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import logging
import tempfile
import unittest
from pbcore.io.dataset.DataSetMetaTypes import dsIdToSuffix
from pbcore.io import (DataSetMetaTypes, divideKeys, keysToRanges,
SubreadSet, getDataSetUuid, getDataSetMetaType)
from pbcore.io.dataset.utils import (xy_to_hn, hn_to_xy, sampleHolesUniformly,
sampleUniformly, quadratic_expand,
prodround)
import pbcore.data as upstreamdata
from utils import _pbtestdata, _check_constools, _internal_data
log = logging.getLogger(__name__)
class TestDataSetUtils(unittest.TestCase):
"""Unit and integrationt tests for the DataSet class and \
associated module functions"""
def test_hn_xy_converters(self):
for x in range(64, 1024, 10):
for y in range(64, 1144, 10):
hn = xy_to_hn(x, y)
ox, oy = hn_to_xy(hn)
self.assertEqual(x, ox)
self.assertEqual(y, oy)
def test_quadratic_expand(self):
i = [[0, 1, 2]]
e = [[0], [1], [2]]
o = quadratic_expand(i)
self.assertEqual(e, o)
i = [[0, 1, 2], [3, 4, 5]]
e = [[0, 3], [1, 3], [2, 3],
[0, 4], [1, 4], [2, 4],
[0, 5], [1, 5], [2, 5]]
o = quadratic_expand(i)
self.assertEqual(e, o)
def test_prodround(self):
i = [1.1, 2.5, 3.8]
e = [1, 2, 4]
o = prodround(i, 8)
self.assertEqual(e, o)
e = [1, 3, 3]
o = prodround(i, 9)
self.assertEqual(e, o)
e = [1, 3, 4]
o = prodround(i, 12)
self.assertEqual(e, o)
def test_sampleUniformly(self):
hns = sampleUniformly(4, [(0, 1), (0, 1)])
self.assertEqual(hns, [[0, 0], [1, 0], [0, 1], [1, 1]])
hns = sampleUniformly(4, [(0, 4), (0, 4)])
self.assertEqual(hns, [[1, 1], [3, 1], [1, 3], [3, 3]])
hns = sampleUniformly(4, [(0, 4), (0, 8)])
self.assertEqual(hns, [[1, 3], [3, 3], [1, 5], [3, 5]])
hns = sampleUniformly(3, [(0, 4), (0, 8)])
self.assertEqual(hns, [[2, 2], [2, 4], [2, 6]])
def test_sampleHolesUniformly(self):
ncols = 1144
nrows = 1024
bounds = [(64, ncols), (64, nrows)]
expected = [xy_to_hn(x, y) for x,y in sampleUniformly(100, bounds)]
all_xy = quadratic_expand([range(64, ncols), range(64, nrows)])
all_holes = [xy_to_hn(x, y) for x, y in all_xy]
samples = sampleHolesUniformly(100, all_holes)
self.assertEqual(expected, samples)
@unittest.skipIf(not _internal_data(),
"Internal data not available")
def test_sampleHolesUniformly_realdata(self):
path = ('/pbi/dept/secondary/siv/testdata/SA3-Sequel/'
'lambda/315/3150128/r54008_20160308_001811/'
'2_B01/m54008_160308_053311.subreads.bam')
ds = SubreadSet(path, strict=True)
samples = sampleHolesUniformly(100, ds.index.holeNumber)
self.assertEqual(len(samples), 100)
def test_get_dataset_uuid(self):
ds = SubreadSet(upstreamdata.getUnalignedBam(), strict=True)
ds_file = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
ds.write(ds_file)
uuid = getDataSetUuid(ds_file)
self.assertEqual(uuid, ds.uuid)
with open(ds_file, "w") as out:
out.write("hello world!")
uuid = getDataSetUuid(ds_file)
self.assertEqual(uuid, None)
def test_get_dataset_metatype(self):
ds = SubreadSet(upstreamdata.getUnalignedBam(), strict=True)
ds_file = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
ds.write(ds_file)
meta_type = getDataSetMetaType(ds_file)
self.assertEqual(meta_type, "PacBio.DataSet.SubreadSet")
def test_dsIdToSuffix(self):
suffixes = ['subreadset.xml', 'hdfsubreadset.xml', 'alignmentset.xml',
'barcodeset.xml', 'consensusreadset.xml',
'consensusalignmentset.xml',
'referenceset.xml', 'contigset.xml']
for dsId, exp in zip(DataSetMetaTypes.ALL, suffixes):
self.assertEqual(dsIdToSuffix(dsId), exp)
def test_divideKeys_keysToRanges(self):
keys = [0, 1, 2, 3, 5, 8, 50]
res = divideKeys(keys, 0)
self.assertEqual(res, [])
res = keysToRanges(res)
self.assertEqual(res, [])
res = divideKeys(keys, 1)
self.assertEqual(res, [[0, 1, 2, 3, 5, 8, 50]])
res = keysToRanges(res)
self.assertEqual(res, [[0, 50]])
res = divideKeys(keys, 2)
self.assertEqual(res, [[0, 1, 2], [3, 5, 8, 50]])
res = keysToRanges(res)
self.assertEqual(res, [[0, 2], [3, 50]])
res = divideKeys(keys, 3)
self.assertEqual(res, [[0, 1], [2, 3], [5, 8, 50]])
res = keysToRanges(res)
self.assertEqual(res, [[0, 1], [2, 3], [5, 50]])
res = divideKeys(keys, 7)
self.assertEqual(res, [[0], [1], [2], [3], [5], [8], [50]])
res = keysToRanges(res)
self.assertEqual(res, [[0, 0], [1, 1], [2, 2], [3, 3],
[5, 5], [8, 8], [50, 50]])
res = divideKeys(keys, 8)
self.assertEqual(res, [[0], [1], [2], [3], [5], [8], [50]])
res = keysToRanges(res)
self.assertEqual(res, [[0, 0], [1, 1], [2, 2], [3, 3],
[5, 5], [8, 8], [50, 50]])
keys = [0, 1, 2, 2, 3, 5, 8, 50, 50]
res = divideKeys(keys, 0)
self.assertEqual(res, [])
res = keysToRanges(res)
self.assertEqual(res, [])
res = divideKeys(keys, 1)
self.assertEqual(res, [[0, 1, 2, 2, 3, 5, 8, 50, 50]])
res = keysToRanges(res)
self.assertEqual(res, [[0, 50]])
res = divideKeys(keys, 2)
self.assertEqual(res, [[0, 1, 2, 2], [3, 5, 8, 50, 50]])
res = keysToRanges(res)
self.assertEqual(res, [[0, 2], [3, 50]])
res = divideKeys(keys, 3)
self.assertEqual(res, [[0, 1, 2], [2, 3, 5], [8, 50, 50]])
res = keysToRanges(res)
self.assertEqual(res, [[0, 2], [2, 5], [8, 50]])
res = divideKeys(keys, 9)
self.assertEqual(res, [[0], [1], [2], [2], [3], [5], [8], [50], [50]])
res = keysToRanges(res)
self.assertEqual(res, [[0, 0], [1, 1], [2, 2], [2, 2], [3, 3],
[5, 5], [8, 8], [50, 50], [50, 50]])
res = divideKeys(keys, 10)
self.assertEqual(res, [[0], [1], [2], [2], [3], [5], [8], [50], [50]])
res = keysToRanges(res)
self.assertEqual(res, [[0, 0], [1, 1], [2, 2], [2, 2], [3, 3],
[5, 5], [8, 8], [50, 50], [50, 50]])
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