def test_overwrite_snp_data():
"""
Testing if the overwrite works.
:return:
"""
"""
Overwrite the snp data, this should not fail, and produce the same values in the class.
"""
snp_a = variants.SNP("rs123", "1", 123, "A", "C", 0.25)
snp_to_overwrite = variants.SNP("rs123", "hahaa", 1e6, "HGH", "lala",
1000.0)
snp_to_overwrite.add_snp_data(snp_a, overwrite=True)
#make sure everythign is the same.
assert snp_to_overwrite.snp_name == snp_a.snp_name
assert snp_to_overwrite.chromosome == snp_a.chromosome
assert snp_to_overwrite.position == snp_a.position
assert snp_to_overwrite.major_allele == snp_a.major_allele
assert snp_to_overwrite.minor_allele == snp_a.minor_allele
assert snp_to_overwrite.minor_allele_frequency == snp_a.minor_allele_frequency
assert snp_to_overwrite.has_position_data == snp_a.has_position_data
assert snp_to_overwrite.has_allele_data == snp_a.has_allele_data
assert snp_to_overwrite.has_frequency_data == snp_a.has_frequency_data
def test_update_position():
snp_a = variants.SNP("rs123", "1", 123, "A", "C", 0.25)
snp_no_position = variants.SNP("rs123", None, None, "A", "C", 0.25)
snp_no_position.add_snp_data(snp_a)
assert snp_no_position.chromosome == snp_a.chromosome
assert snp_no_position.position == snp_a.position
snp_with_position = variants.SNP("rs123", "2", 124, "A", "C", 0.25)
snp_with_position.add_snp_data(snp_a)
assert snp_with_position.chromosome != snp_a.chromosome
assert snp_with_position.position != snp_a.position
def test_adding_snp_to_genetic_association():
beta = 0.1
se = 0.05
snp_a = variants.SNP("rs123", "1", 123, "A", "C", 0.25)
assoc_a = association.GeneticAssociation("CeD",
"rs123",
200,
beta,
se,
r_squared=None,
chromosome=None,
position=None,
major_allele=None,
minor_allele=None,
minor_allele_frequency=None,
reference_allele=None,
effect_allele=None)
assoc_a.add_snp_data(snp_a)
assert assoc_a.snp_name == snp_a.snp_name
assert assoc_a.chromosome == snp_a.chromosome
assert assoc_a.position == snp_a.position
assert assoc_a.major_allele == snp_a.major_allele
assert assoc_a.minor_allele == snp_a.minor_allele
assert assoc_a.minor_allele_frequency == snp_a.minor_allele_frequency
assert assoc_a.has_position_data == snp_a.has_position_data
assert assoc_a.has_allele_data == snp_a.has_allele_data
assert assoc_a.has_frequency_data == snp_a.has_frequency_data
assert beta == assoc_a.beta
assert beta / se == assoc_a.z_score
assoc_b = association.GeneticAssociation("CeD",
"rs123",
200,
beta,
se,
r_squared=None,
chromosome=None,
position=None,
major_allele="C",
minor_allele="A",
minor_allele_frequency=None,
reference_allele=None,
effect_allele=None)
assoc_b.add_snp_data(snp_a)
assert beta == (-1 * assoc_b.beta)
assert beta / se == (-1 * assoc_b.z_score)
def test_add_snp_snp_acceptance():
"""
Tests some snps
:return:
"""
# making sure that this does not throw an error when the data is the same.
snp_a = variants.SNP("rs123", "1", 123, "A", "C", 0.25)
snp_b = variants.SNP("1:123", "1", 123, "A", "C", 0.25)
failed = False
try:
snp_a.add_snp_data(snp_a)
snp_a.add_snp_data(snp_b)
except ValueError:
failed = True
assert not failed
# now making sure that this throws an error when comparing snps.
snp_c = variants.SNP(("2:123", "2", 123, "A", "C", 0.25))
failed = False
try:
snp_a.add_snp_data(snp_c)
except ValueError:
failed = True
assert failed
snp_d = variants.SNP("rs126", "1", 123, "A", "C", 0.25)
failed = False
try:
snp_a.add_snp_data(snp_d)
except ValueError:
failed = True
assert failed
def test_adding_minor_allele_frequency():
"""
:return:
"""
"""
Tests if minor allele frequency data is correct.
"""
snp_a = variants.SNP("rs123", "1", 123, "A", "C", 0.25)
snp_to_add_maf = variants.SNP("rs123", "1", 123, "A", "C")
snp_to_add_maf.add_snp_data(snp_a)
assert snp_to_add_maf.minor_allele_frequency == snp_a.minor_allele_frequency
"""
Tests if minor allele frequency will be flipped.
"""
maf = 0.77
snp_to_add_maf = variants.SNP("rs123", "1", 123, "C", "A", maf)
snp_to_add_maf.add_snp_data(snp_a)
assert snp_to_add_maf.minor_allele_frequency == (1 - maf)
"""
Tests if this will produce a runtime warning as there could be allele frequency differences
"""
warning_given = False
snp_to_add_maf = variants.SNP("rs123", "1", 123, "C", "A", 1 - maf)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
snp_to_add_maf.add_snp_data(snp_a)
if len(w) == 1:
warning_given = True
assert warning_given
def test_update_alleles():
"""
This function is used to ensure the alleles are correct when adding snp data.
:return:
"""
"""
Making sure the allele data is added correctly
"""
snp_a = variants.SNP("rs123", "1", 123, "A", "C", 0.25)
snp_no_alleles = variants.SNP("rs123", None, None, None, None, 0.25)
snp_no_alleles.add_snp_data(snp_a)
assert snp_no_alleles.major_allele == snp_a.major_allele
assert snp_no_alleles.minor_allele == snp_a.minor_allele
"""
Making sure the snp data is added when there is only one allele present.
"""
snp_only_major_allele = variants.SNP("rs123", None, None, "A", None, 0.25)
snp_only_major_allele.add_snp_data(snp_a)
assert snp_only_major_allele.minor_allele == snp_a.minor_allele
snp_only_minor_allele = variants.SNP("rs123", None, None, None, "C", 0.25)
snp_only_minor_allele.add_snp_data(snp_a)
assert snp_only_major_allele.minor_allele == snp_a.minor_allele
"""
Making sure the snp data is added when the alleles are flipped.
"""
allele_frequency = 0.75
snp_flipped_alleles = variants.SNP("rs123", "1", 123, "C", "A",
allele_frequency)
snp_flipped_alleles.add_snp_data(snp_a)
assert snp_flipped_alleles.major_allele == snp_a.major_allele
assert snp_flipped_alleles.minor_allele == snp_a.minor_allele
assert snp_flipped_alleles.minor_allele_frequency == (1 - allele_frequency)
"""
Making sure the snp data is added when there is only a major allele. which is the minor allele in the reference.
"""
snp_flipped_only_major = variants.SNP("rs123", "1", 123, "C", None,
allele_frequency)
snp_flipped_only_major.add_snp_data(snp_a)
assert snp_flipped_alleles.major_allele == snp_a.major_allele
assert snp_flipped_alleles.minor_allele == snp_a.minor_allele
assert snp_flipped_alleles.minor_allele_frequency == (1 - allele_frequency)
"""
Making sure the snp data is added when there is only a minor allele. which is the major allele in the reference.
"""
snp_flipped_only_major = variants.SNP("rs123", "1", 123, None, "A",
allele_frequency)
snp_flipped_only_major.add_snp_data(snp_a)
assert snp_flipped_alleles.major_allele == snp_a.major_allele
assert snp_flipped_alleles.minor_allele == snp_a.minor_allele
assert snp_flipped_alleles.minor_allele_frequency == (1 - allele_frequency)
"""
Check that it fails when both the alleles are wrong.
"""
snp_both_wrong_alleles = variants.SNP("rs123", "1", 123, "G", "T", 0.25)
failed = False
try:
snp_both_wrong_alleles.add_snp_data(snp_a)
except ValueError:
failed = True
assert failed
"""
Check that it fails when only a single allele is wrong.
"""
snp_both_wrong_alleles = variants.SNP("rs123", "1", 123, "A", "T", 0.25)
failed = False
try:
snp_both_wrong_alleles.add_snp_data(snp_a)
except ValueError:
failed = True
assert failed
snp_both_wrong_alleles = variants.SNP("rs123", "1", 123, "T", "A", 0.25)
failed = False
try:
snp_both_wrong_alleles.add_snp_data(snp_a)
except ValueError:
failed = True
assert failed