def remove_low_call_rate_samples(variations,
min_call_rate,
rates=True,
filter_id='sample_call_rate',
calc_histogram=False,
n_bins=DEF_NUM_BINS,
limits=None):
num_missing_gts = calc_missing_gt_per_sample(variations, rates=rates)
if rates:
num_called = 1 - num_missing_gts
else:
num_called = utils_array.get_shape_item(variations.gt,
0) - num_missing_gts
selected_samples = num_called >= min_call_rate
variations = keep_samples_with_mask(variations, selected_samples)[FLT_VARS]
num_selected_samples = va.count_nonzero(selected_samples)
num_filtered_samples = va.count_nonzero(va.logical_not(selected_samples))
flt_stats = {
N_SAMPLES_KEPT: num_selected_samples,
N_SAMPLES_FILTERED_OUT: num_filtered_samples
}
if calc_histogram:
limits = (0, 1) if rates else (0, len(variations.num_variations))
counts, bin_edges = va.histogram(num_called,
n_bins=n_bins,
limits=limits)
flt_stats[COUNT] = counts
flt_stats[BIN_EDGES] = bin_edges
flt_stats[HIST_RANGE] = [min_call_rate]
return {FLT_VARS: variations, FLT_ID: filter_id, FLT_STATS: flt_stats}
def keep_variable_variations(variations,
max_alleles,
filter_id='variable_variations'):
gts = variations[GT_FIELD]
some_not_missing_gts = va.any(gts != MISSING_INT, axis=2)
selected_vars1 = va.any(some_not_missing_gts, axis=1)
allele_counts = count_alleles(gts,
max_alleles=max_alleles,
count_missing=False)
num_alleles_per_snp = va.sum(allele_counts > 0, axis=1)
selected_vars2 = num_alleles_per_snp > 1
selected_vars = va.logical_and(selected_vars1, selected_vars2)
selected_variations = variations.get_vars(selected_vars)
num_selected_vars = va.count_nonzero(selected_vars)
num_filtered = va.count_nonzero(va.logical_not(selected_vars))
flt_stats = {N_KEPT: num_selected_vars, N_FILTERED_OUT: num_filtered}
return {
FLT_VARS: selected_variations,
FLT_ID: filter_id,
FLT_STATS: flt_stats
}
def calc_diversities(variations,
max_alleles,
min_num_genotypes,
min_call_dp_for_het_call=MIN_DP_FOR_CALL_HET,
polymorphic_threshold=0.95):
diversities = {}
mafs = calc_maf_by_gt(variations,
max_alleles,
min_num_genotypes=min_num_genotypes)
mafs_no_nan = mafs[va.logical_not(va.isnan(mafs))]
num_variable_vars = va.sum(mafs_no_nan < 0.9999999999)
diversities['num_variable_vars'] = num_variable_vars
snp_is_poly = mafs_no_nan <= polymorphic_threshold
num_poly = va.sum(snp_is_poly)
diversities['num_polymorphic_vars'] = num_poly
exp_het = calc_expected_het(variations,
max_alleles=max_alleles,
min_num_genotypes=min_num_genotypes)
diversities['exp_het'] = va.nanmean(exp_het)
obs_het = calc_obs_het(variations,
min_call_dp_for_het_call=min_call_dp_for_het_call,
min_num_genotypes=min_num_genotypes)
diversities['obs_het'] = va.nanmean(obs_het)
diversities['num_total_variations'] = variations.num_variations
return diversities
def remove_low_call_rate_vars(variations,
min_call_rate,
rates=True,
filter_id='call_rate',
calc_histogram=False,
n_bins=DEF_NUM_BINS,
limits=None):
num_missing_gts = calc_missing_gt(variations, rates=rates)
if rates:
num_called = 1 - num_missing_gts
else:
num_called = variations.gt.shape[1] - num_missing_gts
selected_vars = num_called >= min_call_rate
variations = variations.get_vars(selected_vars)
num_selected_vars = va.count_nonzero(selected_vars)
num_filtered = va.count_nonzero(va.logical_not(selected_vars))
flt_stats = {N_KEPT: num_selected_vars, N_FILTERED_OUT: num_filtered}
if calc_histogram:
limits = (0, 1) if rates else (0, len(variations.num_samples))
counts, bin_edges = va.histogram(num_called,
n_bins=n_bins,
limits=limits)
flt_stats[COUNT] = counts
flt_stats[BIN_EDGES] = bin_edges
flt_stats['limits'] = [min_call_rate]
return {FLT_VARS: variations, FLT_ID: filter_id, FLT_STATS: flt_stats}
def _filter_by_snp_position(variations, regions, filter_id, reverse=False):
selected_vars = _select_variations_in_region(variations, regions)
if reverse:
selected_vars = va.logical_not(selected_vars)
selected_variations = variations.get_vars(selected_vars)
# print('sel', selected_variations.shape)
num_selected_vars = va.count_nonzero(selected_vars)
num_filtered = va.count_nonzero(va.logical_not(selected_vars))
flt_stats = {N_KEPT: num_selected_vars, N_FILTERED_OUT: num_filtered}
return {
FLT_VARS: selected_variations,
FLT_ID: filter_id,
FLT_STATS: flt_stats
}
def _call_is_het(variations, is_missing=None):
is_hom = _call_is_hom(variations, is_missing=is_missing)
# if is_hom.shape[0] == 0:
# return is_hom, is_missing
is_het = va.logical_not(is_hom)
if is_missing is not None:
is_het[is_missing] = False
return is_het
def hmean(array, axis=0, dtype=None):
if axis is None:
array = array.ravel()
size = array.shape[0]
else:
size = array.shape[axis]
with np.errstate(divide='ignore'):
inverse_mean = va.sum(1.0 / array, axis=axis, dtype=dtype)
is_inf = va.logical_not(va.isfinite(inverse_mean))
hmean = size / inverse_mean
hmean[is_inf] = np.nan
return hmean
def _calc_obs_het_counts(variations, axis, min_call_dp_for_het_call,
max_call_dp_for_het_call=None):
is_missing = va.any(variations[GT_FIELD] == MISSING_INT, axis=2)
if min_call_dp_for_het_call is not None or max_call_dp_for_het_call is not None:
dps = variations[DP_FIELD]
if min_call_dp_for_het_call is not None:
low_dp = dps < min_call_dp_for_het_call
is_missing = va.logical_or(is_missing, low_dp)
if max_call_dp_for_het_call is not None:
high_dp = dps > max_call_dp_for_het_call
is_missing = va.logical_or(is_missing, high_dp)
is_het = _call_is_het(variations, is_missing=is_missing)
return (va.sum(is_het, axis=axis),
va.sum(va.logical_not(is_missing), axis=axis))
def _get_gts_non_missing_in_both(vars1, vars2):
num_missing_gts1 = calc_missing_gt(vars1, rates=True)
num_missing_gts2 = calc_missing_gt(vars2, rates=True)
is_called = va.logical_not(
va.logical_or(num_missing_gts1, num_missing_gts2))
gts1 = vars1[GT_FIELD]
gts2 = vars2[GT_FIELD]
gts1 = gts1[is_called]
gts2 = gts2[is_called]
indi1 = gts1[:, 0]
indi2 = gts2[:, 0]
return indi1, indi2
def _select_vars(variations, stats, min_allowable=None, max_allowable=None):
with np.errstate(invalid='ignore'):
selector_max = None if max_allowable is None else stats <= max_allowable
selector_min = None if min_allowable is None else stats >= min_allowable
if selector_max is None and selector_min is not None:
selected_vars = selector_min
elif selector_max is not None and selector_min is None:
selected_vars = selector_max
elif selector_max is not None and selector_min is not None:
selected_vars = selector_min & selector_max
else:
selected_vars = _filter_no_row(variations)
variations = variations.get_vars(selected_vars)
num_selected_vars = va.count_nonzero(selected_vars)
num_filtered = va.count_nonzero(va.logical_not(selected_vars))
flt_stats = {N_KEPT: num_selected_vars, N_FILTERED_OUT: num_filtered}
return {FLT_VARS: variations, FLT_STATS: flt_stats}
