qpxc transform quantify --method ibaq fails with KeyError: 'Condition'

[hanying-yang]

Bug: qpxc transform quantify --method ibaq fails with KeyError: 'Condition'

Thank you for developing QPX and mokume (and ibaqpy). I’m testing the iBAQ quantification workflow from a QPX DIA-NN feature parquet and ran into a missing Condition column error.

Command:

qpxc transform quantify \
  --feature-path diann.feature.parquet \
  --method ibaq \
  --fasta HomoSapiens_SwissProt_231115.fasta \
  -o protein_ibaq.tsv

The feature file loads and QPX prepares the peptide table:

Loaded 1033729 QPX feature rows from diann.feature.parquet
Prepared 1033729 peptide rows: 14173 proteins, 47 samples
Running iBAQ quantification ...

But it fails in mokume:

File ".../mokume/quantification/ibaq.py", line 371, in peptides_to_protein
  map_size = data.groupby([PROTEIN_NAME, SAMPLE_ID, CONDITION]).size().to_dict()
KeyError: 'Condition'

From reading the source, it looks like __qpx_feature_to_peptide_df(...) does not create a Condition column, but
mokume.quantification.peptides_to_protein expects one.

Environment:

qpx: 1.0.1
mokume: 0.1.0
Python: 3.10

This may be related to issue #185, which also mentions a missing Condition column error.