mavis.pairing.pairing
mavis.pairing.pairing.product_key()
unique id for the product row
def product_key(bpp):
Args
- bpp
mavis.pairing.pairing.predict_transcriptome_breakpoint()
for a given genomic breakpoint and the target transcript. Predicts the possible transcriptomic breakpoints that would be expected based on the splicing model for abrogated splice sites
def predict_transcriptome_breakpoint(breakpoint, transcript):
Args
- breakpoint (
Breakpoint): the genomic breakpoint - transcript (
PreTranscript): the transcript
Note
mavis.pairing.pairing.equivalent()
compares two events by breakpoint position to see if they are equivalent
def equivalent(event1, event2, distances=None):
Args
- event1
- event2
- distances
mavis.pairing.pairing.pair_by_distance()
for a set of input calls, pair by distance
def pair_by_distance(calls, distances, log=DEVNULL, against_self=False):
Args
- calls
- distances
- log
- against_self
mavis.pairing.pairing.inferred_equivalent()
comparison of events using product prediction and breakpoint prediction
def inferred_equivalent(event1, event2, reference_transcripts, distances=None):
Args
- event1
- event2
- reference_transcripts
- distances