Convert N/A values to NoneType objects.

1 files changed, 12 insertions, 5 deletions

diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index b1eae90..ec70c5c 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -6,7 +6,7 @@ import json
 from pathlib import Path
 from functools import reduce, partial
 from zipfile import ZipFile, is_zipfile
-from typing import Union, Iterator, Iterable, Callable, Optional
+from typing import Union, Iterator, Iterable, Callable, Optional, Sequence
 
 import yaml
 
@@ -572,14 +572,21 @@ def read_text_file(filepath: Union[str, Path]) -> Iterator[str]:
             yield line
 
 
-def read_csv_file(filepath: Union[str, Path],
-                  separator: str = ",",
-                  comment_char: str = "#") -> Iterator[tuple[str, ...]]:
+def read_csv_file(
+        filepath: Union[str, Path],
+        separator: str = ",",
+        comment_char: str = "#",
+        na_strings: Sequence[str] = ["NA"]
+) -> Iterator[tuple[str, ...]]:
     """Read a file as a csv file."""
+    def __none_if_na__(val):
+        return None if val in na_strings else val
+
     for line in read_text_file(filepath):
         if line.startswith(comment_char):
             continue
-        yield tuple(field.strip() for field in line.split(separator))
+        yield tuple(__none_if_na__(field.strip())
+                    for field in line.split(separator))
 
 
 def read_csv_file_headers(