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
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