Merge pull request #328 from theGreatHerrLebert/feature/timsim-gui

Feature/timsim gui
theGreatHerrLebert · Feb 21, 2025 · 68d6d8c · 68d6d8c
2 parents a22ccb4 + 847bb6b
commit 68d6d8c
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Showing 4 changed files with 12 additions and 10 deletions.
diff --git a/imspy/imspy/timstof/dbsearch/imspy_dda.py b/imspy/imspy/timstof/dbsearch/imspy_dda.py
@@ -210,6 +210,7 @@ def main():
     parser.set_defaults(c_terminal=None)
 
     parser.add_argument("--calibrate_mz", dest="calibrate_mz", action="store_true", help="Calibrate mz (default: False)")
+    parser.set_defaults(calibrate_mz=None)
 
     parser.add_argument(
         "--no_decoys",
@@ -314,6 +315,7 @@ def main():
     parser.add_argument("--tims2rescore_table", dest="tims2rescore_table", action="store_true", help="Write PSM table that can be passed to tims2rescore")
     parser.set_defaults(tims2rescore_table=None)
     parser.add_argument("--use_mgf", action="store_true", help="Use Bruker DataAnalysis parsed MGF files stored in the .d folders instead of raw data.")
+    parser.set_defaults(use_mgf=None)
 
     args = parser.parse_args()
 
@@ -411,7 +413,9 @@ def main():
         for file in dirs:
             if file.endswith(".d"):
                 path = os.path.join(root, file)
-                if args.use_mgf:
+                if params['use_mgf']:
+                    if args.verbose:
+                        print(f"Looking for mgf in folder `{path}` ...")
                     mgf_path = None
                     mgf_path_cnt = 0
                     for potential_mgf_path in Path(path).iterdir():
@@ -422,8 +426,6 @@ def main():
                     mgfs.append(mgf_path)
                 paths.append(path)
 
-
-
     # Get the write folder path
     write_folder_path = str(Path(args.path))
 
@@ -563,7 +565,7 @@ def main():
 
         fragments = None
 
-        if args.use_mgf:
+        if params['use_mgf']:
             mgf_path = mgfs[file_id]
             fragments = mgf_to_sagepy_query(mgf_path, top_n=params['take_top_n'])
         else:
@@ -659,13 +661,13 @@ def main():
 
             psm_dict = scorer.score_collection_psm(
                 db=indexed_db,
-                spectrum_collection=fragments if args.use_mgf else fragments['processed_spec'].values,
+                spectrum_collection=fragments if params['use_mgf'] else fragments['processed_spec'].values,
                 num_threads=params['num_threads'],
             )
 
             if params['calibrate_mz']:
 
-                if args.use_mgf:
+                if params['use_mgf']:
                     raise NotImplementedError("Mass calibration is not yet supported in --use_mgf mode.")
 
                 if args.verbose:

diff --git a/imspy/pyproject.toml b/imspy/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "imspy"
-version = "0.3.12"
+version = "0.3.13"
 description = ""
 authors = [
     { name = "theGreatHerrLebert", email = "davidteschner@googlemail.com" }
@@ -19,7 +19,7 @@ dependencies = [
     "wandb>=0.12.1",
     "mokapot>=0.10.0",
     "sagepy>=0.3.8",
-    "imspy-connector>=0.3.12",
+    "imspy-connector>=0.3.13",
     "scipy>=1.7.1",
     "tqdm>=4.66",
     "pyarrow>=13.0",

diff --git a/imspy_connector/Cargo.toml b/imspy_connector/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "imspy-connector"
-version = "0.3.12"
+version = "0.3.13"
 edition = "2021"
 
 [lib]

diff --git a/imspy_connector/pyproject.toml b/imspy_connector/pyproject.toml
@@ -7,7 +7,7 @@ name = "imspy_connector"
 dependencies = [
     "opentims-bruker-bridge>=1.1.0",
 ]
-version = "0.3.12"
+version = "0.3.13"
 requires-python = ">=3.11"
 classifiers = [
     "Programming Language :: Rust",