def read_fam_file(in_file):
out = {}
header = ped.get_ped_fields(in_file)
with open(in_file) as in_handle:
for line in in_handle:
if not line.startswith("#"):
field = line.split(None, 7)[:7]
if len(field) > 1:
info = dict(zip(header, field))
out[info["name"]] = info
return out
def read_fam_file(in_file):
out = {}
header = ped.get_ped_fields(in_file)
with open(in_file) as in_handle:
for line in in_handle:
if not line.startswith("#"):
field = line.split(None, 8)[:8]
if len(field) > 1:
info = dict(zip(header, field))
out[info["name"]] = info
return out
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:
add_columns(header, c, args.clear)
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])