def filter_peaks_based_on_peak_shape_worker2(max_peaks, i_list, rt_list,
max_peaks_all):
max_fold_change_score = -1
best_rt = -1
best_i = -1
for rt, i in max_peaks:
rt_left, rt_right = chrom.get_peak_boundary(rt_list, i_list, rt)
i_apex = float(i)
i_left = peak_groups.get_intensity_for_closest_rt(
rt_left, rt_list, i_list)
i_right = peak_groups.get_intensity_for_closest_rt(
rt_right, rt_list, i_list)
fold_change_left = i_apex / (i_left + 1.0)
fold_change_right = i_apex / (i_right + 1.0)
fold_change_score = fold_change_left * fold_change_right
if fold_change_score > max_fold_change_score:
max_fold_change_score = fold_change_score
best_rt = rt
best_i = i
max_peaks_all.append((best_rt, best_i))
return max_peaks_all
def filter_peaks_based_on_peak_shape_worker2(max_peaks, i_list, rt_list, max_peaks_all):
max_fold_change_score = -1
best_rt = -1
best_i = -1
for rt, i in max_peaks:
rt_left, rt_right = chrom.get_peak_boundary(rt_list, i_list, rt)
i_apex = float(i)
i_left = peak_groups.get_intensity_for_closest_rt(rt_left, rt_list, i_list)
i_right = peak_groups.get_intensity_for_closest_rt(rt_right, rt_list, i_list)
fold_change_left = i_apex / (i_left + 1.0)
fold_change_right = i_apex / (i_right + 1.0)
fold_change_score = fold_change_left * fold_change_right
if fold_change_score > max_fold_change_score:
max_fold_change_score = fold_change_score
best_rt = rt
best_i = i
max_peaks_all.append((best_rt, best_i))
return max_peaks_all
def filter_peaks_based_on_peak_shape_worker(max_peaks, i_list, rt_list, max_peaks_all):
for rt, i in max_peaks:
rt_left, rt_right = chrom.get_peak_boundary(rt_list, i_list, rt)
i_apex = float(i)
i_left = peak_groups.get_intensity_for_closest_rt(rt_left, rt_list, i_list)
i_right = peak_groups.get_intensity_for_closest_rt(rt_right, rt_list, i_list)
fold_change_left = i_apex / (i_left + 1.0)
fold_change_right = i_apex / (i_right + 1.0)
if fold_change_left >= parameters.PEAK_SHAPE_FOLD_VARIATION_CRUDE and fold_change_right >= parameters.PEAK_SHAPE_FOLD_VARIATION_CRUDE:
max_peaks_all.append((rt, i))
return max_peaks_all
def filter_peaks_based_on_peak_shape_worker(max_peaks, i_list, rt_list,
max_peaks_all):
for rt, i in max_peaks:
rt_left, rt_right = chrom.get_peak_boundary(rt_list, i_list, rt)
i_apex = float(i)
i_left = peak_groups.get_intensity_for_closest_rt(
rt_left, rt_list, i_list)
i_right = peak_groups.get_intensity_for_closest_rt(
rt_right, rt_list, i_list)
fold_change_left = i_apex / (i_left + 1.0)
fold_change_right = i_apex / (i_right + 1.0)
if fold_change_left >= parameters.PEAK_SHAPE_FOLD_VARIATION_CRUDE and fold_change_right >= parameters.PEAK_SHAPE_FOLD_VARIATION_CRUDE:
max_peaks_all.append((rt, i))
return max_peaks_all
def find_matched_fragments(chrom_data, tg, sample, rt):
# fold_change = 0.1 by default
matched_fragments = []
matched_fragments_rt_list = []
matched_fragments_i_list = []
matched_fragments_peak_rt_left = []
matched_fragments_peak_rt_right = []
for fragment in chrom_data[tg][sample].keys():
if fragment != tg:
if hasattr(chrom_data[tg][sample][fragment], 'peak_apex_rt_list'):
peak_apex_rt_list = chrom_data[tg][sample][fragment].peak_apex_rt_list
peak_apex_i_list = chrom_data[tg][sample][fragment].peak_apex_i_list
if peak_apex_rt_list != 'NA':
for rt0, i in zip(peak_apex_rt_list, peak_apex_i_list):
if abs(rt - rt0) < parameters.MAX_RT_TOLERANCE: # 10 s for 2hr gradient
matched_fragments.append(fragment)
matched_fragments_rt_list.append(rt0)
matched_fragments_i_list.append(i)
rt_list = chrom_data[tg][sample][fragment].rt_list
i_list = chrom_data[tg][sample][fragment].i_list
rt_left, rt_right = chrom.get_peak_boundary(rt_list, i_list, rt0)
matched_fragments_peak_rt_left.append(rt_left)
matched_fragments_peak_rt_right.append(rt_right)
break
return matched_fragments, matched_fragments_rt_list, matched_fragments_i_list, matched_fragments_peak_rt_left, matched_fragments_peak_rt_right
