From c168bab304a13580595fc9b41e6fdd66c8e9d85c Mon Sep 17 00:00:00 2001 From: Daniel Considine Date: Wed, 20 Mar 2024 14:32:07 +0000 Subject: [PATCH] Revert "Delete src/gentropy/datasource/gnomad/ld.py" This reverts commit 00dc4d879b01161691a736f2a29bfeba2860f849. --- src/gentropy/datasource/gnomad/ld.py | 526 +++++++++++++++++++++++++++ 1 file changed, 526 insertions(+) create mode 100644 src/gentropy/datasource/gnomad/ld.py diff --git a/src/gentropy/datasource/gnomad/ld.py b/src/gentropy/datasource/gnomad/ld.py new file mode 100644 index 000000000..4d4007d0f --- /dev/null +++ b/src/gentropy/datasource/gnomad/ld.py @@ -0,0 +1,526 @@ +"""Step to import filtered version of a LD matrix (block matrix).""" +from __future__ import annotations + +import sys +from dataclasses import dataclass, field +from functools import reduce +from typing import TYPE_CHECKING + +import hail as hl +import numpy as np +import pyspark.sql.functions as f +from hail.linalg import BlockMatrix +from pyspark.sql import Window + +from gentropy.common.session import Session +from gentropy.common.spark_helpers import get_top_ranked_in_window, get_value_from_row +from gentropy.common.utils import _liftover_loci, convert_gnomad_position_to_ensembl +from gentropy.dataset.ld_index import LDIndex + +if TYPE_CHECKING: + from pyspark.sql import DataFrame + + +@dataclass +class GnomADLDMatrix: + """Toolset ot interact with GnomAD LD dataset (version: r2.1.1). + + Datasets are accessed in Hail's native format, as provided by the [GnomAD consortium](https://gnomad.broadinstitute.org/downloads/#v2-linkage-disequilibrium). + + Attributes: + ld_matrix_template (str): Template for the LD matrix path. Defaults to "gs://gcp-public-data--gnomad/release/2.1.1/ld/gnomad.genomes.r2.1.1.{POP}.common.adj.ld.bm". + ld_index_raw_template (str): Template for the LD index path. Defaults to "gs://gcp-public-data--gnomad/release/2.1.1/ld/gnomad.genomes.r2.1.1.{POP}.common.ld.variant_indices.ht". + grch37_to_grch38_chain_path (str): Path to the chain file used to lift over the coordinates. Defaults to "gs://hail-common/references/grch37_to_grch38.over.chain.gz". + ld_populations (list[str]): List of populations to use to build the LDIndex. Defaults to ["afr", "amr", "asj", "eas", "fin", "nfe", "nwe", "seu"]. + """ + + ld_matrix_template: str = "gs://gcp-public-data--gnomad/release/2.1.1/ld/gnomad.genomes.r2.1.1.{POP}.common.adj.ld.bm" + ld_index_raw_template: str = "gs://gcp-public-data--gnomad/release/2.1.1/ld/gnomad.genomes.r2.1.1.{POP}.common.ld.variant_indices.ht" + grch37_to_grch38_chain_path: str = ( + "gs://hail-common/references/grch37_to_grch38.over.chain.gz" + ) + ld_populations: list[str] = field( + default_factory=lambda: [ + "afr", # African-American + "amr", # American Admixed/Latino + "asj", # Ashkenazi Jewish + "eas", # East Asian + "fin", # Finnish + "nfe", # Non-Finnish European + "nwe", # Northwestern European + "seu", # Southeastern European + ] + ) + + @staticmethod + def _aggregate_ld_index_across_populations( + unaggregated_ld_index: DataFrame, + ) -> DataFrame: + """Aggregate LDIndex across populations. + + Args: + unaggregated_ld_index (DataFrame): Unaggregate LDIndex index dataframe each row is a variant pair in a population + + Returns: + DataFrame: Aggregated LDIndex index dataframe each row is a variant with the LD set across populations + + Examples: + >>> data = [("1.0", "var1", "X", "var1", "pop1"), ("1.0", "X", "var2", "var2", "pop1"), + ... ("0.5", "var1", "X", "var2", "pop1"), ("0.5", "var1", "X", "var2", "pop2"), + ... ("0.5", "var2", "X", "var1", "pop1"), ("0.5", "X", "var2", "var1", "pop2")] + >>> df = spark.createDataFrame(data, ["r", "variantId", "chromosome", "tagvariantId", "population"]) + >>> GnomADLDMatrix._aggregate_ld_index_across_populations(df).printSchema() + root + |-- variantId: string (nullable = true) + |-- chromosome: string (nullable = true) + |-- ldSet: array (nullable = false) + | |-- element: struct (containsNull = false) + | | |-- tagVariantId: string (nullable = true) + | | |-- rValues: array (nullable = false) + | | | |-- element: struct (containsNull = false) + | | | | |-- population: string (nullable = true) + | | | | |-- r: string (nullable = true) + + """ + return ( + unaggregated_ld_index + # First level of aggregation: get r/population for each variant/tagVariant pair + .withColumn("r_pop_struct", f.struct("population", "r")) + .groupBy("chromosome", "variantId", "tagVariantId") + .agg( + f.collect_set("r_pop_struct").alias("rValues"), + ) + # Second level of aggregation: get r/population for each variant + .withColumn("r_pop_tag_struct", f.struct("tagVariantId", "rValues")) + .groupBy("variantId", "chromosome") + .agg( + f.collect_set("r_pop_tag_struct").alias("ldSet"), + ) + ) + + @staticmethod + def _convert_ld_matrix_to_table( + block_matrix: BlockMatrix, min_r2: float + ) -> DataFrame: + """Convert LD matrix to table. + + Args: + block_matrix (BlockMatrix): LD matrix + min_r2 (float): Minimum r2 value to keep in the table + + Returns: + DataFrame: LD matrix as a Spark DataFrame + """ + table = block_matrix.entries(keyed=False) + return ( + table.filter(hl.abs(table.entry) >= min_r2**0.5) + .to_spark() + .withColumnRenamed("entry", "r") + ) + + @staticmethod + def _create_ldindex_for_population( + population_id: str, + ld_matrix_path: str, + ld_index_raw_path: str, + grch37_to_grch38_chain_path: str, + min_r2: float, + ) -> DataFrame: + """Create LDIndex for a specific population. + + Args: + population_id (str): Population ID + ld_matrix_path (str): Path to the LD matrix + ld_index_raw_path (str): Path to the LD index + grch37_to_grch38_chain_path (str): Path to the chain file used to lift over the coordinates + min_r2 (float): Minimum r2 value to keep in the table + + Returns: + DataFrame: LDIndex for a specific population + """ + # Prepare LD Block matrix + ld_matrix = GnomADLDMatrix._convert_ld_matrix_to_table( + BlockMatrix.read(ld_matrix_path), min_r2 + ) + + # Prepare table with variant indices + ld_index = GnomADLDMatrix._process_variant_indices( + hl.read_table(ld_index_raw_path), + grch37_to_grch38_chain_path, + ) + + return GnomADLDMatrix._resolve_variant_indices(ld_index, ld_matrix).select( + "*", + f.lit(population_id).alias("population"), + ) + + @staticmethod + def _process_variant_indices( + ld_index_raw: hl.Table, grch37_to_grch38_chain_path: str + ) -> DataFrame: + """Creates a look up table between variants and their coordinates in the LD Matrix. + + !!! info "Gnomad's LD Matrix and Index are based on GRCh37 coordinates. This function will lift over the coordinates to GRCh38 to build the lookup table." + + Args: + ld_index_raw (hl.Table): LD index table from GnomAD + grch37_to_grch38_chain_path (str): Path to the chain file used to lift over the coordinates + + Returns: + DataFrame: Look up table between variants in build hg38 and their coordinates in the LD Matrix + """ + ld_index_38 = _liftover_loci( + ld_index_raw, grch37_to_grch38_chain_path, "GRCh38" + ) + + return ( + ld_index_38.to_spark() + # Filter out variants where the liftover failed + .filter(f.col("`locus_GRCh38.position`").isNotNull()) + .withColumn( + "chromosome", f.regexp_replace("`locus_GRCh38.contig`", "chr", "") + ) + .withColumn( + "position", + convert_gnomad_position_to_ensembl( + f.col("`locus_GRCh38.position`"), + f.col("`alleles`").getItem(0), + f.col("`alleles`").getItem(1), + ), + ) + .select( + "chromosome", + "position", + f.concat_ws( + "_", + f.col("chromosome"), + f.col("position"), + f.col("`alleles`").getItem(0), + f.col("`alleles`").getItem(1), + ).alias("variantId"), + f.col("idx"), + ) + # Filter out ambiguous liftover results: multiple indices for the same variant + .withColumn("count", f.count("*").over(Window.partitionBy(["variantId"]))) + .filter(f.col("count") == 1) + .drop("count") + ) + + @staticmethod + def _resolve_variant_indices( + ld_index: DataFrame, ld_matrix: DataFrame + ) -> DataFrame: + """Resolve the `i` and `j` indices of the block matrix to variant IDs (build 38). + + Args: + ld_index (DataFrame): Dataframe with resolved variant indices + ld_matrix (DataFrame): Dataframe with the filtered LD matrix + + Returns: + DataFrame: Dataframe with variant IDs instead of `i` and `j` indices + """ + ld_index_i = ld_index.selectExpr( + "idx as i", "variantId as variantIdI", "chromosome" + ) + ld_index_j = ld_index.selectExpr("idx as j", "variantId as variantIdJ") + return ( + ld_matrix.join(ld_index_i, on="i", how="inner") + .join(ld_index_j, on="j", how="inner") + .drop("i", "j") + ) + + @staticmethod + def _transpose_ld_matrix(ld_matrix: DataFrame) -> DataFrame: + """Transpose LD matrix to a square matrix format. + + Args: + ld_matrix (DataFrame): Triangular LD matrix converted to a Spark DataFrame + + Returns: + DataFrame: Square LD matrix without diagonal duplicates + + Examples: + >>> df = spark.createDataFrame( + ... [ + ... (1, 1, 1.0, "1", "AFR"), + ... (1, 2, 0.5, "1", "AFR"), + ... (2, 2, 1.0, "1", "AFR"), + ... ], + ... ["variantIdI", "variantIdJ", "r", "chromosome", "population"], + ... ) + >>> GnomADLDMatrix._transpose_ld_matrix(df).show() + +----------+----------+---+----------+----------+ + |variantIdI|variantIdJ| r|chromosome|population| + +----------+----------+---+----------+----------+ + | 1| 2|0.5| 1| AFR| + | 1| 1|1.0| 1| AFR| + | 2| 1|0.5| 1| AFR| + | 2| 2|1.0| 1| AFR| + +----------+----------+---+----------+----------+ + + """ + ld_matrix_transposed = ld_matrix.selectExpr( + "variantIdI as variantIdJ", + "variantIdJ as variantIdI", + "r", + "chromosome", + "population", + ) + return ld_matrix.filter(f.col("variantIdI") != f.col("variantIdJ")).unionByName( + ld_matrix_transposed + ) + + def as_ld_index( + self: GnomADLDMatrix, + min_r2: float, + ) -> LDIndex: + """Create LDIndex dataset aggregating the LD information across a set of populations. + + **The basic steps to generate the LDIndex are:** + + 1. Convert LD matrix to a Spark DataFrame. + 2. Resolve the matrix indices to variant IDs by lifting over the coordinates to GRCh38. + 3. Aggregate the LD information across populations. + + Args: + min_r2 (float): Minimum r2 value to keep in the table + + Returns: + LDIndex: LDIndex dataset + """ + ld_indices_unaggregated = [] + for pop in self.ld_populations: + try: + ld_matrix_path = self.ld_matrix_template.format(POP=pop) + ld_index_raw_path = self.ld_index_raw_template.format(POP=pop) + pop_ld_index = self._create_ldindex_for_population( + pop, + ld_matrix_path, + ld_index_raw_path.format(pop), + self.grch37_to_grch38_chain_path, + min_r2, + ) + ld_indices_unaggregated.append(pop_ld_index) + except Exception as e: + print(f"Failed to create LDIndex for population {pop}: {e}") # noqa: T201 + sys.exit(1) + + ld_index_unaggregated = ( + GnomADLDMatrix._transpose_ld_matrix( + reduce(lambda df1, df2: df1.unionByName(df2), ld_indices_unaggregated) + ) + .withColumnRenamed("variantIdI", "variantId") + .withColumnRenamed("variantIdJ", "tagVariantId") + ) + return LDIndex( + _df=self._aggregate_ld_index_across_populations(ld_index_unaggregated), + _schema=LDIndex.get_schema(), + ) + + def get_ld_variants( + self: GnomADLDMatrix, + gnomad_ancestry: str, + chromosome: str, + start: int, + end: int, + ) -> DataFrame | None: + """Return melted LD table with resolved variant id based on ancestry and genomic location. + + Args: + gnomad_ancestry (str): GnomAD major ancestry label eg. `nfe` + chromosome (str): chromosome label + start (int): window upper bound + end (int): window lower bound + + Returns: + DataFrame | None: LD table with resolved variant id based on ancestry and genomic location + """ + # Extracting locus: + ld_index_df = ( + self._process_variant_indices( + hl.read_table(self.ld_index_raw_template.format(POP=gnomad_ancestry)), + self.grch37_to_grch38_chain_path, + ) + .filter( + (f.col("chromosome") == chromosome) + & (f.col("position") >= start) + & (f.col("position") <= end) + ) + .select("chromosome", "position", "variantId", "idx") + ) + + if ld_index_df.limit(1).count() == 0: + # If the returned slice from the ld index is empty, return None + return None + + # Compute start and end indices + start_index = get_value_from_row( + get_top_ranked_in_window( + ld_index_df, Window.partitionBy().orderBy(f.col("position").asc()) + ).collect()[0], + "idx", + ) + end_index = get_value_from_row( + get_top_ranked_in_window( + ld_index_df, Window.partitionBy().orderBy(f.col("position").desc()) + ).collect()[0], + "idx", + ) + + return self._extract_square_matrix( + ld_index_df, gnomad_ancestry, start_index, end_index + ) + + def _extract_square_matrix( + self: GnomADLDMatrix, + ld_index_df: DataFrame, + gnomad_ancestry: str, + start_index: int, + end_index: int, + ) -> DataFrame: + """Return LD square matrix for a region where coordinates are normalised. + + Args: + ld_index_df (DataFrame): Look up table between a variantId and its index in the LD matrix + gnomad_ancestry (str): GnomAD major ancestry label eg. `nfe` + start_index (int): start index of the slice + end_index (int): end index of the slice + + Returns: + DataFrame: square LD matrix resolved to variants. + """ + return ( + self.get_ld_matrix_slice( + gnomad_ancestry, start_index=start_index, end_index=end_index + ) + .join( + ld_index_df.select( + f.col("idx").alias("idx_i"), + f.col("variantId").alias("variantIdI"), + ), + on="idx_i", + how="inner", + ) + .join( + ld_index_df.select( + f.col("idx").alias("idx_j"), + f.col("variantId").alias("variantIdJ"), + ), + on="idx_j", + how="inner", + ) + .select("variantIdI", "variantIdJ", "r") + ) + + def get_ld_matrix_slice( + self: GnomADLDMatrix, + gnomad_ancestry: str, + start_index: int, + end_index: int, + ) -> DataFrame: + """Extract a slice of the LD matrix based on the provided ancestry and stop and end indices. + + - The half matrix is completed into a full square. + - The returned indices are adjusted based on the start index. + + Args: + gnomad_ancestry (str): LD population label eg. `nfe` + start_index (int): start index of the slice + end_index (int): end index of the slice + + Returns: + DataFrame: square slice of the LD matrix melted as dataframe with idx_i, idx_j and r columns + """ + # Extracting block matrix slice: + half_matrix = BlockMatrix.read( + self.ld_matrix_template.format(POP=gnomad_ancestry) + ).filter(range(start_index, end_index + 1), range(start_index, end_index + 1)) + + # Return converted Dataframe: + return ( + (half_matrix + half_matrix.T) + .entries() + .to_spark() + .select( + (f.col("i") + start_index).alias("idx_i"), + (f.col("j") + start_index).alias("idx_j"), + f.when(f.col("i") == f.col("j"), f.col("entry") / 2) + .otherwise(f.col("entry")) + .alias("r"), + ) + ) + + @staticmethod + def get_locus_index( + session: Session, + study_locus_row: DataFrame, + window_size: int, + ld_index_path: str, + major_population: str = "nfe", + ) -> DataFrame: + """Extract hail matrix index from StudyLocus rows. + + Args: + session (Session): Spark session + study_locus_row (DataFrame): Study-locus row + window_size (int): Window size to extract from gnomad matrix + ld_index_path (str): Optional path to the LD index parquet + major_population (str): Major population to extract from gnomad matrix, default is "nfe" + Returns: + DataFrame: Returns the index of the gnomad matrix for the locus + """ + _df = ( + study_locus_row.withColumn("start", f.col("position") - (window_size / 2)) + .withColumn("end", f.col("position") + (window_size / 2)) + .alias("_df") + ) + + _matrix_index = session.spark.read.parquet( + ld_index_path.format(POP=major_population) + ) + + _index_joined = ( + _df.alias("df") + .join( + _matrix_index.alias("matrix_index"), + (f.col("df.chromosome") == f.col("matrix_index.chromosome")) + & (f.col("df.start") <= f.col("matrix_index.position")) + & (f.col("df.end") >= f.col("matrix_index.position")), + ) + .select( + "matrix_index.chromosome", + "matrix_index.position", + "referenceAllele", + "alternateAllele", + "idx", + ) + .sort("idx") + ) + + return _index_joined + + @staticmethod + def get_locus_matrix( + locus_index: DataFrame, + gnomad_ancestry: str, + ) -> np.ndarray: + """Extract the LD block matrix for a locus. + + Args: + locus_index (DataFrame): hail matrix variant index table + gnomad_ancestry (str): GnomAD major ancestry label eg. `nfe` + + Returns: + np.ndarray: LD block matrix for the locus + """ + idx = [row["idx"] for row in locus_index.select("idx").collect()] + + half_matrix = ( + BlockMatrix.read( + GnomADLDMatrix.ld_matrix_template.format(POP=gnomad_ancestry) + ) + .filter(idx, idx) + .to_numpy() + ) + + return (half_matrix + half_matrix.T) - np.diag(np.diag(half_matrix))