mavis/annotate/splicing

class SplicingPattern

inherits list

SplicingPattern.generate_patterns()

returns a list of splice sites to be connected as a splicing pattern

@classmethod
def generate_patterns(
    cls, sites: Iterable['SpliceSite'], is_reverse=False
) -> List['SplicingPattern']:

Args

• sites (Iterable[SpliceSite])
• is_reverse

Returns

• List[SplicingPattern]: List of positions to be spliced together

Note

see theory - predicting splicing patterns

class SpliceSite

inherits BioInterval

predict_splice_sites()

looks for the expected splice site sequence patterns in the input strings and returns a list of putative splice sites

def predict_splice_sites(input_sequence: str, is_reverse: bool = False) -> List[SpliceSite]:

Args

• input_sequence (str): input sequence with respect to the positive/forward strand
• is_reverse (bool): True when the sequences is transcribed on the reverse strand

Returns

• List[SpliceSite]