splicing module

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

Bases: mavis.annotate.base.BioInterval

__or__(other)[source]
class mavis.annotate.splicing.SplicingPattern(*args, splice_type='normal')[source]

Bases: list

static classify(pattern, original_sites)[source]
mavis.annotate.splicing.predict_splice_sites(input_sequence, is_reverse=False)[source]

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