Post processing

PhEvalDiseaseResult dataclass

Bases: PhEvalResult

Minimal data required from tool-specific output for disease prioritisation

Parameters:

Name	Type	Description	Default
disease_name	str	Disease name for the result entry	required
disease_identifier	str	Identifier for the disease result entry in the OMIM namespace	required
score	str	Score for the disease result entry	required

Notes

While we recommend providing the disease identifier in the OMIM namespace, any matching format used in Phenopacket interpretations is acceptable for result matching purposes in the analysis.

Source code in src/pheval/post_processing/post_processing.py

@dataclass
class PhEvalDiseaseResult(PhEvalResult):
    """Minimal data required from tool-specific output for disease prioritisation
    Args:
        disease_name (str): Disease name for the result entry
        disease_identifier (str): Identifier for the disease result entry in the OMIM namespace
        score (str): Score for the disease result entry
    Notes:
        While we recommend providing the disease identifier in the OMIM namespace,
        any matching format used in Phenopacket interpretations is acceptable for result matching purposes
        in the analysis.
    """

    disease_name: str
    disease_identifier: str
    score: float

PhEvalGeneResult dataclass

Bases: PhEvalResult

Minimal data required from tool-specific output for gene prioritisation result

Parameters:

Name	Type	Description	Default
gene_symbol	str	The gene symbol for the result entry	required
gene_identifier	str	The ENSEMBL gene identifier for the result entry	required
score	float	The score for the gene result entry	required

Notes

While we recommend providing the gene identifier in the ENSEMBL namespace, any matching format used in Phenopacket interpretations is acceptable for result matching purposes in the analysis.

Source code in src/pheval/post_processing/post_processing.py

@dataclass
class PhEvalGeneResult(PhEvalResult):
    """Minimal data required from tool-specific output for gene prioritisation result
    Args:
        gene_symbol (str): The gene symbol for the result entry
        gene_identifier (str): The ENSEMBL gene identifier for the result entry
        score (float): The score for the gene result entry
    Notes:
        While we recommend providing the gene identifier in the ENSEMBL namespace,
        any matching format used in Phenopacket interpretations is acceptable for result matching purposes
        in the analysis.
    """

    gene_symbol: str
    gene_identifier: str
    score: float

PhEvalResult dataclass

Base class for PhEval results.

Source code in src/pheval/post_processing/post_processing.py

@dataclass
class PhEvalResult:
    """Base class for PhEval results."""

PhEvalVariantResult dataclass

Bases: PhEvalResult

Minimal data required from tool-specific output for variant prioritisation

Parameters:

Name	Type	Description	Default
chromosome	str	The chromosome position of the variant recommended to be provided in the following format.	required
start	int	The start position of the variant	required
end	int	The end position of the variant	required
ref	str	The reference allele of the variant	required
alt	str	The alternate allele of the variant	required
score	float	The score for the variant result entry	required

Notes

While we recommend providing the variant's chromosome in the specified format, any matching format used in Phenopacket interpretations is acceptable for result matching purposes in the analysis.

Source code in src/pheval/post_processing/post_processing.py

@dataclass
class PhEvalVariantResult(PhEvalResult):
    """Minimal data required from tool-specific output for variant prioritisation
    Args:
        chromosome (str): The chromosome position of the variant recommended to be provided in the following format.
        This includes numerical designations from 1 to 22 representing autosomal chromosomes,
        as well as the sex chromosomes X and Y, and the mitochondrial chromosome MT.
        start (int): The start position of the variant
        end (int): The end position of the variant
        ref (str): The reference allele of the variant
        alt (str): The alternate allele of the variant
        score (float): The score for the variant result entry
    Notes:
        While we recommend providing the variant's chromosome in the specified format,
        any matching format used in Phenopacket interpretations is acceptable for result matching purposes
        in the analysis.
    """

    chromosome: str
    start: int
    end: int
    ref: str
    alt: str
    score: float

RankedPhEvalDiseaseResult dataclass

Bases: PhEvalDiseaseResult

PhEval disease result with corresponding rank

Parameters:

Name	Type	Description	Default
rank	int	The rank for the result entry	required

Source code in src/pheval/post_processing/post_processing.py

@dataclass
class RankedPhEvalDiseaseResult(PhEvalDiseaseResult):
    """PhEval disease result with corresponding rank
    Args:
        rank (int): The rank for the result entry
    """

    rank: int

    @staticmethod
    def from_disease_result(pheval_disease_result: PhEvalDiseaseResult, rank: int):
        """Return RankedPhEvalDiseaseResult from a PhEvalDiseaseResult and rank
        Args:
            pheval_disease_result (PhEvalDiseaseResult): The disease result entry
            rank (int): The corresponding rank for the result entry

        Returns:
            RankedPhEvalDiseaseResult: The result as a RankedPhEvalDiseaseResult
        """
        return RankedPhEvalDiseaseResult(
            disease_name=pheval_disease_result.disease_name,
            disease_identifier=pheval_disease_result.disease_identifier,
            score=pheval_disease_result.score,
            rank=rank,
        )

from_disease_result(pheval_disease_result, rank) staticmethod

Return RankedPhEvalDiseaseResult from a PhEvalDiseaseResult and rank

Parameters:

Name	Type	Description	Default
pheval_disease_result	PhEvalDiseaseResult	The disease result entry	required
rank	int	The corresponding rank for the result entry	required

Returns:

Name	Type	Description
RankedPhEvalDiseaseResult		The result as a RankedPhEvalDiseaseResult

Source code in src/pheval/post_processing/post_processing.py

@staticmethod
def from_disease_result(pheval_disease_result: PhEvalDiseaseResult, rank: int):
    """Return RankedPhEvalDiseaseResult from a PhEvalDiseaseResult and rank
    Args:
        pheval_disease_result (PhEvalDiseaseResult): The disease result entry
        rank (int): The corresponding rank for the result entry

    Returns:
        RankedPhEvalDiseaseResult: The result as a RankedPhEvalDiseaseResult
    """
    return RankedPhEvalDiseaseResult(
        disease_name=pheval_disease_result.disease_name,
        disease_identifier=pheval_disease_result.disease_identifier,
        score=pheval_disease_result.score,
        rank=rank,
    )

RankedPhEvalGeneResult dataclass

Bases: PhEvalGeneResult

PhEval gene result with corresponding rank

Parameters:

Name	Type	Description	Default
rank	int	The rank for the result entry	required

Source code in src/pheval/post_processing/post_processing.py

@dataclass
class RankedPhEvalGeneResult(PhEvalGeneResult):
    """PhEval gene result with corresponding rank
    Args:
        rank (int): The rank for the result entry
    """

    rank: int

    @staticmethod
    def from_gene_result(pheval_gene_result: PhEvalGeneResult, rank: int):
        """Return RankedPhEvalGeneResult from a PhEvalGeneResult and rank
        Args:
            pheval_gene_result (PhEvalGeneResult): The gene result entry
            rank (int): The corresponding rank for the result entry

        Returns:
            RankedPhEvalGeneResult: The result as a RankedPhEvalGeneResult
        """
        return RankedPhEvalGeneResult(
            gene_symbol=pheval_gene_result.gene_symbol,
            gene_identifier=pheval_gene_result.gene_identifier,
            score=pheval_gene_result.score,
            rank=rank,
        )

from_gene_result(pheval_gene_result, rank) staticmethod

Return RankedPhEvalGeneResult from a PhEvalGeneResult and rank

Parameters:

Name	Type	Description	Default
pheval_gene_result	PhEvalGeneResult	The gene result entry	required
rank	int	The corresponding rank for the result entry	required

Returns:

Name	Type	Description
RankedPhEvalGeneResult		The result as a RankedPhEvalGeneResult

Source code in src/pheval/post_processing/post_processing.py

@staticmethod
def from_gene_result(pheval_gene_result: PhEvalGeneResult, rank: int):
    """Return RankedPhEvalGeneResult from a PhEvalGeneResult and rank
    Args:
        pheval_gene_result (PhEvalGeneResult): The gene result entry
        rank (int): The corresponding rank for the result entry

    Returns:
        RankedPhEvalGeneResult: The result as a RankedPhEvalGeneResult
    """
    return RankedPhEvalGeneResult(
        gene_symbol=pheval_gene_result.gene_symbol,
        gene_identifier=pheval_gene_result.gene_identifier,
        score=pheval_gene_result.score,
        rank=rank,
    )

RankedPhEvalVariantResult dataclass

Bases: PhEvalVariantResult

PhEval variant result with corresponding rank

Parameters:

Name	Type	Description	Default
rank	int	The rank for the result entry	required

Source code in src/pheval/post_processing/post_processing.py

@dataclass
class RankedPhEvalVariantResult(PhEvalVariantResult):
    """PhEval variant result with corresponding rank
    Args:
        rank (int): The rank for the result entry
    """

    rank: int

    @staticmethod
    def from_variant_result(pheval_variant_result: PhEvalVariantResult, rank: int):
        """Return RankedPhEvalVariantResult from a PhEvalVariantResult and rank
        Args:
            pheval_variant_result (PhEvalVariantResult): The variant result entry
            rank (int): The corresponding rank for the result entry

        Returns:
            RankedPhEvalVariantResult: The result as a RankedPhEvalVariantResult
        """
        return RankedPhEvalVariantResult(
            chromosome=pheval_variant_result.chromosome,
            start=pheval_variant_result.start,
            end=pheval_variant_result.end,
            ref=pheval_variant_result.ref,
            alt=pheval_variant_result.alt,
            score=pheval_variant_result.score,
            rank=rank,
        )

from_variant_result(pheval_variant_result, rank) staticmethod

Return RankedPhEvalVariantResult from a PhEvalVariantResult and rank

Parameters:

Name	Type	Description	Default
pheval_variant_result	PhEvalVariantResult	The variant result entry	required
rank	int	The corresponding rank for the result entry	required

Returns:

Name	Type	Description
RankedPhEvalVariantResult		The result as a RankedPhEvalVariantResult

Source code in src/pheval/post_processing/post_processing.py

@staticmethod
def from_variant_result(pheval_variant_result: PhEvalVariantResult, rank: int):
    """Return RankedPhEvalVariantResult from a PhEvalVariantResult and rank
    Args:
        pheval_variant_result (PhEvalVariantResult): The variant result entry
        rank (int): The corresponding rank for the result entry

    Returns:
        RankedPhEvalVariantResult: The result as a RankedPhEvalVariantResult
    """
    return RankedPhEvalVariantResult(
        chromosome=pheval_variant_result.chromosome,
        start=pheval_variant_result.start,
        end=pheval_variant_result.end,
        ref=pheval_variant_result.ref,
        alt=pheval_variant_result.alt,
        score=pheval_variant_result.score,
        rank=rank,
    )

ResultSorter

Class for sorting PhEvalResult instances based on a given sort order.

Source code in src/pheval/post_processing/post_processing.py

class ResultSorter:
    """Class for sorting PhEvalResult instances based on a given sort order."""

    def __init__(self, pheval_results: [PhEvalResult], sort_order: SortOrder):
        """
        Initialise ResultSorter

        Args:
            pheval_results ([PhEvalResult]): List of PhEvalResult instances to be sorted
            sort_order (SortOrder): Sorting order to be applied
        """
        self.pheval_results = pheval_results
        self.sort_order = sort_order

    def _sort_by_decreasing_score(self) -> [PhEvalResult]:
        """
        Sort results in descending order based on the score

        Returns:
            [PhEvalResult]: Sorted list of PhEvalResult instances.
        """
        return sorted(self.pheval_results, key=operator.attrgetter("score"), reverse=True)

    def _sort_by_increasing_score(self) -> [PhEvalResult]:
        """
        Sort results in ascending order based on the score

        Returns:
            [PhEvalResult]: Sorted list of PhEvalResult instances.
        """
        return sorted(self.pheval_results, key=operator.attrgetter("score"), reverse=False)

    def sort_pheval_results(self) -> [PhEvalResult]:
        """
        Sort results based on the specified sort order.

        Returns:
            [PhEvalResult]: Sorted list of PhEvalResult instances.
        """
        return (
            self._sort_by_increasing_score()
            if self.sort_order == SortOrder.ASCENDING
            else self._sort_by_decreasing_score()
        )

__init__(pheval_results, sort_order)

Initialise ResultSorter

Parameters:

Name	Type	Description	Default
pheval_results	[PhEvalResult]	List of PhEvalResult instances to be sorted	required
sort_order	SortOrder	Sorting order to be applied	required

Source code in src/pheval/post_processing/post_processing.py

def __init__(self, pheval_results: [PhEvalResult], sort_order: SortOrder):
    """
    Initialise ResultSorter

    Args:
        pheval_results ([PhEvalResult]): List of PhEvalResult instances to be sorted
        sort_order (SortOrder): Sorting order to be applied
    """
    self.pheval_results = pheval_results
    self.sort_order = sort_order

sort_pheval_results()

Sort results based on the specified sort order.

Returns:

Type	Description
[PhEvalResult]	[PhEvalResult]: Sorted list of PhEvalResult instances.

Source code in src/pheval/post_processing/post_processing.py

def sort_pheval_results(self) -> [PhEvalResult]:
    """
    Sort results based on the specified sort order.

    Returns:
        [PhEvalResult]: Sorted list of PhEvalResult instances.
    """
    return (
        self._sort_by_increasing_score()
        if self.sort_order == SortOrder.ASCENDING
        else self._sort_by_decreasing_score()
    )

SortOrder

Bases: Enum

Enumeration representing sorting orders.

Source code in src/pheval/post_processing/post_processing.py

class SortOrder(Enum):
    """Enumeration representing sorting orders."""

    ASCENDING = 1
    """Ascending sort order."""
    DESCENDING = 2
    """Descending sort order."""

ASCENDING = 1 class-attribute

Ascending sort order.

DESCENDING = 2 class-attribute

Descending sort order.

calculate_end_pos(variant_start, variant_ref)

Calculate the end position for a variant

Parameters:

Name	Type	Description	Default
variant_start	int	The start position of the variant	required
variant_ref	str	The reference allele of the variant	required

Returns:

Name	Type	Description
int	int	The end position of the variant

Source code in src/pheval/post_processing/post_processing.py

def calculate_end_pos(variant_start: int, variant_ref: str) -> int:
    """Calculate the end position for a variant
    Args:
        variant_start (int): The start position of the variant
        variant_ref (str): The reference allele of the variant

    Returns:
        int: The end position of the variant
    """
    return variant_start + len(variant_ref) - 1

generate_pheval_result(pheval_result, sort_order_str, output_dir, tool_result_path)

Generate PhEval variant, gene or disease TSV result based on input results.

Parameters:

Name	Type	Description	Default
pheval_result	[PhEvalResult]	List of PhEvalResult instances to be processed.	required
sort_order_str	str	String representation of the desired sorting order.	required
output_dir	Path	Path to the output directory.	required
tool_result_path	Path	Path to the tool-specific result file.	required

Raises:

Type	Description
ValueError	If the results are not all the same type or an error occurs during file writing.

Source code in src/pheval/post_processing/post_processing.py

def generate_pheval_result(
    pheval_result: [PhEvalResult],
    sort_order_str: str,
    output_dir: Path,
    tool_result_path: Path,
) -> None:
    """
    Generate PhEval variant, gene or disease TSV result based on input results.

    Args:
        pheval_result ([PhEvalResult]): List of PhEvalResult instances to be processed.
        sort_order_str (str): String representation of the desired sorting order.
        output_dir (Path): Path to the output directory.
        tool_result_path (Path): Path to the tool-specific result file.

    Raises:
        ValueError: If the results are not all the same type or an error occurs during file writing.
    """
    if not pheval_result:
        info_log.warning(f"No results found for {tool_result_path.name}")
        return
    ranked_pheval_result = _create_pheval_result(pheval_result, sort_order_str)
    if all(isinstance(result, PhEvalGeneResult) for result in pheval_result):
        _write_pheval_gene_result(ranked_pheval_result, output_dir, tool_result_path)
    elif all(isinstance(result, PhEvalVariantResult) for result in pheval_result):
        _write_pheval_variant_result(ranked_pheval_result, output_dir, tool_result_path)
    elif all(isinstance(result, PhEvalDiseaseResult) for result in pheval_result):
        _write_pheval_disease_result(ranked_pheval_result, output_dir, tool_result_path)
    else:
        raise ValueError("Results are not all of the same type.")