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from __future__ import print_function
import sys
sys.path.append('..') # this is an assumption and is probably wrong
from base.utils import parse_date
import argparse
import json
from numpy import ndarray
from augur.argparse_ import ExtendOverwriteDefault
def get_trait(attributes, trait, dateFormat):
if trait in ["num_date", "date"]:
try:
date = parse_date(attributes["raw_date"], dateFormat)[1]
except KeyError:
return "unknown"
if isinstance(date, (list, tuple, ndarray)):
return (date[0] + date[1]) / 2
return date
else:
try:
return attributes[trait]
except KeyError:
return "unknown"
if __name__=="__main__":
parser = argparse.ArgumentParser(description = "Process a given JSONs")
parser.add_argument('--json', required=True, type=str, help="prepared JSON")
parser.add_argument('--trait', required=True, type=str, help="prepared JSON")
parser.add_argument('--header', nargs='*', action='extend', type=str, help="header fields")
parser.add_argument('--date_format', nargs='*', action=ExtendOverwriteDefault, default=["%Y-%m-%d"], type=str, help="if needed. default: [%%Y-%%m-%%d]")
params = parser.parse_args()
with open(params.json, 'r') as fh:
data = json.load(fh)
try:
print("\t".join(params.header))
except KeyError:
pass
for seq, val in data["sequences"].items():
print("{}\t{}".format(seq, get_trait(val["attributes"], params.trait, params.date_format)))
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