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
- ivc
- Returns
- tuple
(chromosome name, half-open end of fiveprime exon, first position of threeprime exon, strand)
- plastid.genomics.splicing.junction_pat = re.compile('([^@]+)@([0-9]+)\\^([0-9]+)\\(([+-])\\)f([0-9]+)')¶
Regex for matching splice junctions in plastid’s notation