Argument parsing (early version)

convert_to_modelcif.py

+#!/usr/bin/env python3
+
+"""Take the output of the AlphaPulldown pipeline and turn it into a ModelCIF
+file with a lot of metadata in place."""
+
+from absl import app
+from absl import flags
+
+
+FLAGS = flags.FLAGS
+flags.DEFINE_list(
+    "metadata",
+    None,
+    "JSON files with information about experiment setup, one file per feature",
+)
+flags.DEFINE_string("af2_output", None, "Results of AlphaFold2 modelling")
+flags.DEFINE_integer(
+    "model_selected",
+    None,
+    "Model to be converted into ModelCIF, use '--select_all' to convert all "
+    + "models found in '--af2_output'",
+)
+flags.DEFINE_bool(
+    "select_all",
+    False,
+    "Convert all models found in '--af2_output' into ModelCIF, excludes "
+    + "'--model_selected'",
+)
+
+
+def _mark_model_selection_as_mutual_exclusive():
+    """Create & register a validator for model selection.
+
+    Enforce only one option is set, either '--select_all' or '--model_selected'.
+    Enforce that at least one of '--select_all' or '--model_selected' is set
+    (so this options will not pop up in `flags.mark_flags_as_required`).
+    """
+
+    def _validate_mutual_exclusion_model_selection(flags_dict):
+        not_set_count = 0
+        if flags_dict["model_selected"] is None:
+            not_set_count += 1
+        if flags_dict["select_all"] is False:
+            not_set_count += 1
+
+        if not_set_count == 1:
+            return True
+        return False
+
+    flags.register_multi_flags_validator(
+        ["model_selected", "select_all"],
+        _validate_mutual_exclusion_model_selection,
+        "Exactly one (and only one) argument needs to be set.",
+    )
+
+
+_mark_model_selection_as_mutual_exclusive()
+flags.mark_flags_as_required(["metadata", "af2_output"])
+# ToDo: implement a flags.register_validator() for 'metadata', checking that
+#       the file exists and is readable.
+# ToDo: implement a flags.register_validator() for 'af2_output', checking that
+#       the file directory exists and is readable (overkill: check directory
+#       structure).
+
+
+def main(argv):
+    """Run as script."""
+    """
+    Here, the metadata json files for each feature are in features_monomers/
+    directory. The models are in models/ directory, and usually there are many
+    complexes modelled using different permutations of the monomeric features.
+    For the sake of size, I send you the models of only one dimer
+    cage_B_and_cage_C/ that was generated using features_monomers/cage_B.pkl
+    and features_monomers/cage_C.pkl accordingly.
+    Please note that typically all the cage_?_feature_metadata.json files are
+    identical in terms of used databases and software versions and generated
+    in one go.
+    However, theoretically they could be generated using different binaries/DBs
+    versions, so maybe it makes sense to compare them and store both/all
+    versions if they are different. This merging can be done on our
+    AlphaPulldown side and may be added now or later on. Let me know if it is
+    critical for you now.
+    """
+    del argv  # Unused.
+
+
+if __name__ == "__main__":
+    app.run(main)
+
+#  LocalWords:  ToDo