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_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
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_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 main():
version = "1.3.0"
parser = argparse.ArgumentParser(description='Map GWAS summary statistics to VCF/BCF')
parser.add_argument('-v', '--version', action='version', version='%(prog)s {}'.format(version))
parser.add_argument('--out', dest='out', required=False,
help='Path to output VCF/BCF. If not present then must be specified as \'out\' in json file')
parser.add_argument('--data', dest='data', required=False,
help='Path to GWAS summary stats. If not present then must be specified as \'data\' in json file')
parser.add_argument('--ref', dest='ref', required=True, help='Path to reference FASTA')
parser.add_argument('--dbsnp', dest='dbsnp', required=False, help='Path to reference dbSNP VCF')
parser.add_argument('--json', dest='json', required=True, help='Path to parameters JSON')
parser.add_argument('--id', dest='id', required=False,
help='Study identifier. If not present then must be specified as \'id\' in json file')
parser.add_argument('--cohort_controls', type=int, dest='cohort_controls', required=False, default=None,
help='Total study number of controls (if case/control) or total sample size if continuous. Overwrites value if present in json file.')
parser.add_argument('--cohort_cases', type=int, dest='cohort_cases', required=False, default=None,
help='Total study number of cases. Overwrites value if present in json file.')
parser.add_argument('--csi', dest='csi', action='store_true', default=False, required=False,
help='Default is to index tbi but use this flag to index csi')
parser.add_argument("--log", dest="log", required=False, default='INFO',
choices=['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'],
help="Set the logging level")
parser.add_argument('--alias', dest='alias', required=False,
help='Optional chromosome alias file')
args = parser.parse_args()
# set logging level
if args.log:
logging.basicConfig(level=getattr(logging, args.log), format='%(asctime)s %(levelname)s %(message)s')
logging.info("Gwas2VCF {}".format(version))
logging.info("Arguments: {}".format(vars(args)))
logging.info("Reading JSON parameters")
try:
schema = Param(strict=True)
with open(args.json) as f:
j = schema.load(json.load(f)).data
logging.info("Parameters: {}".format(j))
except json.decoder.JSONDecodeError as e:
logging.error("Could not read json parameter file: {}".format(e))
sys.exit()
except marshmallow.exceptions.ValidationError as e:
logging.error("Could not validate json parameter file: {}".format(e))
sys.exit()
logging.info("Checking input arguments")
if args.data is None:
if 'data' in j.keys():
vars(args)['data'] = j['data']
else:
logging.error("'data' filename not provided in arguments or json file")
sys.exit()
if args.out is None:
if 'out' in j.keys():
vars(args)['out'] = j['out']
else:
logging.error("out filename not provided in arguments or json file")
sys.exit()
if args.id is None:
if 'id' in j.keys():
vars(args)['id'] = j['id']
else:
logging.error("id not provided in arguments or json file")
sys.exit()
if args.cohort_cases is None and 'cohort_cases' in j.keys():
vars(args)['cohort_cases'] = j['cohort_cases']
if args.cohort_controls is None and 'cohort_controls' in j.keys():
vars(args)['cohort_controls'] = j['cohort_controls']
# check values are valid
if args.cohort_cases is not None:
if args.cohort_cases < 1:
logging.error("Total study number of cases must be a positive number")
sys.exit()
if args.cohort_controls is not None:
if args.cohort_controls < 1:
logging.error("Total study number of controls must be a positive number")
sys.exit()
if not os.path.isfile(args.data):
logging.error("{} file does not exist".format(args.data))
sys.exit()
if not os.path.isfile(args.ref):
logging.error("{} file does not exist".format(args.ref))
sys.exit()
if not os.path.exists(os.path.dirname(args.out)):
logging.error("{} output directory does not exist".format(args.out))
sys.exit()
if args.dbsnp is not None:
dbsnp = pysam.VariantFile(args.dbsnp)
else:
dbsnp = None
if args.alias is not None:
alias = {}
with open(args.alias) as f:
for line in f:
(key, val) = line.strip().split("\t")
alias[key] = val
else:
alias = None
# read in data
# harmonise, left align and trim on-the-fly and write to pickle format
# keep file index for each record and chromosome position to write out karyotypically sorted records later
with pysam.FastaFile(args.ref) as fasta:
gwas, idx, sample_metadata = Gwas.read_from_file(
args.data,
fasta,
j['chr_col'],
j['pos_col'],
j['ea_col'],
j['oa_col'],
j['beta_col'],
j['se_col'],
j['pval_col'],
j['delimiter'],
j['header'],
ncase_field=j.get('ncase_col'),
rsid_field=j.get('snp_col'),
ea_af_field=j.get('eaf_col'),
nea_af_field=j.get('oaf_col'),
imp_z_field=j.get('imp_z_col'),
imp_info_field=j.get('imp_info_col'),
ncontrol_field=j.get('ncontrol_col'),
alias=alias,
dbsnp=dbsnp
)
if dbsnp is not None:
dbsnp.close()
# metadata
file_metadata = {
'Gwas2VCF_command': ' '.join(sys.argv[1:]) + "; " + version,
'file_date': datetime.now().isoformat()
}
if args.cohort_controls is not None:
sample_metadata['TotalControls'] = args.cohort_controls
if args.cohort_cases is not None:
sample_metadata['TotalCases'] = args.cohort_cases
if 'ncase_col' in j or args.cohort_cases is not None:
sample_metadata['StudyType'] = 'CaseControl'
else:
sample_metadata['StudyType'] = 'Continuous'
# write to VCF
# loop over sorted chromosome position and get record using random access
Vcf.write_to_file(gwas, idx, args.out, fasta, j['build'], args.id, sample_metadata, file_metadata, args.csi)
# close temp file to release disk space
gwas.close()
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"