nonexplicit error message about keggcharter HOT 5 CLOSED

Submitted a new version - 0.3.5 - which will soon be available. Do check if this has been improved

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Installed the new version (0.4.1) and this now happens:

keggcharter.py -f reCOGnizer_results.tsv -o test -ecc "EC number" -mm "Fatty acid metabolism"

Created /shared/homes/152324/miniconda3/envs/keggcharter_env/bin/kc_kgmls
Created /shared/homes/152324/miniconda3/envs/keggcharter_env/bin/kc_csvs
2022-12-14 14:21:48: Arguments valid.
/shared/homes/152324/miniconda3/envs/keggcharter_env/bin/keggcharter.py:117: DtypeWarning: Columns (10) have mixed types. Specify dtype option on import or set low_memory=False.
  return pd.read_csv(file, sep='\t')
2022-12-14 14:22:16: Data successfully read.
Converting 1703 EC numbers to KOs through the KEGG API: 100%|███████████████████████████████████████████████████████████████████| 12/12 [00:13<00:00,  1.16s/it]
Converting 2365 KOs to EC numbers through the KEGG API: 100%|█████████████████████████████████████████████████████████████████████████████████████████| 16/16 [00:17<00:00,  1.08s/it]
2022-12-14 14:25:27: Results saved to test/KEGGCharter_results.tsv
Traceback (most recent call last):
  File "/shared/homes/152324/miniconda3/envs/keggcharter_env/bin/keggcharter.py", line 489, in <module>
    main()
  File "/shared/homes/152324/miniconda3/envs/keggcharter_env/bin/keggcharter.py", line 437, in main
    args.genomic_columns = args.genomic_columns.split(',')
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'split'

I don't have in this case a genomic column. As it is optional, keggcharter.py should not be complaining about it, right?

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KEGGCharter always counts on one column of taxonomy and another of quantification to build the maps for. In KEGGCharter, this information can be inputted alternatively using the -it NAME_OF_TAXONOMY and -iq parameters, which will input taxonomy and quantification, respectively, replace the -tc and -gcols/-tcols parameters. -it requires NAME_OF_TAXONOMY as it is the value that will appear represented in the maps.

As you had complained before, this is not intuitively expressed in the interface. I will update when I have the time.

from keggcharter.

Hello quick question is quantification mandatory for the use of KEGGCharter or is there a way to make this data optional as currently my lab can't obtain quantification levels of our proteins?

Thank you very much.

from keggcharter.

You can input a mock quantification with the -iq parameter. In the future, I hope to make this more intuitive.

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