scout/parse/case.py
def parse_ped(ped_stream, family_type='ped'):
    """Parse out minimal family information from a PED file.

    Args:
        ped_stream(iterable(str))
        family_type(str): Format of the pedigree information

    Returns:
        family_id(str), samples(list[dict])
    """
    pedigree = FamilyParser(ped_stream, family_type=family_type)

    if len(pedigree.families) != 1:
        raise PedigreeError("Only one case per ped file is allowed")

    family_id = list(pedigree.families.keys())[0]
    family = pedigree.families[family_id]

    samples = [{
        'sample_id': ind_id,
        'father': individual.father,
        'mother': individual.mother,
        # Convert sex to human readable
        'sex': SEX_MAP[individual.sex],
        'phenotype': PHENOTYPE_MAP[int(individual.phenotype)],
    } for ind_id, individual in family.individuals.items()]

    return family_id, samples
def parse_ped(ped_stream, family_type='ped'):
    pedigree = FamilyParser(ped_stream, family_type=family_type)

    if len(pedigree.families) != 1:
        raise PedigreeError("Only one case per ped file is allowed")

    family_id = list(pedigree.families.keys())[0]
    family = pedigree.families[family_id]

    samples = [{
        'sample_id': ind_id,
        'father': individual.father,
        'mother': individual.mother,
        # Convert sex to human readable
        'sex': SEX_MAP[individual.sex],
        'phenotype': PHENOTYPE_MAP[int(individual.phenotype)],
    } for ind_id, individual in family.individuals.items()]

    return family_id, samples
def parse_ped ( ped_stream , family_type = 'ped' ) : pedigree = FamilyParser ( ped_stream , family_type = family_type ) if len ( pedigree . families ) != 1 : raise PedigreeError ( "Only one case per ped file is allowed" ) family_id = list ( pedigree . families . keys ( ) ) [ 0 ] family = pedigree . families [ family_id ] samples = [ { 'sample_id' : ind_id , 'father' : individual . father , 'mother' : individual . mother , # Convert sex to human readable 'sex' : SEX_MAP [ individual . sex ] , 'phenotype' : PHENOTYPE_MAP [ int ( individual . phenotype ) ] , } for ind_id , individual in family . individuals . items ( ) ] return family_id , samples
Parse out minimal family information from a PED file.

    Args:
        ped_stream(iterable(str))
        family_type(str): Format of the pedigree information

    Returns:
        family_id(str), samples(list[dict])
Parse out minimal family information from a PED file .