change fasta_to_ali

build_modeller.py

@@ -6,6 +6,10 @@ import time
 from typing import List
 import sys
 import glob
+import pyfastx
+from Bio import SeqIO
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
 
 @dataclass
 class PDBModeler:
@@ -108,13 +112,13 @@ class PDBModeler:
         if ali_file.exists():
             ali_file.unlink()
 
-        with open(self.fasta_file, 'r') as f:
-            seq = f.readlines()[1].strip()
+        fx = pyfastx.Fasta(self.fasta_file.as_posix(), build_index=True)
+        assert len(fx) == 1, "FASTA file should contain only one sequence"
 
         with open(ali_file, 'w') as f:
             f.write(f'>P1;{self.sequence}\n')
             f.write(f'sequence:{self.sequence}:::::::0.00: 0.00\n')
-            f.write(f'{seq}*')
+            f.write(f'{fx[0].seq}*')
 
         return ali_file