def _aggregate(self, covgs, threshold=5):
del_phylo_groups = []
for phylo_group, covg_dict in covgs.items():
percent_coverage = covg_dict["percent_coverage"]
length = covg_dict["length"]
bases_covered = self._bases_covered(percent_coverage, length)
total_bases = covg_dict["total_bases"]
total_percent_covered = round(bases_covered / total_bases, 3)
_median = covg_dict.get("median", [0])
minimum_percentage_coverage_required = percent_coverage_from_expected_coverage(
self.expected_depth) * self.threshold.get(
phylo_group, DEFAULT_THRESHOLD)
if total_percent_covered < minimum_percentage_coverage_required or median(
_median) < 0.1 * self.expected_depth:
# Remove low coverage nodes
_index = [
i for i, d in enumerate(_median)
if d > 0.1 * self.expected_depth
]
percent_coverage = [percent_coverage[i] for i in _index]
length = [length[i] for i in _index]
bases_covered = self._bases_covered(percent_coverage, length)
_median = [_median[i] for i in _index]
total_percent_covered = round(bases_covered / total_bases, 3)
if total_percent_covered > threshold:
if phylo_group == "Mycobacterium_llatzerense": # Mistake in panel
phylo_group = "Mycobacterium_mucogenicum"
covgs[phylo_group] = {
"percent_coverage": total_percent_covered,
"median_depth": median(_median)
}
else:
del_phylo_groups.append(phylo_group)
for phylo_group in del_phylo_groups:
del covgs[phylo_group]
def estimate_depth(self):
depth = []
for variant_covg in self.variant_covgs.values():
if variant_covg.reference_coverage.median_depth > 0:
depth.append(variant_covg.reference_coverage.median_depth)
for spcs in self.gene_presence_covgs.values():
__median_depth = median(
[spc.median_depth for spc in spcs.values()])
if __median_depth > 0:
depth.append(__median_depth)
_median = median(depth)
if _median < 1:
return 1
else:
return _median
def calc_expected_depth(self):
# Get all of the panels with % coverage > 30
_median = []
for phylo_group, coverage_dict in self.phylo_group_covgs.items():
_median.extend(coverage_dict["median"])
if _median:
return median(_median)
else:
return 0