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test_esid.py
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"""Tests for variantkey esid module."""
# test_esid.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:size, 1:start, 2:esize, 3:esid, 4:hsid, 5:estr, 6:istr
esidTestData = np.array([
(36, 0, 10, 0xa411493515597619, 0xb3a5fdb8808cb7dc, b"0123456789", b"0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ"),
(36, 1, 10, 0xa4524d45565d8661, 0xb3a5fdb8808cb7dc, b"123456789A", b"0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ"),
(36, 10, 10, 0xa8628e49669e8a6a, 0xd93e382010f46f32, b"ABCDEFGHIJ", b"0223456789ABCDEFGHIJKLMNOPQRSTUVWXYZ"),
(36, 25, 10, 0xac31cb3d35db7e39, 0xbfc379f4a71cb3be, b"PQRSTUVWXY", b"0133456789ABCDEFGHIJKLMNOPQRSTUVWXYZ"),
(36, 26, 10, 0xac72cf4d76df8e7a, 0xdba299d06b54215d, b"QRSTUVWXYZ", b"1123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ"),
(36, 35, 1, 0x1ec0000000000000, 0x996dcdc8ef7c89c1, b"[", b"0123456789ABCDEFGHIJKLMNOPQRSTUVWXY["),
(6, 0, 6, 0x6411493515000000, 0xa81279395d9c891e, b"012345", b"012345"),
(6, 1, 5, 0x54524d4540000000, 0xa81279395d9c891e, b"12345", b"012345"),
(6, 3, 3, 0x34d4540000000000, 0xa81279395d9c891e, b"345", b"012345"),
(6, 5, 1, 0x1540000000000000, 0xa81279395d9c891e, b"5", b"012345"),
(10, 0, 10, 0xafc1083105187209, 0x838c148028a06998, b"_!\"#$%&'()", b" !\"#$%&'()"),
(10, 0, 10, 0xa28b30d38f411493, 0x96e42cf7aefeccf0, b"*+,-./0123", b"*+,-./0123"),
(10, 0, 10, 0xa51559761969b71d, 0xb391c7f288e446ee, b"456789:;<=", b"456789:;<="),
(10, 0, 10, 0xa79f8218a39259a7, 0xcc0de20381405e0a, b">?@ABCDEFG", b">?@ABCDEFG"),
(10, 0, 10, 0xaa29aabb2dbafc31, 0xbbfc630eacb6c552, b"HIJKLMNOPQ", b"HIJKLMNOPQ"),
(10, 0, 10, 0xacb3d35db7e39ebb, 0x803eda0a1781a117, b"RSTUVWXYZ[", b"RSTUVWXYZ["),
(10, 0, 10, 0xaf3dfbf8218a3925, 0x878ef2947ee3cc2b, b"\\]^_@ABCDE", b"\\]^_`abcde"),
(10, 0, 10, 0xa9a7a29aabb2dbaf, 0xbaadaef07826969b, b"FGHIJKLMNO", b"fghijklmno"),
(10, 0, 10, 0xac31cb3d35db7e39, 0xd3da4d5e28be3590, b"PQRSTUVWXY", b"pqrstuvwxy"),
(6, 0, 6, 0x6ebbf3dfbf000000, 0xeadc752a50c5b850, b"Z[\\]^_", b"z{|}~\t"),
(15, 0, 10, 0xa4524d45565d8452, 0x9af6ee553ba41827, b"1234567812", b"123456781234567"),
(14, 0, 10, 0xa4524d45565d8452, 0xc94e10e9fe153fd2, b"1234567812", b"12345678123456"),
(13, 0, 10, 0xa4524d45565d8452, 0x9b56411c7abdefe6, b"1234567812", b"1234567812345"),
(12, 0, 10, 0xa4524d45565d8452, 0xcbec35944ff1c863, b"1234567812", b"123456781234"),
(11, 0, 10, 0xa4524d45565d8452, 0x929920298cf56b9b, b"1234567812", b"12345678123"),
(10, 0, 10, 0xa4524d45565d8452, 0xbdf006d50a33ad90, b"1234567812", b"1234567812"),
(9, 0, 9, 0x94524d45565d8440, 0xde094182e93557ae, b"123456781", b"123456781"),
(8, 0, 8, 0x84524d45565d8000, 0xccbc926a73ece95c, b"12345678", b"12345678"),
(7, 0, 7, 0x74524d45565c0000, 0xd18b960e2f99c279, b"1234567", b"1234567"),
(6, 0, 6, 0x64524d4556000000, 0x811c9c02fcc22096, b"123456", b"123456"),
(5, 0, 5, 0x54524d4540000000, 0xd863467dedd1cab1, b"12345", b"12345"),
(4, 0, 4, 0x44524d4000000000, 0xbef404ecb71e4cd9, b"1234", b"1234"),
(3, 0, 3, 0x34524c0000000000, 0xfad470644116fa54, b"123", b"123"),
(2, 0, 2, 0x2452000000000000, 0xd94ae1e7173e781d, b"12", b"12"),
(1, 0, 1, 0x1440000000000000, 0xfc73100baa96ad81, b"1", b"1"),
(0, 0, 0, 0x0000000000000000, 0x8000000000000000, b"", b""),
])
# 0:size, 1:esize, 2:esid, 3:estr, 4:istr
esidNumTestData = np.array([
(1, 1, 0x1680000000000000, b":", b":"),
(1, 1, 0x1840000000000000, b"A", b"A"),
(2, 2, 0x285a000000000000, b"A:", b"A:"),
(2, 2, 0x2691000000000000, b":1", b":1"),
(2, 2, 0x2862000000000000, b"AB", b"Ab"),
(3, 3, 0x3862680000000000, b"AB:", b"Ab:"),
(3, 3, 0x38628c0000000000, b"ABC", b"AbC"),
(4, 4, 0x48628da000000000, b"ABC:", b"AbC:"),
(4, 4, 0x48628e4000000000, b"ABCD", b"AbCd"),
(5, 5, 0x58628e4680000000, b"ABCD:", b"AbCd:"),
(5, 5, 0x58628e4940000000, b"ABCDE", b"AbCdE"),
(6, 6, 0x68628e495a000000, b"ABCDE:", b"AbCdE:"),
(6, 6, 0x68628e4966000000, b"ABCDEF", b"AbCdEf"),
(7, 7, 0x78628e4966680000, b"ABCDEF:", b"AbCdEf:"),
(7, 7, 0x78628e49669c0000, b"ABCDEFG", b"AbCdEfG"),
(8, 8, 0x88628e49669da000, b"ABCDEFG:", b"AbCdEfG:"),
(8, 8, 0x88628e49669e8000, b"ABCDEFGH", b"AbCdEfGh"),
(9, 9, 0x98628e49669e8680, b"ABCDEFGH:", b"AbCdEfGh:"),
(5, 5, 0x58628da400000000, b"ABC:0", b"AbC:0"),
(5, 5, 0x58628da440000000, b"ABC:1", b"AbC:1"),
(12, 12, 0xd8628c0000bc614e, b"ABC:12345678", b"AbC:12345678"),
(13, 13, 0xd8628c0008bc614e, b"ABC:012345678", b"AbC:012345678"),
(14, 14, 0xd8628c0010bc614e, b"ABC:0012345678", b"AbC:0012345678"),
(15, 15, 0xd8628c0018bc614e, b"ABC:00012345678", b"AbC:00012345678"),
(16, 16, 0xd8628c0020bc614e, b"ABC:000012345678", b"AbC:000012345678"),
(17, 17, 0xd8628c0028bc614e, b"ABC:0000012345678", b"AbC:0000012345678"),
(18, 18, 0xd8628c0030bc614e, b"ABC:00000012345678", b"AbC:00000012345678"),
(19, 19, 0xd8628c0038bc614e, b"ABC:000000012345678", b"AbC:000000012345678"),
(20, 19, 0xd8628c0038bc614e, b"ABC:000000012345678", b"AbC:0000000012345678"),
(21, 19, 0xd8628c0038bc614e, b"ABC:000000012345678", b"AbC:00000000012345678"),
(22, 19, 0xd8628c0038bc614e, b"ABC:000000012345678", b"AbC:000000000012345678"),
(23, 19, 0xd8628c0038bc614e, b"ABC:000000012345678", b"AbC:0000000000012345678"),
(7, 7, 0x78628e495a400000, b"ABCDE:0", b"AbCdE:0"),
(7, 7, 0x78628e495a440000, b"ABCDE:1", b"AbCdE:1"),
(14, 14, 0xf8628e4940bc614e, b"ABCDE:12345678", b"AbCdE:12345678"),
(15, 15, 0xf8628e4948bc614e, b"ABCDE:012345678", b"AbCdE:012345678"),
(16, 16, 0xf8628e4950bc614e, b"ABCDE:0012345678", b"AbCdE:0012345678"),
(17, 17, 0xf8628e4958bc614e, b"ABCDE:00012345678", b"AbCdE:00012345678"),
(18, 18, 0xf8628e4960bc614e, b"ABCDE:000012345678", b"AbCdE:000012345678"),
(19, 19, 0xf8628e4968bc614e, b"ABCDE:0000012345678", b"AbCdE:0000012345678"),
(20, 20, 0xf8628e4970bc614e, b"ABCDE:00000012345678", b"AbCdE:00000012345678"),
(21, 21, 0xf8628e4978bc614e, b"ABCDE:000000012345678", b"AbCdE:000000012345678"),
(22, 21, 0xf8628e4978bc614e, b"ABCDE:000000012345678", b"AbCdE:0000000012345678"),
(23, 21, 0xf8628e4978bc614e, b"ABCDE:000000012345678", b"AbCdE:00000000012345678"),
(24, 21, 0xf8628e4978bc614e, b"ABCDE:000000012345678", b"AbCdE:000000000012345678"),
(25, 21, 0xf8628e4978bc614e, b"ABCDE:000000012345678", b"AbCdE:0000000000012345678"),
(9, 9, 0x98628e49669da400, b"ABCDEFG:0", b"AbCdEfG:0"),
(9, 9, 0x98628e49669da440, b"ABCDEFG:1", b"AbCdEfG:1"),
(16, 14, 0xf8628e4940bc614e, b"ABCDE:12345678", b"AbCdEfG:12345678"),
(17, 15, 0xf8628e4948bc614e, b"ABCDE:012345678", b"AbCdEfG:012345678"),
(18, 16, 0xf8628e4950bc614e, b"ABCDE:0012345678", b"AbCdEfG:0012345678"),
(19, 17, 0xf8628e4958bc614e, b"ABCDE:00012345678", b"AbCdEfG:00012345678"),
(20, 18, 0xf8628e4960bc614e, b"ABCDE:000012345678", b"AbCdEfG:000012345678"),
(21, 19, 0xf8628e4968bc614e, b"ABCDE:0000012345678", b"AbCdEfG:0000012345678"),
(22, 20, 0xf8628e4970bc614e, b"ABCDE:00000012345678", b"AbCdEfG:00000012345678"),
(23, 21, 0xf8628e4978bc614e, b"ABCDE:000000012345678", b"AbCdEfG:000000012345678"),
(24, 21, 0xf8628e4978bc614e, b"ABCDE:000000012345678", b"AbCdEfG:0000000012345678"),
(25, 21, 0xf8628e4978bc614e, b"ABCDE:000000012345678", b"AbCdEfG:00000000012345678"),
(26, 21, 0xf8628e4978bc614e, b"ABCDE:000000012345678", b"AbCdEfG:000000000012345678"),
(27, 21, 0xf8628e4978bc614e, b"ABCDE:000000012345678", b"AbCdEfG:0000000000012345678"),
])
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_string_id(self):
h = npvk.encode_string_id(esidTestData[:, 6], esidTestData[:, 1])
np.testing.assert_array_equal(h, esidTestData[:, 3].astype(np.uint64))
def test_encode_string_id_scalar_start(self):
h = npvk.encode_string_id(esidTestData[14:16, 6], 0)
np.testing.assert_array_equal(h, esidTestData[14:16, 3].astype(np.uint64))
def test_encode_string_num_id(self):
h = npvk.encode_string_num_id(esidNumTestData[:, 4], b':')
np.testing.assert_array_equal(h, esidNumTestData[:, 2].astype(np.uint64))
def test_decode_string_id(self):
esid, elen = npvk.decode_string_id(esidTestData[:, 3])
np.testing.assert_array_equal(esid, esidTestData[:, 5].astype(np.string_))
np.testing.assert_array_equal(elen, esidTestData[:, 2].astype(np.uint8))
def test_decode_string_num_id(self):
esid, elen = npvk.decode_string_id(esidNumTestData[:, 2])
np.testing.assert_array_equal(esid, esidNumTestData[:, 3].astype(np.string_))
np.testing.assert_array_equal(elen, esidNumTestData[:, 1].astype(np.uint8))
def test_hash_string_id(self):
h = npvk.hash_string_id(esidTestData[:, 6])
np.testing.assert_array_equal(h, esidTestData[:, 4].astype(np.uint64))