param.py

from marshmallow import Schema, ValidationError, fields, validates_schema


class Param(Schema):
    chr_col = fields.Int(required=True, description="Column number for chromosome")
    pos_col = fields.Int(required=True, description="Column number for base position")
    ea_col = fields.Int(required=True, description="Column number for effect allele")
    oa_col = fields.Int(required=True, description="Column number for other allele")
    beta_col = fields.Int(required=True, description="Column number for effect")
    se_col = fields.Int(required=True, description="Column number for standard error")
    pval_col = fields.Int(
        required=True, description="Column number for association P value"
    )
    delimiter = fields.Str(required=True, description="Input file column delimiter")
    header = fields.Bool(required=True, description="Does the input file have a header")
    ncase_col = fields.Int(
        required=False, description="Column number for number of cases"
    )
    snp_col = fields.Int(
        required=False, description="Column number for variant identifier"
    )
    eaf_col = fields.Int(
        required=False, description="Column number for effect allele variant frequency"
    )
    oaf_col = fields.Int(
        required=False, description="Column number for other allele variant frequency"
    )
    imp_z_col = fields.Int(
        required=False,
        description="Column number for summary statistics imputation Z score",
    )
    imp_info_col = fields.Int(
        required=False,
        description="Column number for summary statistics imputation INFO score",
    )
    ncontrol_col = fields.Int(
        required=False,
        description="Column number for number of controls (if case/control) or total sample size if continuous",
    )
    build = fields.Str(
        required=True,
        description="Name of the genome build i.e. GRCh36, GRCh37, GRCh38",
    )
    data = fields.Str(
        required=False,
        description="Path to input file, required if not passed in main command line parameters",
    )
    out = fields.Str(
        required=False,
        description="Path to output vcf file, required if not passed in main command line parameters",
    )
    id = fields.Str(
        required=False,
        description="Unique identified or name of GWAS study, required if not passed in main command line parameters",
    )
    cohort_cases = fields.Float(
        required=False, description="Total study number of cases"
    )
    cohort_controls = fields.Float(
        required=False,
        description="Total study number of controls (if case/control) or total sample size if continuous",
    )
    jsonmeta = fields.Str(
        required=False, description="Path to input metadata file file"
    )
    md5 = fields.Str(required=False, description="md5 checksum for input file")

    @validates_schema(pass_original=True)
    def check_unknown_fields(self, data, original_data):
        unknown = set(original_data) - set(self.fields)
        if unknown:
            raise ValidationError("Unknown field", unknown)