Add psm_reader_kwargs option to config

compomics · Sep 14, 2023 · 20fd311 · 20fd311
1 parent 13e210c
commit 20fd311
Show file tree

Hide file tree

Showing 3 changed files with 7 additions and 0 deletions.
diff --git a/docs/source/config_schema.md b/docs/source/config_schema.md
@@ -22,6 +22,7 @@
       - *string*
       - *null*
   - **`psm_file_type`** *(string)*: PSM file type. By default inferred from file extension. Default: `"infer"`.
+  - **`psm_reader_kwargs`** *(object)*: Keyword arguments passed to the PSM reader. Default: `{}`.
   - **`spectrum_path`**: Path to spectrum file or directory with spectrum files.
     - **One of**
       - *string*

diff --git a/ms2rescore/core.py b/ms2rescore/core.py
@@ -43,6 +43,7 @@ def rescore(configuration: Dict, psm_list: PSMList = None) -> None:
             config["psm_file"],
             filetype=config["psm_file_type"],
             show_progressbar=True,
+            **config["psm_reader_kwargs"],
         )
 
     logger.debug("Finding decoys...")

diff --git a/ms2rescore/package_data/config_schema.json b/ms2rescore/package_data/config_schema.json
@@ -69,6 +69,11 @@
                     "type": "string",
                     "default": "infer"
                 },
+                "psm_reader_kwargs": {
+                    "description": "Keyword arguments passed to the PSM reader.",
+                    "type": "object",
+                    "default": {}
+                },
                 "spectrum_path": {
                     "description": "Path to spectrum file or directory with spectrum files",
                     "oneOf": [{ "type": "string" }, { "type": "null" }]