Merge pull request #41 from TRON-Bioinformatics/fix-cn-less-one

Fix CN less one

.github/workflows/unit_tests.yml

@@ -16,7 +16,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel
-        pip install virtualenv tox==3.23.0 tox-wheel==0.6.0 tox-gh-actions
+        pip install virtualenv tox==3.26.0 tox-wheel==1.0.0 tox-gh-actions
     - name: Build, install and run unit tests
       run: |
         tox

setup.py

@@ -42,6 +42,7 @@
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3 :: Only',
         "License :: OSI Approved :: MIT License",
         "Operating System :: Unix"

tox.ini

@@ -1,11 +1,12 @@
 [tox]
-envlist = {py37, py38, py39}
+envlist = {py37, py38, py39, py310}
 
 [gh-actions]
 python =
     3.7: py37
     3.8: py38
     3.9: py39
+    3.10: py310
 
 [testenv]
 wheel = true

vafator/__init__.py

@@ -1 +1 @@
-VERSION='2.0.3'
+VERSION='2.1.0'

vafator/power.py

@@ -46,7 +46,7 @@ def calculate_expected_vaf(self, sample: str, variant: Optional[Variant]) -> flo
         In a scenario with purity = 1, tumor CN = 2 and normal CN = 2 => expected VAF = 0.5
         """
         purity = self.purities.get(sample, DEFAULT_PURITY)
-        tumor_ploidy = self.tumor_ploidies.get(sample, default_ploidy_manager).get_ploidy(variant=variant)
+        tumor_ploidy = max(1, self.tumor_ploidies.get(sample, default_ploidy_manager).get_ploidy(variant=variant))
         corrected_tumor_ploidy = purity * tumor_ploidy + ((1 - purity) * self.normal_ploidy)
         expected_vaf = purity / corrected_tumor_ploidy
         return expected_vaf

vafator/tests/test_annotator.py

@@ -3,7 +3,7 @@
 from unittest import TestCase
 from cyvcf2 import VCF
 
-from ploidies import PloidyManager
+from vafator.ploidies import PloidyManager
 from vafator.annotator import Annotator
 import vafator.tests.utils as test_utils
 import time

vafator/tests/test_pileups.py

@@ -3,7 +3,7 @@
 import pkg_resources
 import pysam
 
-from tests.utils import VafatorVariant
+from vafator.tests.utils import VafatorVariant
 from vafator.pileups import get_variant_pileup, get_metrics
 
 

vafator/tests/test_ploidy_manager.py

@@ -2,7 +2,7 @@
 
 import pkg_resources
 
-from tests.utils import VafatorVariant
+from vafator.tests.utils import VafatorVariant
 from vafator.ploidies import PloidyManager, default_ploidy_manager
 
 

vafator/tests/test_power_calculator.py

@@ -1,11 +1,9 @@
 from unittest import TestCase
-
-import numpy as np
 import pkg_resources
 
-from ploidies import PloidyManager
-from power import PowerCalculator
-from tests.utils import VafatorVariant
+from vafator.ploidies import PloidyManager
+from vafator.power import PowerCalculator
+from vafator.tests.utils import VafatorVariant
 
 
 class PowerCalculatorTest(TestCase):
@@ -26,6 +24,11 @@ def test_power_calculator(self):
         self.assertAlmostEqual(power.calculate_power(dp=10, ac=10, sample='tumor', variant=None), 1.0)
         self.assertAlmostEqual(power.calculate_power(dp=10, ac=11, sample='tumor', variant=None), 1.0)
 
+    def test_eaf_copy_number_below_one(self):
+        power = PowerCalculator(
+            tumor_ploidies={'tumor': PloidyManager(genome_wide_ploidy=0.5)}, purities={'tumor': 0.9})
+        self.assertLessEqual(power.calculate_expected_vaf(sample='tumor', variant=None), 1.0)
+
     def test_varying_purity(self):
         power1 = PowerCalculator(
             tumor_ploidies={'tumor': PloidyManager(genome_wide_ploidy=2.5)}, purities={'tumor': 0.8})

vafator/tests/test_rank_sum_test.py

@@ -1,5 +1,4 @@
 from unittest import TestCase
-
 from vafator.rank_sum_test import calculate_rank_sum_test