Create protein_converter.py

Author: sinamajidian

archive/scripts/protein_converter.py

@@ -0,0 +1,22 @@
+import sys
+from Bio import SeqIO
+
+# Get input and output file paths from command-line arguments
+# Daniel Paiva Agustinho
+input_file = sys.argv[1]
+output_file = sys.argv[2]
+
+with open(input_file, "r") as input_handle:
+    with open(output_file, "w") as output_handle:
+        for record in SeqIO.parse(input_handle, "fasta"):
+            protein_seq = record.seq.translate()
+
+            # Extract the entire original header
+            original_header = record.description
+
+            # Create a new sequence record with the original header
+            protein_seq = SeqIO.SeqRecord(
+                protein_seq, id=record.id, description=original_header
+            )
+            SeqIO.write(protein_seq, output_handle, "fasta")
+print("done",str(output_file))