Adding filter for mtRNA (#110)

euxhenh · Nov 27, 2023 · a35fc3e · a35fc3e
1 parent 98f20d6
commit a35fc3e
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Showing 2 changed files with 31 additions and 1 deletion.
diff --git a/src/grinch/filters.py b/src/grinch/filters.py
@@ -5,10 +5,12 @@
 import numpy as np
 from anndata import AnnData
 from pydantic import NonNegativeFloat, NonNegativeInt, validate_call
-from sklearn.utils.validation import check_non_negative
+from sklearn.utils.validation import check_non_negative, column_or_1d
 
 from .aliases import OBS, VAR
+from .base import StorageMixin
 from .conf import BaseConfigurable
+from .processors import ReadKey
 from .utils import any_not_None, true_inside
 from .utils.decorators import plt_interactive
 from .utils.plotting import plot1d
@@ -132,6 +134,8 @@ class Config(BaseFilter.Config):
         max_counts: NonNegativeFloat | None = None
         min_cells: NonNegativeInt | None = None
         max_cells: NonNegativeInt | None = None
+        remove_MT_genes: bool = False
+        gene_names_key: ReadKey = "var_names"  # only used if remove_MT_genes
 
     cfg: Config
 
@@ -170,6 +174,11 @@ def _filter(self, adata: AnnData) -> None:
                 self.cfg.max_cells,
             )
 
+        if self.cfg.remove_MT_genes:
+            gene_names = StorageMixin.read(adata, self.cfg.gene_names_key)
+            gene_names = np.char.upper(column_or_1d(gene_names).astype(str))
+            to_keep &= ~np.char.startswith(gene_names, 'MT-')
+
         if to_keep.sum() < 1:
             raise ValueError(
                 "Filtering options are too stringent. "

diff --git a/tests/test_filters.py b/tests/test_filters.py
@@ -235,11 +235,13 @@ def test_gene_all(X):
             "min_counts": 6,
             "min_cells": 1,
             "max_cells": 2,
+            "remove_MT_genes": True,
         }
     )
     cfg = instantiate(cfg)
     filter_genes = cfg.create()
     adata = AnnData(X)
+    adata.var_names = ["G1", "MT2", "MT-3", "G4"]
     X_original = adata.X.copy()
     filter_genes(adata)
     assert_allclose(X_original, X)
@@ -249,6 +251,25 @@ def test_gene_all(X):
     assert_allclose(adata.var[VAR.N_CELLS], [2])
 
 
+@pytest.mark.parametrize("X", X_mods)
+def test_gene_MT(X):
+    cfg = OmegaConf.create(
+        {
+            "_target_": "src.grinch.FilterGenes.Config",
+            "remove_MT_genes": True,
+        }
+    )
+    cfg = instantiate(cfg)
+    filter_genes = cfg.create()
+    adata = AnnData(X)
+    adata.var_names = ["G1", "MT2", "MT-3", "G4"]
+    X_original = adata.X.copy()
+    filter_genes(adata)
+    assert_allclose(X_original, X)
+    X_filtered = X[:, [0, 1, 3]]
+    assert_allclose(X_filtered, adata.X)
+
+
 @pytest.mark.parametrize("X", X_mods)
 def test_gene_inplace(X):
     cfg = OmegaConf.create(