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Add --lookup-mac and --expand-mac to pyard command #259

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Merged
merged 2 commits into from
Aug 17, 2023
Merged

Add --lookup-mac and --expand-mac to pyard command #259

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f2e6fcc
Lookup MAC based on Allele List
pbashyal-nmdp Aug 16, 2023
01f982a
`--expand-mac` takes a MAC and converts to allele list
pbashyal-nmdp Aug 16, 2023
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26 changes: 25 additions & 1 deletion scripts/pyard
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ import sys

from pyard.constants import VALID_REDUCTION_TYPES
import pyard.misc
from pyard.exceptions import InvalidAlleleError, InvalidTypingError
from pyard.exceptions import InvalidAlleleError, InvalidTypingError, InvalidMACError
from pyard.misc import get_data_dir, get_imgt_version

if __name__ == "__main__":
Expand Down Expand Up @@ -70,6 +70,12 @@ if __name__ == "__main__":
help="Validate the provided GL String",
)
parser.add_argument("--cwd", dest="cwd", help="Perform CWD redux")
parser.add_argument(
"--expand-mac", dest="expand_mac", help="Expand MAC to Allele List"
)
parser.add_argument(
"--lookup-mac", dest="lookup_mac", help="Lookup MAC for an Allele List"
)

args = parser.parse_args()

Expand All @@ -89,6 +95,24 @@ if __name__ == "__main__":
print(f"{mapping[0]} = {'/'.join(mapping[1])}")
sys.exit(0)

# Handle --expand-mac option
if args.expand_mac:
try:
allele_list = ard.expand_mac(args.expand_mac)
print(allele_list)
except InvalidMACError as e:
print(e.message, file=sys.stderr)
sys.exit(0)

# Handle --lookup-mac option
if args.lookup_mac:
try:
mac = ard.lookup_mac(args.lookup_mac)
print(mac)
except InvalidMACError as e:
print(e.message, file=sys.stderr)
sys.exit(0)

try:
if args.validate:
ard.validate(args.cwd)
Expand Down