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Merge pull request #9 from nextstrain/testing_strain_name
Changing json names to show strain name.
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import pandas as pd | ||
import json | ||
import argparse | ||
from augur.io import read_metadata | ||
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def replace_name_recursive(node, lookup, saveoldcolumn): | ||
if node["name"] in lookup: | ||
if saveoldcolumn == "accession": | ||
node["node_attrs"][saveoldcolumn] = node["name"] | ||
elif saveoldcolumn == "genbank_accession": | ||
node["node_attrs"][saveoldcolumn] = {} | ||
node["node_attrs"][saveoldcolumn]["value"] = node["name"] | ||
else: | ||
node["node_attrs"][saveoldcolumn] = node["name"] | ||
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if node["name"] in lookup: | ||
node["name"] = lookup[node["name"]] | ||
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if "children" in node: | ||
for child in node["children"]: | ||
replace_name_recursive(child, lookup, saveoldcolumn) | ||
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if __name__=="__main__": | ||
parser = argparse.ArgumentParser( | ||
description="Swaps out the strain names in the Auspice JSON with the final strain name", | ||
formatter_class=argparse.ArgumentDefaultsHelpFormatter | ||
) | ||
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parser.add_argument('--input-auspice-json', type=str, required=True, help="input auspice_json") | ||
parser.add_argument('--metadata', type=str, required=True, help="input data") | ||
parser.add_argument('--metadata-id-columns', nargs="+", help="names of possible metadata columns containing identifier information, ordered by priority. Only one ID column will be inferred.") | ||
parser.add_argument('--display-strain-name', type=str, required=True, help="field to use as strain name in auspice") | ||
parser.add_argument('--output', type=str, metavar="JSON", required=True, help="output Auspice JSON") | ||
args = parser.parse_args() | ||
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metadata = read_metadata(args.metadata, id_columns=args.metadata_id_columns) | ||
name_lookup = {} | ||
for ri, row in metadata.iterrows(): | ||
strain_id = row.name | ||
name_lookup[strain_id] = args.display_strain_name if pd.isna(row[args.display_strain_name]) else row[args.display_strain_name] | ||
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with open(args.input_auspice_json, 'r') as fh: | ||
data = json.load(fh) | ||
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replace_name_recursive(data['tree'], name_lookup, "genbank_accession") | ||
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with open(args.output, 'w') as fh: | ||
json.dump(data, fh) |