def _prepare_samples(self):
"""
private method to load sample information
"""
if not self.args.no_genotypes:
self.samples = self.vcf_reader.samples
self.sample_to_id = {}
for idx, sample in enumerate(self.samples):
self.sample_to_id[sample] = idx + 1
self.ped_hash = {}
if self.args.ped_file is not None:
header = get_ped_fields(self.args.ped_file)
for line in open(self.args.ped_file, 'r'):
if line.startswith("#"):
continue
fields = line.split()
linedict = dict(zip(header, line.split()))
self.ped_hash[fields[1]] = fields
sample_list = []
for sample in self.samples:
i = self.sample_to_id[sample]
if sample in self.ped_hash:
fields = self.ped_hash[sample]
sample_list = [i] + fields
elif len(self.ped_hash) > 0:
sys.exit("EXITING: sample %s found in the VCF but "
"not in the PED file.\n" % (sample))
else:
# if there is no ped file given, just fill in the name and
# sample_id and set the other required fields to None
sample_list = [i, None, sample]
sample_list += list(repeat(None, len(default_ped_fields) - 2))
database.insert_sample(self.c, sample_list)
def create_sample_table(cursor, args):
NUM_BUILT_IN = 6
fields = get_ped_fields(args.ped_file)
required = "sample_id integer"
optional_fields = ["family_id", "name", "paternal_id", "maternal_id", "sex", "phenotype"]
optional_fields += fields[NUM_BUILT_IN:] + ["PRIMARY KEY(sample_id ASC)"]
optional = " text default NULL,".join(optional_fields)
structure = """{0}, {1}""".format(required, optional)
creation = "create table if not exists samples ({0})".format(structure)
cursor.execute(creation)
def create_sample_table(cursor, args):
NUM_BUILT_IN = 6
fields = get_ped_fields(args.ped_file)
required = "sample_id integer"
optional_fields = ["family_id", "name", "paternal_id", "maternal_id",
"sex", "phenotype"]
optional_fields += fields[NUM_BUILT_IN:] + ["PRIMARY KEY(sample_id ASC)"]
optional = " text default NULL,".join(optional_fields)
structure = '''{0}, {1}'''.format(required, optional)
creation = "create table if not exists samples ({0})".format(structure)
cursor.execute(creation)
def amend_sample(args):
loaded_subjects = get_subjects(args)
ped_dict = load_ped_file(args.sample)
header = get_ped_fields(args.sample)
with database_transaction(args.db) as c:
for k, v in loaded_subjects.items():
if k in ped_dict:
item_list = map(quote_string, ped_dict[k])
sample = zip(header, item_list)
set_str = ",".join([str(x) + "=" + str(y) for (x, y) in sample])
sql_query = "update samples set {0} where sample_id={1}"
c.execute(sql_query.format(set_str, v.sample_id))
def amend_sample(args):
loaded_subjects = get_subjects(args)
ped_dict = load_ped_file(args.sample)
header = get_ped_fields(args.sample)
with database_transaction(args.db) as c:
for k, v in loaded_subjects.items():
if k in ped_dict:
item_list = map(quote_string, ped_dict[k])
sample = zip(header, item_list)
set_str = ",".join(
[str(x) + "=" + str(y) for (x, y) in sample])
sql_query = "update samples set {0} where sample_id={1}"
c.execute(sql_query.format(set_str, v.sample_id))
def create_sample_table(cursor, metadata, args):
NUM_BUILT_IN = 6
cols = [sql.Column("sample_id", sql.Integer, primary_key=True)]
fields = get_ped_fields(args.ped_file)
optional_fields = ["family_id", "name", "paternal_id", "maternal_id",
"sex", "phenotype"]
optional_fields += fields[NUM_BUILT_IN:]
for field in optional_fields:
if field == "name":
cols.append(sql.Column(field, sql.String(50)))
else:
cols.append(sql.Column(field, sql.TEXT))
t = sql.Table("samples", metadata, *cols)
t.drop(checkfirst=True)
metadata.create_all(tables=[t])
def create_sample_table(cursor, metadata, args):
NUM_BUILT_IN = 6
cols = [sql.Column("sample_id", sql.Integer, primary_key=True)]
fields = get_ped_fields(args.ped_file)
optional_fields = [
"family_id", "name", "paternal_id", "maternal_id", "sex", "phenotype"
]
optional_fields += fields[NUM_BUILT_IN:]
for field in optional_fields:
if field == "name":
cols.append(sql.Column(field, sql.String(50)))
else:
cols.append(sql.Column(field, sql.TEXT))
t = sql.Table("samples", metadata, *cols)
t.drop(checkfirst=True)
metadata.create_all(tables=[t])
