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import logging
import tempfile
import unittest
from pbcore.io.dataset.DataSetMetaTypes import dsIdToSuffix
from pbcore.io import (DataSetMetaTypes, divideKeys,
SubreadSet, getDataSetUuid, getDataSetMetaType)
import pbcore.data as upstreamdata
from utils import _pbtestdata, _check_constools, _internal_data
log = logging.getLogger(__name__)
def keysToRanges(keys):
key_ranges = [[min(k), max(k)] for k in keys]
return key_ranges
class TestDataSetUtils(unittest.TestCase):
"""Unit and integrationt tests for the DataSet class and \
associated module functions"""
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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