Add dataflow/move_anndata_slots component#1163
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jakubmajercik wants to merge 6 commits into
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dorien-er
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Apr 15, 2026
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DriesSchaumont
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Apr 29, 2026
| @@ -0,0 +1,141 @@ | |||
| name: move_anndata_slots | |||
| namespace: "dataflow" | |||
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Let's use metadata as the namespace.
| Move slots (.obs, .var, .obsm, .varm, .obsp, .varp, .uns) from a modality | ||
| in a source MuData file into a modality in a target MuData file. | ||
| The specified slots are copied from the source modality into the target | ||
| modality, overwriting any existing data at those slots. |
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What happens if the dimensions not match? (Please add it in the description if they need to match)
| needs_var = any(par[s] for s in ("var", "varm", "varp")) | ||
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| mismatches = [] | ||
| if needs_obs and set(source_mod.obs_names) != set(target_mod.obs_names): |
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I think its best to use https://pandas.pydata.org/docs/reference/api/pandas.Index.get_indexer.html#pandas.Index.get_indexer here. It will return -1 if no match is found.
This will use the same method as reindexing (which is used later in this script). I will take into account dtypes etc..
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| "Index mismatch between source and target modalities: " | ||
| + " and ".join(mismatches) | ||
| + " indices do not match." | ||
| ) |
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Use string formatting here.
| ) | ||
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| # Reindex source to match target order if needed. | ||
| if needs_obs and not (source_mod.obs_names == target_mod.obs_names).all(): |
| run_component( | ||
| [ | ||
| "--input_source", | ||
| str(source_h5mu_path), |
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I dont think str is a requirement here anymore. Check other places as well.
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Changelog
Add a new
dataflow/move_anndata_slotscomponent that selectively moves AnnData slots (.obs,.var,.obsm,.varm,.obsp,.varp,.uns) from a modality in a source MuData file into a modality in a target MuData file, without performing a full merge. Supports cross-modality transfers via--target_modality.Issue ticket number and link
N/A
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I have performed a self-review of my code
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Proposed changes are described in the CHANGELOG.md
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