plastid.genomics.splicing module

Utility functions for systematically naming splice junctions and retrieving their sequences

plastid.genomics.splicing.get_junction_tuple(ivc)[source]

Convert a SegmentChain representing a splice junction to a tuple

Parameters:
ivc : SegmentChain

A two-exon fragment representing a splice junction

Returns:
tuple

(chromosome name, half-open end of fiveprime exon, first position of threeprime exon, strand)

plastid.genomics.splicing.junction_pat = <_sre.SRE_Pattern object>

Regex for matching splice junctions in plastid’s notation