statgen 0.3.2__tar.gz → 0.3.3__tar.gz

{statgen-0.3.2 → statgen-0.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: statgen
-Version: 0.3.2
+Version: 0.3.3
 Summary: Statistical genetics data objects and loaders for Python and MATLAB/Octave.
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown

{statgen-0.3.2 → statgen-0.3.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "statgen"
-version = "0.3.2"
+version = "0.3.3"
 description = "Statistical genetics data objects and loaders for Python and MATLAB/Octave."
 readme = "README.md"
 requires-python = ">=3.10"

{statgen-0.3.2 → statgen-0.3.3}/statgen/__init__.py

@@ -1,5 +1,5 @@
 from ._verbosity import get_verbosity, set_verbosity
 
-__version__ = "0.3.2"
+__version__ = "0.3.3"
 
 __all__ = ["__version__", "get_verbosity", "set_verbosity"]

statgen-0.3.3/statgen/_annotation_painting.py

@@ -0,0 +1,146 @@
+from pathlib import Path
+
+import numpy as np
+import pandas as pd
+from scipy import sparse
+
+IGNORED_CHR = {"Y", "MT"}
+
+
+def merge_intervals(starts: np.ndarray, ends: np.ndarray) -> np.ndarray:
+    if starts.size == 0:
+        return np.empty((0, 2), dtype=np.int64)
+
+    order = np.lexsort((ends, starts))
+    s = starts[order]
+    e = ends[order]
+
+    running_max_end = np.maximum.accumulate(e)
+    new_group = np.empty(len(s), dtype=bool)
+    new_group[0] = True
+    new_group[1:] = s[1:] > running_max_end[:-1]
+
+    group_starts_idx = np.where(new_group)[0]
+    merged_starts = s[group_starts_idx]
+    merged_ends = np.maximum.reduceat(e, group_starts_idx)
+
+    return np.column_stack([merged_starts.astype(np.int64), merged_ends.astype(np.int64)])
+
+
+def binary_intervals_by_chr_from_arrays(
+    chr_values: np.ndarray,
+    starts: np.ndarray,
+    ends: np.ndarray,
+) -> dict[str, np.ndarray]:
+    intervals_by_chr: dict[str, np.ndarray] = {}
+    grouped = pd.DataFrame({"chr": chr_values, "start": starts, "end": ends}).groupby(
+        "chr", sort=False
+    )
+    for chr_label, grp in grouped:
+        if chr_label in IGNORED_CHR:
+            continue
+        intervals_by_chr[str(chr_label)] = merge_intervals(
+            grp["start"].to_numpy(dtype=np.int64),
+            grp["end"].to_numpy(dtype=np.int64),
+        )
+    return intervals_by_chr
+
+
+def validate_numeric_non_overlapping(
+    chr_values: np.ndarray,
+    starts: np.ndarray,
+    ends: np.ndarray,
+    path: Path,
+    row_base0: int = 0,
+) -> None:
+    source = pd.DataFrame(
+        {
+            "chr": chr_values,
+            "start": starts,
+            "end": ends,
+            "row0": np.arange(starts.size, dtype=np.int64),
+        }
+    )
+    for chr_label, grp in source.groupby("chr", sort=False):
+        if chr_label in IGNORED_CHR or grp.shape[0] <= 1:
+            continue
+        order = np.lexsort((grp["end"].to_numpy(), grp["start"].to_numpy()))
+        s = grp["start"].to_numpy(dtype=np.int64)[order]
+        e = grp["end"].to_numpy(dtype=np.int64)[order]
+        rows = grp["row0"].to_numpy(dtype=np.int64)[order]
+        prev_max = np.maximum.accumulate(e)[:-1]
+        overlap = s[1:] < prev_max
+        if overlap.any():
+            j = int(np.flatnonzero(overlap)[0]) + 1
+            raise ValueError(
+                f"{path}: row {row_base0 + int(rows[j]) + 1}: "
+                f"numeric annotation intervals overlap on chromosome {chr_label}"
+            )
+
+
+def paint_mask(bp: np.ndarray, intervals: np.ndarray) -> np.ndarray:
+    n = bp.size
+    if intervals.size == 0:
+        return np.zeros(n, dtype=np.float64)
+
+    pos0 = np.asarray(bp, dtype=np.int64) - 1
+    starts = intervals[:, 0]
+    ends = intervals[:, 1]
+
+    idx = np.searchsorted(starts, pos0, side="right") - 1
+    valid = idx >= 0
+    out = np.zeros(n, dtype=np.float64)
+    if valid.any():
+        valid_idx = idx[valid]
+        inside = pos0[valid] < ends[valid_idx]
+        out[np.flatnonzero(valid)[inside]] = 1.0
+    return out
+
+
+def paint_numeric_sparse(
+    bp: np.ndarray,
+    intervals: np.ndarray,
+    values: np.ndarray,
+) -> sparse.csr_matrix:
+    n = bp.size
+    k = values.shape[1]
+    if intervals.size == 0:
+        return sparse.csr_matrix((n, k), dtype=np.float64)
+
+    pos0 = np.asarray(bp, dtype=np.int64) - 1
+    starts = intervals[:, 0]
+    ends = intervals[:, 1]
+    idx = np.searchsorted(starts, pos0, side="right") - 1
+    valid = idx >= 0
+    if not valid.any():
+        return sparse.csr_matrix((n, k), dtype=np.float64)
+
+    valid_idx = idx[valid]
+    inside = pos0[valid] < ends[valid_idx]
+    if not inside.any():
+        return sparse.csr_matrix((n, k), dtype=np.float64)
+
+    hit_rows = np.flatnonzero(valid)[inside]
+    hit_values = values[valid_idx[inside], :]
+    row_idx, col_idx = np.nonzero(hit_values)
+    if row_idx.size == 0:
+        return sparse.csr_matrix((n, k), dtype=np.float64)
+
+    return sparse.csr_matrix(
+        (hit_values[row_idx, col_idx], (hit_rows[row_idx], col_idx)),
+        shape=(n, k),
+        dtype=np.float64,
+    )
+
+
+def paint_binary_column(intervals_by_chr: dict[str, np.ndarray], reference) -> sparse.csr_matrix:
+    n = int(reference.num_snp)
+    mask = np.zeros(n, dtype=np.float64)
+    for ref_shard, off in zip(reference.shards, reference.shard_offsets):
+        start = int(off["start0"])
+        stop = int(off["stop0"])
+        intervals = intervals_by_chr.get(ref_shard.label)
+        if intervals is None:
+            continue
+        mask[start:stop] = paint_mask(ref_shard.bp, intervals)
+    return sparse.csr_matrix(mask.reshape(-1, 1))