Mercurial > repos > ebi-gxa > decoupler_pseudobulk
comparison decoupler_pseudobulk.py @ 2:130e25d3ce92 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 85a3118a571246d88aaad26733d0c62009cb736b
| author | ebi-gxa |
|---|---|
| date | Fri, 13 Oct 2023 15:19:51 +0000 |
| parents | 046d8ff974ff |
| children | 93f61ea19336 |
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| 1:046d8ff974ff | 2:130e25d3ce92 |
|---|---|
| 163 # Load AnnData object from file | 163 # Load AnnData object from file |
| 164 adata = anndata.read_h5ad(args.adata_file) | 164 adata = anndata.read_h5ad(args.adata_file) |
| 165 | 165 |
| 166 # Merge adata.obs fields specified in args.adata_obs_fields_to_merge | 166 # Merge adata.obs fields specified in args.adata_obs_fields_to_merge |
| 167 if args.adata_obs_fields_to_merge: | 167 if args.adata_obs_fields_to_merge: |
| 168 fields = args.adata_obs_fields_to_merge.split(",") | 168 # first split potential groups by ":" and iterate over them |
| 169 check_fields(fields, adata) | 169 for group in args.adata_obs_fields_to_merge.split(":"): |
| 170 adata = merge_adata_obs_fields(fields, adata) | 170 fields = group.split(",") |
| 171 check_fields(fields, adata) | |
| 172 adata = merge_adata_obs_fields(fields, adata) | |
| 171 | 173 |
| 172 check_fields([args.groupby, args.sample_key], adata) | 174 check_fields([args.groupby, args.sample_key], adata) |
| 173 | 175 |
| 174 factor_fields = None | 176 factor_fields = None |
| 175 if args.factor_fields: | 177 if args.factor_fields: |
| 272 parser.add_argument("adata_file", type=str, help="Path to the AnnData file") | 274 parser.add_argument("adata_file", type=str, help="Path to the AnnData file") |
| 273 parser.add_argument( | 275 parser.add_argument( |
| 274 "-m", | 276 "-m", |
| 275 "--adata_obs_fields_to_merge", | 277 "--adata_obs_fields_to_merge", |
| 276 type=str, | 278 type=str, |
| 277 help="Fields in adata.obs to merge, comma separated", | 279 help="Fields in adata.obs to merge, comma separated. You can have more than one set of fields, separated by semi-colon ;", |
| 278 ) | 280 ) |
| 279 parser.add_argument( | 281 parser.add_argument( |
| 280 "--groupby", | 282 "--groupby", |
| 281 type=str, | 283 type=str, |
| 282 required=True, | 284 required=True, |