Remove whitespace in bulk RNA expression (#337)

* remove whitespace in bulk RNA annotation

* reformat

* add details of random whitespace issue

pertpy/tools/_metadata/_cell_line.py

@@ -108,6 +108,12 @@ def __init__(self):
                 zip_file.extract("rnaseq_read_count_20220624.csv", path=settings.cachedir)
 
         self.bulk_rna_sanger = pd.read_csv(bulk_rna_sanger_file_path, skiprows=[2, 3], header=[0, 1], index_col=[0, 1])
+
+        # issue: read count values contain random whitespace, not sure what it supposes to mean
+        # solution: remove the white space and convert to int before depmap updates the metadata
+        self.bulk_rna_sanger = self.bulk_rna_sanger.applymap(
+            lambda x: int(x.replace(" ", "")) if isinstance(x, str) else x
+        )
         self.bulk_rna_sanger = self.bulk_rna_sanger.T
         self.bulk_rna_sanger.index = self.bulk_rna_sanger.index.droplevel("model_id")
         self.bulk_rna_sanger.columns = self.bulk_rna_sanger.columns.droplevel("gene_id")
@@ -396,7 +402,8 @@ def annotate_bulk_rna_expression(
             sanger_rna_exp.index = adata.obs.index
             adata.obsm["bulk_rna_expression_sanger"] = sanger_rna_exp
         else:
-            ccle_expression = self.bulk_rna_broad.reindex(adata.obs[query_id])
+            broad_rna_exp = self.bulk_rna_broad[self.bulk_rna_broad.index.isin(adata.obs[query_id])]
+            ccle_expression = broad_rna_exp.reindex(adata.obs[query_id])
             ccle_expression.index = adata.obs.index
             adata.obsm["bulk_rna_expression_broad"] = ccle_expression