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"""Test cases for procedures defined in computations.parsers"""
import unittest
import os
import pytest
from gn3.computations.parsers import parse_genofile
class TestParsers(unittest.TestCase):
"""Test cases for some various parsers"""
@pytest.mark.unit_test
def test_parse_genofile_without_existing_file(self):
"""Assert that an error is raised if the genotype file is absent"""
self.assertRaises(FileNotFoundError, parse_genofile,
"/non-existent-file")
@pytest.mark.unit_test
def test_parse_genofile_with_existing_file(self):
"""Test that a genotype file is parsed correctly"""
samples = ["bxd1", "bxd2"]
genotypes = [
{"chr": "1", "locus": "rs31443144",
"cm": "1.50", "mb": "3.010274",
"values": [-1, -1],
"dicvalues": {'bxd1': -1, 'bxd2': -1}},
{"chr": "2", "locus": "rs27644551",
"cm": "93.26", "mb": "173.542999",
"values": [1, 1],
"dicvalues": {'bxd1': 1, 'bxd2': 1}},
{"chr": "3", "locus": "rs31187985",
"cm": "17.12", "mb": "41.921845",
"values": [1, 1],
"dicvalues": {'bxd1': 1, 'bxd2': 1}},
{"chr": "4", "locus": "rs30254612",
"cm": "2.15", "mb": "3.718812",
"values": [-1, 1],
"dicvalues": {'bxd1': -1, 'bxd2': 1}},
{"chr": "5", "locus": "UNCHS047057",
"cm": "3.10", "mb": "4.199559",
"values": [-1, -1],
"dicvalues": {'bxd1': -1, 'bxd2': -1}},
{"chr": "X", "locus": "ChrXp_no_data",
"cm": "1.40", "mb": "3.231738",
"values": [1, -1],
"dicvalues": {'bxd1': 1, 'bxd2': -1}},
{"chr": "X", "locus": "Affy_17539964",
"cm": "1.40", "mb": "7.947581",
"values": [1, -1],
"dicvalues": {'bxd1': 1, 'bxd2': -1}},
]
test_genotype_file = os.path.abspath(os.path.join(
os.path.dirname(__file__),
"../test_data/genotype.txt"
))
self.assertEqual(parse_genofile(
test_genotype_file), (samples, genotypes))
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