rather fix in phenotype

micom-dev · Mar 1, 2024 · f4a7007 · f4a7007
1 parent 5578ca1
commit f4a7007
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Showing 2 changed files with 21 additions and 9 deletions.
diff --git a/micom/measures.py b/micom/measures.py
@@ -31,10 +31,16 @@ def production_rates(results):
     """
     fluxes = results.exchanges
     pos = fluxes[(fluxes.direction == "export") & (fluxes.taxon != "medium")]
-    rates = pos.groupby(["sample_id", "metabolite"]).apply(
-        lambda df: pd.Series({"flux": np.sum(df.abundance * df.flux.abs())})
-    ).reset_index()
-    rates = pd.merge(rates, results.annotations, on="metabolite")
+    rates = (
+        pos.groupby(["sample_id", "metabolite"])
+        .apply(lambda df: pd.Series({"flux": np.sum(df.abundance * df.flux.abs())}))
+        .reset_index()
+    )
+    rates = pd.merge(
+        rates,
+        results.annotations.drop_duplicates(subset=["metabolite"]),
+        on="metabolite",
+    )
     return rates
 
 
@@ -63,8 +69,14 @@ def consumption_rates(results):
     """
     fluxes = results.exchanges
     neg = fluxes[(fluxes.direction == "import") & (fluxes.taxon != "medium")]
-    rates = neg.groupby(["sample_id", "metabolite"]).apply(
-        lambda df: pd.Series({"flux": np.sum(df.abundance * df.flux.abs())})
-    ).reset_index()
-    rates = pd.merge(rates, results.annotations, on="metabolite")
+    rates = (
+        neg.groupby(["sample_id", "metabolite"])
+        .apply(lambda df: pd.Series({"flux": np.sum(df.abundance * df.flux.abs())}))
+        .reset_index()
+    )
+    rates = pd.merge(
+        rates,
+        results.annotations.drop_duplicates(subset=["metabolite"]),
+        on="metabolite",
+    )
     return rates
diff --git a/micom/viz/prediction.py b/micom/viz/prediction.py
@@ -65,7 +65,7 @@ def plot_fit(
 
     """
     exchanges = results.exchanges
-    anns = results.annotations
+    anns = results.annotations.drop_duplicates(subset=["metabolite"])
     anns.index = anns.metabolite
     if flux_type == "import":
         exchanges = exchanges[