def test_gwas_unpickle():
g1 = [
Gwas("1", 101, "A", "T", 1, 0, 5e-8, 1000, 0.4, "rs1234", None, None,
None),
Gwas("1", 105, "A", "T", 1, 0, 5e-8, 1000, 0.4, "rs1234", None, None,
None),
Gwas("1", 102, "A", "T", 1, 0, 5e-8, 1000, 0.4, "rs1234", None, None,
None)
]
g2 = []
idx = []
results = tempfile.TemporaryFile()
for result in g1:
heappush(idx, (result.pos, results.tell()))
pickle.dump(result, results)
while idx:
pos = heappop(idx)
results.seek(pos[1])
result = pickle.load(results)
g2.append(result)
assert g2[0].pos == 101
assert g2[1].pos == 102
assert g2[2].pos == 105
results.close()
def test_are_alleles_iupac():
g = Gwas('test', 1, 'A', 'T', None, None, None, None, None, None, None,
None, None)
g.check_alleles_are_vaild()
with pytest.raises(AssertionError):
g = Gwas('test', 1, 'A', 'wdeT', None, None, None, None, None, None,
None, None, None)
g.check_alleles_are_vaild()
def test_check_reference_allele():
with pysam.FastaFile(os.path.join(os.path.dirname(__file__),
"test.fasta")) as fasta:
g = Gwas('test', 1, 'A', 'T', 1, None, None, None, None, None, None,
None, None)
g.check_reference_allele(fasta)
with pytest.raises(AssertionError):
g = Gwas('test', 1, 'T', 'A', 1, None, None, None, None, None,
None, None, None)
g.check_reference_allele(fasta)
def test_normalise():
with pysam.FastaFile(os.path.join(os.path.dirname(__file__),
"test.fasta")) as fasta:
# SNV
g = Gwas('test', 1, 'A', 'T', None, None, None, None, None, None, None,
None, None)
g.check_reference_allele(fasta)
g.normalise(fasta, padding=5)
assert g.chrom == "test"
assert g.pos == 1
assert g.ref == "A"
assert g.alt == "T"
# left pad SNV
g = Gwas('test', 10, 'ACACA', 'ACACT', None, None, None, None, None,
None, None, None, None)
g.check_reference_allele(fasta)
g.normalise(fasta, padding=5)
assert g.chrom == "test"
assert g.pos == 14
assert g.ref == "A"
assert g.alt == "T"
# right pad SNV
g = Gwas('test', 10, 'ACACA', 'TCACA', None, None, None, None, None,
None, None, None, None)
g.check_reference_allele(fasta)
g.normalise(fasta, padding=5)
assert g.chrom == "test"
assert g.pos == 10
assert g.ref == "A"
assert g.alt == "T"
# left pad ins
g = Gwas('test', 10, 'ACA', 'ACAGT', None, None, None, None, None,
None, None, None, None)
g.check_reference_allele(fasta)
g.normalise(fasta, padding=5)
assert g.chrom == "test"
assert g.pos == 12
assert g.ref == "A"
assert g.alt == "AGT"
# left-align pad del
g = Gwas('test', 10, 'ACACA', 'ACA', None, None, None, None, None,
None, None, None, None)
g.check_reference_allele(fasta)
g.normalise(fasta, padding=5)
assert g.chrom == "test"
assert g.pos == 9
assert g.ref == "TAC"
assert g.alt == "T"
def test_update_dbsnp():
with pysam.VariantFile(
os.path.join(os.path.dirname(__file__), "dbsnp.vcf.gz")) as dbsnp:
g = Gwas('test', 1, 'A', 'T', 1, None, None, None, None, None, None,
None, None)
assert g.dbsnpid is None
g.update_dbsnp(dbsnp)
assert g.dbsnpid == "rs1234"
g = Gwas('test', 2, 'A', 'T', 1, None, None, None, None, None, None,
None, None)
assert g.dbsnpid is None
g.update_dbsnp(dbsnp)
assert g.dbsnpid is None
def test_reverse_sign():
g = Gwas('test', 1, 'A', 'T', 1, None, None, None, None, None, None, None,
None)
g.reverse_sign()
assert g.chrom == "test"
assert g.pos == 1
assert g.ref == "T"
assert g.alt == "A"
assert g.b == -1