Update tests

scripts/adjust_matrix_coordinates.py

@@ -40,7 +40,7 @@ def main(counts_matrix: str, coordinates_file: str, update_coordinates: bool, ou
         return 1
 
     if not outfile:
-        outfile = "adjusted_{}".format(os.path.basename(counts_matrix))
+        outfile = f"adjusted_{os.path.basename(counts_matrix)}"
 
     # Get a map of the new coordinates
     new_coordinates = dict()
@@ -70,7 +70,7 @@ def main(counts_matrix: str, coordinates_file: str, update_coordinates: bool, ou
             new_x, new_y = new_coordinates[(x, y)]
             if not update_coordinates:
                 new_x, new_y = x, y
-            new_index_values.append("{0}x{1}".format(new_x, new_y))
+            new_index_values.append(f"{new_x}x{new_y}")
         except KeyError:
             counts_table.drop(index, inplace=True)
 

scripts/convertEnsemblToNames.py

@@ -29,7 +29,7 @@ def main(st_data_file: str, annotation: str, output_file: str) -> int:
         try:
             gene_map[line["gene_id"]] = line["gene_name"]
         except KeyError as e:
-            print("Error, parsing annotation file, missing key {}".format(e))
+            print(f"Error, parsing annotation file, missing key {e}")
             return 1
     assert (len(gene_map) > 0)
 
@@ -38,14 +38,14 @@ def main(st_data_file: str, annotation: str, output_file: str) -> int:
 
     # Check that the annotation file given was valid
     if len(gene_map) < len(st_data.columns):
-        print("Error, the annotation file given is invalid or does not match the ST data")
+        print(f"Error, the annotation file given is invalid or does not match the ST data")
         return 1
 
     # Checks that there are no duplicated genes ids in the input data
     gene_ids_counter = Counter(st_data.columns)
     for gene_id, count in gene_ids_counter.most_common():
         if count > 1:
-            print("Error, Ensembl ID {} was found {} times in the input matrix.".format(gene_id, count))
+            print(f"Error, Ensembl ID {gene_id} was found {count} times in the input matrix.")
             return 1
 
     # Iterates the genes IDs to get gene names
@@ -62,11 +62,9 @@ def main(st_data_file: str, annotation: str, output_file: str) -> int:
                 # so we keep the Ensembl ID.
                 # We assume input Ensembl ids are unique as we checked this before
                 gene_name = gene_id
-                print("Warning, gene name {} was already matched so the original "
-                                 "Ensembl ID {} will be kept".format(gene_name, gene_id))
+                print(f"Warning, gene name {gene_name} was already matched so the original Ensembl ID {gene_id} will be kept")
         except KeyError:
-            print("Warning, {} was not found in the annotation, "
-                             "so the original Ensembl ID will be kept".format(gene_id))
+            print(f"Warning, {gene_id} was not found in the annotation so the original Ensembl ID will be kept")
             gene_name = gene_id
         adjustedList.append(gene_name)
 

scripts/filter_gene_type_matrix.py

@@ -51,7 +51,7 @@ def main(counts_matrix: str, gene_types_keep: List[str], outfile: str, annotatio
             if gene_types[gene] not in gene_types_keep:
                 genes_drop.append(gene)
         except KeyError:
-            print("Warning, {} was not found in the annotation\n".format(gene))
+            print(f"Warning, {gene} was not found in the annotation")
 
     if len(genes_drop) > 0:
         counts_table.drop(genes_drop, axis=1, inplace=True)