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c87881a | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 | #!/usr/bin/env python3
from __future__ import annotations
import argparse
import json
from pathlib import Path
from bgc_retrieval.external_prepare import extract_benchmark_proteins, write_mapping_outputs
def main() -> None:
parser = argparse.ArgumentParser()
parser.add_argument(
"--benchmark-dir", default="data/external/bgc-clustering-benchmark"
)
parser.add_argument("--output-dir", default="data/external/processed")
parser.add_argument("--source-commit", default="bb8500d60f90cb43397cc41de5aed396725aa800")
args = parser.parse_args()
benchmark = Path(args.benchmark_dir)
output = Path(args.output_dir)
mapping_counts = write_mapping_outputs(
benchmark / "source_data/NPAtlas_bm_v1.tsv",
output / "gold_bgc_product_mapping.csv",
output / "all_bgc_product_metadata.csv",
output / "ambiguous_product_exclusions.csv",
)
sequence_counts = extract_benchmark_proteins(
benchmark / "benchmark_bgc",
output / "external_proteins.fasta",
output / "external_atlas.csv",
output / "external_sequence_provenance.json",
args.source_commit,
)
concise_sequences = {
key: value for key, value in sequence_counts.items() if key != "source_manifest"
}
print(json.dumps({**mapping_counts, **concise_sequences}, indent=2, sort_keys=True))
if __name__ == "__main__":
main()
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