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RuntimeError when trying to run online MapMyCells mouse brain taxonomy programmatically #26

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Winterwind opened this issue Nov 4, 2024 · 0 comments

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@Winterwind
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Hi there,
First off, I'd like to say thank you for making this wonderful tool!

I'm having an issue where I am trying to run MapMyCells using the code from this repo, and I am trying to do so with the online 10x Whole Mouse Brain taxonomy (CCN20230722) that is used on the MapMyCells website. I am also trying to do so programmatically so I don't have to use the otherwise unwieldy command line expression to run it. My python code to perform a test run looks like this (I am also using the sample mouse brain h5ad file provided on the website to test it out):

from cell_type_mapper.cli.from_specified_markers import (
    FromSpecifiedMarkersRunner
)

config = {
    'precomputed_stats': {
        'path': '/Users/ariandjahed/LocalRepos/Other/cell_type_mapper/taxonomies/10x_Whole_Mouse_Brain_taxonomy_(CCN20230722)/precomputed_stats_ABC_revision_230821.h5'
    },
    'query_markers': {
        'serialized_lookup': '/Users/ariandjahed/LocalRepos/Other/cell_type_mapper/taxonomies/10x_Whole_Mouse_Brain_taxonomy_(CCN20230722)/mouse_markers_230821.json'
    },
    'type_assignment': {
        'n_processors': 4,
        'normalization': 'raw'
    },
    'query_path': 'wholemousebrain_ccn20230722_example_10kcells_550genes.h5ad',
    'extended_result_path': 'mapping_output.json',
    'csv_result_path': 'mapping_output.csv',
    'drop_level': 'CCN20230722_SUPT',
    'cloud_safe': False
}

mapping_runner = FromSpecifiedMarkersRunner(
    args=[], input_data=config)

mapping_runner.run()

However, I am getting the following error, and I can't seem to figure out what is causing it:

Traceback (most recent call last):
  File "/Users/ariandjahed/LocalRepos/SharedRepos/Bonsai_SpatialTranscriptomics/mapmycells_data/test_with_local_repo/mapmycellstest.py", line 26, in <module>
    mapping_runner.run()
  File "/Users/ariandjahed/LocalRepos/Other/cell_type_mapper/src/cell_type_mapper/cli/from_specified_markers.py", line 71, in run
    run_mapping(
  File "/Users/ariandjahed/LocalRepos/Other/cell_type_mapper/src/cell_type_mapper/cli/from_specified_markers.py", line 144, in run_mapping
    output = _run_mapping(
             ^^^^^^^^^^^^^
  File "/Users/ariandjahed/LocalRepos/Other/cell_type_mapper/src/cell_type_mapper/cli/from_specified_markers.py", line 310, in _run_mapping
    create_marker_cache_from_specified_markers(
  File "/Users/ariandjahed/LocalRepos/Other/cell_type_mapper/src/cell_type_mapper/type_assignment/marker_cache_v2.py", line 115, in create_marker_cache_from_specified_markers
    marker_lookup = validate_marker_lookup(
                    ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/ariandjahed/LocalRepos/Other/cell_type_mapper/src/cell_type_mapper/type_assignment/marker_cache_v2.py", line 775, in validate_marker_lookup
    raise RuntimeError(error_msg)
RuntimeError: After comparing query data to reference data, no valid marker genes could be found at any level in the taxonomy.
Example of genes in query set:
['2900052N01Rik', '4930509J09Rik', '9330158H04Rik', 'A630012P03Rik', 'A830036E02Rik']

What would you advise? Any help would be appreciated.
Thank you so much in advance!

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