mavis.annotate.fusion
class mavis.annotate.fusion.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.
mavis.annotate.fusion.FusionTranscript.__init__()
def __init__(self):
mavis.annotate.fusion.determine_prime()
determine the side of the transcript 5' or 3' which is 'kept' given the breakpoint
def determine_prime(transcript, breakpoint):
Args
- transcript (
Transcript
): the transcript - breakpoint (
Breakpoint
): the breakpoint
Returns
PRIME
: 5' or 3'
Raises
AttributeError
: if the orientation of the breakpoint or the strand of the transcript is not specified