def get_peak_group_values(pg, rt, ref_pg):
pg_best = data_holder.NestedDict()
pg_best['peak_rt'] = rt
# use peak width from ref_pg to compute the boundary of this peak group
ref_pg_width = ref_pg['rt_right'] - ref_pg['rt_left']
pg_best['rt_left'], pg_best['rt_right'] = get_boundary_for_pg_best(pg, rt, ref_pg_width)
for fragment in pg[rt]['ms2']['rt_list'].keys():
# get the rt and i list only for the peak group
pg_best['ms2']['rt_list'][fragment], pg_best['ms2']['i_list'][fragment] = \
chrom.get_chrom_range(pg_best['rt_left'], pg_best['rt_right'],
pg[rt]['ms2']['rt_list'][fragment], pg[rt]['ms2']['i_list'][fragment])
pg_best['ms2']['peak_apex_i'][fragment], pg_best['ms2']['if_found_peak'][fragment] = get_fragment_intensity_for_peak_group(
pg[rt]['ms2']['peak_apex_rt_list'][fragment], pg[rt]['ms2']['peak_apex_i_list'][fragment], rt)
# get the rt and i list only for the peak group
pg_best['ms1']['rt_list'], pg_best['ms1']['i_list'] = \
chrom.get_chrom_range(
pg_best['rt_left'], pg_best['rt_right'], pg[rt]['ms1']['rt_list'], pg[rt]['ms1']['i_list'])
pg_best['ms1']['peak_apex_i'], pg_best['ms1']['if_found_peak'] = get_fragment_intensity_for_peak_group(
pg[rt]['ms1']['peak_apex_rt_list'], pg[rt]['ms1']['peak_apex_i_list'], rt)
return pg_best
def check_if_the_top1_fragment_is_good_in_ref_sample(pg, ref_pg):
# check the top1 fragment is a good one, otherwise, remove it
top1 = find_top_n_fragment(1, ref_pg)
# ref_pg_rt_apex = ref_pg['peak_rt']
ref_pg_rt_left = ref_pg['rt_left']
ref_pg_rt_right = ref_pg['rt_right']
top1_rt_list = ref_pg['ms2']['rt_list'][top1]
top1_i_list = ref_pg['ms2']['i_list'][top1]
top1_rt_list_in_range, top1_i_list_in_range = \
chrom.get_chrom_range(ref_pg_rt_left, ref_pg_rt_right, top1_rt_list, top1_i_list)
if_ref_good = dia_quant.check_if_displayed_peak_a_good_one(top1_rt_list, top1_i_list, 1, 3)
return if_ref_good
def check_if_top1_fragment_good_in_this_pg(pg, ref_pg, if_top1_fragment_good_in_ref_sample, rt):
if_top1_fragment_good_in_this_pg = 1
if if_top1_fragment_good_in_ref_sample == 0:
if_top1_fragment_good_in_this_pg = 0
else:
top1 = find_top_n_fragment(1, ref_pg)
top1_rt_list = pg[rt]['ms2']['rt_list'][top1]
top1_i_list = pg[rt]['ms2']['i_list'][top1]
ref_pg_width = ref_pg['rt_right'] - ref_pg['rt_left']
pg_rt_left, pg_rt_right = get_boundary_for_pg_best(pg, rt, ref_pg_width)
top1_rt_list_in_range, top1_i_list_in_range = \
chrom.get_chrom_range(pg_rt_left, pg_rt_right, top1_rt_list, top1_i_list)
if_top1_fragment_good_in_this_pg = dia_quant.check_if_displayed_peak_a_good_one(
top1_rt_list, top1_i_list, 1, 3)
return if_top1_fragment_good_in_this_pg
