def test_parse_conservation(cyvcf2_variant):
variant = cyvcf2_variant
## GIVEN a variant with some GERP information
variant.INFO['GERP++_RS_prediction_term'] = 'Conserved'
## WHEN parsing conservation
## THEN assert that the field is parsed correct
assert parse_conservation(variant, 'GERP++_RS_prediction_term') == ['Conserved']
def test_parse_conservation(cyvcf2_variant):
variant = cyvcf2_variant
## GIVEN a variant with some GERP information
variant.INFO['dbNSFP_GERP___RS'] = 3.7
## WHEN parsing conservation
## THEN assert that the field is parsed correct
assert parse_conservation(variant, 'dbNSFP_GERP___RS') == ['Conserved']
def test_parse_conservation_wrong_term(cyvcf2_variant):
variant = cyvcf2_variant
## GIVEN a variant with wrong GERP information
variant.INFO['GERP++_RS_prediction_term'] = 'Conservation'
## WHEN parsing conservation
## THEN assert that nothing is returned
assert parse_conservation(variant, 'GERP++_RS_prediction_term') == []
def test_parse_conservation(cyvcf2_variant):
variant = cyvcf2_variant
## GIVEN a variant with some GERP information
variant.INFO['dbNSFP_GERP___RS'] = 3.7
## WHEN parsing conservation
## THEN assert that the field is parsed correct
assert parse_conservation(variant, 'dbNSFP_GERP___RS') == ['Conserved']
def test_parse_conservation_multiple_terms(cyvcf2_variant):
variant = cyvcf2_variant
## GIVEN a variant with multiple GERP annotations
variant.INFO['GERP++_RS_prediction_term'] = 'Conserved, NotConserved'
## WHEN parsing conservation
## THEN assert that all terms are returned
assert parse_conservation(variant, 'GERP++_RS_prediction_term') == ['Conserved', 'NotConserved']
def test_parse_conservation_multiple_terms(cyvcf2_variant):
variant = cyvcf2_variant
## GIVEN a variant with multiple GERP annotations
variant.INFO['dbNSFP_GERP___RS'] = 3.7, -0.34
## WHEN parsing conservation
## THEN assert that all terms are returned
assert parse_conservation(variant, 'dbNSFP_GERP___RS') == ['Conserved', 'NotConserved']
def test_parse_conservation_multiple_terms(cyvcf2_variant):
variant = cyvcf2_variant
## GIVEN a variant with multiple GERP annotations
variant.INFO['dbNSFP_GERP___RS'] = 3.7, -0.34
## WHEN parsing conservation
## THEN assert that all terms are returned
assert parse_conservation(
variant, 'dbNSFP_GERP___RS') == ['Conserved', 'NotConserved']