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authorMuriithi Frederick Muriuki2021-09-01 09:11:17 +0300
committerMuriithi Frederick Muriuki2021-09-01 09:11:17 +0300
commita1c217cf277feda3815a8435d6c8909f1b5546a1 (patch)
tree04644c259b0d1f9437c783fccc20da7e07ca5ca4 /tests/unit
parentb975e0cfd1d0adc5f51e66292d29d4651d3f053f (diff)
downloadgenenetwork3-a1c217cf277feda3815a8435d6c8909f1b5546a1.tar.gz
Parse data lines into markers
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/genotypes.py: parse data lines in file to genetic markers. * tests/unit/db/test_genotypes.py: test that parsing works. Add some tests to check that the parsing of the markers works as expected, and add the code to actually parse the markers.
Diffstat (limited to 'tests/unit')
-rw-r--r--tests/unit/db/test_genotypes.py38
1 files changed, 37 insertions, 1 deletions
diff --git a/tests/unit/db/test_genotypes.py b/tests/unit/db/test_genotypes.py
index 4fa8a53..ba90191 100644
--- a/tests/unit/db/test_genotypes.py
+++ b/tests/unit/db/test_genotypes.py
@@ -1,11 +1,13 @@
"""Tests gn3.db.genotypes"""
from unittest import TestCase
-from gn3.db.genotypes import parse_genotype_labels, parse_genotype_header
+from gn3.db.genotypes import (
+ parse_genotype_labels, parse_genotype_header, parse_genotype_data_line)
class TestGenotypes(TestCase):
"""Tests for functions in `gn3.db.genotypes`."""
def test_parse_genotype_labels(self):
+ """Test that the genotype labels are parsed correctly."""
self.assertEqual(
parse_genotype_labels([
"@name: test_group\t", "@filler: test_filler ",
@@ -17,6 +19,7 @@ class TestGenotypes(TestCase):
("het", "test_het"), ("unk", "test_unk")))
def test_parse_genotype_header(self):
+ """Test that the genotype header is parsed correctly."""
for header, expected in [
[("Chr\tLocus\tcM\tMb\tBXD1\tBXD2\tBXD5\tBXD6\tBXD8\tBXD9\t"
"BXD11\tBXD12\tBXD13\tBXD14\tBXD15\tBXD16\tBXD18\tBXD19"),
@@ -35,3 +38,36 @@ class TestGenotypes(TestCase):
("nprgy", 13))]]:
with self.subTest(header=header):
self.assertEqual(parse_genotype_header(header), expected)
+
+ def test_parse_genotype_data_line(self):
+ """Test parsing of data lines."""
+ for line, geno_obj, parlist, expected in [
+ ["1\trs31443144\t1.50\t3.010274\tB\tB\tD\tD\tD\tB\tB\tD\tB\tB",
+ {"mat": "test_mat", "pat": "test_pat", "het": "test_het",
+ "unk": "test_unk", "cm_column": 2, "Mbmap": True,
+ "mb_column": 3},
+ tuple(),
+ (("chr", "1"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", 3.0),
+ ("genotype",
+ ("U", "U", "U", "U", "U", "U", "U", "U", "U", "U")))],
+ ["1\trs31443144\t1.50\t3.010274\tB\tB\tD\tD\tD\tB\tB\tD\tB\tB",
+ {"mat": "test_mat", "pat": "test_pat", "het": "test_het",
+ "unk": "test_unk", "cm_column": 2, "Mbmap": True,
+ "mb_column": 3},
+ ("some", "parlist", "content"),
+ (("chr", "1"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", 3.0),
+ ("genotype",
+ (-1, 1, "U", "U", "U", "U", "U", "U", "U", "U")))],
+ ["1\trs31443144\t1.50\t3.010274\tB\tB\tD\tH\tD\tB\tU\tD\tB\tB",
+ {"mat": "B", "pat": "D", "het": "H", "unk": "U",
+ "cm_column": 2, "Mbmap": True, "mb_column": 3},
+ tuple(),
+ (("chr", "1"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", 3.0),
+ ("genotype", (-1, -1, 1, 0, 1, -1, "U", 1, -1, -1)))]]:
+ with self.subTest(line = line):
+ self.assertEqual(
+ parse_genotype_data_line(line, geno_obj, parlist),
+ expected)