Producing sequence for splicing isoforms

Question

[tomas4482]

After detection of alternative splicing events using rMATs or SplAdder, I could have the coordinates of events. For simply spliced-out or spliced-in events like exon skipping/intron retention, it is easy to produce the sequence from the coordinates by removing or inserting sequences to all the reference annotated transcripts. But for A3SS, A5SS, mutual exclusive exons, they have multiple connections between different exons. It is not easy to generate sequences for them.

Is there any method or tool can be used to do this task?