, "G"] == 3
assert df_snp_second_pos.loc[2, "C"] == 0
assert df_snp_second_pos.loc[2, "T"] == 0
assert df_snp_second_pos.loc[3, "start_pos"] == 9
assert df_snp_second_pos.loc[3, "stop_pos"] == 10
assert df_snp_second_pos.loc[3, "ref_duplex"] == "TA"
assert df_snp_second_pos.loc[3, "G"] == 0
assert df_snp_second_pos.loc[3, "C"] == 0
assert df_snp_second_pos.loc[3, "T"] == 0
