mavis.annotate.base

class mavis.annotate.base.ReferenceName

inherits str

Class for reference sequence names. Ensures that hg19/hg38 chromosome names match.

int: the start position

@property
def start(self):

Args

int: the end position

@property
def end(self):

Args

Tuple: a tuple representing the items expected to be unique. for hashing and comparing

def key(self):

get the sequence for the current annotation object

def get_seq(self, reference_genome=None, ignore_cache=False):

Args

Raises

pulls strand information from the current object, or follows reference objects until the strand is found

def get_strand(self):

Returns

Raises

AttributeError: raised if the strand is not set on this or any of its reference objects

True if the gene is on the reverse/negative strand.

@property
def is_reverse(self):

Args

Raises

pulls chromosome information from the current object, or follows reference objects until the chromosome is found

def get_chr(self):

Returns

Raises

AttributeError: raised if the chromosome is not set on this or any of its reference objects

creates a dictionary representing the current object

def to_dict(self):

Returns