def load_genotypes(self,
Structural_Variant=None,
SVs=None,
Ped=None,
ids=None,
gen=None,
no_anno=None,
tmp_dir=None):
svs = BedTool(
list(
set([(format_chrom(x[0]), x[1], x[2])
for x in Structural_Variant.raw]))).sort()
if no_anno == False:
Annot = Annotation()
Annot.check_overlap(svs, Structural_Variant.raw, gen, tmp_dir)
self.Annotations = Annot
for locus in SVs:
Variant = SVs[locus]
self.quals[locus] = Variant.med_ref, Variant.med_alt
self.filters[
locus] = Variant.standard_filter, Variant.denovo_filter
for sample_id in ids:
gt = './.'
if (locus[0] == 'chrX'
or locus[0] == 'chrY') and Ped.males.get(
sample_id
) != None and Structural_Variant.par[locus] == False:
gt = '.'
if Variant.gt.get(locus + (sample_id, )) != None:
gt = Variant.gt[locus + (sample_id, )]
for allele in gt.split(':').pop(0).split('/'):
if allele == '.': continue
if self.allele_freq.get(locus) == None:
self.allele_freq[locus] = [int(allele), 1]
else:
self.allele_freq[locus] = [
self.allele_freq[locus][0] + int(allele),
self.allele_freq[locus][1] + 1
]
if self.genotypes.get(locus) == None:
self.genotypes[locus] = [gt]
else:
self.genotypes[locus].append(gt)
