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MannLabs · Jan 25, 2024 · 88faa2b · 88faa2b
1 parent a38eb30
commit 88faa2b
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Showing 5 changed files with 186 additions and 118 deletions.
diff --git a/alphadia/features.py b/alphadia/features.py
@@ -864,10 +864,11 @@ def fragment_features(
     is_y = fragments.type == 121
 
     if np.sum(is_b) > 0 and np.sum(is_y) > 0:
-
         min_y = fragments.position[is_y].min()
         max_b = fragments.position[is_b].max()
-        overlapping = (is_y & (fragments.position < max_b)) | (is_b & (fragments.position > min_y))
+        overlapping = (is_y & (fragments.position < max_b)) | (
+            is_b & (fragments.position > min_y)
+        )
 
         # n_overlapping
         feature_array[43] = overlapping.sum()

diff --git a/alphadia/plexscoring.py b/alphadia/plexscoring.py
@@ -1678,9 +1678,8 @@ def collect_candidates(
             "mean_ms2_mass_error",
             "n_overlapping",
             "mean_overlapping_intensity",
-            "mean_overlapping_mass_error"
+            "mean_overlapping_mass_error",
         ]
-
 
         precursor_idx, rank, features = psm_proto_df.to_precursor_df()
 

diff --git a/alphadia/plotting/reporting/demo/reporting_demo.ipynb b/alphadia/plotting/reporting/demo/reporting_demo.ipynb
@@ -27,9 +27,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "default_file = 'default.yaml'\n",
-    "experiment_file_1 = 'config.yaml'\n",
-    "experiment_file_2 = 'config2.yaml'"
+    "default_file = \"default.yaml\"\n",
+    "experiment_file_1 = \"config.yaml\"\n",
+    "experiment_file_2 = \"config2.yaml\""
    ]
   },
   {
@@ -40,14 +40,15 @@
    "source": [
     "import pandas as pd\n",
     "import numpy as np\n",
+    "\n",
     "default = Config(\"default\")\n",
     "default.from_yaml(default_file)\n",
     "\n",
     "experiment_1 = Config(\"experiment 1\")\n",
     "experiment_1.from_yaml(experiment_file_1)\n",
     "\n",
     "experiment_2 = Config(\"experiment 2\")\n",
-    "experiment_2.from_yaml(experiment_file_2)\n"
+    "experiment_2.from_yaml(experiment_file_2)"
    ]
   },
   {
@@ -215,7 +216,7 @@
     }
    ],
    "source": [
-    "#Lets visualize the default config using the implemented print_recursively method to print it in visually appealing way\n",
+    "# Lets visualize the default config using the implemented print_recursively method to print it in visually appealing way\n",
     "print_recursively(default.config)"
    ]
   },
@@ -286,8 +287,10 @@
     }
    ],
    "source": [
-    "#Lets visualize the experiment 1 config using the implemented print_recursively method to print it in visually appealing way\n",
-    "print_recursively(experiment_1.config, style='new') #style='new' to visually differentiate between the two configs"
+    "# Lets visualize the experiment 1 config using the implemented print_recursively method to print it in visually appealing way\n",
+    "print_recursively(\n",
+    "    experiment_1.config, style=\"new\"\n",
+    ")  # style='new' to visually differentiate between the two configs"
    ]
   },
   {
@@ -358,7 +361,9 @@
     }
    ],
    "source": [
-    "print_recursively(experiment_2.config, style='new') #style='new' to visually differentiate between the two configs"
+    "print_recursively(\n",
+    "    experiment_2.config, style=\"new\"\n",
+    ")  # style='new' to visually differentiate between the two configs"
    ]
   },
   {
@@ -569,10 +574,10 @@
     }
    ],
    "source": [
-    "#Get the table of modifications\n",
+    "# Get the table of modifications\n",
     "table = get_update_table(default, [experiment_1, experiment_2])\n",
     "\n",
-    "#Write the table to a tsv file\n",
+    "# Write the table to a tsv file\n",
     "table.to_csv(\"config_modifications2.csv\", sep=\"\\t\")\n",
     "\n",
     "table.head(20)"
@@ -764,7 +769,7 @@
     }
    ],
    "source": [
-    "#Update the default config with a list of experiments\n",
+    "# Update the default config with a list of experiments\n",
     "default.update([experiment_1, experiment_2], print_modifications=True)"
    ]
   },
@@ -934,7 +939,7 @@
     }
    ],
    "source": [
-    "#Overloaded print function to print the config in a visually appealing way\n",
+    "# Overloaded print function to print the config in a visually appealing way\n",
     "print(default)"
    ]
   },
@@ -945,11 +950,13 @@
    "outputs": [],
    "source": [
     "# Validate the updated config with target.yaml\n",
-    "target_file = 'target.yaml'\n",
+    "target_file = \"target.yaml\"\n",
     "target = Config(\"target\")\n",
     "target.from_yaml(target_file)\n",
     "\n",
-    "assert default.config == target.config, \"The updated config is not equal to the target config\""
+    "assert (\n",
+    "    default.config == target.config\n",
+    "), \"The updated config is not equal to the target config\""
    ]
   }
  ],