Prepare corpus

prepare_corpus(phenopacket_dir, variant_analysis, gene_analysis, disease_analysis, gene_identifier, hg19_template_vcf, hg38_template_vcf, hg19_vcf_dir, hg38_vcf_dir, output_dir)

Prepare a corpus of Phenopackets for analysis, optionally checking for complete variant records and updating gene identifiers.

Parameters:

Name	Type	Description	Default
phenopacket_dir	Path	The path to the directory containing Phenopackets.	required
variant_analysis	bool	If True, check for complete variant records in the Phenopackets.	required
gene_analysis	bool	If True, check for complete gene records in the Phenopackets.	required
disease_analysis	bool	If True, check for complete disease records in the Phenopackets.	required
gene_identifier	str	Identifier for updating gene identifiers, if applicable.	required
hg19_template_vcf	Path	Path to the hg19 template VCF file (optional), to spike variants into	required
hg38_template_vcf	Path	Path to the hg38 template VCF file (optional), to spike variants into	required
hg19_vcf_dir	Path	Path to the directory containing hg19 template VCF files (optional).	required
hg38_vcf_dir	Path	Path to the directory containing hg38 template VCF files (optional).	required
output_dir	Path	The directory to save the prepared Phenopackets and, optionally, VCF files.	required

Notes

To spike variants into VCFs for variant-based analysis at least one of hg19_template_vcf, hg38_template_vcf, hg19_vcf_dir or hg38_vcf_dir is required.

Source code in src/pheval/prepare/prepare_corpus.py

def prepare_corpus(
    phenopacket_dir: Path,
    variant_analysis: bool,
    gene_analysis: bool,
    disease_analysis: bool,
    gene_identifier: str,
    hg19_template_vcf: Path,
    hg38_template_vcf: Path,
    hg19_vcf_dir: Path,
    hg38_vcf_dir: Path,
    output_dir: Path,
) -> None:
    """
    Prepare a corpus of Phenopackets for analysis, optionally checking for complete variant records and updating
    gene identifiers.

    Args:
        phenopacket_dir (Path): The path to the directory containing Phenopackets.
        variant_analysis (bool): If True, check for complete variant records in the Phenopackets.
        gene_analysis (bool): If True, check for complete gene records in the Phenopackets.
        disease_analysis (bool): If True, check for complete disease records in the Phenopackets.
        gene_identifier (str): Identifier for updating gene identifiers, if applicable.
        hg19_template_vcf (Path): Path to the hg19 template VCF file (optional), to spike variants into
        VCFs for variant-based analysis at least one of hg19_template_vcf or hg38_template_vcf is required.
        hg38_template_vcf (Path): Path to the hg38 template VCF file (optional), to spike variants into
        VCFs for variant-based analysis at least one of hg19_template_vcf or hg38_template_vcf is required.
        hg19_vcf_dir (Path): Path to the directory containing hg19 template VCF files (optional).
        hg38_vcf_dir (Path): Path to the directory containing hg38 template VCF files (optional).
        output_dir (Path): The directory to save the prepared Phenopackets and, optionally, VCF files.
    Notes:
        To spike variants into VCFs for variant-based analysis at least one of hg19_template_vcf, hg38_template_vcf,
        hg19_vcf_dir or hg38_vcf_dir is required.
    """
    output_dir.joinpath("phenopackets").mkdir(exist_ok=True, parents=True)
    for phenopacket_path in all_files(phenopacket_dir):
        phenopacket_util = PhenopacketUtil(phenopacket_reader(phenopacket_path))
        if not phenopacket_util.observed_phenotypic_features():
            info_log.warning(
                f"Removed {phenopacket_path.name} from the corpus due to no observed phenotypic features."
            )
            continue
        if variant_analysis:
            if phenopacket_util.check_incomplete_variant_record():
                info_log.warning(
                    f"Removed {phenopacket_path.name} from the corpus due to missing variant fields."
                )
                continue
        if gene_analysis:
            if phenopacket_util.check_incomplete_gene_record():
                info_log.warning(
                    f"Removed {phenopacket_path.name} from the corpus due to missing gene fields."
                )
                continue
        if disease_analysis:
            if phenopacket_util.check_incomplete_disease_record():
                info_log.warning(
                    f"Removed {phenopacket_path.name} from the corpus due to missing disease fields."
                )
                continue
        if hg19_template_vcf or hg38_template_vcf:
            output_dir.joinpath("vcf").mkdir(exist_ok=True)
            create_spiked_vcf(
                output_dir.joinpath("vcf"),
                phenopacket_path,
                hg19_template_vcf,
                hg38_template_vcf,
                hg19_vcf_dir,
                hg38_vcf_dir,
            )
        if gene_identifier:
            create_updated_phenopacket(
                gene_identifier, phenopacket_path, output_dir.joinpath("phenopackets")
            )
        else:
            # if not updating phenopacket gene identifiers then copy phenopacket as is to output directory
            shutil.copy(
                phenopacket_path, output_dir.joinpath(f"phenopackets/{phenopacket_path.name}")
            )