smftools 0.2.3__py3-none-any.whl → 0.2.5__py3-none-any.whl

smftools/preprocessing/filter_adata_by_nan_proportion.py

@@ -1,26 +1,38 @@
 ## filter_adata_by_nan_proportion
 
-def filter_adata_by_nan_proportion(adata, threshold, axis='obs'):
-    """
-    Filters an anndata object on a nan proportion threshold in a given matrix axis.
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    import anndata as ad
+
+
+def filter_adata_by_nan_proportion(
+    adata: "ad.AnnData", threshold: float, axis: str = "obs"
+) -> "ad.AnnData":
+    """Filter an AnnData object on NaN proportion in a matrix axis.
+
+    Args:
+        adata: AnnData object to filter.
+        threshold: Maximum allowed NaN proportion.
+        axis: Whether to filter based on ``"obs"`` or ``"var"`` NaN content.
 
-    Parameters:
-        adata (AnnData):
-        threshold (float): The max np.nan content to allow in the given axis.
-        axis (str): Whether to filter the adata based on obs or var np.nan content
     Returns:
-        filtered_adata
+        anndata.AnnData: Filtered AnnData object.
+
+    Raises:
+        ValueError: If ``axis`` is not ``"obs"`` or ``"var"``.
     """
     import numpy as np
-    import anndata as ad
 
-    if axis == 'obs':
+    if axis == "obs":
         # Calculate the proportion of NaN values in each read
         nan_proportion = np.isnan(adata.X).mean(axis=1)
         # Filter reads to keep reads with less than a certain NaN proportion
         filtered_indices = np.where(nan_proportion <= threshold)[0]
         filtered_adata = adata[filtered_indices, :].copy()
-    elif axis == 'var':
+    elif axis == "var":
         # Calculate the proportion of NaN values at a given position
         nan_proportion = np.isnan(adata.X).mean(axis=0)
         # Filter positions to keep positions with less than a certain NaN proportion
@@ -28,4 +40,4 @@ def filter_adata_by_nan_proportion(adata, threshold, axis='obs'):
         filtered_adata = adata[:, filtered_indices].copy()
     else:
         raise ValueError("Axis must be either 'obs' or 'var'")
-    return filtered_adata
+    return filtered_adata

smftools/preprocessing/filter_reads_on_length_quality_mapping.py

@@ -1,28 +1,41 @@
-from typing import Optional, Union, Sequence
+from typing import Optional, Sequence, Union
+
+import anndata as ad
 import numpy as np
 import pandas as pd
-import anndata as ad
+
+from smftools.logging_utils import get_logger
+
+logger = get_logger(__name__)
+
 
 def filter_reads_on_length_quality_mapping(
     adata: ad.AnnData,
     filter_on_coordinates: Union[bool, Sequence] = False,
     # New single-range params (preferred):
-    read_length: Optional[Sequence[float]] = None,          # e.g. [min, max]
-    length_ratio: Optional[Sequence[float]] = None,         # e.g. [min, max]
-    read_quality: Optional[Sequence[float]] = None,         # e.g. [min, max]  (commonly min only)
-    mapping_quality: Optional[Sequence[float]] = None,      # e.g. [min, max]  (commonly min only)
-    uns_flag: str = "reads_removed_failing_length_quality_mapping_qc",
+    read_length: Optional[Sequence[float]] = None,  # e.g. [min, max]
+    length_ratio: Optional[Sequence[float]] = None,  # e.g. [min, max]
+    read_quality: Optional[Sequence[float]] = None,  # e.g. [min, max]  (commonly min only)
+    mapping_quality: Optional[Sequence[float]] = None,  # e.g. [min, max]  (commonly min only)
+    uns_flag: str = "filter_reads_on_length_quality_mapping_performed",
     bypass: bool = False,
-    force_redo: bool = True
+    force_redo: bool = True,
 ) -> ad.AnnData:
-    """
-    Filter AnnData by coordinate window, read length, length ratios, read quality and mapping quality.
-
-    New: you may pass `read_length=[min, max]` (or tuple) to set both min/max in one argument.
-    If `read_length` is given it overrides scalar min/max variants (which are not present in this signature).
-    Same behavior supported for `length_ratio`, `read_quality`, `mapping_quality`.
-
-    Returns a filtered copy of the input AnnData and marks adata.uns[uns_flag] = True.
+    """Filter AnnData by coordinates, read length, quality, and mapping metrics.
+
+    Args:
+        adata: AnnData object to filter.
+        filter_on_coordinates: Optional coordinate window as a two-value sequence.
+        read_length: Read length range as ``[min, max]``.
+        length_ratio: Length ratio range as ``[min, max]``.
+        read_quality: Read quality range as ``[min, max]``.
+        mapping_quality: Mapping quality range as ``[min, max]``.
+        uns_flag: Flag in ``adata.uns`` indicating prior completion.
+        bypass: Whether to skip processing.
+        force_redo: Whether to rerun even if ``uns_flag`` is set.
+
+    Returns:
+        anndata.AnnData: Filtered copy of the input AnnData.
     """
     # early exit
     already = bool(adata.uns.get(uns_flag, False))
@@ -37,7 +50,9 @@ def filter_reads_on_length_quality_mapping(
         try:
             low, high = tuple(filter_on_coordinates)
         except Exception:
-            raise ValueError("filter_on_coordinates must be False or an iterable of two numbers (low, high).")
+            raise ValueError(
+                "filter_on_coordinates must be False or an iterable of two numbers (low, high)."
+            )
         try:
             var_coords = np.array([float(v) for v in adata_work.var_names])
             if low > high:
@@ -50,10 +65,17 @@ def filter_reads_on_length_quality_mapping(
                 selected_cols = list(adata_work.var_names[lo_idx : hi_idx + 1])
             else:
                 selected_cols = list(adata_work.var_names[col_mask_bool])
-            print(f"Subsetting adata to coordinates between {low} and {high}: keeping {len(selected_cols)} variables.")
+            logger.info(
+                "Subsetting adata to coordinates between %s and %s: keeping %s variables.",
+                low,
+                high,
+                len(selected_cols),
+            )
             adata_work = adata_work[:, selected_cols].copy()
         except Exception:
-            print("Warning: could not interpret adata.var_names as numeric coordinates — skipping coordinate filtering.")
+            logger.warning(
+                "Could not interpret adata.var_names as numeric coordinates — skipping coordinate filtering."
+            )
 
     # --- helper to coerce range inputs ---
     def _coerce_range(range_arg):
@@ -85,72 +107,83 @@ def filter_reads_on_length_quality_mapping(
     # read length filter
     if (rl_min is not None) or (rl_max is not None):
         if "mapped_length" not in adata_work.obs.columns:
-            print("Warning: 'mapped_length' not found in adata.obs — skipping read_length filter.")
+            logger.warning("'mapped_length' not found in adata.obs — skipping read_length filter.")
         else:
             vals = pd.to_numeric(adata_work.obs["mapped_length"], errors="coerce")
             mask = pd.Series(True, index=adata_work.obs.index)
             if rl_min is not None:
-                mask &= (vals >= rl_min)
+                mask &= vals >= rl_min
             if rl_max is not None:
-                mask &= (vals <= rl_max)
+                mask &= vals <= rl_max
             mask &= vals.notna()
             combined_mask &= mask
-            print(f"Planned read_length filter: min={rl_min}, max={rl_max}")
+            logger.info("Planned read_length filter: min=%s, max=%s", rl_min, rl_max)
 
     # length ratio filter
     if (lr_min is not None) or (lr_max is not None):
         if "mapped_length_to_reference_length_ratio" not in adata_work.obs.columns:
-            print("Warning: 'mapped_length_to_reference_length_ratio' not found in adata.obs — skipping length_ratio filter.")
+            logger.warning(
+                "'mapped_length_to_reference_length_ratio' not found in adata.obs — skipping length_ratio filter."
+            )
         else:
-            vals = pd.to_numeric(adata_work.obs["mapped_length_to_reference_length_ratio"], errors="coerce")
+            vals = pd.to_numeric(
+                adata_work.obs["mapped_length_to_reference_length_ratio"], errors="coerce"
+            )
             mask = pd.Series(True, index=adata_work.obs.index)
             if lr_min is not None:
-                mask &= (vals >= lr_min)
+                mask &= vals >= lr_min
             if lr_max is not None:
-                mask &= (vals <= lr_max)
+                mask &= vals <= lr_max
             mask &= vals.notna()
             combined_mask &= mask
-            print(f"Planned length_ratio filter: min={lr_min}, max={lr_max}")
+            logger.info("Planned length_ratio filter: min=%s, max=%s", lr_min, lr_max)
 
     # read quality filter (supporting optional range but typically min only)
     if (rq_min is not None) or (rq_max is not None):
         if "read_quality" not in adata_work.obs.columns:
-            print("Warning: 'read_quality' not found in adata.obs — skipping read_quality filter.")
+            logger.warning("'read_quality' not found in adata.obs — skipping read_quality filter.")
         else:
             vals = pd.to_numeric(adata_work.obs["read_quality"], errors="coerce")
             mask = pd.Series(True, index=adata_work.obs.index)
             if rq_min is not None:
-                mask &= (vals >= rq_min)
+                mask &= vals >= rq_min
             if rq_max is not None:
-                mask &= (vals <= rq_max)
+                mask &= vals <= rq_max
             mask &= vals.notna()
             combined_mask &= mask
-            print(f"Planned read_quality filter: min={rq_min}, max={rq_max}")
+            logger.info("Planned read_quality filter: min=%s, max=%s", rq_min, rq_max)
 
     # mapping quality filter (supporting optional range but typically min only)
     if (mq_min is not None) or (mq_max is not None):
         if "mapping_quality" not in adata_work.obs.columns:
-            print("Warning: 'mapping_quality' not found in adata.obs — skipping mapping_quality filter.")
+            logger.warning(
+                "'mapping_quality' not found in adata.obs — skipping mapping_quality filter."
+            )
         else:
             vals = pd.to_numeric(adata_work.obs["mapping_quality"], errors="coerce")
             mask = pd.Series(True, index=adata_work.obs.index)
             if mq_min is not None:
-                mask &= (vals >= mq_min)
+                mask &= vals >= mq_min
             if mq_max is not None:
-                mask &= (vals <= mq_max)
+                mask &= vals <= mq_max
             mask &= vals.notna()
             combined_mask &= mask
-            print(f"Planned mapping_quality filter: min={mq_min}, max={mq_max}")
+            logger.info("Planned mapping_quality filter: min=%s, max=%s", mq_min, mq_max)
 
     # Apply combined mask and report
     s0 = adata_work.n_obs
     combined_mask_bool = combined_mask.astype(bool).values
     adata_work = adata_work[combined_mask_bool].copy()
     s1 = adata_work.n_obs
-    print(f"Combined filters applied: kept {s1} / {s0} reads (removed {s0 - s1})")
+    logger.info("Combined filters applied: kept %s / %s reads (removed %s)", s1, s0, s0 - s1)
 
     final_n = adata_work.n_obs
-    print(f"Filtering complete: start={start_n}, final={final_n}, removed={start_n - final_n}")
+    logger.info(
+        "Filtering complete: start=%s, final=%s, removed=%s",
+        start_n,
+        final_n,
+        start_n - final_n,
+    )
 
     # mark as done
     adata_work.uns[uns_flag] = True