base module

class mavis.annotate.base.BioInterval(reference_object, start, end=None, name=None, seq=None, data=None, strand=None)

Bases: object

Parameters:

• reference_object – the object this interval is on
• start (int) start of the interval (inclusive) –
• end (int) – end of the interval (inclusive)
• name – optional
• seq (str) – the seq relating to this interval

Example

>>> b = BioInterval('1', 12572784, 12578898, 'q22.2')
>>> b[0]
12572784
>>> b[1]
12578898

__len__()

Example

>>> b = BioInterval('1', 12572784, 12578898, 'q22.2')
>>> len(b)
6115

end

the end position

Type:int

get_chr()

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

Returns:the chromosome of this or any of its reference objects Return type:str Raises:AttributeError – raised if the chromosome is not set on this or any of its reference objects

get_seq(reference_genome=None, ignore_cache=False)

get the sequence for the current annotation object

Raises:NotImplementedError – abstract method

get_strand()

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

Returns:the strand of this or any of its reference objects Return type:STRAND Raises:AttributeError – raised if the strand is not set on this or any of its reference objects

is_reverse

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

Raises:AttributeError – if the strand is not specified

key()

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

start

the start position

Type:int

to_dict()

creates a dictionary representing the current object

Returns:the dictionary of attribute values Return type:dict by str

class mavis.annotate.base.ReferenceName

Bases: str

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

Example

>>> ReferenceName('chr1') == ReferenceName('1')
True