pheval 0.4.7__py3-none-any.whl → 0.5.0__py3-none-any.whl

pheval/analyse/parse_benchmark_summary.py

@@ -1,81 +0,0 @@
-from dataclasses import dataclass
-from pathlib import Path
-from typing import List
-
-import pandas as pd
-
-from pheval.analyse.benchmark_db_manager import BenchmarkDBManager
-from pheval.analyse.benchmarking_data import BenchmarkRunResults
-from pheval.analyse.binary_classification_stats import BinaryClassificationStats
-from pheval.analyse.rank_stats import RankStats
-
-
-@dataclass
-class BenchmarkSummaryResults:
-    gene_results: List[BenchmarkRunResults]
-    disease_results: List[BenchmarkRunResults]
-    variant_results: List[BenchmarkRunResults]
-
-
-def parse_benchmark_results(benchmark_summary_table: pd.DataFrame) -> List[BenchmarkRunResults]:
-    """
-    Parse benchmark results from a DataFrame.
-
-    Args:
-        benchmark_summary_table (pd.DataFrame): DataFrame containing benchmark results.
-
-    Returns:
-        List[BenchmarkRunResults]: A list of BenchmarkRunResults objects parsed from the DataFrame.
-    """
-    results = []
-    for _, row in benchmark_summary_table.iterrows():
-        benchmarking_result = BenchmarkRunResults(
-            rank_stats=RankStats(
-                top=row["top"],
-                top3=row["top3"],
-                top5=row["top5"],
-                top10=row["top10"],
-                found=row["found"],
-                total=row["total"],
-                mrr=row["mean_reciprocal_rank"],
-            ),
-            benchmark_name=row["results_directory_path"],
-            binary_classification_stats=BinaryClassificationStats(),
-        )
-        results.append(benchmarking_result)
-    return results
-
-
-def parse_benchmark_db(benchmarking_db: Path) -> BenchmarkSummaryResults:
-    """
-    Read the summary benchmark TSV output generated from the benchmark-comparison command.
-
-    Args:
-        benchmarking_db (Path): Path to the benchmark db.
-
-    Returns:
-        BenchmarkSummaryResults: A dataclass containing all benchmarking results contained in the db.
-    """
-    db_connector = BenchmarkDBManager(benchmarking_db)
-    gene_benchmarking_results, disease_benchmarking_results, variant_benchmarking_results = (
-        None,
-        None,
-        None,
-    )
-    if db_connector.check_table_exists("gene_summary"):
-        gene_benchmarking_results = parse_benchmark_results(
-            db_connector.conn.execute("SELECT * FROM gene_summary").fetchdf()
-        )
-    if db_connector.check_table_exists("disease_summary"):
-        disease_benchmarking_results = parse_benchmark_results(
-            db_connector.conn.execute("SELECT * FROM disease_summary").fetchdf()
-        )
-    if db_connector.check_table_exists("variant_summary"):
-        variant_benchmarking_results = parse_benchmark_results(
-            db_connector.conn.execute("SELECT * FROM variant_summary").fetchdf()
-        )
-    return BenchmarkSummaryResults(
-        gene_results=gene_benchmarking_results,
-        disease_results=disease_benchmarking_results,
-        variant_results=variant_benchmarking_results,
-    )

pheval/analyse/parse_corpus.py

@@ -1,219 +0,0 @@
-from pathlib import Path
-from typing import List
-
-from pheval.analyse.benchmark_db_manager import BenchmarkDBManager
-from pheval.analyse.benchmark_generator import (
-    BenchmarkRunOutputGenerator,
-    DiseaseBenchmarkRunOutputGenerator,
-    GeneBenchmarkRunOutputGenerator,
-    VariantBenchmarkRunOutputGenerator,
-)
-from pheval.utils.file_utils import all_files
-from pheval.utils.phenopacket_utils import (
-    GenomicVariant,
-    PhenopacketUtil,
-    ProbandCausativeGene,
-    ProbandDisease,
-    phenopacket_reader,
-)
-
-
-def _obtain_causative_diseases(phenopacket_path: Path) -> List[ProbandDisease]:
-    """
-    Obtain known diseases from a Phenopacket.
-    Args:
-       phenopacket_path (Path): Path to the Phenopacket file.
-
-    Returns:
-       List[ProbandDisease]: A list of known diseases associated with the proband,
-       extracted from the Phenopacket.
-    """
-    phenopacket = phenopacket_reader(phenopacket_path)
-    phenopacket_util = PhenopacketUtil(phenopacket)
-    return phenopacket_util.diagnoses()
-
-
-def _obtain_causative_variants(phenopacket_path: Path) -> List[GenomicVariant]:
-    """
-    Obtain known variants from a Phenopacket.
-    Args:
-       phenopacket_path (Path): Path to the Phenopacket file.
-
-    Returns:
-       List[GenomicVariant]: A list of known variants associated with the proband,
-       extracted from the Phenopacket.
-    """
-    phenopacket = phenopacket_reader(phenopacket_path)
-    phenopacket_util = PhenopacketUtil(phenopacket)
-    return phenopacket_util.diagnosed_variants()
-
-
-def _obtain_causative_genes(phenopacket_path: Path) -> List[ProbandCausativeGene]:
-    """
-    Obtain known genes from a Phenopacket.
-    Args:
-       phenopacket_path (Path): Path to the Phenopacket file.
-    Returns:
-       List[ProbandCausativeGene]: A list of known genes associated with the proband,
-       extracted from the Phenopacket.
-    """
-    phenopacket = phenopacket_reader(phenopacket_path)
-    phenopacket_util = PhenopacketUtil(phenopacket)
-    return phenopacket_util.diagnosed_genes()
-
-
-class CorpusParser:
-    """Class for parsing phenopacket corpus and retrieving known variants/genes/diseases."""
-
-    def __init__(self, benchmark_name: str, phenopacket_dir: Path) -> None:
-        """
-        Initialise the CorpusParser class.
-        Args:
-            phenopacket_dir (Path): Path to the Phenopacket directory.
-        """
-        self.phenopacket_dir = phenopacket_dir
-        self.conn = BenchmarkDBManager(benchmark_name).conn
-        self.table_name = phenopacket_dir.parents[0].name
-
-    def _create_gene_table(self) -> None:
-        """
-        Create the Gene benchmarking table if it doesn't already exist.
-        """
-        self.conn.execute(
-            f"""
-                    CREATE TABLE IF NOT EXISTS "{self.table_name}_gene" (
-                        identifier VARCHAR(255) PRIMARY KEY,
-                        phenopacket VARCHAR,
-                        gene_symbol VARCHAR,
-                        gene_identifier VARCHAR
-                    )
-                    """
-        )
-
-    def _create_variant_table(self) -> None:
-        """
-        Create the Variant benchmarking table if it doesn't already exist.
-        """
-        self.conn.execute(
-            f"""
-                    CREATE TABLE IF NOT EXISTS "{self.table_name}_variant" (
-                        identifier VARCHAR(255) PRIMARY KEY,
-                        phenopacket VARCHAR,
-                        chrom VARCHAR,
-                        pos INTEGER,
-                        "ref" VARCHAR,
-                        alt VARCHAR
-                    )
-                    """
-        )
-
-    def _create_disease_table(self):
-        """
-        Create the Disease benchmarking table if it doesn't already exist.
-        """
-        self.conn.execute(
-            f"""
-                    CREATE TABLE IF NOT EXISTS "{self.table_name}_disease" (
-                        identifier VARCHAR(255) PRIMARY KEY,
-                        phenopacket VARCHAR,
-                        disease_identifier VARCHAR,
-                        disease_name VARCHAR
-                    )
-                    """
-        )
-
-    def _create_tables(self, benchmark_generator: BenchmarkRunOutputGenerator) -> None:
-        """
-        Create tables based on the benchmarking analysis specified.
-        Args:
-            benchmark_generator (BenchmarkRunOutputGenerator): Class instance of the benchmark generator type.
-        """
-
-        if isinstance(benchmark_generator, GeneBenchmarkRunOutputGenerator):
-            self._create_gene_table()
-        if isinstance(benchmark_generator, VariantBenchmarkRunOutputGenerator):
-            self._create_variant_table()
-        if isinstance(benchmark_generator, DiseaseBenchmarkRunOutputGenerator):
-            self._create_disease_table()
-
-    def _insert_genes(self, phenopacket_path: Path, genes: List[ProbandCausativeGene]) -> None:
-        """
-        Insert known disease-causing genes into the Gene benchmarking table.
-        Args:
-            phenopacket_path(Path): Path to the Phenopacket file.
-            genes(List[ProbandCausativeGene]): List of known genes associated with the proband.
-        """
-        for gene in genes:
-            identifier = f"{phenopacket_path.name}-{gene.gene_symbol}"
-            self.conn.execute(
-                f"""
-                INSERT OR IGNORE INTO "{self.table_name}_gene" (identifier, phenopacket, gene_symbol, gene_identifier)
-                VALUES (?, ?, ?, ?)
-                """,
-                (identifier, phenopacket_path.name, gene.gene_symbol, gene.gene_identifier),
-            )
-
-    def _insert_variants(self, phenopacket_path: Path, variants: List[GenomicVariant]) -> None:
-        """
-        Insert known variants into the Variant benchmarking table.
-        Args:
-            phenopacket_path (Path): Path to the Phenopacket file.:
-            variants (List[GenomicVariant]): List of known variants associated with the proband.
-        """
-        for variant in variants:
-            identifier = (
-                f"{phenopacket_path.name}-{variant.chrom}-{variant.pos}-{variant.ref}-{variant.alt}"
-            )
-            self.conn.execute(
-                f"""
-                INSERT OR IGNORE INTO "{self.table_name}_variant" (identifier, phenopacket, chrom, pos, "ref", alt)
-                VALUES (?, ?, ?, ?, ?, ?)
-                """,
-                (
-                    identifier,
-                    phenopacket_path.name,
-                    variant.chrom,
-                    variant.pos,
-                    variant.ref,
-                    variant.alt,
-                ),
-            )
-
-    def _insert_diseases(self, phenopacket_path: Path, diseases: List[ProbandDisease]) -> None:
-        """
-        Insert known diseases into the Disease benchmarking table.
-        Args:
-            phenopacket_path (Path): Path to the Phenopacket file.:
-            diseases (List[ProbandDisease]): List of known diseases associated with the proband.
-        """
-        for disease in diseases:
-            identifier = f"{phenopacket_path.name}-{disease.disease_identifier}"
-            self.conn.execute(
-                f"""INSERT OR IGNORE INTO "{self.table_name}_disease" """
-                f"""(identifier, phenopacket, disease_identifier, disease_name) VALUES (?, ?, ?, ?)""",
-                (
-                    identifier,
-                    phenopacket_path.name,
-                    disease.disease_identifier,
-                    disease.disease_name,
-                ),
-            )
-
-    def parse_corpus(self, benchmark_generator: BenchmarkRunOutputGenerator) -> None:
-        """
-        Parse the phenopacket corpus and add known genes/variants/diseases to relevant benchmarking tables.
-        Args:
-            benchmark_generator (BenchmarkRunOutputGenerator): Class instance of the benchmark generator type.
-        """
-        self._create_tables(benchmark_generator)
-        for phenopacket_path in all_files(self.phenopacket_dir):
-            if isinstance(benchmark_generator, GeneBenchmarkRunOutputGenerator):
-                genes = _obtain_causative_genes(phenopacket_path)
-                self._insert_genes(phenopacket_path, genes)
-            if isinstance(benchmark_generator, VariantBenchmarkRunOutputGenerator):
-                variants = _obtain_causative_variants(phenopacket_path)
-                self._insert_variants(phenopacket_path, variants)
-            if isinstance(benchmark_generator, DiseaseBenchmarkRunOutputGenerator):
-                diseases = _obtain_causative_diseases(phenopacket_path)
-                self._insert_diseases(phenopacket_path, diseases)
-        self.conn.close()

pheval/analyse/prioritisation_result_types.py

@@ -1,52 +0,0 @@
-from dataclasses import dataclass
-from pathlib import Path
-
-from pheval.utils.phenopacket_utils import GenomicVariant, ProbandDisease
-
-
-@dataclass
-class GenePrioritisationResult:
-    """
-    Store rank data for causative genes.
-
-    Attributes:
-        phenopacket_path (Path): Path to the phenopacket.
-        gene (str): The causative gene.
-        rank (int): The assigned rank for the gene. Defaults to 0.
-    """
-
-    phenopacket_path: Path
-    gene: str
-    rank: int = 0
-
-
-@dataclass
-class VariantPrioritisationResult:
-    """
-    Store rank data for variants.
-
-    Attributes:
-        phenopacket_path (Path): Path to the phenopacket.
-        variant (GenomicVariant): The genomic variant.
-        rank (int): The assigned rank for the variant. Defaults to 0.
-    """
-
-    phenopacket_path: Path
-    variant: GenomicVariant
-    rank: int = 0
-
-
-@dataclass
-class DiseasePrioritisationResult:
-    """
-    Store rank data for known diseases.
-
-    Attributes:
-        phenopacket_path (Path): Path to the phenopacket.
-        disease (ProbandDisease): The proband disease.
-        rank (int): The assigned rank for the disease. Defaults to 0.
-    """
-
-    phenopacket_path: Path
-    disease: ProbandDisease
-    rank: int = 0

pheval/analyse/variant_prioritisation_analysis.py

@@ -1,159 +0,0 @@
-from pathlib import Path
-
-from pheval.analyse.assess_prioritisation_base import AssessPrioritisationBase
-from pheval.analyse.benchmark_db_manager import BenchmarkDBManager
-from pheval.analyse.benchmarking_data import BenchmarkRunResults
-from pheval.analyse.binary_classification_stats import BinaryClassificationStats
-from pheval.analyse.rank_stats import RankStats
-from pheval.analyse.run_data_parser import RunConfig
-from pheval.post_processing.post_processing import RankedPhEvalVariantResult
-from pheval.utils.file_utils import all_files
-from pheval.utils.phenopacket_utils import GenomicVariant
-
-
-class AssessVariantPrioritisation(AssessPrioritisationBase):
-    """Class for assessing variant prioritisation based on thresholds and scoring orders."""
-
-    def assess_variant_prioritisation(
-        self,
-        standardised_variant_result_path: Path,
-        phenopacket_path: Path,
-        binary_classification_stats: BinaryClassificationStats,
-    ) -> None:
-        """
-        Assess variant prioritisation.
-
-        This method assesses the prioritisation of variants based on the provided criteria
-        and records ranks using a PrioritisationRankRecorder.
-
-        Args:
-            standardised_variant_result_path (Path): Path to standardised variant TSV result.
-            phenopacket_path (Path): Path to the phenopacket.
-            binary_classification_stats (BinaryClassificationStats): BinaryClassificationStats class instance.
-        """
-        relevant_ranks = []
-        df = self.conn.execute(
-            f"""SELECT * FROM "{self.table_name}" WHERE phenopacket = '{phenopacket_path.name}'"""
-        ).fetchdf()
-        for _i, row in df.iterrows():
-            causative_variant = GenomicVariant(
-                chrom=row["chrom"],
-                pos=int(row["pos"]),
-                ref=row["ref"],
-                alt=row["alt"],
-            )
-            result = (
-                self.conn.execute(
-                    (
-                        f"SELECT * FROM '{standardised_variant_result_path}' "
-                        f"WHERE "
-                        f"chromosome == '{causative_variant.chrom}' AND "
-                        f"start == {causative_variant.pos} AND "
-                        f"ref == '{causative_variant.ref}' AND "
-                        f"alt == '{causative_variant.alt}'"
-                    )
-                    if standardised_variant_result_path.exists()
-                    else "SELECT NULL WHERE FALSE"
-                )
-                .fetchdf()
-                .to_dict(orient="records")
-            )
-
-            if len(result) > 0:
-                variant_match = self._record_matched_entity(RankedPhEvalVariantResult(**result[0]))
-                relevant_ranks.append(variant_match)
-                primary_key = (
-                    f"{phenopacket_path.name}-{causative_variant.chrom}-{causative_variant.pos}-"
-                    f"{causative_variant.ref}-{causative_variant.alt}"
-                )
-                self.conn.execute(
-                    f'UPDATE "{self.table_name}" SET "{self.column}" = ? WHERE identifier = ?',
-                    (variant_match, primary_key),
-                )
-            elif len(result) == 0:
-                relevant_ranks.append(0)
-        binary_classification_stats.add_classification(
-            (
-                self.db_connection.parse_table_into_dataclass(
-                    str(standardised_variant_result_path), RankedPhEvalVariantResult
-                )
-                if standardised_variant_result_path.exists()
-                else []
-            ),
-            relevant_ranks,
-        )
-
-
-def assess_phenopacket_variant_prioritisation(
-    phenopacket_path: Path,
-    run: RunConfig,
-    variant_binary_classification_stats: BinaryClassificationStats,
-    variant_benchmarker: AssessVariantPrioritisation,
-) -> None:
-    """
-    Assess variant prioritisation for a Phenopacket by comparing PhEval standardised variant results
-    against the recorded causative variants for a proband in the Phenopacket.
-
-    Args:
-        phenopacket_path (Path): Path to the Phenopacket.
-        run (RunConfig): Run configuration.
-        variant_binary_classification_stats (BinaryClassificationStats): BinaryClassificationStats class instance.
-        variant_benchmarker (AssessVariantPrioritisation): AssessVariantPrioritisation class instance.
-    """
-    standardised_variant_result_path = run.results_dir.joinpath(
-        f"pheval_variant_results/{phenopacket_path.stem}-pheval_variant_result.tsv"
-    )
-    variant_benchmarker.assess_variant_prioritisation(
-        standardised_variant_result_path,
-        phenopacket_path,
-        variant_binary_classification_stats,
-    )
-
-
-def benchmark_variant_prioritisation(
-    benchmark_name: str,
-    run: RunConfig,
-    score_order: str,
-    threshold: float,
-):
-    """
-    Benchmark a directory based on variant prioritisation results.
-
-    Args:
-        benchmark_name (str): Name of the benchmark.
-        run (RunConfig): Run configuration.
-        score_order (str): The order in which scores are arranged.
-        threshold (float): Threshold for assessment.
-
-    Returns:
-        BenchmarkRunResults: An object containing benchmarking results for variant prioritisation,
-        including ranks and rank statistics for the benchmarked directory.
-    """
-    variant_binary_classification_stats = BinaryClassificationStats()
-    db_connection = BenchmarkDBManager(benchmark_name)
-    variant_benchmarker = AssessVariantPrioritisation(
-        db_connection,
-        f"{run.phenopacket_dir.parents[0].name}" f"_variant",
-        run.run_identifier,
-        threshold,
-        score_order,
-    )
-    for phenopacket_path in all_files(run.phenopacket_dir):
-        assess_phenopacket_variant_prioritisation(
-            phenopacket_path,
-            run,
-            variant_binary_classification_stats,
-            variant_benchmarker,
-        )
-    variant_rank_stats = RankStats()
-    variant_rank_stats.add_ranks(
-        benchmark_name=benchmark_name,
-        table_name=f"{run.phenopacket_dir.parents[0].name}_variant",
-        column_name=str(run.run_identifier),
-    )
-    return BenchmarkRunResults(
-        benchmark_name=run.run_identifier,
-        rank_stats=variant_rank_stats,
-        binary_classification_stats=variant_binary_classification_stats,
-        phenopacket_dir=run.phenopacket_dir,
-    )