change documentation for scoring (#78)

* scoring and documentation

CHANGELOG.md

@@ -5,6 +5,21 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [3.1.0]
+
+### Changed
+
+- Scoring formula changed to:
+    $$
+    score = 0.8 * \sum_{tool}^{tools provided} f(fusion, tool) + 0.2 * \sum_{db}^{dbs provided} g(fusion, db)*w(db)
+    $$
+
+    Weights for databases are as follows:
+
+    * COSMIC (50)
+    * MITELMAN (50)
+    * FusionGDB2 (0)
+
 ## [3.0.0]
 
 ### Added

docs/score.md

@@ -10,7 +10,7 @@ report different results, for example FusionCatcher will work best on somatic sa
 You can customize weight of individual tool by specific parameter `<tool-name>_weight 30`.
 The sum of the weights has to be 100!
 
-Currently weights for databases are not adjustable. The weights for databases are as follows:
+Weights for databases are as follows:
 
 * COSMIC (50)
 * MITELMAN (50)
@@ -24,5 +24,11 @@ Currently weights for databases are not adjustable. The weights for databases ar
 The final formula for calculating score is:
 
 $$
-score = 0.5 * \sum_{tool}^{tools} f(fusion, tool)*w(tool) + 0.5 * \sum_{db}^{dbs} g(fusion, db)*w(db)
-$$
+score = 0.8 * \sum_{tool}^{tools provided} f(fusion, tool) + 0.2 * \sum_{db}^{dbs provided} g(fusion, db)*w(db)
+$$
+
+Weights for databases are as follows:
+
+* COSMIC (50)
+* MITELMAN (50)
+* FusionGDB2 (0)

fusion_report/app.py

@@ -207,7 +207,16 @@ def score(self, params: Namespace) -> None:
         at https://github.com/matq007/fusion-report/docs/scoring-fusion
         """
         tools_provided = 0
-        for tool in ['ericscript', 'fusioncatcher', 'starfusion', 'arriba', 'pizzly', "squid", "dragen", 'jaffa']:
+        for tool in [
+            "ericscript",
+            "fusioncatcher",
+            "starfusion",
+            "arriba",
+            "pizzly",
+            "squid",
+            "dragen",
+            "jaffa",
+        ]:
             if getattr(params, tool) is not None:
                 tools_provided += 1
 
@@ -224,14 +233,13 @@ def score(self, params: Namespace) -> None:
 
             # database estimation
             db_hits: float = sum(
-                float(Settings.FUSION_WEIGHTS[db_name.lower()]) for db_name in fusion.dbs)
+                float(Settings.FUSION_WEIGHTS[db_name.lower()]) for db_name in fusion.dbs
+            )
 
-            db_score: float = db_hits/db_provided
+            db_score: float = db_hits / db_provided
 
             score: float = float("%0.3f" % (0.8 * tool_score + 0.2 * db_score))
-            score_explained = (
-                f'0.8 * ({len(fusion.tools)} / {tools_provided}) + 0.2 * ({(db_hits)} / {db_provided})'
-            )
+            score_explained = f"0.8 * ({len(fusion.tools)} / {tools_provided}) + 0.2 * ({(db_hits)} / {db_provided})"
             fusion.score, fusion.score_explained = score, score_explained
 
     @staticmethod