Skip to content

Commit

Permalink
✅ SynonymousPE update
Browse files Browse the repository at this point in the history
  • Loading branch information
@Goosang-Yu
Goosang-Yu committed Jan 25, 2024
1 parent 71048c1 commit cc5932f
Showing 1 changed file with 93 additions and 35 deletions.
128 changes: 93 additions & 35 deletions genet/design/functional.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -144,11 +144,13 @@ def __init__(self,
# step 2: pegRNA의 strand 방향에 따라 synonymous Mut 생성 함수 결정
if self.wt_seq in self.ref_seq:
self.strand = '+'
self.rtt_frame = (frame - self.edit_pos + 1) % 3 # rtt 시작점의 frame, LHA 길이를 이용한 계산
#self.rtt_frame = (frame - self.edit_pos + 1) % 3 # rtt 시작점의 frame, LHA 길이를 이용한 계산
self.rtt_frame = (frame - (self.edit_pos - 1) % 3) % 3 #frame - (self.edit_pos - 1)가 음수가 되었을 때 결과 값이 다름.

elif reverse_complement(self.wt_seq) in self.ref_seq:
self.strand = '-'
self.rtt_frame = (self.edit_pos + frame) % 3 # revcom_rtt_dna의 3' end가 위치하는 지점의 frame. 시작점이 거기이기 때문.
#self.rtt_frame = (self.edit_pos + frame) % 3 # revcom_rtt_dna의 3' end가 위치하는 지점의 frame. 시작점이 거기이기 때문.
self.rtt_frame = (self.edit_pos + frame - 1) % 3

else: raise ValueError('Reference sequence is not matched with pegRNA information!\nPlease chech your ref_seq')

Expand Down Expand Up @@ -228,19 +230,21 @@ def generate(self, rtt_frame:int, strand:str) -> pd.DataFrame:

if strand == '+':
codon_le = rtt_frame
codon_re = (3 - (rtt_frame + self.rtt_len)) % 3
#codon_re = (3 - (rtt_frame + self.rtt_len)) % 3
codon_re = -(rtt_frame + self.rtt_len) % 3

codon_RTT = self.ed_seq[21-codon_le:21+self.rtt_len+codon_re]

dict_codon_Pos = {codon_RTT: [i for i in range(codon_le, len(codon_RTT)-codon_re)]}

else:
codon_re = abs(self.frame - ep) % 3 # added abs()
#codon_re = (self.frame - ep) % 3
codon_re = 2 - rtt_frame
codon_le = -(codon_re + self.rtt_len) % 3

codon_RTT = self.ed_seq[21-codon_re:21+self.rtt_len+codon_le]
codon_RTT = reverse_complement(codon_RTT)

dict_codon_Pos = {codon_RTT: [i for i in range(codon_le, len(codon_RTT) - codon_re)]} #due to revcom sequence

### 결과가 안 맞으면, 여기까지 (codon_RTT)를 다시 한번 살펴보기, 특히 (-) strand! #######
Expand Down Expand Up @@ -281,10 +285,13 @@ def generate(self, rtt_frame:int, strand:str) -> pd.DataFrame:

# priority 결정하는 부분 ##########################################
# 1/ Edit class에 따라서 분류하고, 각 class에 따라 값을 할당
if mut_pos in [5, 6]: edit_class = 'PAM_edit'; priority = 1
if (mut_pos in [5, 6]) and (rtt_dna_mut[4:6] not in ['GG', 'GA', 'AG']):
if mut_pos < ep : edit_class = 'PAM_edit_LHA'; priority = 1
else : edit_class = 'PAM_edit_RHA'; priority = 1

elif mut_pos < ep : edit_class = 'LHA_edit'; priority = 2 + ep - mut_pos
elif mut_pos > ep : edit_class = 'RHA_edit'; priority = 3 + ep + mut_pos

# 2/ GC contents가 변화하면 값 증가
if gc_fraction(codon) != gc_fraction(mut_codon): priority += 1

Expand All @@ -300,11 +307,20 @@ def generate(self, rtt_frame:int, strand:str) -> pd.DataFrame:
aa_mut_codon = mut_codon

if codon_intron_5 > 0:
aa_wt_codon = codon[(codon_intron_5 // 3) * 3:]
aa_wt_codon = codon[((codon_intron_5 // 3) - 1) * 3:]
aa_mut_codon = mut_codon[(codon_intron_5 // 3) * 3:]

# partial codon 부분의 mutation filtering (+ strand)
partial_len = len(codon) - len(aa_wt_codon)
if snv_pos in [partial_len, partial_len-1]: continue

if codon_intron_3 > 0:
aa_wt_codon = codon[:-(codon_intron_3 // 3) * 3]
aa_mut_codon = mut_codon[:-(codon_intron_3 // 3) * 3]
aa_wt_codon = codon[:-((codon_intron_3 // 3) + 1) * 3]
aa_mut_codon = mut_codon[:-((codon_intron_3 // 3) + 1) * 3]

# partial codon 부분의 mutation filtering (- strand)
partial_len = len(aa_wt_codon)
if snv_pos in [partial_len, partial_len+1]: continue

aa_wt = translate(aa_wt_codon)
aa_mut = translate(aa_mut_codon)
Expand Down Expand Up @@ -338,13 +354,14 @@ def generate(self, rtt_frame:int, strand:str) -> pd.DataFrame:
# def End: generate


def stack(self, num:int):
def stack(self, num:int, max_rha_edit:int = 2):
"""만들 수 있는 Synonymous Mut 들의 조합을 추가로 만들어서,
그 중에서도 synonymous mut이 존재하는지 확인하고,
가능한 조합을 return 하는 method.
Args:
num (int): Synonymous Mutation을 쌓을 최대 제한 수
max_rha_edit (int) : 허용할 RHA edit의 최대 제한 수. (지정 안하면 제한 안둠.)
Returns:
_type_: str, list
Expand All @@ -369,43 +386,84 @@ def stack(self, num:int):
selected_mut_codon = best_syn.Codon_Mut

synMut_cnt = 1
stacked_pos = []
synMut_RHA_cnt = 1 if best_syn.Edit_class == 'RHA_edit' else 0
stacked_pos = [best_syn.Mut_pos]

for i in range(1, len(syn_dedup)):

temp_syn = syn_dedup.iloc[i]

if best_syn.Edit_class != 'PAM_edit_RHA':
mut_pos = temp_syn.Codon_MutPos - 1
mut_nt = temp_syn.Codon_Mut[mut_pos]

mut_pos = temp_syn.Codon_MutPos - 1
mut_nt = temp_syn.Codon_Mut[mut_pos]
stacked_mut_codon = list(selected_mut_codon)
stacked_mut_codon[mut_pos] = mut_nt
stacked_mut_codon = ''.join(stacked_mut_codon)

stacked_mut_codon = list(selected_mut_codon)
stacked_mut_codon[mut_pos] = mut_nt
stacked_mut_codon = ''.join(stacked_mut_codon)
# Silent Mut check
aa_mut_codon = temp_syn.Codon_Mut

# Silent Mut check
aa_mut_codon = temp_syn.Codon_Mut
if codon_intron_5 > 0:
aa_mut_codon = stacked_mut_codon[(codon_intron_5 // 3) * 3:]
if codon_intron_3 > 0:
aa_mut_codon = stacked_mut_codon[:-(codon_intron_3 // 3) * 3]

if codon_intron_5 > 0:
aa_mut_codon = stacked_mut_codon[(codon_intron_5 // 3) * 3:]
if codon_intron_3 > 0:
aa_mut_codon = stacked_mut_codon[:-(codon_intron_3 // 3) * 3]
aa_origin = translate(aa_origin_codon)
aa_mut = translate(aa_mut_codon)

aa_origin = translate(aa_origin_codon)
aa_mut = translate(aa_mut_codon)
if aa_origin == aa_mut:

# 만약 조건에 맞는 mutation을 찾으면, origin_codon을 업데이트
selected_mut_codon = stacked_mut_codon
aa_origin_codon = stacked_mut_codon

if aa_origin == aa_mut:

# 만약 조건에 맞는 mutation을 찾으면, origin_codon을 업데이트
selected_mut_codon = stacked_mut_codon
aa_origin_codon = stacked_mut_codon
if codon_intron_5 > 0: aa_origin_codon = stacked_mut_codon[(codon_intron_5 // 3) * 3:]
if codon_intron_3 > 0: aa_origin_codon = stacked_mut_codon[:-(codon_intron_3 // 3) * 3]

synMut_cnt += 1
synMut_RHA_cnt += 1 if temp_syn.Edit_class == 'RHA_edit' else 0
stacked_pos.append(temp_syn.Mut_pos)

if (synMut_cnt == num) or (synMut_RHA_cnt == max_rha_edit): break

elif best_syn.Edit_class == 'PAM_edit_RHA':
if temp_syn.Edit_class in 'PAM_edit_RHA': continue
elif temp_syn.Edit_class not in ['PAM_edit_RHA', 'RHA_edit']:

mut_pos = temp_syn.Codon_MutPos - 1
mut_nt = temp_syn.Codon_Mut[mut_pos]

stacked_mut_codon = list(selected_mut_codon)
stacked_mut_codon[mut_pos] = mut_nt
stacked_mut_codon = ''.join(stacked_mut_codon)

# Silent Mut check
aa_mut_codon = temp_syn.Codon_Mut

if codon_intron_5 > 0:
aa_mut_codon = stacked_mut_codon[(codon_intron_5 // 3) * 3:]
if codon_intron_3 > 0:
aa_mut_codon = stacked_mut_codon[:-(codon_intron_3 // 3) * 3]

aa_origin = translate(aa_origin_codon)
aa_mut = translate(aa_mut_codon)

if aa_origin == aa_mut:

# 만약 조건에 맞는 mutation을 찾으면, origin_codon을 업데이트
selected_mut_codon = stacked_mut_codon
aa_origin_codon = stacked_mut_codon

if codon_intron_5 > 0: aa_origin_codon = stacked_mut_codon[(codon_intron_5 // 3) * 3:]
if codon_intron_3 > 0: aa_origin_codon = stacked_mut_codon[:-(codon_intron_3 // 3) * 3]
if codon_intron_5 > 0: aa_origin_codon = stacked_mut_codon[(codon_intron_5 // 3) * 3:]
if codon_intron_3 > 0: aa_origin_codon = stacked_mut_codon[:-(codon_intron_3 // 3) * 3]

synMut_cnt += 1
stacked_pos.append(temp_syn.Mut_pos)
synMut_cnt += 1
synMut_RHA_cnt += 1 if temp_syn.Edit_class == 'RHA_edit' else 0
stacked_pos.append(temp_syn.Mut_pos)

if synMut_cnt == num: break
if (synMut_cnt == num) or (synMut_RHA_cnt == max_rha_edit): break
else : break

if strand == '+':
rtt_dna_mut = selected_mut_codon[self.codon_le:len(selected_mut_codon)-self.codon_re]
Expand Down

0 comments on commit cc5932f

Please sign in to comment.