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"""
This module deals with partial correlations.
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()))
def dictify_by_samples(samples_vals_vars: Sequence[Sequence]) -> dict:
"""
Build a sequence of dictionaries from a sequence of separate sequences of
samples, values and variances.
This is a partial migration of
`web.webqtl.correlation.correlationFunction.fixStrains` function in GN1.
This implementation extracts code that will find common use, and that will
find use in more than one place.
"""
return tuple(
{
sample: {"sample_name": sample, "value": val, "variance": var}
for sample, val, var in zip(*trait_line)
} for trait_line in zip(*(samples_vals_vars[0:3])))
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