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authorFrederick Muriuki Muriithi2021-09-27 04:48:53 +0300
committerFrederick Muriuki Muriithi2021-09-27 04:48:53 +0300
commit19783a18c2bc7941fc5980e593f19fb1d18c3623 (patch)
treef3a6e241be3c6224b9647c8258c516a7b741a28c /tests
parent8d9bc0f29ce9208306915b079818e6f0c31785e2 (diff)
downloadgenenetwork3-19783a18c2bc7941fc5980e593f19fb1d18c3623.tar.gz
Update terminology: `strain` to `sample`
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Update the terminology used: use `sample` in place of `strain` according to Zachary's direction at https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926043306
Diffstat (limited to 'tests')
-rw-r--r--tests/unit/computations/test_parsers.py4
-rw-r--r--tests/unit/test_heatmaps.py70
2 files changed, 37 insertions, 37 deletions
diff --git a/tests/unit/computations/test_parsers.py b/tests/unit/computations/test_parsers.py
index 19c3067..b51b0bf 100644
--- a/tests/unit/computations/test_parsers.py
+++ b/tests/unit/computations/test_parsers.py
@@ -15,7 +15,7 @@ class TestParsers(unittest.TestCase):
def test_parse_genofile_with_existing_file(self):
"""Test that a genotype file is parsed correctly"""
- strains = ["bxd1", "bxd2"]
+ samples = ["bxd1", "bxd2"]
genotypes = [
{"chr": "1", "locus": "rs31443144",
"cm": "1.50", "mb": "3.010274",
@@ -51,4 +51,4 @@ class TestParsers(unittest.TestCase):
"../test_data/genotype.txt"
))
self.assertEqual(parse_genofile(
- test_genotype_file), (strains, genotypes))
+ test_genotype_file), (samples, genotypes))
diff --git a/tests/unit/test_heatmaps.py b/tests/unit/test_heatmaps.py
index fd91cf9..b54e2f3 100644
--- a/tests/unit/test_heatmaps.py
+++ b/tests/unit/test_heatmaps.py
@@ -5,41 +5,41 @@ from gn3.heatmaps import (
get_lrs_from_chr,
export_trait_data,
compute_traits_order,
- retrieve_strains_and_values,
+ retrieve_samples_and_values,
process_traits_data_for_heatmap)
from tests.unit.sample_test_data import organised_trait_1, organised_trait_2
-strainlist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"]
+samplelist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"]
trait_data = {
"mysqlid": 36688172,
"data": {
- "B6cC3-1": {"strain_name": "B6cC3-1", "value": 7.51879, "variance": None, "ndata": None},
- "BXD1": {"strain_name": "BXD1", "value": 7.77141, "variance": None, "ndata": None},
- "BXD12": {"strain_name": "BXD12", "value": 8.39265, "variance": None, "ndata": None},
- "BXD16": {"strain_name": "BXD16", "value": 8.17443, "variance": None, "ndata": None},
- "BXD19": {"strain_name": "BXD19", "value": 8.30401, "variance": None, "ndata": None},
- "BXD2": {"strain_name": "BXD2", "value": 7.80944, "variance": None, "ndata": None},
- "BXD21": {"strain_name": "BXD21", "value": 8.93809, "variance": None, "ndata": None},
- "BXD24": {"strain_name": "BXD24", "value": 7.99415, "variance": None, "ndata": None},
- "BXD27": {"strain_name": "BXD27", "value": 8.12177, "variance": None, "ndata": None},
- "BXD28": {"strain_name": "BXD28", "value": 7.67688, "variance": None, "ndata": None},
- "BXD32": {"strain_name": "BXD32", "value": 7.79062, "variance": None, "ndata": None},
- "BXD39": {"strain_name": "BXD39", "value": 8.27641, "variance": None, "ndata": None},
- "BXD40": {"strain_name": "BXD40", "value": 8.18012, "variance": None, "ndata": None},
- "BXD42": {"strain_name": "BXD42", "value": 7.82433, "variance": None, "ndata": None},
- "BXD6": {"strain_name": "BXD6", "value": 8.09718, "variance": None, "ndata": None},
- "BXH14": {"strain_name": "BXH14", "value": 7.97475, "variance": None, "ndata": None},
- "BXH19": {"strain_name": "BXH19", "value": 7.67223, "variance": None, "ndata": None},
- "BXH2": {"strain_name": "BXH2", "value": 7.93622, "variance": None, "ndata": None},
- "BXH22": {"strain_name": "BXH22", "value": 7.43692, "variance": None, "ndata": None},
- "BXH4": {"strain_name": "BXH4", "value": 7.96336, "variance": None, "ndata": None},
- "BXH6": {"strain_name": "BXH6", "value": 7.75132, "variance": None, "ndata": None},
- "BXH7": {"strain_name": "BXH7", "value": 8.12927, "variance": None, "ndata": None},
- "BXH8": {"strain_name": "BXH8", "value": 6.77338, "variance": None, "ndata": None},
- "BXH9": {"strain_name": "BXH9", "value": 8.03836, "variance": None, "ndata": None},
- "C3H/HeJ": {"strain_name": "C3H/HeJ", "value": 7.42795, "variance": None, "ndata": None},
- "C57BL/6J": {"strain_name": "C57BL/6J", "value": 7.50606, "variance": None, "ndata": None},
- "DBA/2J": {"strain_name": "DBA/2J", "value": 7.72588, "variance": None, "ndata": None}}}
+ "B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None, "ndata": None},
+ "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None, "ndata": None},
+ "BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None, "ndata": None},
+ "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None, "ndata": None},
+ "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None, "ndata": None},
+ "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None, "ndata": None},
+ "BXD21": {"sample_name": "BXD21", "value": 8.93809, "variance": None, "ndata": None},
+ "BXD24": {"sample_name": "BXD24", "value": 7.99415, "variance": None, "ndata": None},
+ "BXD27": {"sample_name": "BXD27", "value": 8.12177, "variance": None, "ndata": None},
+ "BXD28": {"sample_name": "BXD28", "value": 7.67688, "variance": None, "ndata": None},
+ "BXD32": {"sample_name": "BXD32", "value": 7.79062, "variance": None, "ndata": None},
+ "BXD39": {"sample_name": "BXD39", "value": 8.27641, "variance": None, "ndata": None},
+ "BXD40": {"sample_name": "BXD40", "value": 8.18012, "variance": None, "ndata": None},
+ "BXD42": {"sample_name": "BXD42", "value": 7.82433, "variance": None, "ndata": None},
+ "BXD6": {"sample_name": "BXD6", "value": 8.09718, "variance": None, "ndata": None},
+ "BXH14": {"sample_name": "BXH14", "value": 7.97475, "variance": None, "ndata": None},
+ "BXH19": {"sample_name": "BXH19", "value": 7.67223, "variance": None, "ndata": None},
+ "BXH2": {"sample_name": "BXH2", "value": 7.93622, "variance": None, "ndata": None},
+ "BXH22": {"sample_name": "BXH22", "value": 7.43692, "variance": None, "ndata": None},
+ "BXH4": {"sample_name": "BXH4", "value": 7.96336, "variance": None, "ndata": None},
+ "BXH6": {"sample_name": "BXH6", "value": 7.75132, "variance": None, "ndata": None},
+ "BXH7": {"sample_name": "BXH7", "value": 8.12927, "variance": None, "ndata": None},
+ "BXH8": {"sample_name": "BXH8", "value": 6.77338, "variance": None, "ndata": None},
+ "BXH9": {"sample_name": "BXH9", "value": 8.03836, "variance": None, "ndata": None},
+ "C3H/HeJ": {"sample_name": "C3H/HeJ", "value": 7.42795, "variance": None, "ndata": None},
+ "C57BL/6J": {"sample_name": "C57BL/6J", "value": 7.50606, "variance": None, "ndata": None},
+ "DBA/2J": {"sample_name": "DBA/2J", "value": 7.72588, "variance": None, "ndata": None}}}
slinked = (
(((0, 2, 0.16381088984330505),
@@ -66,7 +66,7 @@ class TestHeatmap(TestCase):
["all", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)]]:
with self.subTest(dtype=dtype):
self.assertEqual(
- export_trait_data(trait_data, strainlist, dtype=dtype),
+ export_trait_data(trait_data, samplelist, dtype=dtype),
expected)
def test_export_trait_data_dtype_all_flags(self):
@@ -106,7 +106,7 @@ class TestHeatmap(TestCase):
with self.subTest(dtype=dtype, vflag=vflag, nflag=nflag):
self.assertEqual(
export_trait_data(
- trait_data, strainlist, dtype=dtype, var_exists=vflag,
+ trait_data, samplelist, dtype=dtype, var_exists=vflag,
n_exists=nflag),
expected)
@@ -164,8 +164,8 @@ class TestHeatmap(TestCase):
self.assertEqual(
compute_traits_order(slinked), (0, 2, 1, 7, 5, 9, 3, 6, 8, 4))
- def test_retrieve_strains_and_values(self):
- """Test retrieval of strains and values."""
+ def test_retrieve_samples_and_values(self):
+ """Test retrieval of samples and values."""
for orders, slist, tdata, expected in [
[
[2],
@@ -185,9 +185,9 @@ class TestHeatmap(TestCase):
[6, None, None, 4, None]],
[[3, ["s1", "s4"], [6, 4]]]
]]:
- with self.subTest(strainlist=slist, traitdata=tdata):
+ with self.subTest(samplelist=slist, traitdata=tdata):
self.assertEqual(
- retrieve_strains_and_values(orders, slist, tdata), expected)
+ retrieve_samples_and_values(orders, slist, tdata), expected)
def test_get_lrs_from_chr(self):
"""Check that function gets correct LRS values"""