revert to load_module for parsing af flags

alphapulldown/create_individual_features.py

@@ -4,13 +4,12 @@
 # This script is just to create msa and structural features for each sequences and store them in pickle
 # #
 
-from alphafold import run_alphafold as run_af
 from alphapulldown.objects import MonomericObject
 from alphafold.data.pipeline import DataPipeline
 from alphafold.data.tools import hmmsearch
 from alphafold.data import templates
 from absl import logging, app
-from alphapulldown.utils import save_meta_data, create_uniprot_runner, parse_fasta
+from alphapulldown.utils import save_meta_data, create_uniprot_runner, parse_fasta, get_flags_from_af
 import contextlib
 from datetime import datetime
 from pathlib import Path
@@ -25,7 +24,7 @@ def output_meta_file(file_path):
     with open(file_path, "w") as outfile:
         yield outfile.name
 
-flags = run_af.flags
+flags = get_flags_from_af()
 flags.DEFINE_bool("save_msa_files", False, "save msa output or not")
 flags.DEFINE_bool(
     "skip_existing", False, "skip existing monomer feature pickles or not"

alphapulldown/create_individual_features_with_templates.py

@@ -3,9 +3,8 @@
 # create_individual_features using custom multimeric templates
 #
 
-from alphafold import run_alphafold as run_af
 from alphapulldown.objects import MonomericObject
-from alphapulldown.utils import create_uniprot_runner
+from alphapulldown.utils import create_uniprot_runner, get_flags_from_af
 from alphapulldown.create_custom_template_db import create_db
 from alphafold.data.pipeline import DataPipeline
 from alphafold.data.tools import hmmsearch
@@ -19,7 +18,7 @@
 from create_individual_features import create_and_save_monomer_objects, iter_seqs
 
 
-flags = run_af.flags
+flags = get_flags_from_af()
 
 flags.DEFINE_integer("job_index", None, "index of job in the description file, starting from 1")
 

alphapulldown/utils.py

@@ -12,6 +12,7 @@
 import pickle
 import logging
 from alphapulldown.plot_pae import plot_pae
+import alphafold
 from alphafold.model import config
 from alphafold.model import model
 from alphafold.model import data
@@ -26,6 +27,7 @@
 import re
 import hashlib
 import glob
+import importlib
 
 COMMON_PATTERNS = [
     r"[Vv]ersion\s*(\d+\.\d+(?:\.\d+)?)",  # version 1.0 or version 1.0.0
@@ -48,6 +50,25 @@
     'ColabFold' : ["https://wwwuser.gwdg.de/~compbiol/colabfold/colabfold_envdb_202108.tar.gz"],
 }
 
+def get_flags_from_af():
+    """
+    A function to load flags from alphafold imported as a module
+    """
+    def load_module(file_name, module_name):
+        spec = importlib.util.spec_from_file_location(module_name, file_name)
+        module = importlib.util.module_from_spec(spec)
+        sys.modules[module_name] = module
+        spec.loader.exec_module(module)
+        return module
+    PATH_TO_RUN_ALPHAFOLD = os.path.join(os.path.dirname(alphafold.__file__), "run_alphafold.py")
+    try:
+        run_af = load_module(PATH_TO_RUN_ALPHAFOLD, "run_alphafold")
+        return run_af.flags
+    except FileNotFoundError:
+        PATH_TO_RUN_ALPHAFOLD = os.path.join(os.path.dirname(os.path.dirname(alphafold.__file__)), "run_alphafold.py")
+        run_af = load_module(PATH_TO_RUN_ALPHAFOLD, "run_alphafold")
+        return run_af.flags
+
 
 def create_uniprot_runner(jackhmmer_binary_path, uniprot_database_path):
     """create a uniprot runner object"""