update

test.py

@@ -1,6 +1,13 @@
 from tcr_pmhc_complexes import FastaFile
 from pathlib import Path
 import glob
+from analysis_pdb import PDBAnalyzer
+
+def download_fasta_for_pdb(pdb_id, pdb_directory):
+    """Download the FASTA file for a given PDB ID into the specified directory."""
+    pdb_analyzer = PDBAnalyzer(pdb_file=Path(pdb_directory) / f"{pdb_id}.pdb")
+    fasta_file = pdb_analyzer.download_fasta(pdb_id)
+    return fasta_file
 
 def test_fasta_file(file_path):
     fasta_file = FastaFile(file=Path(file_path))
@@ -17,15 +24,33 @@ def test_fasta_file(file_path):
         print(f"Description: {header_info.description}")
         print(f"Sequence: {seq.sequence.sequence[:30]}...")
         print(f"Sequence Length: {len(seq.sequence.sequence)}\n")
+    return fasta_file
 
-# Discover all .fasta files within directories matching the pattern
+# Discover all runner_* directories
 runner_directories = glob.glob('/mnt/mydrive/analysis_pdb-dev/pdb_test1/runner_*')
-fasta_files = [file for directory in runner_directories for file in Path(directory).glob('*.fasta')]
+fasta_files = []
+
+for directory in runner_directories:
+    pdb_file = Path(directory).joinpath(f'{directory[-4:]}.pdb')
+    fasta_file = Path(directory).joinpath(f'{directory[-4:]}.fasta')
+    if pdb_file.exists() and fasta_file.exists():
+        fasta_files.append(fasta_file)
+    else:
+        print(f'File {fasta_file} does not exist, download...')
+        ins = PDBAnalyzer(pdb_file)
+        ins.download_fasta()
+
+# Check if the number of directories matches the number of PDB files
+if len(runner_directories) != len(fasta_files):
+    print("Warning: Number of runner directories does not match number of PDB files.")
 
 # Add the standard FASTA file to the list of files to be tested
-fasta_files.append(Path('/mnt/mydrive/analysis_pdb-dev/test.fasta'))
+# fasta_files.append(Path('/mnt/mydrive/analysis_pdb-dev/test.fasta'))
+
+# # Test each FASTA file
+# for file_path in fasta_files:
+#     test_fasta_file(file_path)
+
+
+
 
-# Test each FASTA file
-for file_path in fasta_files:
-    test_fasta_file(file_path)
-# test_fasta_file('/mnt/mydrive/analysis_pdb-dev/test.fasta')exit