mavis/annotate/base
class ReferenceName
inherits str
Class for reference sequence names. Ensures that hg19/hg38 chromosome names match.
class BioInterval
Attributes
- position (Interval)
- name (
Optional[str]
) - data (
Dict
) - seq (
Optional[str]
) - reference_object (
Any
) - strand (
Optional[str]
)
BioInterval.start()
the start position
@property
def start(self) -> int:
Args
- self
Returns
int
BioInterval.end()
the end position
@property
def end(self) -> int:
Args
- self
Returns
int
BioInterval.key()
Tuple: a tuple representing the items expected to be unique. for hashing and comparing
def key(self):
BioInterval.get_seq()
get the sequence for the current annotation object
def get_seq(self, reference_genome: Optional[ReferenceGenome] = None, ignore_cache=False):
Args
- reference_genome (Optional[ReferenceGenome])
- ignore_cache
Raises
NotImplementedError
: abstract method
BioInterval.get_strand()
pulls strand information from the current object, or follows reference objects until the strand is found
def get_strand(self):
Returns
- STRAND: the strand of this or any of its reference objects
Raises
AttributeError
: raised if the strand is not set on this or any of its reference objects
BioInterval.is_reverse()
True if the gene is on the reverse/negative strand.
@property
def is_reverse(self):
Args
- self
Raises
AttributeError
: if the strand is not specified
BioInterval.get_chr()
pulls chromosome information from the current object, or follows reference objects until the chromosome is found
def get_chr(self):
Returns
str
: the chromosome of this or any of its reference objects
Raises
AttributeError
: raised if the chromosome is not set on this or any of its reference objects
BioInterval.to_dict()
creates a dictionary representing the current object
def to_dict(self):
Returns
Dict[str]
: the dictionary of attribute values