From 3479a77a7cf9e4952ffdb80190606265f7309b78 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Thu, 24 Oct 2019 09:19:51 +0200
Subject: [PATCH] Convert single use fixtures to regular tests
---
tests/test_evaluate.py | 37 ++++++-------------------------------
1 file changed, 6 insertions(+), 31 deletions(-)
diff --git a/tests/test_evaluate.py b/tests/test_evaluate.py
index ec17739..712f755 100644
--- a/tests/test_evaluate.py
+++ b/tests/test_evaluate.py
@@ -83,19 +83,7 @@ def test_no_call(BLANK_NA12878):
assert BLANK_NA12878['alleles_no_call'] == 8
-@pytest.fixture(scope='module')
-def NA12878_BLANK():
- filename = 'tests/cases/gatk.vcf.gz'
- call = VCF(filename, gts012=True)
- positive = VCF(filename, gts012=True)
- d, disc = site_concordancy(call, positive, call_samples=['NA12878'],
- positive_samples=['BLANK'],
- min_gq=30, min_dp=20)
- return d
-
-
-@pytest.fixture(scope='module')
-def NA12878_call_truncated():
+def test_truncated_call_file():
""" When the call set is truncated, i.e. is missing variants which are
present in the positive vcf file """
@@ -106,17 +94,10 @@ def NA12878_call_truncated():
d, disc = site_concordancy(call, positive, call_samples=['NA12878'],
positive_samples=['BLANK'],
min_gq=30, min_dp=20)
- return d
-
-
-def test_truncated_called_no_call(NA12878_call_truncated):
- """ Variants which are missing from the call vcf count towards
- alleles_no_call """
- assert NA12878_call_truncated['alleles_no_call'] == 12
+ assert d['alleles_no_call'] == 12
-@pytest.fixture(scope='module')
-def NA12878_positive_truncated():
+def test_truncated_positive_file():
""" When the positive set is truncated, i.e. the called vcf file contains
variants which are absent from the positive vcf file """
filename = 'tests/cases/gatk.vcf.gz'
@@ -126,16 +107,10 @@ def NA12878_positive_truncated():
d, disc = site_concordancy(call, positive, call_samples=['NA12878'],
positive_samples=['BLANK'],
min_gq=30, min_dp=20)
- return d
-
-
-def test_truncated_positive_no_call(NA12878_positive_truncated):
- """ Variants which are missing from the positive vcf do not count towards
- alleles_no_call """
- assert NA12878_positive_truncated['alleles_no_call'] == 0
+ assert d['alleles_no_call'] == 0
-def test_phased_positive():
+def test_phased_positive_file():
""" Test error message when the positive vcf contains phased variants """
filename = 'tests/cases/gatk.vcf.gz'
phased = 'tests/cases/dummy_phased_blank.vcf.gz'
@@ -147,7 +122,7 @@ def test_phased_positive():
positive_samples=['BLANK'])
-def test_phased_call():
+def test_phased_call_file():
""" Test error message when the call vcf contains phased variants """
filename = 'tests/cases/gatk.vcf.gz'
phased = 'tests/cases/dummy_phased_blank.vcf.gz'
--
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