def test_liftover_bad_request():
"""Test variant liftover with non-valid request params"""
# WHEN sending a liftover request with non-standard chromosome (M instead of MT)
chromosome = "M"
start = 7278
end = 7278
# THEN the service should not return mappings
mappings = liftover("GRCh37", chromosome, start, end)
assert mappings is None
def test_liftover_37_38():
"""Test variant liftover from GRCh37 to GRCh38"""
# WHEN sending a liftover request with suitable coordinates in genome build 37
chromosome = "X"
start = 1000000
end = 1000000
# THEN the service should return valid mappings
mappings = liftover("GRCh37", chromosome, start, end)
# Each mapping should have the expected output format
assert isinstance(mappings, list)
assert isinstance(mappings[0], dict)
for item in ["assembly", "seq_region_name", "start", "end"]:
assert mappings[0]["mapped"][item]
# And genome assembly should be GRCh38
assert mappings[0]["mapped"]["assembly"] == "GRCh38"
def test_liftover_MT_variant():
"""Test liftover for a mitochondrial variant from GRCh37 to GRCh38"""
# GIVEN a mitochondrial variant
chromosome = "MT"
start = 7278
end = 7278
# THEN the service should return valid mappings
mappings = liftover("GRCh37", chromosome, start, end)
# Each mapping should have the expected output format
assert isinstance(mappings, list)
assert isinstance(mappings[0], dict)
for item in ["assembly", "seq_region_name", "start", "end"]:
assert mappings[0]["mapped"][item]
# And genome assembly should be GRCh38
assert mappings[0]["mapped"]["assembly"] == "GRCh38"
def lift_variant(variant):
"""Perform a variant liftover using Ensebl REST API and return eventual variant in the other genome build
Args:
variant(dict): example:
{'assembly': 'GRCh38', 'referenceName': '12', 'start': 14641142, 'end': 14641142, 'referenceBases': 'C', 'alternateBases': 'T'}
Returns:
lifted_variants(list of dict): example:
[{'assembly': 'GRCh37', 'referenceName': '12', 'start': 14794076, 'end': 14794076, 'referenceBases': 'C', 'alternateBases': 'T'}]
"""
lifted_vars = []
mappings = liftover(
variant.get("assembly"),
variant.get("referenceName"),
variant.get("start") + 1, # coordinates are 0-based in MatchMaker
variant.get("end") + 1 if variant.get("end") else variant.get("end"),
)
if mappings is None:
return lifted_vars
for res in mappings:
# Create a variant which is the copy of the original variant
lifted = deepcopy(variant)
mapped = res["mapped"]
# Modify coordinates of this variant according to mapping results
lifted["assembly"] = mapped["assembly"]
lifted["referenceName"] = mapped["seq_region_name"]
lifted["start"] = mapped[
"start"] - 1 # conver back to 0-based coordinates
if variant.get("end") is None:
continue
lifted["end"] = mapped["end"] - 1
lifted_vars.append(lifted)
return lifted_vars