CI
bb7533583f
Build pipeline: vsh-ci-dev-gckj5
Source commit: da62b4ffe3
Source message: Add labels to qc_test component
35 lines
1.5 KiB
Python
35 lines
1.5 KiB
Python
from scipy.sparse import issparse
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def check_arguments(par):
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# check output .obs predictions
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if not par["output_obs_predictions"]:
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par["output_obs_predictions"] = [ t + "_pred" for t in par["reference_obs_targets"]]
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assert len(par["output_obs_predictions"]) == len(par["reference_obs_targets"]), f"Number of output_obs_predictions must match number of reference_obs_targets\npar: {par}"
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# check output .obs uncertainty
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if not par["output_obs_probability"]:
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par["output_obs_probability"] = [ t + "_probability" for t in par["reference_obs_targets"]]
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assert len(par["output_obs_probability"]) == len(par["reference_obs_targets"]), f"Number of output_obs_probability must match number of reference_obs_targets\npar: {par}"
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return par
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def get_reference_features(adata_reference, par, logger):
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if par["reference_obsm_features"] is None:
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logger.info("Using .X of reference data")
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train_data = adata_reference.X
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else:
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logger.info(f"Using .obsm[{par['reference_obsm_features']}] of reference data")
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train_data = adata_reference.obsm[par["reference_obsm_features"]]
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return train_data
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def get_query_features(adata, par, logger):
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if par["input_obsm_features"] is None:
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logger.info("Using .X of query data")
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query_data = adata.X
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else:
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logger.info(f"Using .obsm[{par['input_obsm_features']}] of query data")
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query_data = adata.obsm[par["input_obsm_features"]]
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return query_data
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