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Traceback (most recent call last):
File "/home/ladewie1/micromamba/envs/segger/bin/segger", line 6, in
sys.exit(app())
^^^^^
File "/home/ladewie1/micromamba/envs/segger/lib/python3.11/site-packages/cyclopts/core.py", line 1869, in call
result = _run_maybe_async_command(command, bound, resolved_backend)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ladewie1/micromamba/envs/segger/lib/python3.11/site-packages/cyclopts/_run.py", line 50, in _run_maybe_async_command
return command(*bound.args, **bound.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ladewie1/bin/github/segger/src/segger/cli/segment.py", line 313, in segment
datamodule = ISTDataModule(
^^^^^^^^^^^^^^
File "", line 27, in init
File "/home/ladewie1/bin/github/segger/src/segger/data/data_module.py", line 160, in post_init
self.load()
File "/home/ladewie1/bin/github/segger/src/segger/data/data_module.py", line 172, in load
tx = self.tx = pp.transcripts
^^^^^^^^^^^^^^
File "/home/ladewie1/micromamba/envs/segger/lib/python3.11/functools.py", line 1001, in get
val = self.func(instance)
^^^^^^^^^^^^^^^^^^^
File "/home/ladewie1/bin/github/segger/src/segger/io/preprocessor.py", line 439, in transcripts
.collect()
^^^^^^^^^
File "/home/ladewie1/micromamba/envs/segger/lib/python3.11/site-packages/polars/_utils/deprecation.py", line 97, in wrapper
return function(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ladewie1/micromamba/envs/segger/lib/python3.11/site-packages/polars/lazyframe/opt_flags.py", line 326, in wrapper
return function(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ladewie1/micromamba/envs/segger/lib/python3.11/site-packages/polars/lazyframe/frame.py", line 2440, in collect
return wrap_df(ldf.collect(engine, callback))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
polars.exceptions.ComputeError: cannot compare string with numeric type (i32)
Branch now up to date. Dataset mentioned above runs through. Git history on top of pr #22 . Ready to merge from my side.
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Closes #20 .
☑️ Now supports this dataset: https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast
Adding the following changes:
cell_ids are allUtf8in transcripts, cell_boundaries and nucleus_bandaries filesfeature_nameisUtf8in transcripts fileXeniumPreprocessorV1preprocessor, which uses a differentnull_cell_id. Added detection logic using the metadata.Testing
--> Tested on a xenium v3 dataset. Fixes don't affect outputs, results match previous results.
--> Tested on outdated xenium dataset (https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast) and fails!