ValueError in notebooks/proteomics_data_relaxations.ipynb cell 17 line 1.

[Soratake-HirotakaYajima]

Hello.

I got a ValueError in notebooks/proteomics_data_relaxations.ipynb cell 17 line 1.

I checked excel file that there are not MW row in msb20209536-sup-0010-datasetev9.xlsx sheet 'EV9-AbsoluteMassFractions-2'.

Perhaps, it is lack of data about MW.

Could you tell me about error below.

Best regards.

---

ValueError Traceback (most recent call last)
/Users/userName/geckopy/simult_supp_material/notebooks/proteomics_data_relaxations.ipynb セル 17 line 1
----> 1 ev9_valid["MW"] = extract_proteins(None, prot_dict)["MW"]

File ~/.pyenv/versions/3.8.18/envs/geckopy/lib/python3.8/site-packages/geckopy/experimental/molecular_weights.py:194, in extract_proteins(model, all_proteins, key_fn)
192 df_prot["MW"] = 0
193 for index, row in df_prot.iterrows():
--> 194 df_prot.loc[index, "MW"] = _molecular_weight(row["Sequence"])
195 return df_prot[["uniprot", "protein_id", "MW", "Sequence"]]

File ~/.pyenv/versions/3.8.18/envs/geckopy/lib/python3.8/site-packages/geckopy/experimental/molecular_weights.py:95, in _molecular_weight(seq)
93 weight = sum(weight_table[x] for x in seq) - (len(seq) - 1) * water
94 except KeyError as e:
---> 95 raise ValueError(
96 f"'{e}' is not a valid unambiguous letter for proteins"
97 ) from None
99 return weight

ValueError: ''X'' is not a valid unambiguous letter for proteins

[carrascomj]

Hi! Thank you for opening this issue. Unfortunately, I cannot reproduce this.

I have set up a fresh virtual environment (python3.10), installed latest master from geckopy,

pip install git+https://github.com/ginkgobioworks/geckopy.git

cloned this repository and run the notebook. The molecular weights are properly fetched as they were.

I checked excel file that there are not MW row in msb20209536-sup-0010-datasetev9.xlsx sheet 'EV9-AbsoluteMassFractions-2'. Perhaps, it is lack of data about MW.

The molecular weights are fetched from uniprot, using the extract_proteins function, so there should not be any MW column. The ValueError that you are getting is that a protein sequence was fetched with an unknown "X" aminoacid, whose molecular weight cannot be determined. The extraction, however, runs for me without issues.

Possible solutions to your problem:

1. Try reinstalling geckopy to a fresh environment and running the notebook there.
2. Wait some time. Uniprot may block an IP temporarily if there are too many requests. I don't think that's the issue here because it should error out before spitting out a sequence, but this has happened before to me.
3. I will rerun it with python3.8 as you were and see if that helps me reproduce your issue.

Let me know if there is any progress!

[carrascomj]

Wait, I was on the wrong commit, I can reproduce this now.

The reason I don't get the error with an earlier commit is because the MW fallback was removed for some reason, I have open a pull request for this on upstream geckopy.

Installing geckopy from the branch should work now

pip install git+https://github.com/ginkgobioworks/geckopy.git@fix-re-mw-fallback
# cobrapy may cause some issues, so it is safer to downgrade it
pip install --upgrade "cobra==0.22.1"

Thanks for spotting this!