feat(IPVC-2425): add migration to fix tx-alt-exon-pairs view

[bsgiles73]

This PR addresses an existing issue with a view in the UTA database, tx_alt_exon_pairs_v. This view is used to find transcript and alternate accession exon pairs for the align-exons method. The goal is to find valid pairs that are missing CIGAR stings provided by uta-align.

The query finds transcript exons with the alt_aln_method="transcript" and alignments with alt_aln_method !="transcript". An issue is encountered when we deprecate an existing transcript. This happens when the cds start/end has changed or the exon structure has changed. UTA does not delete the old record, nor does it update the cds or exon values. It updates the alt_aln_method so that it is essentially hidden. Here is an example of an exon set record being updated due to a change in the exon definition of the transcript.

Transcript: exon_set_id: 343991; tx_ac: NM_001173991.2; alt_aln_method: transcript

was updated to...

Transcript: exon_set_id: 343991; tx_ac: NM_001173991.2; alt_aln_method: transcript/70b44909

because the exon structure went from 0,306;306,408;408,501;501,702;702,1306 -> 0,306;306,408;408,501;501,703;703,1306

using the following query you will see that the updated (deprecated) transcript exon set is showing up as alt_aln_methods that will be passed to align_exons. There is no need to align transcript exons from one deprecated structure to the latest. This issue can be addressed by adjusting the WHERE criteria of the view.

alt_aln_method !="transcript" -> alt_aln_method !~ "transcript"

To test this I ran the following query pre and post Alembic migration.

select a.symbol, a.gene_id, a.tx_ac, a.alt_ac, a.alt_aln_method, count(a.ord) as exon_cnt
from (
      -- query from uta.loading.align_exons, filters for exon pairs missing an exon
      --   alignment and transcripts containing a "/" character.
      select *
      from uta.tx_alt_exon_pairs_v as v
      where exon_aln_id is NULL and tx_ac !~ '/'
) as a
where a.tx_ac='NM_001173991.2'
group by a.symbol, a.gene_id, a.tx_ac, a.alt_ac, a.alt_aln_method;

BEFORE:

+-------+-------+--------------+--------------+-------------------+--------+
|symbol |gene_id|tx_ac         |alt_ac        |alt_aln_method     |exon_cnt|
+-------+-------+--------------+--------------+-------------------+--------+
|TMEM216|51259  |NM_001173991.2|AC_000143.1   |splign             |5       |
|TMEM216|51259  |NM_001173991.2|NC_000011.10  |splign             |5       |
|TMEM216|51259  |NM_001173991.2|NC_000011.10  |splign/d0e7701b    |5       |
|TMEM216|51259  |NM_001173991.2|NC_000011.9   |blat               |5       |
|TMEM216|51259  |NM_001173991.2|NC_000011.9   |splign             |5       |
|TMEM216|51259  |NM_001173991.2|NC_018922.2   |splign             |5       |
|TMEM216|51259  |NM_001173991.2|NG_032976.1   |splign             |5       |
|TMEM216|51259  |NM_001173991.2|NM_001173991.2|transcript/6bcc9051|5       |
|TMEM216|51259  |NM_001173991.2|NM_001173991.2|transcript/70b44909|5       |
+-------+-------+--------------+--------------+-------------------+--------+

AFTER:

+-------+-------+--------------+------------+---------------+--------+
|symbol |gene_id|tx_ac         |alt_ac      |alt_aln_method |exon_cnt|
+-------+-------+--------------+------------+---------------+--------+
|TMEM216|51259  |NM_001173991.2|AC_000143.1 |splign         |5       |
|TMEM216|51259  |NM_001173991.2|NC_000011.10|splign         |5       |
|TMEM216|51259  |NM_001173991.2|NC_000011.10|splign/d0e7701b|5       |
|TMEM216|51259  |NM_001173991.2|NC_000011.9 |blat           |5       |
|TMEM216|51259  |NM_001173991.2|NC_000011.9 |splign         |5       |
|TMEM216|51259  |NM_001173991.2|NC_018922.2 |splign         |5       |
|TMEM216|51259  |NM_001173991.2|NG_032976.1 |splign         |5       |
+-------+-------+--------------+------------+---------------+--------+