Merge pull request #424 from MannLabs/list-config

Improved config for fragment types
MannLabs · Jan 24, 2025 · abfefaf · abfefaf
2 parents 65a9583 + 3cb5ca1
commit abfefaf
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Showing 7 changed files with 75 additions and 14 deletions.
diff --git a/alphadia/constants/default.yaml b/alphadia/constants/default.yaml
@@ -46,8 +46,13 @@ library_prediction:
     - 200
     - 2000
   nce: 25.0
-  # semicolon separated list of fragment types. Supported types are: a, b, c, x, y, z, b_modloss, y_modloss
-  fragment_types: 'b;y'
+
+  # list of fragment types (see alphabase.peptide.fragment.FRAGMENT_TYPES for supported types)
+  # Supported types are: a, b, c, x, y, z, b_modloss, y_modloss, b_H2O, y_H2O, b_NH3, y_NH3, c_lossH, z_addH
+  fragment_types:
+    - 'b'
+    - 'y'
+
   # maximum charge state for predicted fragments
   max_fragment_charge: 2
   instrument: Lumos
@@ -327,8 +332,9 @@ transfer_library:
   # if true, the library is created for transfer learning
   enabled: False
 
-  # semicolon separated list of fragment types to include in the library. possible values are 'a', 'b', 'c', 'x', 'y', 'z'
-  fragment_types: 'b;y'
+  # list of fragment types (see alphabase.peptide.fragment.FRAGMENT_TYPES for supported types)
+  # Supported types are: a, b, c, x, y, z, b_modloss, y_modloss, b_H2O, y_H2O, b_NH3, y_NH3, c_lossH, z_addH
+  fragment_types: ['b', 'y']
 
   # maximum charge for fragments
   max_charge: 2

diff --git a/alphadia/libtransform.py b/alphadia/libtransform.py
@@ -290,7 +290,7 @@ def __init__(
             Default is None, which means the peptdeep default model ("generic") is being used.
             Possible values are ['generic','phospho','digly']
 
-        fragment_types : List[str], optional
+        fragment_types : list[str], optional
             Fragment types to predict. Default is ["b", "y"].
 
         max_fragment_charge : int, optional

diff --git a/alphadia/search_step.py b/alphadia/search_step.py
@@ -218,7 +218,7 @@ def _parse_modifications(mod_str: str) -> list[str]:
                 mp_process_num=thread_count,
                 peptdeep_model_path=prediction_config["peptdeep_model_path"],
                 peptdeep_model_type=prediction_config["peptdeep_model_type"],
-                fragment_types=prediction_config["fragment_types"].split(";"),
+                fragment_types=prediction_config["fragment_types"],
                 max_fragment_charge=prediction_config["max_fragment_charge"],
             )
 

diff --git a/alphadia/workflow/peptidecentric.py b/alphadia/workflow/peptidecentric.py
@@ -1176,7 +1176,7 @@ def requantify_fragments(
             verbosity="progress",
         )
 
-        fragment_types = self.config["transfer_library"]["fragment_types"].split(";")
+        fragment_types = self.config["transfer_library"]["fragment_types"]
         max_charge = self.config["transfer_library"]["max_charge"]
 
         self.reporter.log_string(

diff --git a/gui/src/renderer/components/ParameterInput.js b/gui/src/renderer/components/ParameterInput.js
@@ -172,6 +172,29 @@ const ParameterInput = ({
                     />)
                 break;
 
+            case "multi_select":
+                input = (
+                    <FormControl variant="standard" size="small" sx={{width: "150px", minHeight: "0px"}}>
+                        <Select
+                            multiple
+                            value={parameter.value}
+                            onChange={(event) => {onChange(event.target.value)}}
+                            renderValue={(selected) => (
+                                <Typography>
+                                    {selected.length} selected
+                                </Typography>
+                            )}
+                        >
+                            {parameter.options.map((option) => (
+                                <MenuItem key={option} value={option}>
+                                    {option}
+                                </MenuItem>
+                            ))}
+                        </Select>
+                    </FormControl>
+                )
+                break;
+
             default:
                 input = (
                     <Typography>

diff --git a/gui/workflows/PeptideCentric.v1.json b/gui/workflows/PeptideCentric.v1.json
@@ -210,9 +210,25 @@
                 {
                     "id": "fragment_types",
                     "name": "Fragment types",
-                    "value": "b;y",
-                    "description": "Semicolon separated list of fragment types. \n Supported types: b, y, b_modloss, y_modloss. \n Must be supported by the chosen PeptDeep model.",
-                    "type": "string"
+                    "value": ["b", "y"],
+                    "description":  "List of fragment types to quantify in the library. The PeptDeep model must support the chosen fragment types.",
+                    "type": "multi_select",
+                    "options": [
+                        "b",
+                        "y",
+                        "b_modloss",
+                        "y_modloss",
+                        "a",
+                        "c",
+                        "x",
+                        "z",
+                        "b_H2O",
+                        "y_H2O",
+                        "b_NH3",
+                        "y_NH3",
+                        "c_lossH",
+                        "z_addH"
+                    ]
                 },
                 {
                     "id": "max_fragment_charge",
@@ -574,9 +590,25 @@
                 {
                     "id": "fragment_types",
                     "name": "Fragment types",
-                    "value": "b;y",
-                    "description": "Semicolon separated list of fragment types to include in the library. \n possible values are 'a', 'b', 'c', 'x', 'y', 'z'",
-                    "type": "string"
+                    "value": ["b", "y"],
+                    "description": "List of fragment types to quantify in the library.",
+                    "type": "multi_select",
+                    "options": [
+                        "b",
+                        "y",
+                        "b_modloss",
+                        "y_modloss",
+                        "a",
+                        "c",
+                        "x",
+                        "z",
+                        "b_H2O",
+                        "y_H2O",
+                        "b_NH3",
+                        "y_NH3",
+                        "c_lossH",
+                        "z_addH"
+                    ]
                 },
                 {
                     "id": "max_charge",

diff --git a/tests/unit_tests/test_outputaccumulator.py b/tests/unit_tests/test_outputaccumulator.py
@@ -53,7 +53,7 @@ def prepare_input_data():
         },
         "transfer_library": {
             "enabled": True,
-            "fragment_types": "b;y",
+            "fragment_types": ["b", "y"],
             "max_charge": 2,
             "top_k_samples": 3,
             "norm_delta_max": True,