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uta schema overhaul

4

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...

reece

Use entrez gene_ids rather than symbols to link genes and transcripts

4

The goal is to use entrez gene_ids rather than hgnc symbols to link genes and transcripts, including dropping the hgnc column from the transcript table. Phase 1: * Update gene...

reece

UTA should use cigar strings from NCBI's gff files whenever possible

3

In ~May 2015, NCBI started releasing transcript alignment files with cigar strings. UTA predates these files, and still uses uta_align for alignments. For the future overhaul, UTA should use cigar...

reece

**Originally reported by Reece Hart (Bitbucket: [reece](http://bitbucket.org/reece), GitHub: [reece](http://github.com/reece)) in [biocommons/uta](https://bitbucket.org/biocommons/uta/) [#176](https://bitbucket.org/biocommons/uta/issue/176)** Migrated by [bitbucket-issue-migration](https://github.com/reece/bitbucket-issue-migration) on 2016-09-09 15:15:07 --- When generating sequence alignments, capture sequence edits so that they can...

reece

add min,max bounds to transcript and gene summaries

1

**Originally reported by Reece Hart (Bitbucket: [reece](http://bitbucket.org/reece), GitHub: [reece](http://github.com/reece)) in [biocommons/uta](https://bitbucket.org/biocommons/uta/) [#162](https://bitbucket.org/biocommons/uta/issue/162)** Migrated by [bitbucket-issue-migration](https://github.com/reece/bitbucket-issue-migration) on 2016-09-09 15:15:07 ---

reece

**Originally reported by Reece Hart (Bitbucket: [reece](http://bitbucket.org/reece), GitHub: [reece](http://github.com/reece)) in [biocommons/uta](https://bitbucket.org/biocommons/uta/) [#197](https://bitbucket.org/biocommons/uta/issue/197)** Migrated by [bitbucket-issue-migration](https://github.com/reece/bitbucket-issue-migration) on 2016-09-09 15:15:07 --- Currently, the only way to get the CDS start,end onto aligned...

reece

uta_20150827 is missing ENSP accessions and sequences

2

**Originally reported by Reece Hart (Bitbucket: [reece](http://bitbucket.org/reece), GitHub: [reece](http://github.com/reece)) in [biocommons/uta](https://bitbucket.org/biocommons/uta/) [#194](https://bitbucket.org/biocommons/uta/issue/194)** Migrated by [bitbucket-issue-migration](https://github.com/reece/bitbucket-issue-migration) on 2016-09-09 15:15:07 --- uta_20150827 does not include ENSP sequences or seqinfo. One consequence of...

reece

drop sqlalchemy, rework creation + loading

1

**Originally reported by Reece Hart (Bitbucket: [reece](http://bitbucket.org/reece), GitHub: [reece](http://github.com/reece)) in [biocommons/uta](https://bitbucket.org/biocommons/uta/) [#187](https://bitbucket.org/biocommons/uta/issue/187)** Migrated by [bitbucket-issue-migration](https://github.com/reece/bitbucket-issue-migration) on 2016-09-09 15:15:07 --- I'm incurring lots of overhead and phumphing from using SA and...

reece

**Originally reported by Reece Hart (Bitbucket: [reece](http://bitbucket.org/reece), GitHub: [reece](http://github.com/reece)) in [biocommons/uta](https://bitbucket.org/biocommons/uta/) [#175](https://bitbucket.org/biocommons/uta/issue/175)** Migrated by [bitbucket-issue-migration](https://github.com/reece/bitbucket-issue-migration) on 2016-09-09 15:15:07 ---

reece

**Originally reported by Reece Hart (Bitbucket: [reece](http://bitbucket.org/reece), GitHub: [reece](http://github.com/reece)) in [biocommons/uta](https://bitbucket.org/biocommons/uta/) [#174](https://bitbucket.org/biocommons/uta/issue/174)** Migrated by [bitbucket-issue-migration](https://github.com/reece/bitbucket-issue-migration) on 2016-09-09 15:15:07 --- Add tables to track assemblies. This concept is probably best handled...

reece