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import os
import logging
import tempfile
import unittest
from unittest.case import SkipTest
import numpy as np
from pbcore.io import openIndexedAlignmentFile
from pbcore.io import (DataSet, SubreadSet, ReferenceSet, AlignmentSet,
openDataSet, HdfSubreadSet,
openDataFile)
import pbcore.data.datasets as data
import pbcore.data as upstreamdata
from utils import _pbtestdata, _check_constools, _internal_data
log = logging.getLogger(__name__)
class TestDataSetSplit(unittest.TestCase):
"""Unit and integrationt tests for the DataSet class and \
associated module functions"""
def test_split(self):
ds1 = openDataSet(data.getXml(12))
self.assertTrue(ds1.numExternalResources > 1)
dss = ds1.split()
self.assertTrue(len(dss) == ds1.numExternalResources)
self.assertEqual(sum(ds.numRecords for ds in dss), ds1.numRecords)
self.assertEqual(sum(ds.totalLength for ds in dss), ds1.totalLength)
self.assertEqual(sum(len(ds) for ds in dss), len(ds1))
dss = ds1.split(chunks=1)
self.assertTrue(len(dss) == 1)
self.assertEqual(sum(ds.numRecords for ds in dss), ds1.numRecords)
self.assertEqual(sum(ds.totalLength for ds in dss), ds1.totalLength)
self.assertEqual(sum(len(ds) for ds in dss), len(ds1))
dss = ds1.split(chunks=2)
self.assertTrue(len(dss) == 2)
self.assertEqual(sum(ds.numRecords for ds in dss), ds1.numRecords)
self.assertEqual(sum(ds.totalLength for ds in dss), ds1.totalLength)
self.assertEqual(sum(len(ds) for ds in dss), len(ds1))
dss = ds1.split(chunks=2, ignoreSubDatasets=True)
self.assertTrue(len(dss) == 2)
self.assertEqual(sum(ds.numRecords for ds in dss), ds1.numRecords)
self.assertEqual(sum(ds.totalLength for ds in dss), ds1.totalLength)
self.assertEqual(sum(len(ds) for ds in dss), len(ds1))
self.assertFalse(dss[0].uuid == dss[1].uuid)
self.assertTrue(dss[0].name == dss[1].name)
# Lets try merging and splitting on subdatasets
ds1 = openDataSet(data.getXml(8))
self.assertEquals(ds1.totalLength, 123588)
ds1tl = ds1.totalLength
ds2 = openDataSet(data.getXml(11))
self.assertEquals(ds2.totalLength, 117086)
ds2tl = ds2.totalLength
dss = ds1 + ds2
self.assertTrue(dss.totalLength == (ds1tl + ds2tl))
ds1, ds2 = sorted(dss.split(2, ignoreSubDatasets=False),
key=lambda x: x.totalLength,
reverse=True)
self.assertTrue(ds1.totalLength == ds1tl)
self.assertTrue(ds2.totalLength == ds2tl)
def test_split_zmws(self):
N_RECORDS = 117
test_file = upstreamdata.getUnalignedBam()
ds1 = openDataFile(test_file)
self.assertEqual(len([r for r in ds1]), N_RECORDS)
self.assertEqual(len(ds1), N_RECORDS)
dss = ds1.split(chunks=1, zmws=True)
self.assertEqual(len(dss), 1)
self.assertEqual(sum([len([r for r in ds_]) for ds_ in dss]),
N_RECORDS)
self.assertEqual(sum([len(ds_) for ds_ in dss]),
N_RECORDS)
# We have a lower limit on the number of zmws, now
dss = ds1.split(chunks=12, zmws=True)
self.assertEqual(len(dss), 2)
self.assertEqual(sum([len([r for r in ds_]) for ds_ in dss]),
N_RECORDS)
self.assertEqual(sum([len(ds_) for ds_ in dss]),
N_RECORDS)
self.assertEqual(
dss[0].zmwRanges,
[('m140905_042212_sidney_c100564852550000001823085912221377_s1_X0',
1650, 32328)])
self.assertEqual(
dss[-1].zmwRanges,
[('m140905_042212_sidney_c100564852550000001823085912221377_s1_X0',
32560, 54396)])
ranges = sorted([c.zmwRanges[0][1:] for c in dss])
interspans = []
last = None
for rg in ranges:
if not last is None:
interspans.append((last, rg[0]))
self.assertFalse(last == rg[0])
last = rg[1]
for rg in interspans:
self.assertEqual(len(np.nonzero(np.logical_and(
ds1.index.holeNumber < rg[1],
ds1.index.holeNumber > rg[0]))[0]), 0)
#@unittest.skipUnless(os.path.isdir("/pbi/dept/secondary/siv/testdata"),
# "Missing testadata directory")
@unittest.skip("Too expensive")
def test_large_split_zmws(self):
N_RECORDS = 959539
test_file = ("/pbi/dept/secondary/siv/testdata/SA3-DS/lambda/"
"2372215/0007/Analysis_Results/m150404_101626_42"
"267_c100807920800000001823174110291514_s1_p0.al"
"l.subreadset.xml")
ds1 = openDataFile(test_file)
self.assertEqual(len(ds1), N_RECORDS)
dss = ds1.split(chunks=1, zmws=True)
self.assertEqual(len(dss), 1)
self.assertEqual(sum([len(ds_) for ds_ in dss]),
N_RECORDS)
dss = ds1.split(chunks=12, zmws=True)
self.assertEqual(len(dss), 12)
self.assertEqual(sum([len(ds_) for ds_ in dss]),
N_RECORDS)
self.assertEqual(
dss[0].zmwRanges,
[('m150404_101626_42267_c100807920800000001823174110291514_s1_p0',
7, 14007)])
self.assertEqual(
dss[-1].zmwRanges,
[('m150404_101626_42267_c100807920800000001823174110291514_s1_p0',
149876, 163475)])
ranges = sorted([c.zmwRanges[0][1:] for c in dss])
interspans = []
last = None
for rg in ranges:
if not last is None:
interspans.append((last, rg[0]))
self.assertFalse(last == rg[0])
last = rg[1]
for rg in interspans:
self.assertEqual(len(np.nonzero(np.logical_and(
ds1.index.holeNumber < rg[1],
ds1.index.holeNumber > rg[0]))[0]), 0)
@unittest.skipUnless(os.path.isdir("/pbi/dept/secondary/siv/testdata"),
"Missing testadata directory")
def test_multi_movie_split_zmws(self):
N_RECORDS = 1745161
test_file_1 = ("/pbi/dept/secondary/siv/testdata/SA3-DS/lambda/"
"2372215/0007/Analysis_Results/m150404_101626_42"
"267_c100807920800000001823174110291514_s1_p0.al"
"l.subreadset.xml")
test_file_2 = ("/pbi/dept/secondary/siv/testdata/SA3-DS/lambda/"
"2590980/0008/Analysis_Results/m141115_075238_et"
"han_c100699872550000001823139203261572_s1_p0.al"
"l.subreadset.xml")
ds1 = SubreadSet(test_file_1, test_file_2)
# used to get total:
#self.assertEqual(sum(1 for _ in ds1), N_RECORDS)
self.assertEqual(len(ds1), N_RECORDS)
dss = ds1.split(chunks=1, zmws=True)
self.assertEqual(len(dss), 1)
self.assertEqual(sum([len(ds_) for ds_ in dss]),
N_RECORDS)
dss = ds1.split(chunks=12, zmws=True)
self.assertEqual(len(dss), 12)
self.assertEqual(sum([len(ds_) for ds_ in dss]),
N_RECORDS)
self.assertEqual(
dss[0].zmwRanges,
[('m150404_101626_42267_c100807920800000001823174110291514_s1_p0',
7, 22098)])
self.assertEqual(
dss[-1].zmwRanges,
[('m141115_075238_ethan_c100699872550000001823139203261572_s1_p0',
127814, 163468)])
@SkipTest
def test_split_by_contigs_presplit(self):
# Consumes too much memory for Jenkins
# Test to make sure the result of a split by contigs has an appropriate
# number of records (make sure filters are appropriately aggressive)
ds2 = DataSet(data.getXml(15))
bams = ds2.externalResources.resourceIds
self.assertEqual(len(bams), 2)
refwindows = ds2.refWindows
self.assertEqual(refwindows, [(0, 0, 224992)])
res1 = openIndexedAlignmentFile(bams[0][7:])
res2 = openIndexedAlignmentFile(bams[1][7:])
def count(iterable):
count = 0
for _ in iterable:
count += 1
return count
self.assertEqual(count(res1.readsInRange(*refwindows[0])), 1409)
self.assertEqual(count(res2.readsInRange(*refwindows[0])), 1375)
self.assertEqual(count(ds2.readsInRange(*refwindows[0])), 2784)
self.assertEqual(count(ds2.records), 2784)
ds2.disableFilters()
self.assertEqual(count(ds2.records), 53552)
self.assertEqual(ds2.countRecords(), 53552)
def test_split_by_contigs_with_split_and_maxChunks(self):
# test to make sure the refWindows work when chunks == # refs
ds3 = AlignmentSet(data.getBam())
dss = ds3.split(contigs=True)
self.assertEqual(len(dss), 12)
refWindows = sorted(reduce(lambda x, y: x + y,
[ds.refWindows for ds in dss]))
# not all references have something mapped to them, refWindows doesn't
# care...
self.assertNotEqual(refWindows, sorted(ds3.refWindows))
self.assertEqual(refWindows,
[('B.vulgatus.4', 0, 1449), ('B.vulgatus.5', 0, 1449),
('C.beijerinckii.13', 0, 1433), ('C.beijerinckii.14', 0, 1433),
('C.beijerinckii.9', 0, 1433), ('E.coli.6', 0, 1463),
('E.faecalis.1', 0, 1482), ('E.faecalis.2', 0, 1482),
('R.sphaeroides.1', 0, 1386), ('S.epidermidis.2', 0, 1472),
('S.epidermidis.3', 0, 1472), ('S.epidermidis.4', 0, 1472)])
old_refWindows = refWindows
random_few = [('C.beijerinckii.13', 0, 1433),
('B.vulgatus.4', 0, 1449),
('E.faecalis.1', 0, 1482)]
dss = ds3.split(contigs=True, maxChunks=1)
self.assertEqual(len(dss), 1)
refWindows = sorted(reduce(lambda x, y: x + y,
[ds.refWindows for ds in dss]))
self.assertEqual(refWindows, old_refWindows)
dss = ds3.split(contigs=True, maxChunks=24)
# This isn't expected if num refs >= 100, as map check isn't made
# for now (too expensive)
# There are only 12 refs represented in this set, however...
self.assertEqual(len(dss), 12)
refWindows = sorted(reduce(lambda x, y: x + y,
[ds.refWindows for ds in dss]))
for ref in random_few:
found = False
for window in refWindows:
if ref == window:
found = True
if not found:
log.debug(ref)
self.assertTrue(found)
# test with maxchunks but no breaking contigs
dss = ds3.split(contigs=True, maxChunks=36)
self.assertEqual(len(dss), 12)
refWindows = sorted(reduce(lambda x, y: x + y,
[ds.refWindows for ds in dss]))
for ref in random_few:
found = False
for window in refWindows:
if ref == window:
found = True
self.assertTrue(found)
# test with maxchunks and breaking contigs is allowed (triggers
# targetsize, may result in fewer chunks)
dss = ds3.split(contigs=True, maxChunks=36, breakContigs=True)
self.assertEqual(len(dss), 2)
refWindows = sorted(reduce(lambda x, y: x + y,
[ds.refWindows for ds in dss]))
for ref in random_few:
found = False
for window in refWindows:
if ref == window:
found = True
self.assertTrue(found)
# test with previous setup and smaller targetSize, resulting in more
# chunks
dss = ds3.split(contigs=True, maxChunks=36, breakContigs=True,
targetSize=10)
self.assertEqual(len(dss), 9)
refWindows = sorted(reduce(lambda x, y: x + y,
[ds.refWindows for ds in dss]))
for ref in random_few:
found = False
for window in refWindows:
if ref == window:
found = True
self.assertTrue(found)
# test with byRecords and fewer chunks than atoms
dss = ds3.split(contigs=True, chunks=3, byRecords=True)
self.assertEqual(len(dss), 3)
refWindows = sorted(reduce(lambda x, y: x + y,
[ds.refWindows for ds in dss]))
for ref in random_few:
found = False
for window in refWindows:
if ref == window:
found = True
self.assertTrue(found)
# test with byRecords and more chunks than atoms
orf = random_few
random_few = [('C.beijerinckii.13', 0, 747),
('B.vulgatus.4', 0, 1449),
('E.faecalis.1', 0, 742)]
dss = ds3.split(contigs=True, chunks=16, byRecords=True)
self.assertEqual(len(dss), 16)
refWindows = sorted(reduce(lambda x, y: x + y,
[ds.refWindows for ds in dss]))
for ref in random_few:
found = False
for window in refWindows:
if ref == window:
found = True
self.assertTrue(found)
# test with byRecords and updateCounts
random_few = orf
dss = ds3.split(contigs=True, chunks=3, byRecords=True,
updateCounts=True)
self.assertEqual(len(dss), 3)
sizes = sorted([dset.numRecords for dset in dss])
self.assertListEqual(sizes, [30, 31, 31])
refWindows = sorted(reduce(lambda x, y: x + y,
[ds.refWindows for ds in dss]))
for ref in random_few:
found = False
for window in refWindows:
if ref == window:
found = True
self.assertTrue(found)
# test with byRefLength and updateCounts
random_few = orf
dss = ds3.split(contigs=True, chunks=3, updateCounts=True)
self.assertEqual(len(dss), 3)
sizes = sorted([dset.numRecords for dset in dss])
self.assertListEqual(sizes, [20, 24, 48])
refWindows = sorted(reduce(lambda x, y: x + y,
[ds.refWindows for ds in dss]))
for ref in random_few:
found = False
for window in refWindows:
if ref == window:
found = True
self.assertTrue(found)
def test_split_by_contigs_with_split(self):
# test to make sure the refWindows work when chunks == # refs
ds3 = AlignmentSet(data.getBam())
dss = ds3.split(contigs=True)
self.assertEqual(len(dss), 12)
refWindows = sorted(reduce(lambda x, y: x + y,
[ds.refWindows for ds in dss]))
# not all references have something mapped to them, refWindows doesn't
# care...
self.assertNotEqual(refWindows, sorted(ds3.refWindows))
random_few = [('C.beijerinckii.13', 0, 1433),
('B.vulgatus.4', 0, 1449),
('E.faecalis.1', 0, 1482)]
for reference in random_few:
found = False
for ref in refWindows:
if ref == reference:
found = True
self.assertTrue(found)
old_refWindows = refWindows
dss = ds3.split(contigs=True, chunks=1)
self.assertEqual(len(dss), 1)
refWindows = sorted(reduce(lambda x, y: x + y,
[ds.refWindows for ds in dss]))
self.assertEqual(refWindows, old_refWindows)
dss = ds3.split(contigs=True, chunks=24)
self.assertEqual(len(dss), 24)
refWindows = sorted(reduce(lambda x, y: x + y,
[ds.refWindows for ds in dss]))
random_few = [('E.faecalis.2', 0, 741),
('E.faecalis.2', 741, 1482)]
for ref in random_few:
found = False
for window in refWindows:
if ref == window:
found = True
if not found:
log.debug(ref)
self.assertTrue(found)
dss = ds3.split(contigs=True, chunks=36)
self.assertEqual(len(dss), 36)
refWindows = sorted(reduce(lambda x, y: x + y,
[ds.refWindows for ds in dss]))
random_few = [('E.faecalis.2', 0, 494),
('E.faecalis.2', 494, 988),
('E.faecalis.2', 988, 1482)]
for ref in random_few:
found = False
for window in refWindows:
if ref == window:
found = True
self.assertTrue(found)
def test_refWindows(self):
ds = AlignmentSet(data.getBam())
dss = ds.split(chunks=2, contigs=True)
self.assertEqual(len(dss), 2)
log.debug(dss[0].filters)
log.debug(dss[1].filters)
self.assertTrue(
'( rname = E.faecalis.2 '
in str(dss[0].filters)
or
'( rname = E.faecalis.2 '
in str(dss[1].filters))
ds = AlignmentSet(data.getBam())
ds.filters.addRequirement(rname=[('=', 'E.faecalis.2'),
('=', 'E.faecalis.2')],
tStart=[('<', '99'),
('<', '299')],
tEnd=[('>', '0'),
('>', '100')])
self.assertEqual(str(ds.filters),
'( rname = E.faecalis.2 AND tstart '
'< 99 AND tend > 0 ) OR ( rname = '
'E.faecalis.2 AND tstart < 299 AND tend > 100 )')
self.assertEqual(ds.refWindows, [('E.faecalis.2', 0, 99),
('E.faecalis.2', 100, 299)])
@unittest.skip("Too expensive")
def test_huge_zmw_split(self):
human = ('/pbi/dept/secondary/siv/testdata/SA3-DS/'
'human/JCV_85x_v030/jcv_85x_v030.subreadset.xml')
sset = SubreadSet(human)
ssets = sset.split(zmws=True, maxChunks=5)
@unittest.skipIf(not _internal_data(),
"Internal data not found, skipping")
def test_subreadset_split_metadata_element_name(self):
fn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
log.debug(fn)
sset = SubreadSet("/pbi/dept/secondary/siv/testdata/"
"SA3-Sequel/phi29/315/3150101/"
"r54008_20160219_002905/1_A01/"
"m54008_160219_003234.subreadset.xml")
chunks = sset.split(chunks=5, zmws=False, ignoreSubDatasets=True)
chunks[0].write(fn)
def test_contigset_split(self):
ref = ReferenceSet(data.getXml(9))
exp_n_contigs = len(ref)
refs = ref.split(10)
self.assertEqual(len(refs), 10)
obs_n_contigs = 0
for r in refs:
obs_n_contigs += sum(1 for _ in r)
self.assertEqual(obs_n_contigs, exp_n_contigs)
def test_split_hdfsubreadset(self):
hdfds = HdfSubreadSet(*upstreamdata.getBaxH5_v23())
self.assertEqual(len(hdfds.toExternalFiles()), 3)
hdfdss = hdfds.split(chunks=2, ignoreSubDatasets=True)
self.assertEqual(len(hdfdss), 2)
self.assertEqual(len(hdfdss[0].toExternalFiles()), 2)
self.assertEqual(len(hdfdss[1].toExternalFiles()), 1)
@unittest.skipIf(not _internal_data(),
"Internal data not found, skipping")
def test_barcode_split_cornercases(self):
fn = ('/pbi/dept/secondary/siv/testdata/'
'pblaa-unittest/Sequel/Phi29/m54008_160219_003234'
'.tiny.subreadset.xml')
sset = SubreadSet(fn, skipMissing=True)
ssets = sset.split(chunks=3, barcodes=True)
self.assertEqual([str(ss.filters) for ss in ssets],
["( bc = [0, 0] )",
"( bc = [1, 1] )",
"( bc = [2, 2] )"])
sset = SubreadSet(fn, skipMissing=True)
self.assertEqual(len(sset), 15133)
sset.filters = None
self.assertEqual(str(sset.filters), "")
sset.updateCounts()
self.assertEqual(len(sset), 2667562)
sset.filters.addRequirement(bc=[('=', '[2, 2]')])
self.assertEqual(str(sset.filters), "( bc = [2, 2] )")
sset.updateCounts()
self.assertEqual(len(sset), 4710)
sset.filters = None
self.assertEqual(str(sset.filters), "")
sset.updateCounts()
self.assertEqual(len(sset), 2667562)
sset.filters.addRequirement(bc=[('=', '[2,2]')])
self.assertEqual(str(sset.filters), "( bc = [2,2] )")
sset.updateCounts()
self.assertEqual(len(sset), 4710)
|
