mavis.annotate.splicing

class mavis.annotate.splicing.SplicingPattern

inherits list

mavis.annotate.splicing.SplicingPattern.generate_patterns()

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

@classmethod
def generate_patterns(cls, sites, is_reverse=False):

Args

• sites
• is_reverse

Returns

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

Note

see theory - predicting splicing patterns

class mavis.annotate.splicing.SpliceSite

inherits BioInterval

mavis.annotate.splicing.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, is_reverse=False):

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