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mavis/annotate/constants

PASS_FILENAME

PASS_FILENAME = 'annotations.tab'

SPLICE_SITE_RADIUS

SPLICE_SITE_RADIUS = 2

DONOR_SEQ

DONOR_SEQ = [
    re.compile('(AG)(GT[AG]AG)'),
    re.compile('([CA]AG)(GTA)'),
]

ACCEPTOR_SEQ

ACCEPTOR_SEQ = [
    re.compile('([TC]{8}[ATCG]CAG)([GA][ATCG])'),
    re.compile('([TC]{9}TAG)([GA][ATCG])'),
    re.compile('([TC]{8}[ATCG]AAG)([GA][ATCG])'),
]

class SPLICE_SITE_TYPE

inherits MavisNamespace

Attributes

  • DONOR (int)
  • ACCEPTOR (int)