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Description
This epic is an umbrella for UTA schema overhaul plans
Goals:
Admin changes
- enable schema migrations. This amounts to choosing between keeping SA and using Alembic, or ditching SA (and using direct SQL) with yoyo migrations (presumably).
- use py models?
Updated schema elements
- create index exon_set_alt_ac_method_idx on exon_set(alt_ac, alt_aln_method);
- exon sets defined on sequence digests (rather than accessions)
- sequence aliases (wholesale import from seqrepo?)
- exon-set-relationships view: exon-exon relationships based on digests
- store multiple alignments (currently, only 1 aln per <tx_ac, alt_ac, alt_aln_method>
New schema and content
- cds se on all coding exon sets
- digest table (linked to exon set, I think)
- assembly data
- LRG data
- exon set digests as PK
- alignment digests as PK
- gene-tx table