Improve error messages

src/cfeintact/fisher_exact_test.py

@@ -3,7 +3,8 @@
 
 
 def default_fisher_exact(*args, **kwargs):
-    raise UserError("Cannot import scipy for fisher_exact test.")
+    raise UserError("Cannot import scipy for fisher_exact test. "
+                    "Please check if you have enough RAM for scipy (python -c 'import scipy').")
 
 
 try:
@@ -12,6 +13,7 @@ def default_fisher_exact(*args, **kwargs):
 except ImportError as e:
     logger.warning("Cannot import scipy: %s.", e)
     fisher_exact = default_fisher_exact
-except KeyboardInterrupt as e:
-    logger.warning("Cannot import scipy: %r.", e)
+except KeyboardInterrupt:
+    logger.warning("Cannot import scipy for fisher_exact test. "
+                   "Please check if you have enough RAM for scipy (python -c 'import scipy').")
     fisher_exact = default_fisher_exact

src/cfeintact/intact.py

@@ -573,7 +573,7 @@ def __init__(self, working_dir, fmt):
         self.subtypes = set()
 
         if fmt not in ("json", "csv"):
-            raise UserError(f"Unrecognized output format {fmt!r}.")
+            raise UserError("Unrecognized output format %r.", fmt)
 
     def __enter__(self, *args):
         self.subtypes_file = open(self.subtypes_path, 'w')

src/cfeintact/main.py

@@ -105,8 +105,8 @@ def intact(input_file: str, subtype: str, check_packaging_signal: bool,
             check_unknown_nucleotides, check_small_orfs, check_distance, output_csv,
         )
     except UserError as e:
-        logger.error("%s", e.message)
-        exit(1)
+        logger.fatal(e.fmt, *e.fmt_args)
+        exit(e.code)
 
     exit(0)
 

src/cfeintact/user_error.py

@@ -1,4 +1,6 @@
 
-class UserError(ValueError):
-    def __init__(self, message: str):
-        self.message = message
+class UserError(RuntimeError):
+    def __init__(self, fmt: str, *fmt_args: object):
+        self.fmt = fmt
+        self.fmt_args = fmt_args
+        self.code = 1

src/cfeintact/wrappers.py

@@ -29,8 +29,9 @@ def mafft(sequences: Iterable[SeqRecord]) -> MultipleSeqAlignment:
             subprocess.run(["mafft", "--quiet", alignment_input.name],
                            shell=False, stdout=alignment_output, check=True)
         except Exception as e:
-            raise UserError(f"MAFFT run failed with {e}. "
-                            f"Please check if the input .FASTA file is correctly formatted.") from e
+            raise UserError("MAFFT run failed with %s. "
+                            "Please check if the input FASTA file is correctly formatted.",
+                            e) from e
 
         alignment: MultipleSeqAlignment = AlignIO.read(alignment_output.name, "fasta")
         return alignment
@@ -60,8 +61,9 @@ def blast(alignment_file: str, input_file: str, output_file: str) -> None:
                 check=True,
             )
         except Exception as e:
-            raise UserError(f"BLAST run failed with {e}. "
-                            f"Please check if the input .FASTA file is correctly formatted.") from e
+            raise UserError("BLAST run failed with %s. "
+                            "Please check if the input FASTA file is correctly formatted.",
+                            e) from e
 
         output.write(','.join(fields) + '\n')
         alignment_output.seek(0)