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feat(IPVC-3129): add source to transl excepts #50

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  • Adds Source column to TranslationException model
  • alembic migration
  • changes to check_transl_excepts to generate translation exceptions to account for differences between translated and reported protein sequences.

To test these changes I used a postgres dump of uta_20241219 which has all of the translation exceptions we could get by downloading GBFF files from NCBI. I applied the migration and then ran the check-transl-except using all of the RefSeq NM_ accessions in the database (127,290). The code found all translation exceptions that already existed in the database, and added only those for the missing alternate start codons. Those will be the ones with Internal as the source.

+----------+-------+-------+------------+-------+
| source   | new   | codon | amino_acid | count |
+----------+-------+-------+------------+-------+
| NCBI     | False | TGA   | Sec        | 225   |
+----------+-------+-------+------------+-------+
| NCBI     | False | TGA   | Other      | 26    |
+----------+-------+-------+------------+-------+
| NCBI     | False | GTG   | Met        | 16    |
+----------+-------+-------+------------+-------+
| NCBI     | False | ATA   | Met        | 9     |
+----------+-------+-------+------------+-------+
| NCBI     | False | ACG   | Met        | 5     |
+----------+-------+-------+------------+-------+
| NCBI     | False | ATT   | Met        | 5     |
+----------+-------+-------+------------+-------+
| NCBI     | False | TAG   | Other      | 2     |
+----------+-------+-------+------------+-------+
| NCBI     | False | TGA   | Ser        | 2     |
+----------+-------+-------+------------+-------+
| Internal | True  | CTG   | Met        | 123   |
+----------+-------+-------+------------+-------+
| Internal | True  | TTG   | Met        | 10    |
+----------+-------+-------+------------+-------+

@bsgiles73 bsgiles73 requested a review from sptaylor January 2, 2025 17:47
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