Merge branch 'master' into GH656_avoid_anjl_import

Author: leehart

docs/source/Af1.rst

@@ -71,6 +71,7 @@ SNP data access
     is_accessible
     biallelic_snp_calls
     biallelic_diplotypes
+    biallelic_snps_to_plink
 
 Haplotype data access
 ---------------------

docs/source/Ag3.rst

@@ -72,6 +72,7 @@ SNP data access
     is_accessible
     biallelic_snp_calls
     biallelic_diplotypes
+    biallelic_snps_to_plink
 
 Haplotype data access
 ---------------------

malariagen_data/anoph/plink_params.py

@@ -0,0 +1,18 @@
+"""Parameters for Plink converter functions."""
+
+from typing_extensions import Annotated, TypeAlias
+
+overwrite: TypeAlias = Annotated[
+    bool,
+    """
+    A boolean indicating whether a previously written file with the same name ought
+    to be overwritten. Default is False.
+    """,
+]
+
+output_dir: TypeAlias = Annotated[
+    str,
+    """
+    A string indicating the desired output file location.
+    """,
+]

malariagen_data/anoph/to_plink.py

@@ -0,0 +1,132 @@
+from typing import Optional
+
+import allel  # type: ignore
+import numpy as np
+import os
+import bed_reader
+
+from ..util import dask_compress_dataset
+from .snp_data import AnophelesSnpData
+from . import base_params
+from . import plink_params
+from . import pca_params
+from numpydoc_decorator import doc  # type: ignore
+
+
+class PlinkConverter(
+    AnophelesSnpData,
+):
+    def __init__(
+        self,
+        **kwargs,
+    ):
+        # N.B., this class is designed to work cooperatively, and
+        # so it's important that any remaining parameters are passed
+        # to the superclass constructor.
+        super().__init__(**kwargs)
+
+    @doc(
+        summary="""
+            Write Anopheles biallelic SNP data to the Plink binary file format.
+        """,
+        extended_summary="""
+            This function writes biallelic SNPs to the Plink binary file format. It enables
+            subsetting to specific regions (`region`), selecting specific sample sets, or lists of
+            samples, randomly downsampling sites, and specifying filters based on missing data and
+            minimum minor allele count (see the docs for `biallelic_snp_calls` for more information).
+            The `overwrite` parameter, set to true, will enable overwrite of data with the same
+            SNP selection parameter values.
+        """,
+        returns="""
+        Base path to files containing binary Plink output files. Append .bed,
+        .bim or .fam to obtain paths for the binary genotype table file, variant
+        information file and sample information file respectively.
+        """,
+        notes="""
+            This computation may take some time to run, depending on your computing
+            environment. Unless the `overwrite` parameter is set to `True`, results will be returned
+            from a previous computation, if available.
+        """,
+    )
+    def biallelic_snps_to_plink(
+        self,
+        output_dir: plink_params.output_dir,
+        region: base_params.regions,
+        n_snps: base_params.n_snps,
+        overwrite: plink_params.overwrite = False,
+        thin_offset: base_params.thin_offset = 0,
+        sample_sets: Optional[base_params.sample_sets] = None,
+        sample_query: Optional[base_params.sample_query] = None,
+        sample_indices: Optional[base_params.sample_indices] = None,
+        site_mask: Optional[base_params.site_mask] = base_params.DEFAULT,
+        min_minor_ac: Optional[
+            base_params.min_minor_ac
+        ] = pca_params.min_minor_ac_default,
+        max_missing_an: Optional[
+            base_params.max_missing_an
+        ] = pca_params.max_missing_an_default,
+        random_seed: base_params.random_seed = 42,
+        inline_array: base_params.inline_array = base_params.inline_array_default,
+        chunks: base_params.chunks = base_params.native_chunks,
+    ):
+        # Define output files
+        plink_file_path = f"{output_dir}/{region}.{n_snps}.{min_minor_ac}.{max_missing_an}.{thin_offset}"
+
+        bed_file_path = f"{plink_file_path}.bed"
+
+        # Check to see if file exists and if overwrite is set to false, return existing file
+        if os.path.exists(bed_file_path):
+            if not overwrite:
+                return plink_file_path
+
+        # Get snps
+        ds_snps = self.biallelic_snp_calls(
+            region=region,
+            sample_sets=sample_sets,
+            sample_query=sample_query,
+            sample_indices=sample_indices,
+            site_mask=site_mask,
+            min_minor_ac=min_minor_ac,
+            max_missing_an=max_missing_an,
+            n_snps=n_snps,
+            thin_offset=thin_offset,
+            random_seed=random_seed,
+            inline_array=inline_array,
+            chunks=chunks,
+        )
+
+        # Set up dataset with required vars for plink conversion
+
+        # Compute gt ref counts
+        with self._dask_progress("Computing genotype ref counts"):
+            gt_asc = ds_snps["call_genotype"].data  # dask array
+            gn_ref = allel.GenotypeDaskArray(gt_asc).to_n_ref(fill=-127)
+            gn_ref = gn_ref.compute()
+
+        # Ensure genotypes vary
+        loc_var = np.any(gn_ref != gn_ref[:, 0, np.newaxis], axis=1)
+
+        # Load final data
+        ds_snps_final = dask_compress_dataset(ds_snps, loc_var, dim="variants")
+
+        # Init vars for input to bed reader
+        gn_ref_final = gn_ref[loc_var]
+        val = gn_ref_final.T
+        with self._spinner("Prepare output data"):
+            alleles = ds_snps_final["variant_allele"].values
+            properties = {
+                "iid": ds_snps_final["sample_id"].values,
+                "chromosome": ds_snps_final["variant_contig"].values,
+                "bp_position": ds_snps_final["variant_position"].values,
+                "allele_1": alleles[:, 0],
+                "allele_2": alleles[:, 1],
+            }
+
+        bed_reader.to_bed(
+            filepath=bed_file_path,
+            val=val,
+            properties=properties,
+            count_A1=True,
+        )
+
+        return plink_file_path

malariagen_data/anopheles.py

@@ -46,6 +46,7 @@
 from .anoph.distance import AnophelesDistanceAnalysis
 from .anoph.sample_metadata import AnophelesSampleMetadata, locate_cohorts
 from .anoph.snp_data import AnophelesSnpData
+from .anoph.to_plink import PlinkConverter
 from .anoph.g123 import AnophelesG123Analysis
 from .anoph.fst import AnophelesFstAnalysis
 from .anoph.h12 import AnophelesH12Analysis
@@ -100,6 +101,7 @@ class AnophelesDataResource(
     AnophelesSnpFrequencyAnalysis,
     AnophelesDistanceAnalysis,
     AnophelesPca,
+    PlinkConverter,
     AnophelesIgv,
     AnophelesAimData,
     AnophelesHapData,

notebooks/plink_convert.ipynb

@@ -0,0 +1,50 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import malariagen_data\n",
+    "import os \n",
+    "\n",
+    "ag3 = malariagen_data.Ag3(pre=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ag3.biallelic_snps_to_plink(output_dir=os.getcwd(),\n",
+    "                            region='2L:100000-2000000',\n",
+    "                            n_snps=2000,\n",
+    "                            sample_sets='AG1000G-AO',\n",
+    "                            )"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "malariagen_plink",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}