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-rw-r--r--gn3/partial_correlations.py38
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()))