script: produces sample_input.fasta for 10 strains

Sample Input FASTA/sarsCov2DataExtract.py

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+from Bio import Entrez, SeqIO
+import requests
+
+# replace with YOUR email id.
+Entrez.email = "[email protected]"
+
+# mapping accession numbers to strain names
+accession_to_strain = {
+    "NC_045512": "Wuhan",
+    "OR075545": "XBB.1.16",
+    "OQ608429": "XBB.1.5",
+    "OR598953": "EG.5",
+    "PP292788": "AY.3",
+    "OR813619": "BA.2.86",
+    "OR829491": "CH.1.1",
+    "PP250483": "BF.10",
+    "PP316714": "JN.1",
+    "PP435534": "HV.1",
+    "OQ437945": "B.1.1.7",
+    "PP421053": "P.1",
+    "PP299611": "B.1.617.2",
+    "PP292591": "BE.1",
+    "OQ938406": "DN.2"
+}
+
+output_file = "tool_input.fasta"
+
+with open(output_file, 'w') as outfile:
+    for accession, strain_name in accession_to_strain.items():
+        try:
+            handle = Entrez.efetch(db="nucleotide", id=accession, rettype="fasta", retmode="text")
+            record = SeqIO.read(handle, "fasta")
+
+            # replacing the header with the strain name
+            record.id = strain_name
+            record.description = strain_name
+
+            # writing the modified sequence to the output file
+            SeqIO.write(record, outfile, "fasta")
+            handle.close()
+            print(f"Successfully fetched and added {strain_name}")
+        except Exception as e:
+            print(f"Failed to fetch {accession} ({strain_name}): {e}")
+
+print("Success! All sequences have been written to:", output_file)