94 lines
3.1 KiB
Python
Executable File
94 lines
3.1 KiB
Python
Executable File
"""Check if a sample sheet is valid."""
|
|
import csv
|
|
import sys
|
|
|
|
from .util import get_named_logger, wf_parser # noqa: ABS101
|
|
|
|
|
|
def main(args):
|
|
"""Run the entry point."""
|
|
logger = get_named_logger("checkSheet")
|
|
|
|
barcodes = []
|
|
aliases = []
|
|
sample_types = []
|
|
allowed_sample_types = [
|
|
"test_sample", "positive_control", "negative_control", "no_template_control"
|
|
]
|
|
|
|
try:
|
|
with open(args.sample_sheet, "r") as f:
|
|
csv_reader = csv.DictReader(f)
|
|
n_row = 0
|
|
for row in csv_reader:
|
|
n_row += 1
|
|
if n_row == 1:
|
|
n_cols = len(row)
|
|
else:
|
|
# check we got the same number of fields
|
|
if len(row) != n_cols:
|
|
raise ValueError(
|
|
f"Unexpected number of cells in row number {n_row}."
|
|
)
|
|
try:
|
|
barcodes.append(row["barcode"])
|
|
except KeyError:
|
|
sys.stdout.write("'barcode' column missing")
|
|
sys.exit()
|
|
try:
|
|
aliases.append(row["alias"])
|
|
except KeyError:
|
|
sys.stdout.write("'alias' column missing")
|
|
sys.exit()
|
|
try:
|
|
sample_types.append(row["type"])
|
|
except KeyError:
|
|
pass
|
|
except Exception as e:
|
|
sys.stdout.write(f"Parsing error: {e}")
|
|
sys.exit()
|
|
|
|
# check barcode and alias values are unique
|
|
if len(barcodes) > len(set(barcodes)):
|
|
sys.stdout.write("values in 'barcode' column not unique")
|
|
sys.exit()
|
|
if len(aliases) > len(set(aliases)):
|
|
sys.stdout.write("values in 'alias' column not unique")
|
|
sys.exit()
|
|
|
|
if sample_types:
|
|
# check if "type" column has unexpected values
|
|
unexp_type_vals = set(sample_types) - set(allowed_sample_types)
|
|
|
|
if unexp_type_vals:
|
|
sys.stdout.write(
|
|
f"found unexpected values in 'type' column: {unexp_type_vals}. "
|
|
f"Allowed values are: {allowed_sample_types}"
|
|
)
|
|
sys.exit()
|
|
|
|
if args.required_sample_types:
|
|
for required_type in args.required_sample_types:
|
|
if required_type not in allowed_sample_types:
|
|
sys.stdout.write(f"Not an allowed sample type: {required_type}")
|
|
sys.exit()
|
|
if sample_types.count(required_type) < 1:
|
|
sys.stdout.write(
|
|
f"Sample sheet requires at least 1 of {required_type}")
|
|
sys.exit()
|
|
|
|
logger.info(f"Checked sample sheet {args.sample_sheet}.")
|
|
|
|
|
|
def argparser():
|
|
"""Argument parser for entrypoint."""
|
|
parser = wf_parser("check_sample_sheet")
|
|
parser.add_argument("sample_sheet", help="Sample sheet to check")
|
|
parser.add_argument(
|
|
"--required_sample_types",
|
|
help="List of required sample types. Each sample type provided must "
|
|
"appear at least once in the sample sheet",
|
|
nargs="*"
|
|
)
|
|
return parser
|