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I try to follow the instruction on ibaqpy, see here
and I managed to use quantmsioc convert-feature, but then I run into an issue for quantmsioc convert-ibaq
>>> quantmsioc convert-ibaq \
--feature_file results/quantmsio/feature-00e1d8d0-aecf-421c-bd54-c661c70f415d.feature.parquet \
--sdrf_file hdp_unibio_sdrf.txt \
--output_folder results/ibaq
Determination of memory status is not supported on this
platform, measuring for memoryleaks will never fail
Traceback (most recent call last):
File "/Users/heweb/miniforge3/envs/ibaqpy/bin/quantmsioc", line 8, in <module>
sys.exit(quantms_io_main())
^^^^^^^^^^^^^^^^^
File "/Users/heweb/miniforge3/envs/ibaqpy/lib/python3.12/site-packages/quantmsio/quantmsioc.py", line 79, in quantms_io_main
cli()
File "/Users/heweb/miniforge3/envs/ibaqpy/lib/python3.12/site-packages/click/core.py", line 1442, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/heweb/miniforge3/envs/ibaqpy/lib/python3.12/site-packages/click/core.py", line 1363, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/Users/heweb/miniforge3/envs/ibaqpy/lib/python3.12/site-packages/click/core.py", line 1830, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/heweb/miniforge3/envs/ibaqpy/lib/python3.12/site-packages/click/core.py", line 1226, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/heweb/miniforge3/envs/ibaqpy/lib/python3.12/site-packages/click/core.py", line 794, in invoke
return callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/heweb/miniforge3/envs/ibaqpy/lib/python3.12/site-packages/quantmsio/commands/ibaq_command.py", line 52, in convert_ibaq_file
write_ibaq_feature(sdrf_file, feature_file, output_path)
File "/Users/heweb/miniforge3/envs/ibaqpy/lib/python3.12/site-packages/quantmsio/operate/tools.py", line 332, in write_ibaq_feature
for feature in genereate_ibaq_feature(sdrf_path, parquet_path):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/heweb/miniforge3/envs/ibaqpy/lib/python3.12/site-packages/quantmsio/operate/tools.py", line 293, in genereate_ibaq_feature
experiment_type = sdrf.get_experiment_type_from_sdrf()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/heweb/miniforge3/envs/ibaqpy/lib/python3.12/site-packages/pandas/core/generic.py", line 6299, in __getattr__
return object.__getattribute__(self, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'DataFrame' object has no attribute 'get_experiment_type_from_sdrf'I find the function, but the object registration does seem to be missing.
https://github.com/bigbio/quantms.io/blob/4aa9351edc81b1551e0ff6d594a66be69b40aeb8/quantmsio/core/sdrf.py#L267
If I manage to fix that, I will create an PR...
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