Skeleton for a genomic variant interface

VariantSkeleton.py

class Variant(object):
    """This is the top level class for genomic variants"""
    def __init__(self, filename, filetype=None, gvfreader=None, vcfreader=None):
        """
        Uses the default parser Wrappers unless otherwise specified. 
        Currently supported arguments to filetype are "vcf" and "gvf".
        If filetype is not specified, guessed from file extension.
        """
        self.filename = filename
        if filetype is not None:
            self.filetype = filetype
        else:
            guess_type = self._guess_filetype() # returns 0 for unknown
            if filetype:
                self.filetype = filetype
            else: 
                raise RuntimeError("Unknown filetype, please specify.")
        
        # Use either provided parser instance or instantiate default
        default_vcfreader = PyVCFWrapper
        default_gvfreader = BCBioGFFWrapper
        if self.filetype = "vcf":
            if vcfreader is not None:
                self.parser = vcfreader
            else:
                self.parser = default_vcfreader()
        elif self.filetype = "gvf":
            if gvfreader is not None:
                self.parser = gvfreader
            else:
                self.parser = default_gvfreader()
        else:
            raise RuntimeError('Given filetype is not valid.')
    
    def parse(self):
        # Make instance of parser wrapper
        self.parser.parse(self.filename)
        
    def _guess_filetype(self):
        """Guess filetype based on extension, returns 0 for unknown"""
        # TODO use os.path to determine file extension
        return 0


class Parse(object):
    """Abstract interface class, parser wrappers should inherit from this"""
    def __init__(self):
        """Default constructor for abstract interface class"""
        pass
    
    def parse(self):
        raise NotImplementedError


class PyVCFWrapper(Parse):
    """Wrapper for PyVCF"""
    def __init__(self, filename):
        Parse.__init__(self)
        self.filename = filename
    
    def parse(self):
        """Parse the file"""
        PyVCF.vcf.Reader(self.filename)

class BCBioGFFWrapper(Parse):
    """Wrapper for BCBio.GFF"""
    def __init__(self, filename):
        Parse.__init__(self)
        self.filename = filename
    
    def parse(self):
        """Parse the file"""
        with open(self.filename) as fh:
            BCBio.GFF.parse(fh)