def __init__(self):

self.tmp = ""

def get_complementary(self, c):

if c == 'C':

return "G"

elif c == 'A':

return "T"

elif c == 'T':

return "A"

elif c == 'G':

return "C"

elif c == 'N':

return "N"

else:

print("get_complementary ERROR .... char is [" + c + "]")

exit()

def get_complementary_string(self, trgt_str):

rtrn_str = ""

for tmp_char in trgt_str:

rtrn_str += self.get_complementary(tmp_char)

return rtrn_str

def check_p_m_strand(self, str_genome, str_change):

strnd = "+"

if str_change == "":

return ""

elif str_genome[-1:] != str_change[-1:]:

return "-"

return strnd

def get_p_m_str_list(self, full_cover_p_str, full_cover_m_str, max_len, win_len):

tmp_list = []

if len(full_cover_p_str) > max_len + win_len:

tmp_list.append(full_cover_p_str[-max_len - 1: -1])

tmp_list.append(full_cover_p_str[-max_len - 2: -2])

tmp_list.append(full_cover_p_str[-max_len - 3: -3])

tmp_list.append(full_cover_m_str[-max_len - 1: -1])

tmp_list.append(full_cover_m_str[-max_len - 2: -2])

tmp_list.append(full_cover_m_str[-max_len - 3: -3])

return tmp_list, full_cover_p_str[-max_len - win_len - 1:], full_cover_m_str[-max_len - win_len - 1:], full_cover_p_str[1:win_len + 1]

def get_p_m_str_list_for_n3(self, full_cover_p_str, full_cover_m_str, max_len, win_len):

tmp_list = []

if len(full_cover_p_str) > max_len + win_len:

tmp_list.append(full_cover_p_str[-max_len - 1: -1])

tmp_list.append(full_cover_p_str[-max_len - 2: -1])

tmp_list.append(full_cover_p_str[-max_len - 3: -1])

tmp_list.append(full_cover_m_str[-max_len - 1: -1])

tmp_list.append(full_cover_m_str[-max_len - 2: -1])

tmp_list.append(full_cover_m_str[-max_len - 3: -1])

return tmp_list

def add_in_frm_forwrd_seq(self, idx, chr_key, after_strd_dict, result_dict, p_m_str_list):

if idx in after_strd_dict:

# print(p_m_str_list)

for result_dict_key in after_strd_dict[idx]:

# print("result_dict_key : " + result_dict_key)

# print("p_m_str_list' idx : " + str(result_dict[chr_key][result_dict_key][1]))

result_dict[chr_key][result_dict_key].append(

p_m_str_list[result_dict[chr_key][result_dict_key][1]])

return result_dict

def add_out_frm_forwrd_seq(self, idx, chr_key, after_strd_dict, result_dict, p_m_str_list, n_len_str):

if idx in after_strd_dict:

for result_dict_key in after_strd_dict[idx]:

pm_idx = result_dict[chr_key][result_dict_key][1]

if result_dict[chr_key][result_dict_key][0] == "-":

n_len_str = self.get_complementary_string(n_len_str)

result_dict[chr_key][result_dict_key].append(

n_len_str + p_m_str_list[pm_idx])

return result_dict

def get_frwrd_str_bckwrd_idx(self, mut_seq, p_m_str_n3_list, forward):

m_strand_adder = 0

if forward == "-":

m_strand_adder = 3

frwrd_idx = 0

forward = p_m_str_n3_list[frwrd_idx + m_strand_adder]

bckwrd_idx = 0

is_first_low = False

is_second_low = False

if mut_seq[0].islower():

forward = p_m_str_n3_list[frwrd_idx + m_strand_adder]

frwrd_idx += 1

is_first_low = True

if mut_seq[1].islower():

is_second_low = True

if is_first_low:

frwrd_idx += 1

forward = p_m_str_n3_list[frwrd_idx + m_strand_adder]

else:

bckwrd_idx += 1

if mut_seq[2].islower():

if not is_first_low:

bckwrd_idx += 1

elif not is_second_low:

bckwrd_idx += 1

return forward, frwrd_idx, bckwrd_idx

def get_seqs_bfr_aft_trgt_idx(self, data_dict, init):

chr_path = init[0]

max_len = init[1]

win_len = init[2]

result_dict = {}

util = Util.Utils()

for chr_key, val_list in data_dict.items():

result_dict.update({chr_key: {}})

n3_after_strd_dict = {}

n_len_after_strd_dict = {}

n_mx_len_after_strd_dict = {}

with open(chr_path + chr_key + ".fa", "r") as f:

header = f.readline() # header ignored : >chr19

print("header : " + header)

idx = 1

full_cover_p_str = ""

full_cover_m_str = ""

while True:

c = f.read(1)

if c == "":

print(str(idx))

break

if "\n" in c:

continue

elif "\r" in c:

continue

full_cover_p_str = full_cover_p_str + c.upper()

full_cover_m_str = full_cover_m_str + self.get_complementary(c.upper())

p_m_str_n3_list = self.get_p_m_str_list_for_n3(full_cover_p_str, full_cover_m_str, max_len, win_len)

p_m_str_list, full_cover_p_str, full_cover_m_str, n_len_str = self.get_p_m_str_list(full_cover_p_str, full_cover_m_str, max_len, win_len)

# add forward seq into result_dict

result_dict = self.add_in_frm_forwrd_seq(idx, chr_key, n3_after_strd_dict, result_dict, p_m_str_n3_list)

result_dict = self.add_in_frm_forwrd_seq(idx, chr_key, n_mx_len_after_strd_dict, result_dict, p_m_str_list)

result_dict = self.add_out_frm_forwrd_seq(idx, chr_key, n_len_after_strd_dict, result_dict, p_m_str_list, n_len_str)

if idx in val_list:

for tmp_val in val_list[idx]:

Cellline = tmp_val[0]

Genome_Change = tmp_val[1]

tmp_key = Cellline + "^" + Genome_Change # HCC827^g.chr1:915845C>A

Genomesequence = tmp_val[3]

cDNA_change = tmp_val[4]

Codon_Change = tmp_val[6] # Codon_Change : c.(223-225)Ggt>Tgt

Codon_Change_arr = Codon_Change.split(">") # ['c.(223-225)Ggt', 'Tgt']

# check +/- strand

strnd = self.check_p_m_strand(Genome_Change, cDNA_change)

if len(Codon_Change_arr) > 1:

mut_seq = Codon_Change_arr[1] # mut_seq : Tgt

mut_char_arr = Genome_Change.split(">")

if len(mut_seq) == 3 and len(mut_char_arr) > 1:

# TODO del

mut_char = mut_char_arr[1] # A

# idx_mut_char = mut_seq.find(mut_char)

if strnd == "-":

forward, frwrd_idx, bckwrd_idx = self.get_frwrd_str_bckwrd_idx(mut_seq, p_m_str_n3_list, strnd)

result_dict[chr_key].update({tmp_key: [strnd, bckwrd_idx + 3, forward]})

if idx + 3 + max_len - frwrd_idx in n3_after_strd_dict:

n3_after_strd_dict[idx + 3 + max_len - frwrd_idx].append(tmp_key)

else:

n3_after_strd_dict.update({idx + 3 + max_len - frwrd_idx: [tmp_key]})

else:

forward, frwrd_idx, bckwrd_idx = self.get_frwrd_str_bckwrd_idx(mut_seq, p_m_str_n3_list, strnd)

result_dict[chr_key].update({tmp_key: [strnd, bckwrd_idx, forward]})

if idx + 3 + max_len - frwrd_idx in n3_after_strd_dict:

n3_after_strd_dict[idx + 3 + max_len - frwrd_idx].append(tmp_key)

else:

n3_after_strd_dict.update({idx + 3 + max_len - frwrd_idx: [tmp_key]})

else:

# mut_seq's len is not 3

end_seq = int(re.findall(r'\d+', Genome_Change[Genome_Change.index(":"):])[1])

# if Genomesequence has 'In_Frame'

if 'In_Frame' in Genomesequence:

idx_p_m_str_list = 0

if strnd == "-":

idx_p_m_str_list = 3

forward_str = p_m_str_list[idx_p_m_str_list]

adder = 1

if 'ins'.upper() in Genome_Change.upper():

adder = 0

forward_str = full_cover_p_str[-max_len:]

if strnd == '-':

forward_str = full_cover_m_str[-max_len:]

result_dict[chr_key].update({tmp_key: [strnd, idx_p_m_str_list, forward_str]})

if end_seq + max_len + adder in n_mx_len_after_strd_dict:

n_mx_len_after_strd_dict[end_seq + max_len + adder].append(tmp_key)

else:

n_mx_len_after_strd_dict.update({end_seq + max_len + adder: [tmp_key]})

else:

idx_p_m_str_list = 0

if strnd == "-":

idx_p_m_str_list = 3

forward_str = n_len_str + p_m_str_list[idx_p_m_str_list]

adder = 1

if 'ins'.upper() in Genome_Change.upper():

adder = 0

forward_str = full_cover_p_str[-max_len + win_len:]

if strnd == '-':

forward_str = full_cover_m_str[-max_len + win_len:]

result_dict[chr_key].update(

{tmp_key: [strnd, idx_p_m_str_list, forward_str]})

if end_seq + max_len + win_len + adder in n_len_after_strd_dict:

n_len_after_strd_dict[end_seq + max_len + win_len + adder].append(tmp_key)

else:

n_len_after_strd_dict.update({end_seq + max_len + win_len + adder: [tmp_key]})

elif "_" in Genome_Change:

# deli with '_'

end_seq = int(re.findall(r'\d+', Genome_Change[Genome_Change.index(":"):])[1])

# if Genomesequence has 'In_Frame'

if 'In_Frame' in Genomesequence:

idx_p_m_str_list = 0

if strnd == "-":

idx_p_m_str_list = 3

forward_str = p_m_str_list[idx_p_m_str_list]

adder = 1

if 'ins'.upper() in Genome_Change.upper():

adder = 0

forward_str = full_cover_p_str[-max_len:]

if strnd == '-':

forward_str = full_cover_m_str[-max_len:]

result_dict[chr_key].update(

{tmp_key: [strnd, idx_p_m_str_list, forward_str]})

if end_seq + max_len + adder in n_mx_len_after_strd_dict:

n_mx_len_after_strd_dict[end_seq + max_len + adder].append(tmp_key)

else:

n_mx_len_after_strd_dict.update({end_seq + max_len + adder: [tmp_key]})

else:

idx_p_m_str_list = 0

if strnd == "-":

idx_p_m_str_list = 3

forward_str = n_len_str + p_m_str_list[idx_p_m_str_list]

adder = 1

if 'ins'.upper() in Genome_Change.upper():

adder = 0

forward_str = full_cover_p_str[- max_len - win_len:]

if strnd == "-":

forward_str = full_cover_m_str[- max_len - win_len:]

result_dict[chr_key].update(

{tmp_key: [strnd, idx_p_m_str_list, forward_str]})

if end_seq + max_len + win_len + adder in n_len_after_strd_dict:

n_len_after_strd_dict[end_seq + max_len + win_len + adder].append(tmp_key)

else:

n_len_after_strd_dict.update({end_seq + max_len + win_len + adder: [tmp_key]})

else:

# out of logic

end_seq = idx # + 1

idx_p_m_str_list = 0

if strnd == "-":

idx_p_m_str_list = 3

forward_str = n_len_str + p_m_str_list[idx_p_m_str_list]

adder = 1

if 'ins'.upper() in Genome_Change.upper():

adder = 0

forward_str = full_cover_p_str[- max_len - win_len:]

if strnd == "-":

forward_str = full_cover_m_str[- max_len - win_len:]

result_dict[chr_key].update(

{tmp_key: [strnd, idx_p_m_str_list, forward_str]})

if end_seq + max_len + win_len + adder in n_len_after_strd_dict:

n_len_after_strd_dict[end_seq + max_len + win_len + adder].append(tmp_key)

else:

n_len_after_strd_dict.update({end_seq + max_len + win_len + adder: [tmp_key]})

idx = idx + 1