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Fix MSPreader bug related to dtype of chromosomes #14

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merged 2 commits into from
Nov 26, 2024
Merged

Fix MSPreader bug related to dtype of chromosomes #14

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555adb7
Fix bug in MSPReader related to string chromosomes
miriambt Nov 25, 2024
5b57d7e
Optimize import
miriambt Nov 25, 2024
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14 changes: 10 additions & 4 deletions snputils/ancestry/io/local/read/msp.py
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Original file line number Diff line number Diff line change
@@ -1,10 +1,9 @@
from pathlib import Path
from typing import List, Dict, Optional
from typing import List, Dict, Optional, Union
import logging
import warnings
import numpy as np
import pandas as pd
from typing import Union

from .base import LAIBaseReader
from snputils.ancestry.genobj.local import LocalAncestryObject
Expand Down Expand Up @@ -96,8 +95,15 @@ def _replace_nan_with_none(self, array: Optional[np.ndarray]) -> Optional[np.nda
Returns:
Optional[np.ndarray]: Returns `None` if the array is fully NaN, otherwise returns the original array.
"""
if array is not None and np.isnan(array).all():
return None
if array is not None:
if array.size == 0: # Check if the array is empty
return None
if np.issubdtype(array.dtype, np.number): # Check for numeric types
if np.isnan(array).all(): # Fully NaN numeric array
return None
elif array.dtype == np.object_ or np.issubdtype(array.dtype, np.str_): # String or object types
if all(elem == '' or elem is None for elem in array): # Empty or None strings
return None
return array

def read(self) -> 'LocalAncestryObject':
Expand Down