feat(IPVC-2471): add codon_table to txinfo file

[bsgiles73]

Upon analysis of previous results it was found that we were not setting the codon_table column of the transcript table appropriately for mitochondrial genes or non-coding genes. The value for mitochondrial coding genes should be "2", and for non-coding genes the value really should be NULL. Like cds_start_i, cds_end_i and cds_md5.

This PR makes several updates to accomplish this.

• The alembic migration file was updated to make the new column nullable, a text value, and removed the default.
• Backfills the existing transcript table based on the presence of cds values.
• It adds codon_table to the TxInfo uta format.
• Adds a default of "1" if a RefSeq sequence record has a CDS feature.
• Adds logic to the loading module that sets the value to NULL if the coding has no coding information.

To test these changes I ran the mito workflow on a database that had the gene_id backfill performed.

Run the mito-extract workflow:
=======================
sgiles-MD6M:uta shane.giles$ docker compose -f docker-compose.yml -f misc/mito-transcripts/docker-compose-mito-extract.yml run mito-extract
2024-05-23 01:58:58 INFO     [__main__] downloading files for NC_012920.1
2024-05-23 01:58:58 INFO     [__main__] downloading gb file to /mito-extract/work/NC_012920.1.gbff
2024-05-23 01:59:00 INFO     [__main__] downloading fasta file to /mito-extract/work/NC_012920.1.fna
2024-05-23 01:59:02 INFO     [__main__] processing NCBI GBFF file from /mito-extract/work/NC_012920.1.gbff
2024-05-23 01:59:02 INFO     [__main__] processing NCBI GBFF file from /mito-extract/work/NC_012920.1.fna
2024-05-23 01:59:02 INFO     [__main__] found 37 genes from parsing /mito-extract/work/NC_012920.1.gbff

Verify the codon_table column was in the txinfo file:
=======================================
origin  ac      gene_id gene_symbol     cds_se_i        exons_se_i      codon_table     transl_except
NCBI    NC_012920.1_08526_09207 4508    MT-ATP6 0,681   0,681   2
NCBI    NC_012920.1_09206_09990 4514    MT-CO3  0,784   0,784   2       (pos:9990,aa:TERM)
NCBI    NC_012920.1_09990_10058 4563    MT-TG           0,68

Run the uta-load workflow:
====================
sgiles-MD6M:uta shane.giles$ UTA_ETL_OLD_UTA_VERSION=uta_20210129c UTA_ETL_NEW_UTA_VERSION=uta_20240521 docker compose run uta-load
[+] Creating 1/0
 ✔ Container uta  Running                                                                                                                                                                                                                          0.0s
+ source_uta_v=uta_20210129c
+ dest_uta_v=uta_20240521
...

In the source databaese:
==================
uta=> SELECT t.codon_table, COUNT(*) row_count FROM uta_20210129c.transcript AS t GROUP BY t.codon_table;
 codon_table | row_count
-------------+-----------
 1           |    202275
             |    111952
(2 rows)

In the destination:
==============
uta=> SELECT t.codon_table, COUNT(*) row_count FROM uta_20240521.transcript AS t GROUP BY t.codon_table;
 codon_table | row_count
-------------+-----------
 1           |    202275
 2           |        13
             |    111976
(3 rows)