Mercurial > repos > ebi-gxa > decoupler_pathway_inference
changeset 12:4523224b53ce draft default tip
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 626c1018b662202de10ce77f123fc27f584beb9c
author | ebi-gxa |
---|---|
date | Fri, 13 Jun 2025 09:08:13 +0000 |
parents | db14ac3f6b43 |
children | |
files | decoupler_pseudobulk.py |
diffstat | 1 files changed, 11 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/decoupler_pseudobulk.py Wed Feb 19 16:55:51 2025 +0000 +++ b/decoupler_pseudobulk.py Fri Jun 13 09:08:13 2025 +0000 @@ -324,21 +324,28 @@ >>> check_fields(["bulk_labels", "louvain"], adata, obs=True) """ + # Fields that will be created during the pseudobulking process + pseudobulk_generated_fields = ['psbulk_n_cells', 'psbulk_counts'] + + # Filter out the pseudobulk-generated fields from checking + fields_to_check = [field for field in fields + if field not in pseudobulk_generated_fields] + legend = "" if context: legend = f", passed in {context}," if obs: - if not set(fields).issubset(set(adata.obs.columns)): + if not set(fields_to_check).issubset(set(adata.obs.columns)): raise ValueError( f"Some of the following fields {legend} are not present \ - in adata.obs: {fields}. \ + in adata.obs: {fields_to_check}. \ Possible fields are: {list(set(adata.obs.columns))}" ) else: - if not set(fields).issubset(set(adata.var.columns)): + if not set(fields_to_check).issubset(set(adata.var.columns)): raise ValueError( f"Some of the following fields {legend} are not present \ - in adata.var: {fields}. \ + in adata.var: {fields_to_check}. \ Possible fields are: {list(set(adata.var.columns))}" )