From 081bd53222a40a610257c3d67e9186c09da49106 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 5 May 2022 15:20:30 +0300
Subject: Compute partial correlation with selected traits

Compute partial correlations against a selection of traits rather than against
an entire dataset.
---
 gn3/computations/partial_correlations.py | 55 +++++++++++++++++++++++++++++++-
 gn3/db/partial_correlations.py           |  2 +-
 2 files changed, 55 insertions(+), 2 deletions(-)

(limited to 'gn3')

diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index f82031a..0041684 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -19,8 +19,8 @@ from gn3.settings import TEXTDIR
 from gn3.random import random_string
 from gn3.function_helpers import  compose
 from gn3.data_helpers import parse_csv_line
-from gn3.db.traits import export_informative
 from gn3.db.datasets import retrieve_trait_dataset
+from gn3.db.traits import export_trait_data, export_informative
 from gn3.db.partial_correlations import traits_info, traits_data
 from gn3.db.species import species_name, translate_to_mouse_gene_id
 from gn3.db.correlations import (
@@ -807,3 +807,56 @@ def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911]
             "dataset_type": target_dataset["type"],
             "method": "spearman" if "spearman" in method.lower() else "pearson"
         }}
+
+
+def partial_correlations_with_target_traits(
+        conn: Any, primary_trait_name: str,
+        control_trait_names: Tuple[str, ...],
+        target_trait_names: Tuple[str, ...], method: str) -> dict:
+    """
+    Compute partial correlation against a specific selection of traits.
+    """
+    threshold = 0
+    check_res = check_for_common_errors(
+        conn, primary_trait_name, control_trait_names)
+    if check_res.get("status") == "error":
+        return error_check_results
+
+    target_traits = {
+        trait["name"]: trait
+        for trait in traits_info(conn, threshold, target_trait_names)}
+    target_traits_data = traits_data(conn, target_traits.values())
+
+    def __merge(trait, pcorrs):
+        return {
+            **trait,
+            "noverlap": pcorrs[1],
+            "partial_corr": pcorrs[2],
+            "partial_corr_p_value": pcorrs[3],
+            "corr": pcorrs[4],
+            "corr_p_value": pcorrs[5]}
+
+    all_pcorrs = (
+        __merge(
+            target_traits[target_name],
+            compute_trait_info(
+            check_res["primary_values"], check_res["fixed_control_values"],
+            (export_trait_data(
+                target_data,
+                samplelist=check_res["common_primary_control_samples"]),
+             target_name),
+            method))
+        for target_name, target_data in target_traits_data.items())
+
+    return {
+        "status": "success",
+        "results": {
+            "primary_trait": trait_for_output(check_res["primary_trait"]),
+            "control_traits": tuple(
+                trait_for_output(trait) for trait in
+                check_res["control_traits"]),
+            "correlations": tuple(
+                trait_for_output(trait) for trait in all_pcorrs),
+            "dataset_type": "NOT SET YET",
+            "method": "spearman" if "spearman" in method.lower() else "pearson"
+        }}
diff --git a/gn3/db/partial_correlations.py b/gn3/db/partial_correlations.py
index 72dbf1a..96f953d 100644
--- a/gn3/db/partial_correlations.py
+++ b/gn3/db/partial_correlations.py
@@ -783,7 +783,7 @@ def traits_info(
             partial(temp_traits_info, conn),
             partial(temp_traits_datasets, conn, threshold))
     }
-    return tuple(
+    return (
         trait for sublist in (# type: ignore[var-annotated]
             traits_fns[dataset_type](traits)
             for dataset_type, traits
-- 
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