From 37cf87e94a44ba2ab26a8e458e0c5a90fe5ecc7a Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 1 Nov 2021 08:18:48 +0300
Subject: Retrieve indices of the selected samples

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi

* gn3/computations/partial_correlations.py: New
  function (good_dataset_samples_indexes).
* tests/unit/computations/test_partial_correlations.py: Tests for new
  function (good_dataset_samples_indexes)

  Get the indices of the selected samples. This is a partial migration of the
  `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast`
  function in GN1.
---
 gn3/computations/partial_correlations.py             | 15 +++++++++++++++
 tests/unit/computations/test_partial_correlations.py | 13 ++++++++++++-
 2 files changed, 27 insertions(+), 1 deletion(-)

diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index 151143a..ba4de9e 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -177,3 +177,18 @@ def correlations_of_all_tissue_traits(
     primary_trait_values = tuple(primary_trait_symbol_value_dict.values())[0]
     return batch_computed_tissue_correlation(
         primary_trait_values, symbol_value_dict, method)
+
+def good_dataset_samples_indexes(
+        samples: Tuple[str, ...],
+        samples_from_file: Tuple[str, ...]) -> Tuple[int, ...]:
+    """
+    Return the indexes of the items in `samples_from_files` that are also found
+    in `samples`.
+
+    This is a partial migration of the
+    `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast`
+    function in GeneNetwork1.
+    """
+    return tuple(sorted(
+        samples_from_file.index(good) for good in
+        set(samples).intersection(set(samples_from_file))))
diff --git a/tests/unit/computations/test_partial_correlations.py b/tests/unit/computations/test_partial_correlations.py
index c4ec79a..f7217a9 100644
--- a/tests/unit/computations/test_partial_correlations.py
+++ b/tests/unit/computations/test_partial_correlations.py
@@ -6,7 +6,8 @@ from gn3.computations.partial_correlations import (
     control_samples,
     dictify_by_samples,
     tissue_correlation,
-    find_identical_traits)
+    find_identical_traits,
+    good_dataset_samples_indexes)
 
 sampleslist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"]
 control_traits = (
@@ -260,3 +261,13 @@ class TestPartialCorrelations(TestCase):
             with self.subTest(primary=primary, target=target, method=method):
                 self.assertEqual(
                     tissue_correlation(primary, target, method), expected)
+
+    def test_good_dataset_samples_indexes(self):
+        """
+        Test that `good_dataset_samples_indexes` returns correct indices.
+        """
+        self.assertEqual(
+            good_dataset_samples_indexes(
+                ("a", "e", "i", "k"),
+                ("a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l")),
+            (0, 4, 8, 10))
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