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can't read mudata created with muon (python) #9
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Hey @bio-la, thanks for the detailed report, I think the issue is just with |
thanks for answering this! do you mean that mudataSeurat was built expecting objects created with anndata <0.8, and which version of muon/mudata ? |
Sorry for being unclear. That should be a better way to phrase it: MuDataSeurat was built before AnnData v0.8 spec and hasn't been updated to handle new versions of AnnData files yet. I believe using |
Hey @bio-la, I added new categorical values handling in the latest commits so you might be able to read files written by the latest I.e. this is a small fix to remedy the current issue but also the first step in the direction of this library becoming v0.8-compliant. 😃 tea <- ReadH5MU("muon-tutorials/data/teaseq/pbmc_w3_teaseq.h5mu")
tea
# An object of class Seurat
# 113187 features across 5805 samples within 3 assays
# Active assay: rna (16381 features, 2910 variable features)
# 2 other assays present: atac, prot
# 10 dimensional reductions calculated: MOFA, MOFA_UMAP, UMAP, WNN_UMAP, rnaPCA, rnaUMAP, atacPCA, atacUMAP, protPCA, protUMAP You can also note that it respects |
Hi @gtca ! I was encountering the above issue as well. I installed the latest development version of MuDataSeurat and am now experiencing the following error: library(MuDataSeurat)
## VIASH START
par <- list(
input = "resources_test/pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu",
output = "output.rds"
)
## VIASH END
obj <- ReadH5MU(par$input)
Files which trigger this error: |
* Add initial config generator for cellranger * add back lanes * fix variable * Untar reference input and add fastqs as symlinks * make fixes to pipeline execution script * fix processing of input files * make sure fastqs parameter is added to the csv * fix localcores parameter * fix directory traversal issue * silly commit message * fix pebkac issues * Add beginnings of tests, fix output * os.path.listdir() to os.listdir() * update script * update workflowhelper * clean up bin * test bd rhap using new reference, untar if need be * remove old resources scripts * update bdrhap_5kjrt script * update to new references * painstakingly fix bd rhapsody component * fix bd 5kjrt script * allow velocyto to work with compressed gtf files * fix velocyto * add links to original pages * fix test * fix pbmc script * add something to assert * fix test * Move to pathlib * Fix checking of ouput files. * Shutil doest not accept Path objects on python < 3.9 * Fix paths in tests * Fix paths in tests * CI Only download viash (ci force) * fix names * update changelog #ci force * Allow push run when using: ci force * Undo changes to labels * Use correct conditional check (ci force) * Fix typo (ci force) * Correct conditional (ci force) * Fix typo (ci force) * obsm location was changed in mms test resource * feature_type -> feature_types * `convert/from_h5mu_to_seurat`: Disabled because MuDataSeurat is currently broken, see [https://github.com/PMBio/MuDataSeurat/issues/9](PMBio/MuDataSeurat#9). Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
Thanks a lot, @ilia-kats 🙇 |
I'm experiencing the same issue with anndata v0.10.7 |
Hello, thanks for working on interoperability between seurat and mudata!
I can't read a mudata that I created following your multimodal tutorial using ReadH5MU
I have no problems loading the object with muon in python
I can explore the h5 but it breaks where the error says. it also seems to expect some attributes that I don't have in the mudata
any suggestions?
thanks!
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