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test_regionkey.py
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"""Tests for variantkey regionkey module."""
# test_regionkey.py
# @category Libraries
# @author Nicola Asuni <[email protected]>
# @copyright 2017-2018 GENOMICS plc
# @license MIT (see LICENSE)
# @link https://github.com/genomicsplc/variantkey
import pyvariantkey.variantkey as pyvk
import numpy as np
import os
from unittest import TestCase
# 0:chrom, 1:startpos, 2:endpos, 3:strand, 4:echrom, 5:estrand, 6:rk, 7:rs, 8:chrom_startpos, 9:chrom_endpos
regionsTestData = np.array([
(b"1", 1000, 1100, 0, 1, 0, 0x080001f400002260, b"080001f400002260", 0x00000000100003e8, 0x000000001000044c),
(b"2", 1001, 1201, 1, 2, 1, 0x100001f48000258a, b"100001f48000258a", 0x00000000200003e9, 0x00000000200004b1),
(b"3", 1002, 1302, -1, 3, 2, 0x180001f5000028b4, b"180001f5000028b4", 0x00000000300003ea, 0x0000000030000516),
(b"4", 1003, 1403, 0, 4, 0, 0x200001f580002bd8, b"200001f580002bd8", 0x00000000400003eb, 0x000000004000057b),
(b"5", 1004, 1504, 1, 5, 1, 0x280001f600002f02, b"280001f600002f02", 0x00000000500003ec, 0x00000000500005e0),
(b"10", 1005, 1605, -1, 10, 2, 0x500001f68000322c, b"500001f68000322c", 0x00000000a00003ed, 0x00000000a0000645),
(b"22", 1006, 1706, 0, 22, 0, 0xb00001f700003550, b"b00001f700003550", 0x00000001600003ee, 0x00000001600006aa),
(b"X", 1007, 1807, 1, 23, 1, 0xb80001f78000387a, b"b80001f78000387a", 0x00000001700003ef, 0x000000017000070f),
(b"Y", 1008, 1908, -1, 24, 2, 0xc00001f800003ba4, b"c00001f800003ba4", 0x00000001800003f0, 0x0000000180000774),
(b"MT", 1009, 2009, 0, 25, 0, 0xc80001f880003ec8, b"c80001f880003ec8", 0x00000001900003f1, 0x00000001900007d9),
], dtype=np.string_)
# 0:res, 1:a_chrom, 2:b_chrom, 3:a_startpos, 4:b_startpos, 5:a_endpos, 6:b_endpos, 7:a_rk, 8:a_vk, 9:b_rk
overlapTestData = np.array([
(0, 1, 2, 5, 5, 7, 7, 0x0800000280000038, 0x0800000290920000, 0x1000000280000038), # different chromosome
(0, 1, 1, 0, 3, 2, 7, 0x0800000000000010, 0x0800000010920000, 0x0800000180000038), # -[-]|---|----
(0, 2, 2, 1, 3, 3, 7, 0x1000000080000018, 0x1000000090920000, 0x1000000180000038), # --[-]---|----
(1, 3, 3, 2, 3, 4, 7, 0x1800000100000020, 0x1800000110920000, 0x1800000180000038), # ---[|]--|----
(1, 4, 4, 3, 3, 5, 7, 0x2000000180000028, 0x2000000190920000, 0x2000000180000038), # ----[-]-|----
(1, 5, 5, 4, 3, 6, 7, 0x2800000200000030, 0x2800000210920000, 0x2800000180000038), # ----|[-]|----
(1, 6, 6, 5, 3, 7, 7, 0x3000000280000038, 0x3000000290920000, 0x3000000180000038), # ----|-[ ]----
(1, 10, 10, 6, 3, 8, 7, 0x5000000300000040, 0x5000000310920000, 0x5000000180000038), # ----|--[|]---
(0, 22, 22, 7, 3, 9, 7, 0xb000000380000048, 0xb000000390920000, 0xb000000180000038), # ----|---[-]--
(0, 23, 23, 8, 3, 10, 7, 0xb800000400000050, 0xb800000410920000, 0xb800000180000038), # ----|---|[-]-
(1, 24, 24, 2, 3, 8, 7, 0xc000000100000040, 0xc000000130911200, 0xc000000180000038), # ---[|---|]---
(1, 25, 25, 3, 3, 7, 7, 0xc800000180000038, 0xc8000001a0912000, 0xc800000180000038), # ----[---]----
], dtype=np.string_)
class TestFunctions(TestCase):
@classmethod
def setUpClass(cls):
global npvk
try:
npvk = pyvk.VariantKey(
os.path.realpath(os.path.dirname(os.path.realpath(__file__)) + "/../../c/test/data/genoref.bin"),
os.path.realpath(os.path.dirname(os.path.realpath(__file__)) + "/../../c/test/data/nrvk.10.bin"),
os.path.realpath(os.path.dirname(os.path.realpath(__file__)) + "/../../c/test/data/rsvk.10.bin"),
os.path.realpath(os.path.dirname(os.path.realpath(__file__)) + "/../../c/test/data/vkrs.10.bin"))
except Exception as err:
assert False, "Unable to initialize the class: {0}".format(err)
@classmethod
def tearDownClass(cls):
global npvk
npvk.close()
def test_encode_region_strand(self):
h = npvk.encode_region_strand(regionsTestData[:, 3])
np.testing.assert_array_equal(h, regionsTestData[:, 5].astype(np.uint8))
def test_decode_region_strand(self):
h = npvk.decode_region_strand(regionsTestData[:, 5])
np.testing.assert_array_equal(h, regionsTestData[:, 3].astype(np.int16))
def test_encode_regionkey(self):
h = npvk.encode_regionkey(regionsTestData[:, 4], regionsTestData[:, 1], regionsTestData[:, 2], regionsTestData[:, 5])
np.testing.assert_array_equal(h, regionsTestData[:, 6].astype(np.uint64))
def test_extract_regionkey_chrom(self):
h = npvk.extract_regionkey_chrom(regionsTestData[:, 6])
np.testing.assert_array_equal(h, regionsTestData[:, 4].astype(np.uint8))
def test_extract_regionkey_startpos(self):
h = npvk.extract_regionkey_startpos(regionsTestData[:, 6])
np.testing.assert_array_equal(h, regionsTestData[:, 1].astype(np.uint32))
def test_extract_regionkey_endpos(self):
h = npvk.extract_regionkey_endpos(regionsTestData[:, 6])
np.testing.assert_array_equal(h, regionsTestData[:, 2].astype(np.uint32))
def test_extract_regionkey_strand(self):
h = npvk.extract_regionkey_strand(regionsTestData[:, 6])
np.testing.assert_array_equal(h, regionsTestData[:, 5].astype(np.uint8))
def test_decode_regionkey(self):
echrom, startpos, endpos, estrand = npvk.decode_regionkey(regionsTestData[:, 6])
np.testing.assert_array_equal(echrom, regionsTestData[:, 4].astype(np.uint8))
np.testing.assert_array_equal(startpos, regionsTestData[:, 1].astype(np.uint32))
np.testing.assert_array_equal(endpos, regionsTestData[:, 2].astype(np.uint32))
np.testing.assert_array_equal(estrand, regionsTestData[:, 5].astype(np.uint8))
def test_reverse_regionkey(self):
chrom, startpos, endpos, strand = npvk.reverse_regionkey(regionsTestData[:, 6])
np.testing.assert_array_equal(chrom, regionsTestData[:, 0].astype('|S2'))
np.testing.assert_array_equal(startpos, regionsTestData[:, 1].astype(np.uint32))
np.testing.assert_array_equal(endpos, regionsTestData[:, 2].astype(np.uint32))
np.testing.assert_array_equal(strand, regionsTestData[:, 3].astype(np.int16))
def test_regionkey(self):
h = npvk.regionkey(regionsTestData[:, 0], regionsTestData[:, 1], regionsTestData[:, 2], regionsTestData[:, 3])
np.testing.assert_array_equal(h, regionsTestData[:, 6].astype(np.uint64))
def test_extend_regionkey(self):
rk = npvk.regionkey("X", 10000, 20000, -1)
h = npvk.extend_regionkey(rk, 1000)
self.assertEqual(h, 13258616630331740228)
h = npvk.extend_regionkey(rk, 300000000)
self.assertEqual(h, 13258597305126223868)
def test_regionkey_hex(self):
h = npvk.regionkey_hex(regionsTestData[:, 6])
np.testing.assert_array_equal(h, regionsTestData[:, 7].astype('|S16'))
def test_parse_regionkey_hex(self):
h = npvk.parse_regionkey_hex(regionsTestData[:, 7])
np.testing.assert_array_equal(h, regionsTestData[:, 6].astype(np.uint64))
def test_get_regionkey_chrom_startpos(self):
h = npvk.get_regionkey_chrom_startpos(regionsTestData[:, 6])
np.testing.assert_array_equal(h, regionsTestData[:, 8].astype(np.uint64))
def test_get_regionkey_chrom_endpos(self):
h = npvk.get_regionkey_chrom_endpos(regionsTestData[:, 6])
np.testing.assert_array_equal(h, regionsTestData[:, 9].astype(np.uint64))
def test_are_overlapping_regions(self):
h = npvk.are_overlapping_regions(overlapTestData[:, 1], overlapTestData[:, 3], overlapTestData[:, 5], overlapTestData[:, 2], overlapTestData[:, 4], overlapTestData[:, 6])
np.testing.assert_array_equal(h, overlapTestData[:, 0].astype(np.uint8))
def test_are_overlapping_region_regionkey(self):
h = npvk.are_overlapping_region_regionkey(overlapTestData[:, 1], overlapTestData[:, 3], overlapTestData[:, 5], overlapTestData[:, 9])
np.testing.assert_array_equal(h, overlapTestData[:, 0].astype(np.uint8))
def test_are_overlapping_regionkeys(self):
h = npvk.are_overlapping_regionkeys(overlapTestData[:, 7], overlapTestData[:, 9])
np.testing.assert_array_equal(h, overlapTestData[:, 0].astype(np.uint8))
def test_are_overlapping_variantkey_regionkey(self):
h = npvk.are_overlapping_variantkey_regionkey(overlapTestData[:, 8], overlapTestData[:, 9])
np.testing.assert_array_equal(h, overlapTestData[:, 0].astype(np.uint8))
def test_variantkey_to_regionkey(self):
h = npvk.variantkey_to_regionkey(overlapTestData[:, 8])
np.testing.assert_array_equal(h, overlapTestData[:, 7].astype(np.uint64))