Initial commit: BtToxin Pipeline project structure

scripts/download_bpprc_data.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python3
+"""从 BPPRC/NCBI 下载测试数据"""
+import os
+import argparse
+from pathlib import Path
+from Bio import Entrez, SeqIO
+import logging
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+Entrez.email = "your_email@example.com"
+
+TEST_GENOMES = {
+    'Bacillus_thuringiensis_HD-73': 'NZ_CP004069.1',
+    'Bacillus_thuringiensis_YBT-1520': 'NZ_CP003889.1',
+    'Bacillus_thuringiensis_BMB171': 'NC_014171.1',
+}
+
+def download_genome(accession, output_file):
+    """下载基因组"""
+    try:
+        logger.info(f"Downloading {accession}...")
+        handle = Entrez.efetch(
+            db="nucleotide",
+            id=accession,
+            rettype="fasta",
+            retmode="text"
+        )
+
+        with open(output_file, 'w') as f:
+            f.write(handle.read())
+
+        handle.close()
+        logger.info(f"✓ Downloaded: {output_file}")
+        return True
+    except Exception as e:
+        logger.error(f"✗ Failed: {e}")
+        return False
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--output-dir', default='tests/test_data/genomes')
+    parser.add_argument('--email', required=True)
+    args = parser.parse_args()
+
+    Entrez.email = args.email
+    output_dir = Path(args.output_dir)
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    for name, accession in TEST_GENOMES.items():
+        output_file = output_dir / f"{name}.fna"
+        download_genome(accession, output_file)
+
+if __name__ == '__main__':
+    main()