Enable extra arguents for run-af2 (for custom run_alphafold.py scripts)

run_af2/src/run_af2/_shared.py

@@ -212,7 +212,7 @@ def parse_af2_arguments(parser):
         metavar="<FILE>",
         default=None,
     )
-    opts = parser.parse_args()
+    opts, extra_opts = parser.parse_known_args()
 
     # check that the db_preset setting makes sense
     for arg in db_preset_choices[opts.db_preset]:
@@ -253,7 +253,7 @@ def parse_af2_arguments(parser):
             )
             sys.exit(1)
 
-    return opts
+    return opts, extra_opts
 
 
 #  LocalWords:  argparse ArgumentParser Namespace Bioinformatics Biozentrum af

run_af2/src/run_af2/run_singularity.py

@@ -118,6 +118,7 @@ def _assemble_singularity_call(  # pylint: disable=too-many-arguments
     model_preset,
     is_prokaryote_list,
     data_paths,
+    extra_arg_list,
 ):
     """Assemble the command to run AF2 from the Singularity image."""
     # Since the number of arguments to this function is already high, we allow
@@ -158,6 +159,9 @@ def _assemble_singularity_call(  # pylint: disable=too-many-arguments
     for flag, path in data_paths.items():
         snglrty_cmd.append(f"--{flag}={path}")
 
+    # append extra arguments
+    snglrty_cmd.extend(extra_arg_list)
+
     return snglrty_cmd
 
 
@@ -199,6 +203,7 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
     af2_image_dir="/scicore/home/schwede/GROUP/alphafold_data/",
     snglrty_bin="/usr/bin/singularity",
     tmpdir_var="TMPDIR",
+    extra_arg_list=None,
     # data_dir="/scicore/data/managed/AF2params/frozen_210805T171956/",
     data_dir="/scicore/home/schwede/GROUP/alphafold_data/",
     uniref90_database_path="/scicore/data/managed/UniProt/latest/uniref/"
@@ -274,6 +279,10 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
     :param tmpdir_var: An environment variable defining tmp space, that is not
                        necessarily "/tmp" on some systems.
     :type tmpdir_var: :class:`str`
+    :param extra_arg_list: List of extra arguments appended to the Singularity
+                           call. That is for adding extra arguments in a
+                           modified version of run_alphafold.py.
+    :type extra_arg_list: :class:`list`
     :param data_dir: Holds the params sub directory with model parameters.
                      Corresponds to DOWNLOAD_DIR in AF2.
     :type data_dir: :class:`str`
@@ -321,6 +330,8 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
     # Since the number of arguments to this function is already high, we allow
     # more local variables than defined by PEP8.
     # pylint: disable=too-many-locals
+    if extra_arg_list is None:
+        extra_arg_list = []
     tmpdir = os.getenv(tmpdir_var)
     if tmpdir is None:
         raise ValueError(f"tmpdir_var {tmpdir_var} must not be empty.")
@@ -382,6 +393,7 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
         model_preset,
         is_prokaryote_list,
         data_paths,
+        extra_arg_list,
     )
 
     # set up environment
@@ -412,7 +424,7 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
 
 def main():
     """Execute as script"""
-    opts = _parse_cmdline()
+    opts, extra_arg_list = _parse_cmdline()
 
     # Collect data paths into a dictionary so we can deal with default path on
     # the sciCORE cluster more easily.
@@ -449,7 +461,8 @@ def main():
             opts.db_preset,
             opts.model_preset,
             opts.is_prokaryote_list,
-            af2_image_file=opts.singularity_image,
+            opts.singularity_image,
+            extra_arg_list=extra_arg_list,
             **data_paths,
         )
     except RuntimeError as rte: