diff options
| -rw-r--r-- | gn3/db/traits.py | 24 | ||||
| -rw-r--r-- | gn3/partial_correlations.py | 24 | ||||
| -rw-r--r-- | tests/unit/db/test_traits.py | 86 | ||||
| -rw-r--r-- | tests/unit/test_partial_correlations.py | 87 |
4 files changed, 111 insertions, 110 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py index 1e29aff..1c6aaa7 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -743,3 +743,27 @@ def generate_traits_filename(base_path: str = TMPDIR): """Generate a unique filename for use with generated traits files.""" return "{}/traits_test_file_{}.txt".format( os.path.abspath(base_path), random_string(10)) + +def export_informative(trait_data: dict, inc_var: bool = False) -> tuple: + """ + Export informative strain + + This is a migration of the `exportInformative` function in + web/webqtl/base/webqtlTrait.py module in GeneNetwork1. + + There is a chance that the original implementation has a bug, especially + dealing with the `inc_var` value. It the `inc_var` value is meant to control + the inclusion of the `variance` value, then the current implementation, and + that one in GN1 have a bug. + """ + def __exporter__(acc, data_item): + if not inc_var or data_item["variance"] is not None: + return ( + acc[0] + (data_item["sample_name"],), + acc[1] + (data_item["value"],), + acc[2] + (data_item["variance"],)) + return acc + return reduce( + __exporter__, + filter(lambda td: td["value"] is not None, trait_data["data"].values()), + (tuple(), tuple(), tuple())) diff --git a/gn3/partial_correlations.py b/gn3/partial_correlations.py index 8c37886..df390ed 100644 --- a/gn3/partial_correlations.py +++ b/gn3/partial_correlations.py @@ -6,27 +6,3 @@ GeneNetwork1. """ from functools import reduce - -def export_informative(trait_data: dict, inc_var: bool = False) -> tuple: - """ - Export informative strain - - This is a migration of the `exportInformative` function in - web/webqtl/base/webqtlTrait.py module in GeneNetwork1. - - There is a chance that the original implementation has a bug, especially - dealing with the `inc_var` value. It the `inc_var` value is meant to control - the inclusion of the `variance` value, then the current implementation, and - that one in GN1 have a bug. - """ - def __exporter__(acc, data_item): - if not inc_var or data_item["variance"] is not None: - return ( - acc[0] + (data_item["sample_name"],), - acc[1] + (data_item["value"],), - acc[2] + (data_item["variance"],)) - return acc - return reduce( - __exporter__, - filter(lambda td: td["value"] is not None, trait_data["data"].values()), - (tuple(), tuple(), tuple())) diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py index 0c4ef78..67f0c6f 100644 --- a/tests/unit/db/test_traits.py +++ b/tests/unit/db/test_traits.py @@ -3,6 +3,7 @@ from unittest import mock, TestCase from gn3.db.traits import ( build_trait_name, export_trait_data, + export_informative, set_haveinfo_field, update_sample_data, retrieve_trait_info, @@ -315,3 +316,88 @@ class TestTraitsDBFunctions(TestCase): trait_data, samplelist, dtype=dtype, var_exists=vflag, n_exists=nflag), expected) + + def test_export_informative(self): + """Test that the function exports appropriate data.""" + for trait_data, inc_var, expected in [ + [{"data": { + "sample1": { + "sample_name": "sample1", "value": 9, "variance": None, + "ndata": 13 + }, + "sample2": { + "sample_name": "sample2", "value": 8, "variance": None, + "ndata": 13 + }, + "sample3": { + "sample_name": "sample3", "value": 7, "variance": None, + "ndata": 13 + }, + "sample4": { + "sample_name": "sample4", "value": 6, "variance": None, + "ndata": 13 + }, + }}, 0, ( + ("sample1", "sample2", "sample3", "sample4"), (9, 8, 7, 6), + (None, None, None, None))], + [{"data": { + "sample1": { + "sample_name": "sample1", "value": 9, "variance": None, + "ndata": 13 + }, + "sample2": { + "sample_name": "sample2", "value": 8, "variance": None, + "ndata": 13 + }, + "sample3": { + "sample_name": "sample3", "value": None, "variance": None, + "ndata": 13 + }, + "sample4": { + "sample_name": "sample4", "value": 6, "variance": None, + "ndata": 13 + }, + }}, 0, ( + ("sample1", "sample2", "sample4"), (9, 8, 6), + (None, None, None))], + [{"data": { + "sample1": { + "sample_name": "sample1", "value": 9, "variance": None, + "ndata": 13 + }, + "sample2": { + "sample_name": "sample2", "value": 8, "variance": None, + "ndata": 13 + }, + "sample3": { + "sample_name": "sample3", "value": 7, "variance": None, + "ndata": 13 + }, + "sample4": { + "sample_name": "sample4", "value": 6, "variance": None, + "ndata": 13 + }, + }}, True, (tuple(), tuple(), tuple())], + [{"data": { + "sample1": { + "sample_name": "sample1", "value": 9, "variance": None, + "ndata": 13 + }, + "sample2": { + "sample_name": "sample2", "value": 8, "variance": 0.657, + "ndata": 13 + }, + "sample3": { + "sample_name": "sample3", "value": 7, "variance": None, + "ndata": 13 + }, + "sample4": { + "sample_name": "sample4", "value": 6, "variance": None, + "ndata": 13 + }, + }}, 0, ( + ("sample1", "sample2", "sample3", "sample4"), (9, 8, 7, 6), + (None, 0.657, None, None))]]: + with self.subTest(trait_data=trait_data): + self.assertEqual( + export_informative(trait_data, inc_var), expected) diff --git a/tests/unit/test_partial_correlations.py b/tests/unit/test_partial_correlations.py index 6eea078..f204d4f 100644 --- a/tests/unit/test_partial_correlations.py +++ b/tests/unit/test_partial_correlations.py @@ -1,92 +1,7 @@ """Module contains tests for gn3.partial_correlations""" from unittest import TestCase -from gn3.partial_correlations import export_informative + class TestPartialCorrelations(TestCase): """Class for testing partial correlations computation functions""" - - def test_export_informative(self): - """Test that the function exports appropriate data.""" - for trait_data, inc_var, expected in [ - [{"data": { - "sample1": { - "sample_name": "sample1", "value": 9, "variance": None, - "ndata": 13 - }, - "sample2": { - "sample_name": "sample2", "value": 8, "variance": None, - "ndata": 13 - }, - "sample3": { - "sample_name": "sample3", "value": 7, "variance": None, - "ndata": 13 - }, - "sample4": { - "sample_name": "sample4", "value": 6, "variance": None, - "ndata": 13 - }, - }}, 0, ( - ("sample1", "sample2", "sample3", "sample4"), (9, 8, 7, 6), - (None, None, None, None))], - [{"data": { - "sample1": { - "sample_name": "sample1", "value": 9, "variance": None, - "ndata": 13 - }, - "sample2": { - "sample_name": "sample2", "value": 8, "variance": None, - "ndata": 13 - }, - "sample3": { - "sample_name": "sample3", "value": None, "variance": None, - "ndata": 13 - }, - "sample4": { - "sample_name": "sample4", "value": 6, "variance": None, - "ndata": 13 - }, - }}, 0, ( - ("sample1", "sample2", "sample4"), (9, 8, 6), - (None, None, None))], - [{"data": { - "sample1": { - "sample_name": "sample1", "value": 9, "variance": None, - "ndata": 13 - }, - "sample2": { - "sample_name": "sample2", "value": 8, "variance": None, - "ndata": 13 - }, - "sample3": { - "sample_name": "sample3", "value": 7, "variance": None, - "ndata": 13 - }, - "sample4": { - "sample_name": "sample4", "value": 6, "variance": None, - "ndata": 13 - }, - }}, True, (tuple(), tuple(), tuple())], - [{"data": { - "sample1": { - "sample_name": "sample1", "value": 9, "variance": None, - "ndata": 13 - }, - "sample2": { - "sample_name": "sample2", "value": 8, "variance": 0.657, - "ndata": 13 - }, - "sample3": { - "sample_name": "sample3", "value": 7, "variance": None, - "ndata": 13 - }, - "sample4": { - "sample_name": "sample4", "value": 6, "variance": None, - "ndata": 13 - }, - }}, 0, ( - ("sample1", "sample2", "sample3", "sample4"), (9, 8, 7, 6), - (None, 0.657, None, None))]]: - with self.subTest(trait_data=trait_data): - self.assertEqual( - export_informative(trait_data, inc_var), expected) |