splicing module

class mavis.annotate.splicing.SpliceSite(ref, pos, site_type, intact=True, start=None, end=None, strand=None, seq=None)

Bases: mavis.annotate.base.BioInterval

__or__(other)

class mavis.annotate.splicing.SplicingPattern(*args, splice_type='normal')

Bases: list

classmethod classify(pattern, original_sites)

classmethod generate_patterns(sites, is_reverse=False)

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

Returns:List of positions to be spliced together Return type:list of SplicingPattern

see theory - predicting splicing patterns

mavis.annotate.splicing.predict_splice_sites(input_sequence, is_reverse=False)

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

Parameters:

• 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 of putative splice sites

Return type:

list of SpliceSite