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authorFrederick Muriuki Muriithi2021-11-01 10:49:35 +0300
committerBonfaceKilz2021-11-04 12:45:57 +0300
commit457f2a8473a1d44dfcb66d0c28aa1c7a3a256c85 (patch)
treebb915a212d9699ec7a80ead1e77690da3df61fde /gn3/computations
parent856ee56890f9c10401b717579dc8c0358c7d465d (diff)
downloadgenenetwork3-457f2a8473a1d44dfcb66d0c28aa1c7a3a256c85.tar.gz
Implement `compute_partial_correlations_fast`
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Implement `compute_partial_correlations_fast` that is a partial migration of `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast` in GN1. This function will probably be reworked once the dependencies are fully migrated. It also needs tests to be added.
Diffstat (limited to 'gn3/computations')
-rw-r--r--gn3/computations/partial_correlations.py49
1 files changed, 49 insertions, 0 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index ba4de9e..1a6868a 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -9,6 +9,9 @@ from functools import reduce
from typing import Any, Tuple, Sequence
from scipy.stats import pearsonr, spearmanr
+from gn3.settings import TEXTDIR
+from gn3.data_helpers import parse_csv_line
+
def control_samples(controls: Sequence[dict], sampleslist: Sequence[str]):
"""
Fetches data for the control traits.
@@ -192,3 +195,49 @@ def good_dataset_samples_indexes(
return tuple(sorted(
samples_from_file.index(good) for good in
set(samples).intersection(set(samples_from_file))))
+
+def compute_partial_correlations_fast(# pylint: disable=[R0913, R0914]
+ samples, primary_vals, control_vals, database_filename,
+ fetched_correlations, method: str, correlation_type: str) -> Tuple[
+ float, Tuple[float, ...]]:
+ """
+ This is a partial migration of the
+ `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast`
+ function in GeneNetwork1.
+ """
+ assert method in ("spearman", "pearson")
+ with open(f"{TEXTDIR}/{database_filename}", "r") as dataset_file:
+ dataset = tuple(dataset_file.readlines())
+
+ good_dataset_samples = good_dataset_samples_indexes(
+ samples, parse_csv_line(dataset[0])[1:])
+
+ def __process_trait_names_and_values__(acc, line):
+ trait_line = parse_csv_line(line)
+ trait_name = trait_line[0]
+ trait_data = trait_line[1:]
+ if trait_name in fetched_correlations.keys():
+ return (
+ acc[0] + (trait_name,),
+ acc[1] + tuple(
+ trait_data[i] if i in good_dataset_samples else None
+ for i in range(len(trait_data))))
+ return acc
+
+ processed_trait_names_values: tuple = reduce(
+ __process_trait_names_and_values__, dataset[1:], (tuple(), tuple()))
+ all_target_trait_names: Tuple[str, ...] = processed_trait_names_values[0]
+ all_target_trait_values: Tuple[float, ...] = processed_trait_names_values[1]
+
+ all_correlations = determine_partials(
+ primary_vals, control_vals, all_target_trait_names,
+ all_target_trait_values, method)
+ ## Line 772 to 779 in GN1 are the cause of the weird complexity in the
+ ## return below. Once the surrounding code is successfully migrated and
+ ## reworked, this complexity might go away, by getting rid of the
+ ## `correlation_type` parameter
+ return len(all_correlations), tuple(
+ corr + (
+ (fetched_correlations[corr[0]],) if correlation_type == "literature"
+ else fetched_correlations[corr[0]][0:2])
+ for idx, corr in enumerate(all_correlations))