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import pytest
import numpy as np
import sys
import os
import glob
import sysconfig
from pathlib import Path
import unittest
import pytest
import conftest
build_dir = "build/lib.%s-%s" % (sysconfig.get_platform(), sys.version[0:3])
sys.path.insert(0, os.path.join(os.getcwd(), build_dir))
import HTSeq
data_folder = conftest.get_data_folder()
class TestStretchVector(unittest.TestCase):
def test_init(self):
sv = HTSeq.StretchVector(typecode='d')
self.assertEqual(sv.ivs, [])
self.assertEqual(sv.stretches, [])
def test_setitem_number(self):
sv = HTSeq.StretchVector(typecode='d')
# Set initial stretch
sv[560] = 4.5
self.assertEqual(len(sv.ivs), 1)
self.assertEqual(len(sv.stretches), 1)
np.testing.assert_almost_equal(
sv.stretches[0],
np.ones(1, np.float32) * 4.5,
)
# Overwrite
sv[560] = 4
self.assertEqual(len(sv.ivs), 1)
self.assertEqual(len(sv.stretches), 1)
np.testing.assert_almost_equal(
sv.stretches[0],
np.ones(1, np.float32) * 4,
)
def test_setitem_slice(self):
sv = HTSeq.StretchVector(typecode='d')
# Set initial stretch
sv[100: 300] = 4.5
self.assertEqual(len(sv.ivs), 1)
self.assertEqual(len(sv.stretches), 1)
np.testing.assert_almost_equal(
sv.stretches[0],
np.ones(200, np.float32) * 4.5,
)
# Set overlapping stretch
sv[50:250] = 3
self.assertEqual(len(sv.ivs), 1)
self.assertEqual(len(sv.stretches), 1)
np.testing.assert_almost_equal(
sv.stretches[0][:200],
np.ones(200, np.float32) * 3,
)
np.testing.assert_almost_equal(
sv.stretches[0][200:],
np.ones(50, np.float32) * 4.5,
)
# Set new stretch
sv[400: 450] = np.arange(50)
self.assertEqual(len(sv.ivs), 2)
self.assertEqual(len(sv.stretches), 2)
np.testing.assert_almost_equal(
sv.stretches[1],
np.arange(50).astype(np.float32),
)
# Set overlapping stretch
sv[430: 450] = np.arange(20)
self.assertEqual(len(sv.ivs), 2)
self.assertEqual(len(sv.stretches), 2)
np.testing.assert_almost_equal(
sv.stretches[1][-20:],
np.arange(20).astype(np.float32),
)
def test_getitem_number(self):
sv = HTSeq.StretchVector(typecode='d')
# Set initial stretch
sv[560] = 4.5
self.assertEqual(sv[560], 4.5)
self.assertEqual(sv[580], None)
sv[400: 450] = np.arange(50)
res = sv[350: 430]
self.assertEqual(len(res.ivs), 1)
self.assertEqual(len(res.stretches), 1)
np.testing.assert_almost_equal(
res.stretches[0],
np.arange(30).astype(np.float32),
)
def test_todense(self):
sv = HTSeq.StretchVector(typecode='d')
sv[450: 455] = 6.7
sv[460: 465] = 1.7
res = sv.todense()
np.testing.assert_almost_equal(
res,
np.array([6.7] * 5 + [np.nan] * 5 + [1.7] * 5).astype(np.float32),
)
def test_from_dense(self):
array = np.empty(20, np.float32)
array[:] = np.nan
# All nans
sv = HTSeq.StretchVector.from_dense(array, offset=300)
self.assertEqual(len(sv.ivs), 0)
self.assertEqual(len(sv.stretches), 0)
# All good
array[:] = 78
sv = HTSeq.StretchVector.from_dense(array, offset=300)
self.assertEqual(len(sv.ivs), 1)
self.assertEqual(len(sv.stretches), 1)
# Single flips
array[:5] = np.nan
sv = HTSeq.StretchVector.from_dense(array, offset=300)
self.assertEqual(len(sv.ivs), 1)
self.assertEqual(len(sv.stretches), 1)
self.assertEqual(sv.ivs[0].start, 305)
np.testing.assert_almost_equal(
sv.stretches[0],
78 * np.ones(15).astype(np.float32),
)
array[:] = 78
array[15:] = np.nan
sv = HTSeq.StretchVector.from_dense(array, offset=300)
self.assertEqual(len(sv.ivs), 1)
self.assertEqual(len(sv.stretches), 1)
self.assertEqual(sv.ivs[0].start, 300)
np.testing.assert_almost_equal(
sv.stretches[0],
78 * np.ones(15).astype(np.float32),
)
# Double flip at edges
array[:] = 78
array[:4] = np.nan
array[15:] = np.nan
sv = HTSeq.StretchVector.from_dense(array, offset=300)
self.assertEqual(len(sv.ivs), 1)
self.assertEqual(len(sv.stretches), 1)
self.assertEqual(sv.ivs[0].start, 304)
np.testing.assert_almost_equal(
sv.stretches[0],
78 * np.ones(11).astype(np.float32),
)
# Double flip in the middle
array[:] = 78
array[2:4] = np.nan
sv = HTSeq.StretchVector.from_dense(array, offset=300)
self.assertEqual(len(sv.ivs), 2)
self.assertEqual(len(sv.stretches), 2)
self.assertEqual(sv.ivs[0].start, 300)
self.assertEqual(sv.ivs[0].end, 302)
self.assertEqual(sv.ivs[1].start, 304)
self.assertEqual(sv.ivs[1].end, 320)
np.testing.assert_almost_equal(
sv.stretches[0],
78 * np.ones(2).astype(np.float32),
)
np.testing.assert_almost_equal(
sv.stretches[1],
78 * np.ones(16).astype(np.float32),
)
# Multiple flips
array[:] = 78
array[2:4] = np.nan
array[8:11] = np.nan
array[17:19] = np.nan
sv = HTSeq.StretchVector.from_dense(array, offset=300)
self.assertEqual(len(sv.ivs), 4)
self.assertEqual(len(sv.stretches), 4)
self.assertEqual(sv.ivs[0].start, 300)
self.assertEqual(sv.ivs[0].end, 302)
self.assertEqual(sv.ivs[1].start, 304)
self.assertEqual(sv.ivs[1].end, 308)
self.assertEqual(sv.ivs[2].start, 311)
self.assertEqual(sv.ivs[2].end, 317)
self.assertEqual(sv.ivs[3].start, 319)
self.assertEqual(sv.ivs[3].end, 320)
np.testing.assert_almost_equal(
sv.stretches[0],
78 * np.ones(2).astype(np.float32),
)
np.testing.assert_almost_equal(
sv.stretches[1],
78 * np.ones(4).astype(np.float32),
)
np.testing.assert_almost_equal(
sv.stretches[2],
78 * np.ones(6).astype(np.float32),
)
np.testing.assert_almost_equal(
sv.stretches[3],
78 * np.ones(1).astype(np.float32),
)
if __name__ == '__main__':
suite = TestStretchVector()
suite.test_init()
|
