phred.py

def offset_version_detection(quality_string = ''):
    """Tries to detect phred score offset automatically.
    Args:
        quality_string used to estimate format version and offset
    Returns:
        Phred offset
    Raises:
        ValueError: Cannot evaluate empty quality string
        ValueError: Cannot evaluate phred offset
    """
    pass

    sanger_offset   = 33
    illumina_offset = 64
    if len(quality_string) == 0:
        raise ValueError('Cannot evaluate empty quality string')
        
    minimum_value = min([ord(x) for x in quality_string])
    
    #minimum value needs to be at least 64 for versions [1.3, 1.8) 
    if minimum_value-illumina_offset >= 0:
        return illumina_offset
    #minimum value needs to be at least 33 for sanger
    elif minimum_value-sanger_offset >= 0:
        return sanger_offset
    raise ValueError('Cannot evaluate phred offset')

def phred_score(character, offset):
    return ord(character)-offset