Fix bug in analysis.py

mbarq/analysis.py

@@ -383,12 +383,14 @@ def process_results(self, contrasts_run=()):
         self.logger.info('Writing out final results.')
         if not contrasts_run:
             contrasts_run = self.sd.contrasts
-        try:
-            res = pd.concat([pd.read_table(self.output_dir / f"{self.name}_{i}_vs_{self.sd.baseline}.gene_summary.txt")
-                            .assign(contrast=i) for i in contrasts_run])
-        except:
-            print(f"Warning: No such file or directory: {self.output_dir}/{self.name}_{i}_vs_{self.sd.baseline}.gene_summary.txt")
-
+        contrast_dfs = []
+        for con in contrasts_run:
+            try:
+                contrast_dfs.append(pd.read_table(self.output_dir / f"{self.name}_{con}_vs_{self.sd.baseline}.gene_summary.txt")
+                                .assign(contrast=con))
+            except:
+                print(f"Warning: No such file or directory: {self.output_dir}/{self.name}_{con}_vs_{self.sd.baseline}.gene_summary.txt")
+        res = pd.concat(contrast_dfs)
         bc_res = pd.concat([pd.read_table(self.output_dir / f"{self.name}_{i}_vs_{self.sd.baseline}.sgrna_summary.txt")
                         .assign(contrast=i) for i in contrasts_run]).rename({'sgrna': 'barcode', 'Gene': 'Name'}, axis=1)
         fres = res[['id', 'num', 'neg|lfc', 'neg|fdr', 'pos|fdr', 'contrast']]