def add_genelist(self, list_id, gene_ids, case_obj=None):
"""Create a new gene list and optionally link to cases."""
new_genelist = GeneList(list_id=list_id)
new_genelist.gene_ids = gene_ids
if case_obj:
new_genelist.cases.append(case_obj)
self.session.add(new_genelist)
self.save()
return new_genelist
def add_genelist(self, list_id, gene_ids, case_obj=None):
"""Create a new gene list and optionally link to cases."""
new_genelist = GeneList(list_id=list_id)
new_genelist.gene_ids = gene_ids
if case_obj:
new_genelist.cases.append(case_obj)
self.session.add(new_genelist)
self.save()
return new_genelist
def case_genelist(self, case_obj):
"""Get or create a new case specific gene list record."""
list_id = "{}-HPO".format(case_obj.case_id)
gene_list = self.gene_list(list_id)
if gene_list is None:
gene_list = GeneList(list_id=list_id)
case_obj.gene_lists.append(gene_list)
self.session.add(gene_list)
return gene_list
def test_delete_gene():
gene_list = GeneList(list_id='my cool list')
assert gene_list.list_id == 'my cool list'
assert gene_list.gene_ids == []
gene_ids = ['ADK', 'SKD', 'EGFR']
gene_list.gene_ids = gene_ids
assert gene_list._gene_ids == ','.join(gene_ids)
# remove one gene
gene_list.delete_gene('ADK')
assert gene_list.gene_ids == gene_ids[1:]
# remove multiple genes
gene_list.delete_gene('SKD', 'EGFR')
assert gene_list.gene_ids == []