Merge pull request #394 from malariagen/xpehh

Adding XPEHH

malariagen_data/af1.py

@@ -13,6 +13,7 @@
 H12_CALIBRATION_CACHE_NAME = "af1_h12_calibration_v1"
 H12_GWSS_CACHE_NAME = "af1_h12_gwss_v1"
 G123_GWSS_CACHE_NAME = "af1_g123_gwss_v1"
+XPEHH_GWSS_CACHE_NAME = "af1_xpehh_gwss_v1"
 G123_CALIBRATION_CACHE_NAME = "af1_g123_calibration_v1"
 H1X_GWSS_CACHE_NAME = "af1_h1x_gwss_v1"
 IHS_GWSS_CACHE_NAME = "af1_ihs_gwss_v1"
@@ -75,6 +76,7 @@ class Af1(AnophelesDataResource):
     _h12_calibration_cache_name = H12_CALIBRATION_CACHE_NAME
     _h12_gwss_cache_name = H12_GWSS_CACHE_NAME
     _g123_gwss_cache_name = G123_GWSS_CACHE_NAME
+    _xpehh_gwss_cache_name = XPEHH_GWSS_CACHE_NAME
     _g123_calibration_cache_name = G123_CALIBRATION_CACHE_NAME
     _h1x_gwss_cache_name = H1X_GWSS_CACHE_NAME
     _ihs_gwss_cache_name = IHS_GWSS_CACHE_NAME

malariagen_data/ag3.py

@@ -42,6 +42,7 @@
 H12_GWSS_CACHE_NAME = "ag3_h12_gwss_v1"
 G123_CALIBRATION_CACHE_NAME = "ag3_g123_calibration_v1"
 G123_GWSS_CACHE_NAME = "ag3_g123_gwss_v1"
+XPEHH_GWSS_CACHE_NAME = "ag3_xpehh_gwss_v1"
 H1X_GWSS_CACHE_NAME = "ag3_h1x_gwss_v1"
 IHS_GWSS_CACHE_NAME = "ag3_ihs_gwss_v1"
 
@@ -138,6 +139,7 @@ class Ag3(AnophelesDataResource):
     _h12_calibration_cache_name = H12_CALIBRATION_CACHE_NAME
     _h12_gwss_cache_name = H12_GWSS_CACHE_NAME
     _g123_gwss_cache_name = G123_GWSS_CACHE_NAME
+    _xpehh_gwss_cache_name = XPEHH_GWSS_CACHE_NAME
     _g123_calibration_cache_name = G123_CALIBRATION_CACHE_NAME
     _h1x_gwss_cache_name = H1X_GWSS_CACHE_NAME
     _ihs_gwss_cache_name = IHS_GWSS_CACHE_NAME

malariagen_data/anoph/xpehh_params.py

@@ -0,0 +1,75 @@
+"""Parameter definitions for XPEHH analysis functions."""
+
+from typing import Tuple, Union
+
+import numpy as np
+from typing_extensions import Annotated, TypeAlias
+
+from . import base_params
+
+window_size: TypeAlias = Annotated[
+    int,
+    """
+        The size of window in number of SNPs used to summarise XP-EHH over.
+        If None, per-variant XP-EHH values are returned.
+        """,
+]
+window_size_default: window_size = 200
+min_cohort_size_default: base_params.min_cohort_size = 15
+max_cohort_size_default: base_params.max_cohort_size = 50
+percentiles: TypeAlias = Annotated[
+    Union[int, Tuple[int, ...]],
+    """
+    If window size is specified, this returns the XP-EHH percentiles
+    for each window.
+    """,
+]
+percentiles_default: percentiles = (50, 75, 100)
+filter_min_maf: TypeAlias = Annotated[
+    float,
+    """
+    Minimum minor allele frequency to use for filtering prior to passing
+    haplotypes to allel.xpehh function
+    """,
+]
+filter_min_maf_default: filter_min_maf = 0.05
+map_pos: TypeAlias = Annotated[
+    np.ndarray,
+    """
+    Variant positions (genetic map distance).
+    """,
+]
+min_ehh: TypeAlias = Annotated[
+    float,
+    """
+    Minimum EHH beyond which to truncate integrated haplotype homozygosity
+    calculation.
+    """,
+]
+min_ehh_default: min_ehh = 0.05
+max_gap: TypeAlias = Annotated[
+    int,
+    """
+    Do not report scores if EHH spans a gap larger than this number of
+    base pairs.
+    """,
+]
+max_gap_default: max_gap = 200_000
+gap_scale: TypeAlias = Annotated[
+    int, "Rescale distance between variants if gap is larger than this value."
+]
+gap_scale_default: gap_scale = 20_000
+include_edges: TypeAlias = Annotated[
+    bool,
+    """
+    If True, report scores even if EHH does not decay below min_ehh at the
+    end of the chromosome.
+    """,
+]
+use_threads: TypeAlias = Annotated[
+    bool, "If True, use multiple threads to compute XP-EHH."
+]
+palette: TypeAlias = Annotated[
+    str, "Name of bokeh palette to use for plotting multiple percentiles."
+]
+palette_default: palette = "Blues"