From abb55d7e03bf207ebf00b4c71f1bbdd8f58a0ad3 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 12 Feb 2024 10:44:35 +0300
Subject: Check for errors in the 'phenose' file.

---
 r_qtl/r_qtl2_qc.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

(limited to 'r_qtl/r_qtl2_qc.py')

diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py
index a41c442..f62f142 100644
--- a/r_qtl/r_qtl2_qc.py
+++ b/r_qtl/r_qtl2_qc.py
@@ -97,6 +97,22 @@ def pheno_errors(zfile: ZipFile) -> Iterator[Union[InvalidValue, MissingFile]]:
             zfile, "pheno", (__min_3_decimal_places__,))
         if error is not None)
 
+def phenose_errors(zfile: ZipFile) -> Iterator[Union[InvalidValue, MissingFile]]:
+    """Check for and retrieve phenose errors."""
+    def __min_6_decimal_places__(
+            lineno: int, field: str, value: str) -> Optional[InvalidValue]:
+        if not (re.search(r"^([0-9]+\.[0-9]{6,}|[0-9]+\.?0*)$", value)
+                or re.search(r"^0\.0+$", value)
+                or re.search("^0+$", value)):
+            return InvalidValue(lineno, field, value, (
+                f"Invalid value '{value}'. Expected numerical value "
+                "with at least 6 decimal places."))
+        return None
+    return (
+        error for error in retrieve_errors(
+            zfile, "phenose", (__min_6_decimal_places__,))
+        if error is not None)
+
 def retrieve_errors(zfile: ZipFile, filetype: str, checkers: tuple[Callable]) -> Iterator[
         Union[InvalidValue, MissingFile]]:
     """Check for and retrieve errors from files of type `filetype`."""
-- 
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