integrate mumble into ms2branch

compomics · Aug 21, 2024 · 11fdc51 · 11fdc51
1 parent 6e2d102
commit 11fdc51
Show file tree

Hide file tree

Showing 5 changed files with 64 additions and 0 deletions.
diff --git a/ms2rescore/exceptions.py b/ms2rescore/exceptions.py
@@ -41,3 +41,9 @@ class RescoringError(MS2RescoreError):
     """Error while rescoring PSMs."""
 
     pass
+
+
+class ParseSpectrumError(MS2RescoreError):
+    """Error while rescoring PSMs."""
+
+    pass
diff --git a/ms2rescore/package_data/config_default.json b/ms2rescore/package_data/config_default.json
@@ -12,6 +12,7 @@
             },
             "maxquant": {}
         },
+        "psm_generator": {},
         "rescoring_engine": {
             "mokapot": {
                 "train_fdr": 0.01,

diff --git a/ms2rescore/package_data/config_schema.json b/ms2rescore/package_data/config_schema.json
@@ -62,6 +62,18 @@
                         "mokapot": {}
                     }
                 },
+                "psm_generator": {
+                    "description": "PSM generator and their configuration.",
+                    "type": "object",
+                    "minProperties": 0,
+                    "maxProperties": 1,
+                    "patternProperties": {
+                        ".*": { "$ref": "#/definitions/psm_generator" },
+                        "mumble": {
+                            "$ref": "#/definitions/mumble"
+                        }
+                    }
+                },
                 "config_file": {
                     "description": "Path to configuration file",
                     "oneOf": [{ "type": "string" }, { "type": "null" }]
@@ -179,6 +191,7 @@
                     "type": "boolean",
                     "default": false
                 }
+
             }
         }
     },
@@ -193,6 +206,11 @@
             "type": "object",
             "additionalProperties": true
         },
+        "psm_generator": {
+            "description": "Additional PSM feature generator configuration",
+            "type": "object",
+            "additionalProperties": true
+        },
         "basic": {
             "$ref": "#/definitions/feature_generator",
             "description": "Basic feature generator configuration",
@@ -273,6 +291,30 @@
                 }
             }
         },
+        "mumble": {
+            "$ref": "#/definitions/psm_generator",
+            "description": "Mumble PSM generator configuration using Mubmle",
+            "type": "object",
+            "additionalProperties": true,
+            "properties": {
+                "aa_combinations": {
+                    "description": "Additional amino acid combinations to consider as mass shift",
+                    "type": "integer",
+                    "default": 0
+                },
+                "fasta_file": {
+                    "description": "Maximum number of modifications per peptide",
+                    "oneOf": [{ "type": "string" }, { "type": "null" }],
+                    "default": false
+                },
+                "mass_error": {
+                    "description": "mass error in Da",
+                    "type": "number",
+                    "default": 0.2
+                }
+            }
+        },
+
         "mokapot": {
             "$ref": "#/definitions/rescoring_engine",
             "description": "Mokapot rescoring engine configuration. Additional properties are passed to the Mokapot brew function.",

diff --git a/ms2rescore/parse_psms.py b/ms2rescore/parse_psms.py
@@ -5,6 +5,7 @@
 import numpy as np
 import psm_utils.io
 from psm_utils import PSMList
+from mumble import PSMHandler
 
 from ms2rescore.exceptions import MS2RescoreConfigurationError
 
@@ -90,6 +91,19 @@ def parse_psms(config: Dict, psm_list: Union[PSMList, None]) -> PSMList:
         new_ids = [_match_psm_ids(old_id, pattern) for old_id in psm_list["spectrum_id"]]
         psm_list["spectrum_id"] = new_ids
 
+    # Addition of Modifications for mass shifts in the PSMs with Mumble
+    if "mumble" in config["psm_generator"]:
+        logger.debug("Applying modifications for mass shifts using Mumble...")
+        mumble_config = config["psm_generator"]["mumble"]
+        psm_handler = PSMHandler(
+            **mumble_config,  # TODO how do we store config for mumble?
+        )
+        psm_list = psm_handler.add_modified_psms(
+            psm_list, generate_modified_decoys=True, keep_original=True
+        )
+        if mumble_config["output_file"]:
+            psm_handler.write_modified_psm_list(psm_list, mumble_config["output_file"])
+
     return psm_list
 
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -50,6 +50,7 @@ dependencies = [
     "pyteomics>=4.7.2",
     "rich>=12",
     "tomli>=2; python_version < '3.11'",
+    "mumble"
 ]
 
 [project.optional-dependencies]