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mavis/annotate/fusion

class FusionTranscript

inherits PreTranscript

FusionTranscript is a PreTranscript built from two parent PreTranscripts. It has most of the same functionality as a regular PreTranscript except that it will not have a parent gene and retains a mapping of the new exons to the exons in the PreTranscript they originated from

Additionally the FusionTranscript is always constructed on the positive strand.

The preferred way to construct a FusionTranscript is through the build method.

Attributes

  • last_five_prime_exon (Exon)
  • first_three_prime_exon (Exon)

FusionTranscript.__init__()

def __init__(self):

determine_prime()

determine the side of the transcript 5' or 3' which is 'kept' given the breakpoint

def determine_prime(transcript: Transcript, breakpoint: Breakpoint) -> int:

Args

Returns

  • int: 5' or 3'

Raises

  • AttributeError: if the orientation of the breakpoint or the strand of the transcript is not specified