Fix on input-parameters test

Now differential JSON writes the values
iquasere · Dec 20, 2023 · fffcc88 · fffcc88
1 parent 85ce0b5
commit fffcc88
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Showing 2 changed files with 8 additions and 13 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -73,7 +73,7 @@ jobs:
           docker load --input /tmp/keggcharter.tar
           docker image ls -a
       - name: Run KEGGCharter with "input-quantification" and "input-taxonomy" parameters
-        run: docker run keggcharter /bin/bash -c "keggcharter -f KEGGCharter/cicd/keggcharter_input.tsv -rd resources_directory -keggc 'KEGG' -koc 'KO' -ecc 'EC number' -cogc 'COG ID' -iq -it "My community" -mm 00680"
+        run: docker run keggcharter /bin/bash -c "keggcharter -f KEGGCharter/cicd/keggcharter_input.tsv -rd resources_directory -keggc 'KEGG' -koc 'KO' -ecc 'EC number' -cogc 'COG ID' -iq -it 'My community' -mm 00680"
 
   include-missing-genomes:
     runs-on: ubuntu-latest

diff --git a/keggpathway_map.py b/keggpathway_map.py
@@ -298,11 +298,9 @@ def pathway_boxes_differential(self, dataframe, colormap="coolwarm"):
         dataframe = dataframe.apply(conv_rgb_hex)
         dataframe = dataframe[dataframe.columns.tolist()]
         nrboxes = len(dataframe.columns.tolist())  # number of samples
-        box2colors = {}
         for box in dataframe.index.tolist():
             boxidx = self.ortho_ids_to_pos[box]  # get box index
             box_colors = dataframe.loc[box].tolist()
-            box2colors[box] = box_colors
             paired = nrboxes % 2 == 0
             for i in range(nrboxes):
                 newrecord = create_box_heatmap(
@@ -314,7 +312,6 @@ def pathway_boxes_differential(self, dataframe, colormap="coolwarm"):
                     self.orthologs[boxidx].graphics.append(newrecord)
             if self.orthologs[boxidx].graphics[0].width is not None:  # TODO - should check more deeply why sometimes width is None
                 create_tile_box(self.orthologs[boxidx])
-        return box2colors
 
 
     def grey_boxes(self, box_list):
@@ -457,21 +454,19 @@ def differential_expression_sample(
         if len(df) == 0:
             return 1
         df = df.groupby('Boxes')[samples].sum()
-
-        box2colors = self.pathway_boxes_differential(df)
-
+        df1 = df.copy()
+        self.pathway_boxes_differential(df)
         name = self.name.split(':')[-1]
-        # Write JSON data to a file
-        with open(f'{output}/json/differential_{name}.json', 'w') as file:
-            json.dump(box2colors, file, indent=2)
         self.to_pdf(f'{output}/maps/differential_{name}.pdf')
-
         self.differential_colorbar(df, f'{output}/maps/differential_{name}_legend.png')
-
         self.add_legend(
             f'{output}/maps/differential_{name}.pdf', f'{output}/maps/differential_{name}_legend.png',
             f'{output}/maps/differential_{self.title.replace("/", "|")}.png')
-
+        # Write JSON data to a file
+        df = df1.reset_index()
+        box2quant = {df.iloc[i]['Boxes']: df.iloc[i][samples].tolist() for i in range(len(df))}
+        with open(f'{output}/json/differential_{name}.json', 'w') as file:
+            json.dump(box2quant, file, indent=2)
         return 0
 
     def add_legend(self, kegg_map_file, legend_file, output):