diff options
| -rw-r--r-- | gn3/partial_correlations.py | 16 | ||||
| -rw-r--r-- | tests/unit/test_partial_correlations.py | 42 |
2 files changed, 57 insertions, 1 deletions
diff --git a/gn3/partial_correlations.py b/gn3/partial_correlations.py index 99521c6..4db4807 100644 --- a/gn3/partial_correlations.py +++ b/gn3/partial_correlations.py @@ -44,3 +44,19 @@ def control_samples(controls: Sequence[dict], sampleslist: Sequence[str]): ), [__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]))) diff --git a/tests/unit/test_partial_correlations.py b/tests/unit/test_partial_correlations.py index 0083ef7..6302f74 100644 --- a/tests/unit/test_partial_correlations.py +++ b/tests/unit/test_partial_correlations.py @@ -1,7 +1,7 @@ """Module contains tests for gn3.partial_correlations""" from unittest import TestCase -from gn3.partial_correlations import control_samples +from gn3.partial_correlations import control_samples, dictify_by_samples sampleslist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"] control_traits = ( @@ -85,3 +85,43 @@ class TestPartialCorrelations(TestCase): ((None, None, None, None, None, None), (None, None, None, None), (None, None, None)), (6, 4, 3))) + + def test_dictify_by_samples(self): + """ + Given: + a sequence of sequences with sample names, values and variances, as + in the output of `gn3.partial_correlations.control_samples` or + the output of `gn3.db.traits.export_informative` + When: + the sequence is passed as an argument into the + `gn3.partial_correlations.dictify_by_sample` + Then: + return a sequence of dicts with keys being the values of the sample + names, and each of who's values being sub-dicts with the keys + 'sample_name', 'value' and 'variance' whose values correspond to the + values passed in. + """ + self.assertEqual( + dictify_by_samples( + ((("B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"), + ("BXD12", "BXD16", "BXD19", "BXD2"), + ("B6cC3-1", "BXD1", "BXD2")), + ((7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944), + (8.39265, 8.17443, 8.30401, 7.80944), + (7.51879, 7.77141, 7.80944)), + ((None, None, None, None, None, None), (None, None, None, None), + (None, None, None)), + (6, 4, 3))), + ({"B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None}, + "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None}, + "BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None}, + "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None}, + "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None}, + "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None}}, + {"BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None}, + "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None}, + "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None}, + "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None}}, + {"B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None}, + "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None}, + "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None}})) |