def test_get_location_from_rsid():
with pygwasvcf.GwasVcf(FILE) as g:
g.index_rsid()
chrom, pos = g.get_location_from_rsid("rs10399793")
check_first_row("1", 49298)
with pygwasvcf.GwasVcf(FILE, rsidx_path=FILE + ".rsidx") as g:
chrom, pos = g.get_location_from_rsid("rs10399793")
assert chrom == "1"
assert pos == 49298
def test_get_nc_from_metadata():
with pygwasvcf.GwasVcf(FILE) as g:
metadata = g.get_metadata()
for rec in g.query(contig=CHROM, start=START, stop=STOP):
assert pygwasvcf.VariantRecordGwasFuns.get_nc(
rec, TRAIT, metadata) == 9
del metadata[TRAIT]['TotalCases']
with pytest.raises(KeyError):
for rec in g.query(contig=CHROM, start=START, stop=STOP):
pygwasvcf.VariantRecordGwasFuns.get_nc(rec, TRAIT, metadata)
def test_get_ss_from_metadata():
with pygwasvcf.GwasVcf(FILE) as g:
metadata = g.get_metadata()
for rec in g.query(contig=CHROM, start=START, stop=STOP):
assert pygwasvcf.VariantRecordGwasFuns.get_ss(
rec, TRAIT, metadata) == (463001 + 9)
del metadata[TRAIT]['TotalCases']
for rec in g.query(contig=CHROM, start=START, stop=STOP):
assert pygwasvcf.VariantRecordGwasFuns.get_ss(
rec, TRAIT, metadata) == 463001
def test_get_id_chrpos():
with pygwasvcf.GwasVcf(FILE) as g:
for rec in g.query(contig=CHROM, start=START, stop=STOP):
assert pygwasvcf.VariantRecordGwasFuns.get_id(
rec, TRAIT, create_if_missing=False) is not None
del rec.samples[TRAIT]['ID']
with pytest.raises(KeyError):
assert pygwasvcf.VariantRecordGwasFuns.get_id(
rec, TRAIT, create_if_missing=False)
assert pygwasvcf.VariantRecordGwasFuns.get_id(
rec, TRAIT, create_if_missing=True) == "1-49298-T-C"
def test_get_metadata():
with pygwasvcf.GwasVcf(FILE) as g:
recs = g.get_metadata()
assert TRAIT in recs
assert "TotalVariants" in recs[TRAIT]
assert "VariantsNotRead" in recs[TRAIT]
assert "HarmonisedVariants" in recs[TRAIT]
assert "VariantsNotHarmonised" in recs[TRAIT]
assert "SwitchedAlleles" in recs[TRAIT]
assert "TotalControls" in recs[TRAIT]
assert "TotalCases" in recs[TRAIT]
assert "StudyType" in recs[TRAIT]
def test_index_rsid():
# delete old index if present
if os.path.exists(FILE + ".rsidx"):
os.remove(FILE + ".rsidx")
# index GWAS-VCF
with pygwasvcf.GwasVcf(FILE) as g:
g.index_rsid()
# check index exists
assert os.path.exists(FILE + ".rsidx")
# check contents of index
with sqlite3.connect(FILE + ".rsidx") as dbconn:
cur = dbconn.cursor()
cur.execute("SELECT * FROM rsid_to_coord")
for rec in cur.fetchall():
assert rec[0] is not None
assert isinstance(rec[0], int)
assert rec[1] is not None
assert isinstance(rec[1], str)
assert rec[2] is not None
assert isinstance(rec[2], int)
def read_vcf(fh, alleles, slh=None, trait=None):
with pygwasvcf.GwasVcf(fh) as vcf_in:
traits = vcf_in.get_traits()
if trait is not None:
assert trait in traits
else:
trait = traits[0]
# get global field info from header
metadata = vcf_in.get_metadata()
if alleles:
dtype_dict = {
'SNP': str,
'Z': float,
'N': float,
'A1': str,
'A2': str
}
# Read in data
o = [
[
pygwasvcf.VariantRecordGwasFuns.get_id(
rec, trait,
create_if_missing=True), # rsid or chr-pos-ref-alt
pygwasvcf.VariantRecordGwasFuns.get_beta(rec, trait) /
pygwasvcf.VariantRecordGwasFuns.get_se(rec, trait),
pygwasvcf.VariantRecordGwasFuns.get_ss(
rec, trait, metadata
), # if per-snp sample size unavailable then take from header
rec.alts[0],
rec.ref
] for rec in vcf_in.query()
]
N = pd.Series([x[2] for x in o], dtype='float')
p = pd.DataFrame({
'SNP': pd.Series([x[0] for x in o], dtype='str'),
'Z': pd.Series([x[1] for x in o], dtype='float'),
'N': N,
'A1': pd.Series([x[3] for x in o], dtype='str'),
'A2': pd.Series([x[4] for x in o], dtype='str')
})
else:
dtype_dict = {'SNP': str, 'Z': float, 'N': float}
o = [
[
pygwasvcf.VariantRecordGwasFuns.get_id(
rec, trait,
create_if_missing=True), # rsid or chr-pos-ref-alt
pygwasvcf.VariantRecordGwasFuns.get_beta(rec, trait) /
pygwasvcf.VariantRecordGwasFuns.get_se(rec, trait),
pygwasvcf.VariantRecordGwasFuns.get_ss(
rec, trait, metadata
), # if per-snp sample size unavailable then take from header
] for rec in vcf_in.fetch()
]
N = pd.Series([x[2] for x in o], dtype='float')
p = pd.DataFrame({
'SNP': pd.Series([x[0] for x in o], dtype='str'),
'Z': pd.Series([x[1] for x in o], dtype='float'),
'N': N
})
if slh is not None:
compression = get_compression(slh)
sl = []
if compression == "gzip":
try:
with gzip.open(slh) as f:
for line in f:
sl.append(line.strip())
except (AttributeError, ValueError) as e:
raise ValueError('Improperly formatted snplist file: ' +
str(e.args))
else:
try:
with open(slh) as f:
for line in f:
sl.append(line.strip())
except (AttributeError, ValueError) as e:
raise ValueError('Improperly formatted snplist file: ' +
str(e.args))
f.close()
p = p.loc[p['SNP'].isin(sl)]
return (p)
def test_get_nc():
with pygwasvcf.GwasVcf(FILE) as g:
for rec in g.query(contig=CHROM, start=START, stop=STOP):
with pytest.raises(KeyError):
assert pygwasvcf.VariantRecordGwasFuns.get_nc(rec, TRAIT)
def test_get_id_rsid():
with pygwasvcf.GwasVcf(FILE) as g:
for rec in g.query(contig=CHROM, start=START, stop=STOP):
assert pygwasvcf.VariantRecordGwasFuns.get_id(
rec, TRAIT) == "rs10399793"
def test_get_af():
with pygwasvcf.GwasVcf(FILE) as g:
for rec in g.query(contig=CHROM, start=START, stop=STOP):
assert pygwasvcf.VariantRecordGwasFuns.get_af(
rec, TRAIT) == pytest.approx(0.623765)
def test_query_by_rsid():
with pygwasvcf.GwasVcf(FILE) as g:
g.index_rsid()
for num, row in enumerate(g.query(variant_id="rs10399793")):
check_first_row(row.chrom, row.pos)
assert num == 0
def test_query_by_chr_pos():
with pygwasvcf.GwasVcf(FILE) as g:
for num, row in enumerate(g.query(contig="1", start=49297,
stop=49298)):
check_first_row(row.chrom, row.pos)
assert num == 0
def test_close():
with pygwasvcf.GwasVcf(FILE) as g:
assert not g.is_closed()
assert g.is_closed()
g = pygwasvcf.GwasVcf(FILE)
assert g.is_closed()
def test_query_all():
with pygwasvcf.GwasVcf(FILE) as g:
for num, row in enumerate(g.query()):
if num == 0:
check_first_row(row.chrom, row.pos)
assert num > 0
