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fix: update script to also generate aliases
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5 changes: 3 additions & 2 deletions
5
scripts/generate_new_lineage_definitions.bash
100644 → 100755
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Original file line number | Diff line number | Diff line change |
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@@ -1,4 +1,5 @@ | ||
#!/bin/bash | ||
curl https://raw.githubusercontent.com/cov-lineages/pango-designation/refs/heads/master/pango_designation/alias_key.json > alias_key.json | ||
curl https://raw.githubusercontent.com/cov-lineages/pango-designation/refs/heads/master/lineages.csv | tail -n +2 | cut -d',' -f2 > lineages.csv | ||
python3 alias2lineageDefinitions.py alias_key.json lineages.csv > lineage_definitions.yaml | ||
curl https://raw.githubusercontent.com/cov-lineages/pango-designation/refs/heads/master/lineages.csv > lineages.csv | ||
python3 uniqueValuesFromColumn.py lineages.csv 1 lineage_keys.csv | ||
python3 alias2lineageDefinitions.py alias_key.json lineage_keys.csv > lineage_definitions.yaml |
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,30 @@ | ||
import csv | ||
import argparse | ||
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def extract_unique_values(input_csv, column_idx, output_csv): | ||
unique_values = set() | ||
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with open(input_csv, mode='r', newline='', encoding='utf-8') as infile: | ||
reader = csv.reader(infile) | ||
next(reader, None) | ||
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for row_number, row in enumerate(reader, start=2): # Start from row 2 considering header is row 1 | ||
if len(row) <= column_idx: | ||
raise ValueError(f"Row {row_number} has fewer than {column_idx + 1} columns.") | ||
unique_values.add(row[column_idx]) | ||
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sorted_unique_values = sorted(unique_values) | ||
with open(output_csv, mode='w', newline='', encoding='utf-8') as outfile: | ||
writer = csv.writer(outfile) | ||
for value in sorted_unique_values: | ||
writer.writerow([value]) | ||
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if __name__ == "__main__": | ||
parser = argparse.ArgumentParser(description="Extract unique values from a column of a CSV file. Also strips header line") | ||
parser.add_argument("input_csv", help="Path to the input CSV file") | ||
parser.add_argument("column_idx", type=int, help="Index (0-based) of the column to extract") | ||
parser.add_argument("output_csv", help="Path to the output CSV file") | ||
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args = parser.parse_args() | ||
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extract_unique_values(args.input_csv, args.column_idx, args.output_csv) |
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