Closed mtvector closed 5 months ago
You are passing your ${OUT_PATH}/query_markers.json
in as the argument --input_json
. It should be passed in as --query_markers.serialized_lookup
, i.e. the call you want is
python -m cell_type_mapper.cli.from_specified_markers \
--query_path $QUERY_H5AD \
--query_markers.serialized_lookup ${OUT_PATH}/query_markers.json \
--type_assignment.normalization raw \
--precomputed_stats.path $REF_PATH/precompute_stats.h5 \
--extended_result_path ${OUT_PATH}/hann_results.json \
> ${OUT_PATH}/log_outputs.txt 2>&1
(Note: you also do not want to use --output_json
; --extended_result_path
should point to the JSON file containing your cell type mapping result).
--input_json
is a parameter that the argschema
library always adds to its executables that points to a JSON file containing all of the parameters for the executable, i.e. if you wanted to run
python -m cell_type_mapper.cli.from_specified_markes --input_json config.json
then config.json
would look like
{
'query_path': /path/to/query.h5ad'
'query_markers': {
'serialized_lookup': '/path/to/query_markers.json'
},
'type_assignment': {
'normalization': 'raw'
},
'precomputed_stats': {
'path': '/path/to/precompute_stats.h5'
},
'extended_result_path': '/path/to/output/file.json'
}
Similarly output_json
is an argument where the argschema
library outputs some basic metadata from the run and is actually not used by this module.
Thanks so much Scott, I'm new to this pipeline but that is what I needed to run successfully!
Hi there, Thanks for putting this nice package together. I've tried to create a mapping using the following. Everything works fine up until the last step (or so it seems!)
But this gives a strange error in marshmallow which I don't understand how to fix. It's quite possible I've done something incorrectly upstream of the from_specified_markers call, but I can't figure out what might be wrong with the markers.
Thanks so much for any guidance you can provide!