# 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
# data_105 = list(record.annotations['abif_raw'][e])
# i = len(record.annotations['abif_raw'][e])
# 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], 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)
filename = filename.replace('_CON', '')
elif filename[4] == 'T':
filename = filename.replace('_TIG', '')
abif_file = 'A_' + filename + '.fsa'
record = SeqIO.read(abif_file, 'abi')
print('\nopening fsa file ({}/{}): {}'.format(i, len(file), abif_file))
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))]
if alelle1 != alelle2:
height = []
index_of_peaks = []
for x in range(index_min, index_max):
# print("#",end='')
converted_bp = convert_to_bp(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))]
# <<<<<<< HEAD
# ind = index_of_peaks[height.index(max(height))]
# new_values1.append(max(height))
# new_values3.append(ind)
# new_v_area1.append(np.trapz(data1[ind-80:ind+40]))
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(
fp.findpeaks(data[lower_end_of_window:upper_end_of_window],
spacing=5,
limit=15)))
length.append(
round(
convert_to_bp(detected_peaks[i],
record.annotations['abif_raw']['DATA105'], dye)))
height.append(data[detected_peaks[i]])
for i in range(len(peaks) - 1):
label.append(
model.predict(
[[area_of_peaks[i], no_of_peaks[i], length[i], height[i]]]))
# print(peaks)
# print(len(peaks))
# print(label)
for x in range(len(label) - 1):
if label[x] == 1:
print(length[x])
# print(label)