AllenInstitute / AllenInstitute/cell_type_mapper
RuntimeError when trying to run online MapMyCells mouse brain taxonomy programmatically
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- Dominant language
- Python
- Stars
- 55
- Forks
- 9
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Description
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!
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with cell_type_mapper/cli/from_specified_markers.py and the failing validate_marker_lookup path in cell_type_mapper/type_assignment/marker_cache_v2.py. Compare the query genes, reference files, and configuration used by the sample run; done means the programmatic example completes without the no-valid-marker-genes RuntimeError.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100