# plt.plot(trace[c], color='green')
# plt.plot(trace[d], color='yellow')
# plt.plot(trace[e], color='black')
# plt.show()
# converted_bp = convert_to_bp(1370, record.annotations['abif_raw'][e], dye)
# print(converted_bp)
# converted_index = convert_to_index(240.27, record.annotations['abif_raw'][e])
# print(converted_index)
alelle = 288
height = []
index_of_peaks = []
data1 = list(record.annotations['abif_raw'][a])
for c in range(find_lower(record.annotations['abif_raw'][e], dye),
find_upper(record.annotations['abif_raw'][e], dye)):
converted_bp = convert_to_bp(c, record.annotations['abif_raw'][e], dye)
in_range = converted_bp >= alelle - 1 and converted_bp <= alelle + 1
if in_range:
index_of_peaks.append(c)
height.append(data1[c])
elif converted_bp > alelle:
break
print(height)
print(index_of_peaks)
print(max(height))
print(convert_to_bp(1175, record.annotations['abif_raw'][e], dye))
# Make negative values in array zero
# for x in range(find_lower(record.annotations['abif_raw'][e], dye), find_upper(record.annotations['abif_raw'][e], dye)):
# # print("#",end='')
# converted_bp = convert_to_bp(x, record.annotations['abif_raw'][e], dye)
# in_range = converted_bp >= alelle2 - 1.5 and converted_bp <= alelle2 + 1.5
# if in_range:
# index_of_peaks.append(x)
# height.append(data1[x])
# elif converted_bp > alelle2:
# break
# new_values2.append(max(height))
# new_values4.append(index_of_peaks[height.index(max(height))])
index_min = find_lower(record.annotations['abif_raw'][e], dye)
index_max = find_upper(record.annotations['abif_raw'][e], dye)
data = record.annotations['abif_raw'][a]
height = []
index_of_peaks = []
for x in range(index_min, index_max):
# print("#",end='')
converted_bp = convert_to_bp(x, record.annotations['abif_raw'][e], dye)
in_range = converted_bp >= alelle1 - 1.5 and converted_bp <= alelle1 + 1.5
if in_range:
index_of_peaks.append(x)
height.append(data[x])
elif converted_bp > alelle1+1.5:
break
alelle1_index = index_of_peaks[height.index(max(height))]
# converted_index = convert_to_index(240.27, record.annotations['abif_raw'][e], dye)
# print(converted_index)
alelle = 250
index = 3472
# alelle = 272
# index = 3696
height = []
index_of_peaks = []
data1 = list(record.annotations['abif_raw'][a])
converted_index = convert_to_bp(index, record.annotations['abif_raw'][e], dye)
print(converted_index)
print(find_lower(record.annotations['abif_raw'][e], dye))
print(find_upper(record.annotations['abif_raw'][e], dye))
# for c in range(find_lower(record.annotations['abif_raw'][e], dye), find_upper(record.annotations['abif_raw'][e], dye)):
# converted_bp = convert_to_bp(c, record.annotations['abif_raw'][e], dye)
# in_range = converted_bp >= alelle - 1.5 and converted_bp <= alelle + 1.5
# if in_range:
# index_of_peaks.append(c)
# height.append(data1[c])
# elif converted_bp > alelle + 1.5:
# break
# print(height)
# print(index_of_peaks)
# print(f'the peak of the alelle with length {alelle} bp is: {max(height)}')
dye = [
500, 490, 450, 400, 350, 340, 300, 250, 200, 160, 150, 139, 100, 75, 50, 35
]
file = input('File to analyze: ')
record = SeqIO.read(file + '.fsa', 'abi')
data = record.annotations['abif_raw'][a]
label = []
area_of_peaks = []
no_of_peaks = []
length = []
peaks = []
height = []
index_35 = find_lower(record.annotations['abif_raw']['DATA105'], dye)
index_500 = find_upper(record.annotations['abif_raw']['DATA105'], dye)
detected_peaks = fp.findpeaks(data, spacing=25, limit=25)
for i in range(len(detected_peaks) - 1):
lower_end_of_window = detected_peaks[i] - 80
upper_end_of_window = detected_peaks[i] + 20
if lower_end_of_window < index_35 or upper_end_of_window > index_500:
continue
peaks.append(detected_peaks[i])
area_of_peaks.append(
np.trapz(data[lower_end_of_window:upper_end_of_window]))
no_of_peaks.append(
len(