From abfc0410a2385d8c3d6ee1915fc99b708e1d0dbc Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Wed, 1 Sep 2021 10:49:52 +0300
Subject: Built top-level genotype file parsing function
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: parse genotype files
* tests/unit/db/test_genotypes.py: test parsing is correct
Add the overall genotype files parsing function and tests to check that the
parsing works as expected.
---
tests/unit/db/test_genotypes.py | 101 +++++++++++++++++++++++++++++++++++++++-
1 file changed, 99 insertions(+), 2 deletions(-)
(limited to 'tests')
diff --git a/tests/unit/db/test_genotypes.py b/tests/unit/db/test_genotypes.py
index ba90191..a05ce48 100644
--- a/tests/unit/db/test_genotypes.py
+++ b/tests/unit/db/test_genotypes.py
@@ -1,7 +1,11 @@
"""Tests gn3.db.genotypes"""
from unittest import TestCase
from gn3.db.genotypes import (
- parse_genotype_labels, parse_genotype_header, parse_genotype_data_line)
+ parse_genotype_file,
+ parse_genotype_labels,
+ parse_genotype_header,
+ parse_genotype_marker,
+ build_genotype_chromosomes)
class TestGenotypes(TestCase):
"""Tests for functions in `gn3.db.genotypes`."""
@@ -69,5 +73,98 @@ class TestGenotypes(TestCase):
("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),
+ parse_genotype_marker(line, geno_obj, parlist),
expected)
+
+ def test_build_genotype_chromosomes(self):
+ """
+ Given `markers` and `geno_obj`, test that `build_genotype_chromosomes`
+ builds a sequence of chromosomes with the given markers ordered
+ according to the `chr` value."""
+ for markers, geno_obj, expected in [
+ [[(("chr", "1"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", 3.0),
+ ("genotype", (-1, -1, 1, 0, 1, -1, "U", 1, -1, -1))),
+ (("chr", "2"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", 3.0),
+ ("genotype", (-1, -1, 1, 0, 1, -1, "U", 1, -1, -1)))],
+ {"mat": "B", "pat": "D", "het": "H", "unk": "U",
+ "cm_column": 2, "Mbmap": True, "mb_column": 3},
+ ((("name", "1"), ("mb_exists", True), ("cm_column", 2),
+ ("mb_column", 3),
+ ("loci",
+ ({"chr": "1", "name": "rs31443144", "cM": 2.0, "Mb": 3.0,
+ "genotype": (-1, -1, 1, 0, 1, -1, "U", 1, -1, -1)},))),
+ (("name", "2"), ("mb_exists", True), ("cm_column", 2),
+ ("mb_column", 3),
+ ("loci",
+ ({"chr": "2", "name": "rs31443144", "cM": 2.0, "Mb": 3.0,
+ "genotype": (-1, -1, 1, 0, 1, -1, "U", 1, -1, -1)},))))],
+ [[(("chr", "1"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", None),
+ ("genotype", (-1, 1, 1, 0, 1, -1, "U", 1, -1, -1)))],
+ {"mat": "B", "pat": "D", "het": "H", "unk": "U",
+ "cm_column": 2, "Mbmap": False, "mb_column": None},
+ ((("name", "1"), ("mb_exists", False), ("cm_column", 2),
+ ("mb_column", None),
+ ("loci",
+ ({"chr": "1", "name": "rs31443144", "cM": 2.0, "Mb": None,
+ "genotype": (-1, 1, 1, 0, 1, -1, "U", 1, -1, -1)},))),)]]:
+ with self.subTest(markers = markers):
+ self.assertEqual(
+ build_genotype_chromosomes(geno_obj, markers),
+ expected)
+
+ def test_parse_genotype_file(self):
+ """Test the parsing of genotype files. """
+ self.assertEqual(
+ parse_genotype_file(
+ "tests/unit/db/data/genotypes/genotype_sample1.geno"),
+ {"group": "BXD",
+ "type": "riset",
+ "mat": "B",
+ "pat": "D",
+ "het": "H",
+ "unk": "U",
+ "Mbmap": True,
+ "cm_column": 2,
+ "mb_column": 3,
+ "prgy": ("BXD1", "BXD2", "BXD5", "BXD6", "BXD8", "BXD9"),
+ "nprgy": 6,
+ "chromosomes": (
+ {"name": "1",
+ "mb_exists": True,
+ "cm_column": 2,
+ "mb_column": 3,
+ "loci": (
+ {"chr": "1",
+ "name": "rs31443144",
+ "cM": 2.0,
+ "Mb": 3.0,
+ "genotype": (-1, -1, 1, 1, 1, -1)
+ },
+ {"chr": "1",
+ "name": "rs6269442",
+ "cM": 2.0,
+ "Mb": 3.0,
+ "genotype": (-1, -1, 1, 1, 0, "U")},
+ {"chr": "1",
+ "name": "rs32285189",
+ "cM": 2.0,
+ "Mb": 3.0,
+ "genotype": (-1, "U", 1, 1, 1, -1)})},
+ {"name": "2",
+ "mb_exists": True,
+ "cm_column": 2,
+ "mb_column": 3,
+ "loci": (
+ {"chr": "2",
+ "name": "rs31443144",
+ "cM": 2.0,
+ "Mb": 3.0,
+ "genotype": (-1, -1, 1, 1, 1, -1)},
+ {"chr": "2",
+ "name": "rs6269442",
+ "cM": 2.0,
+ "Mb": 3.0,
+ "genotype": (-1, -1, 1, 1, 0, "U")})})})
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