def judgeIfDenovo(father_SVs, mother_SVs, son_SVs, refdist, typeignore,
overlap_rate, i):
flag = 0
# son_sv.shape[0]
son_sv_pos = int(son_SVs['POS'][i])
son_sv_chrom = str(son_SVs.index[i])
son_sv_end = svEnd(son_SVs.iloc[[i]])
son_sv_start, son_sv_end = getStartAndEnd(son_sv_pos, son_sv_end)
son_sv_type = svType(son_SVs.iloc[[i]])
# if the chrom is the same
if son_sv_chrom in father_SVs.index:
global bench_father_dict
bench_father_df = bench_father_dict[son_sv_chrom]
flag = judgeNeighbour(bench_father_df, son_sv_start, son_sv_chrom,
son_sv_start, son_sv_end, son_sv_type,
typeignore, refdist, overlap_rate)
if flag == 0 and son_sv_type not in ['INS', 'None']:
flag = judgeNeighbour(bench_father_df, son_sv_end, son_sv_chrom,
son_sv_start, son_sv_end, son_sv_type,
typeignore, refdist, overlap_rate)
if flag == 0:
if son_sv_chrom in mother_SVs.index:
global bench_mother_dict
bench_mother_df = bench_mother_dict[son_sv_chrom]
flag = judgeNeighbour(bench_mother_df, son_sv_start, son_sv_chrom,
son_sv_start, son_sv_end, son_sv_type,
typeignore, refdist, overlap_rate)
if flag == 0 and son_sv_type not in ['INS', 'None']:
flag = judgeNeighbour(bench_mother_df, son_sv_end,
son_sv_chrom, son_sv_start, son_sv_end,
son_sv_type, typeignore, refdist,
overlap_rate)
return flag
def judgeNeighbour(bench_df,home_pos,compared_sv_chrom,compared_sv_start,compared_sv_end,compared_sv_type,typeignore,refdist=200,overlap_rate=0.5):
flag = 0
if (bench_df.shape == ()):
if (home_pos < bench_df['POS'].iloc[0]):
left_neighbour_loc,right_neighbour_loc = None,0
else:
left_neighbour_loc,right_neighbour_loc = 0,None
else:
left_neighbour_loc,right_neighbour_loc = binarySearch(bench_df, home_pos, 0, bench_df.shape[0]-1)
if left_neighbour_loc is not None:
if bench_df['POS'].shape == ():
left_neighbour_end = svEnd(bench_df.to_frame().T.iloc[[left_neighbour_loc]])
left_neighbour_type = svType(bench_df.to_frame().T.iloc[[left_neighbour_loc]])
else:
left_neighbour_end = svEnd(bench_df.iloc[[left_neighbour_loc]])
left_neighbour_type = svType(bench_df.iloc[[left_neighbour_loc]])
left_neighbour_start,left_neighbour_end = getStartAndEnd(bench_df['POS'].iloc[left_neighbour_loc],left_neighbour_end)
if judgeIfOverlap(compared_sv_start, compared_sv_end, left_neighbour_start,left_neighbour_end,compared_sv_type,refdist,overlap_rate):
if typeignore == False:
if left_neighbour_type == compared_sv_type:
flag = 1
else:
flag = 1
if flag == 1:
return flag
if right_neighbour_loc is not None:
if bench_df['POS'].shape == ():
right_neighbour_end = svEnd(bench_df.to_frame().T.iloc[[right_neighbour_loc]])
right_neighbour_type = svType(bench_df.to_frame().T.iloc[[right_neighbour_loc]])
else:
right_neighbour_end = svEnd(bench_df.iloc[[right_neighbour_loc]])
right_neighbour_type = svType(bench_df.iloc[[right_neighbour_loc]])
right_neighbour_start,right_neighbour_end = getStartAndEnd(bench_df['POS'].iloc[right_neighbour_loc],right_neighbour_end)
if judgeIfOverlap(compared_sv_start, compared_sv_end, right_neighbour_start,right_neighbour_end,compared_sv_type,refdist,overlap_rate):
if typeignore == False:
if right_neighbour_type == compared_sv_type:
flag = 1
else:
flag = 1
return flag
def judgeIfSame(data_1,data_2,refdist,typeignore,overlap_rate,i):
flag = 0
data_1_sv_pos = int(data_1['POS'].iloc[i])
data_1_sv_chrom = str(data_1.index[i])
data_1_sv_end = svEnd(data_1.iloc[[i]])
data_1_sv_start,data_1_sv_end = getStartAndEnd(data_1_sv_pos, data_1_sv_end)
data_1_sv_type = svType(data_1.iloc[[i]])
# if the chrom is the same
if data_1_sv_chrom in data_2.index:
global bench_dict
bench_df = bench_dict[data_1_sv_chrom]
flag = judgeNeighbour(bench_df,data_1_sv_start,data_1_sv_chrom,data_1_sv_start,data_1_sv_end,data_1_sv_type,typeignore,refdist,overlap_rate)
if flag == 0 and (data_1_sv_type not in ['INS','None']):
flag = judgeNeighbour(bench_df,data_1_sv_end,data_1_sv_chrom,data_1_sv_start,data_1_sv_end,data_1_sv_type,typeignore,refdist,overlap_rate)
return flag