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Diffstat (limited to 'gn3/partial_correlations.py')
| -rw-r--r-- | gn3/partial_correlations.py | 38 |
1 files changed, 38 insertions, 0 deletions
diff --git a/gn3/partial_correlations.py b/gn3/partial_correlations.py index df390ed..99521c6 100644 --- a/gn3/partial_correlations.py +++ b/gn3/partial_correlations.py @@ -5,4 +5,42 @@ It is an attempt to migrate over the partial correlations feature from GeneNetwork1. """ +from typing import Sequence from functools import reduce + +def control_samples(controls: Sequence[dict], sampleslist: Sequence[str]): + """ + Fetches data for the control traits. + + This migrates `web/webqtl/correlation/correlationFunction.controlStrain` in + GN1, with a few modifications to the arguments passed in. + + PARAMETERS: + controls: A map of sample names to trait data. Equivalent to the `cvals` + value in the corresponding source function in GN1. + sampleslist: A list of samples. Equivalent to `strainlst` in the + corresponding source function in GN1 + """ + def __process_control__(trait_data): + def __process_sample__(acc, sample): + if sample in trait_data["data"].keys(): + sample_item = trait_data["data"][sample] + val = sample_item["value"] + if val is not None: + return ( + acc[0] + (sample,), + acc[1] + (val,), + acc[2] + (sample_item["variance"],)) + return acc + return reduce( + __process_sample__, sampleslist, (tuple(), tuple(), tuple())) + + return reduce( + lambda acc, item: ( + acc[0] + (item[0],), + acc[1] + (item[1],), + acc[2] + (item[2],), + acc[3] + (len(item[0]),), + ), + [__process_control__(trait_data) for trait_data in controls], + (tuple(), tuple(), tuple(), tuple())) |