def family_coverage_gene_list(request, family, gene_list):
"""
Table of summary coverages for each gene in the gene list
"""
sample_id_list = [str(individual.pk) for individual in family.get_individuals()]
cache_key = ('family_coverage_gene_list', family.project.project_id, family.family_id, gene_list.slug)
cached_results = server_utils.get_cached_results(cache_key)
if cached_results:
gene_coverages = cached_results
else:
gene_coverages = []
for gene_id in gene_list.gene_id_list():
d = {
'gene_id': gene_id,
'gene_name': get_reference().get_gene_symbol(gene_id),
'totals': get_coverage_store().get_coverage_totals_for_gene(gene_id, sample_id_list)
}
d['coding_size'] = sum(d['totals'].values())
try:
d['percent'] = float(d['totals']['callable'])*100 / d['coding_size']
except ZeroDivisionError:
d['percent'] = 0
gene_coverages.append(d)
server_utils.save_results_cache(cache_key, gene_coverages)
return render(request, 'coverage/family_coverage_gene_list.html', {
'project': family.project,
'family': family,
'gene_list': gene_list,
'gene_coverages': gene_coverages,
})
def family_coverage_gene_list(request, family, gene_list):
"""
Table of summary coverages for each gene in the gene list
"""
sample_id_list = [str(individual.pk) for individual in family.get_individuals()]
cache_key = ('family_coverage_gene_list', family.project.project_id, family.family_id, gene_list.slug)
cached_results = server_utils.get_cached_results(cache_key)
if cached_results:
gene_coverages = cached_results
else:
gene_coverages = []
for gene_id in gene_list.gene_id_list():
d = {
'gene_id': gene_id,
'gene_name': get_reference().get_gene_symbol(gene_id),
'totals': get_coverage_store().get_coverage_totals_for_gene(gene_id, sample_id_list)
}
d['coding_size'] = sum(d['totals'].values())
try:
d['percent'] = float(d['totals']['callable'])*100 / d['coding_size']
except ZeroDivisionError:
d['percent'] = 0
gene_coverages.append(d)
server_utils.save_results_cache(cache_key, gene_coverages)
return render(request, 'coverage/family_coverage_gene_list.html', {
'project': family.project,
'family': family,
'gene_list': gene_list,
'gene_coverages': gene_coverages,
})