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| author | Muriithi Frederick Muriuki | 2021-09-01 07:35:40 +0300 |
|---|---|---|
| committer | Muriithi Frederick Muriuki | 2021-09-01 07:35:40 +0300 |
| commit | b975e0cfd1d0adc5f51e66292d29d4651d3f053f (patch) | |
| tree | 9a995096f469c897b3ccb24b48c380cf27d0d4b3 /tests/unit/db | |
| parent | 221c773daea839ecf0e50c196484bb91e3a6db33 (diff) | |
| download | genenetwork3-b975e0cfd1d0adc5f51e66292d29d4651d3f053f.tar.gz | |
Parse the genotype file's data header
* gn3/db/genotypes.py: parse data header
* tests/unit/db/test_genotypes.py: check that header's parse works correctly.
Add tests to check that the parser works as expected. Add code to implement
the parsing and pass the tests.
Diffstat (limited to 'tests/unit/db')
| -rw-r--r-- | tests/unit/db/test_genotypes.py | 22 |
1 files changed, 21 insertions, 1 deletions
diff --git a/tests/unit/db/test_genotypes.py b/tests/unit/db/test_genotypes.py index 0264764..4fa8a53 100644 --- a/tests/unit/db/test_genotypes.py +++ b/tests/unit/db/test_genotypes.py @@ -1,6 +1,6 @@ """Tests gn3.db.genotypes""" from unittest import TestCase -from gn3.db.genotypes import parse_genotype_labels +from gn3.db.genotypes import parse_genotype_labels, parse_genotype_header class TestGenotypes(TestCase): """Tests for functions in `gn3.db.genotypes`.""" @@ -15,3 +15,23 @@ class TestGenotypes(TestCase): (("group", "test_group"), ("filler", "test_filler"), ("type", "test_type"), ("mat", "test_mat"), ("pat", "test_pat"), ("het", "test_het"), ("unk", "test_unk"))) + + def test_parse_genotype_header(self): + for header, expected in [ + [("Chr\tLocus\tcM\tMb\tBXD1\tBXD2\tBXD5\tBXD6\tBXD8\tBXD9\t" + "BXD11\tBXD12\tBXD13\tBXD14\tBXD15\tBXD16\tBXD18\tBXD19"), + (("Mbmap", True), ("cm_column", 2), ("mb_column", 3), + ("prgy", + ("BXD1", "BXD2", "BXD5", "BXD6", "BXD8", "BXD9", "BXD11", + "BXD12", "BXD13", "BXD14", "BXD15", "BXD16", "BXD18", + "BXD19")), + ("nprgy", 14))], + [("Chr\tLocus\tcM\tBXD1\tBXD2\tBXD5\tBXD6\tBXD8\tBXD9\tBXD11" + "\tBXD12\tBXD13\tBXD14\tBXD15\tBXD16\tBXD18"), + (("Mbmap", False), ("cm_column", 2), ("mb_column", None), + ("prgy", + ("BXD1", "BXD2", "BXD5", "BXD6", "BXD8", "BXD9", "BXD11", + "BXD12", "BXD13", "BXD14", "BXD15", "BXD16", "BXD18")), + ("nprgy", 13))]]: + with self.subTest(header=header): + self.assertEqual(parse_genotype_header(header), expected) |