No TAXID for Ecoli and incompatibility of the Ecoli specific annotation file

[FH96]

Hi,

This is my first time to do GO term analysis and I'm new to it. I want to use goatools for Ecoli. The taxID for ecoli is not in the gene2go file that is downloaded by default, I searched for 562 which is Ecoli in general, 83333 that is for Ecoli k12 and also 469008 which is the taxID for Ecoli BL21 and it says "AssertionError: **FATAL: NO TAXIDS: gene2go" for all of them.

Thus I tried to download the Ecoli annotation from Gene Ontology database. However, the formatting of this file is different from the gene2go file and again I face error reading this GAF file:

**NOTE: DEFAULT TAXID STORED FROM gene2go IS 9606 (human)
1
0) tax_id UniProtKB

1. DB_ID A0A385XJ53
2. GO_ID insA9
3. Evidence_Code involved_in
4. Qualifier GO:0006310
5. GO_term GO_REF:0000043
6. DB_Reference IEA
7. NS UniProtKB-KW:KW-0233
   Traceback (most recent call last):
   File "/Users/fh/Documents/project/python code/venv/lib/python3.12/site-packages/goatools/anno/init/reader_genetogo.py", line 74, in init_associations
   taxid = int(vals[0])
   ^^^^^^^^^^^^
   ValueError: invalid literal for int() with base 10: 'UniProtKB'
   **FATAL: invalid literal for int() with base 10: 'UniProtKB'
   **FATAL: ecocyc2.gaf[1]:
   UniProtKB A0A385XJ53 insA9 involved_in GO:0006310 GO_REF:0000043 IEA UniProtKB-KW:KW-0233 P Insertion element IS1 9 protein InsA insA9|b4709 protein taxon:83333 20240729 UniProt

Probably I can rearrange the E.coli file to match Gene2GOreader function, except "DB reference" that I'm not sure about.
Also I'm wondering if there is another way to get a compatible file for E.coli.

Thank you.