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|
from functools import reduce
import logging
import numpy as np
import os
import pytest
import tempfile
from pbcore.io import openIndexedAlignmentFile
from pbcore.io import (DataSet, SubreadSet, ReferenceSet, AlignmentSet,
openDataSet, openDataFile)
import pbcore.data.datasets as data
import pbcore.data as upstreamdata
log = logging.getLogger(__name__)
class TestDataSetSplit:
"""Unit and integrationt tests for the DataSet class and \
associated module functions"""
def test_split(self):
ds1 = openDataSet(data.getXml(11))
assert ds1.numExternalResources > 1
dss = list(ds1.split())
assert len(dss) == ds1.numExternalResources
assert sum(ds.numRecords for ds in dss) == ds1.numRecords
assert sum(ds.totalLength for ds in dss) == ds1.totalLength
assert sum(len(ds) for ds in dss) == len(ds1)
dss = list(ds1.split(chunks=1))
assert len(dss) == 1
assert sum(ds.numRecords for ds in dss) == ds1.numRecords
assert sum(ds.totalLength for ds in dss) == ds1.totalLength
assert sum(len(ds) for ds in dss) == len(ds1)
dss = list(ds1.split(chunks=2))
assert len(dss) == 2
assert sum(ds.numRecords for ds in dss) == ds1.numRecords
assert sum(ds.totalLength for ds in dss) == ds1.totalLength
assert sum(len(ds) for ds in dss) == len(ds1)
dss = list(ds1.split(chunks=2, ignoreSubDatasets=True))
assert len(dss) == 2
assert sum(ds.numRecords for ds in dss) == ds1.numRecords
assert sum(ds.totalLength for ds in dss) == ds1.totalLength
assert sum(len(ds) for ds in dss) == len(ds1)
assert not dss[0].uuid == dss[1].uuid
assert dss[0].name == dss[1].name
# Lets try merging and splitting on subdatasets
ds1 = openDataSet(data.getXml(7))
assert ds1.totalLength == 123588
ds1tl = ds1.totalLength
ds2 = openDataSet(data.getXml(10))
assert ds2.totalLength == 117086
ds2tl = ds2.totalLength
dss = ds1 + ds2
assert dss.totalLength == (ds1tl + ds2tl)
ds1, ds2 = sorted(dss.split(2, ignoreSubDatasets=False),
key=lambda x: x.totalLength,
reverse=True)
assert ds1.totalLength == ds1tl
assert ds2.totalLength == ds2tl
def test_split_zmws(self):
N_RECORDS = 117
test_file = upstreamdata.getUnalignedBam()
ds1 = openDataFile(test_file)
assert len([r for r in ds1]) == N_RECORDS
assert len(ds1) == N_RECORDS
dss = list(ds1.split(chunks=1, zmws=True))
assert len(dss) == 1
assert sum([len([r for r in ds_]) for ds_ in dss]) == N_RECORDS
assert sum([len(ds_) for ds_ in dss]) == N_RECORDS
# We have a lower limit on the number of zmws, now
dss = list(ds1.split(chunks=12, zmws=True))
assert len(dss) == 2
assert sum([len([r for r in ds_]) for ds_ in dss]) == N_RECORDS
assert sum([len(ds_) for ds_ in dss]) == N_RECORDS
assert dss[0].zmwRanges == [
('m140905_042212_sidney_c100564852550000001823085912221377_s1_X0',
1650, 32328)]
assert 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]))
assert not last == rg[0]
last = rg[1]
for rg in interspans:
assert len(np.nonzero(np.logical_and(
ds1.index.holeNumber < rg[1],
ds1.index.holeNumber > rg[0]))[0]) == 0
def test_split_zmws_targetsize(self):
N_RECORDS = 117
N_ZMWS = 48
test_file = upstreamdata.getUnalignedBam()
ds1 = openDataFile(test_file)
assert len([r for r in ds1]) == N_RECORDS
assert len(ds1) == N_RECORDS
assert len(set(ds1.index.holeNumber)) == N_ZMWS
# with no split
dss = list(ds1.split(targetSize=1000, zmws=True))
assert len(dss) == 1
assert sum([len([r for r in ds_]) for ds_ in dss]) == N_RECORDS
assert sum([len(ds_) for ds_ in dss]) == N_RECORDS
exp = [48]
obs = sorted([len(set(ds.index.holeNumber)) for ds in dss])
assert exp == obs
# with a split
dss = list(ds1.split(targetSize=25, zmws=True))
assert len(dss) == 2
assert sum([len([r for r in ds_]) for ds_ in dss]) == N_RECORDS
assert sum([len(ds_) for ds_ in dss]) == N_RECORDS
exp = [24, 24]
obs = sorted([len(set(ds.index.holeNumber)) for ds in dss])
assert exp == obs
# with a split
dss = list(ds1.split(targetSize=5, zmws=True))
assert len(dss) == 10
assert sum([len([r for r in ds_]) for ds_ in dss]) == N_RECORDS
assert sum([len(ds_) for ds_ in dss]) == N_RECORDS
exp = [4, 4, 5, 5, 5, 5, 5, 5, 5, 5]
obs = sorted([len(set(ds.index.holeNumber)) for ds in dss])
assert exp == obs
@pytest.mark.skip(reason="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)
assert len(ds1) == N_RECORDS
dss = list(ds1.split(chunks=1, zmws=True))
assert len(dss) == 1
assert sum([len(ds_) for ds_ in dss]) == N_RECORDS
dss = list(ds1.split(chunks=12, zmws=True))
assert len(dss) == 12
assert sum([len(ds_) for ds_ in dss]) == N_RECORDS
assert dss[0].zmwRanges == [
('m150404_101626_42267_c100807920800000001823174110291514_s1_p0',
7, 14009)]
assert dss[-1].zmwRanges == [
('m150404_101626_42267_c100807920800000001823174110291514_s1_p0',
149881, 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]))
assert not last == rg[0]
last = rg[1]
for rg in interspans:
assert len(np.nonzero(np.logical_and(
ds1.index.holeNumber < rg[1],
ds1.index.holeNumber > rg[0]))[0]) == 0
@pytest.mark.internal_data
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:
#assert sum(1 for _ in ds1) == N_RECORDS
assert len(ds1) == N_RECORDS
dss = list(ds1.split(chunks=1, zmws=True))
assert len(dss) == 1
assert sum([len(ds_) for ds_ in dss]) == N_RECORDS
dss = list(ds1.split(chunks=12, zmws=True))
assert len(dss) == 12
assert sum([len(ds_) for ds_ in dss]) == N_RECORDS
assert dss[0].zmwRanges == [
('m150404_101626_42267_c100807920800000001823174110291514_s1_p0',
7, 22099)]
assert dss[-1].zmwRanges == [
('m141115_075238_ethan_c100699872550000001823139203261572_s1_p0',
127819, 163468)]
@pytest.mark.internal_data
def test_multi_movie_split_zmws_existing_simple_filters(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:
#assert sum(1 for _ in ds1) == N_RECORDS
assert len(ds1) == N_RECORDS
ds1.filters.addRequirement(rq=[('>', '0.7'), ('<', '0.5')])
FILT_RECORDS = 1732613
assert len(ds1) == FILT_RECORDS
ds1._index = None
ds1.updateCounts()
assert len(ds1) == FILT_RECORDS
dss = list(ds1.split(chunks=1, zmws=True))
dss[0]._index = None
dss[0].updateCounts()
assert len(dss) == 1
assert len(dss[0]) == FILT_RECORDS
assert sum([len(ds_) for ds_ in dss]) == FILT_RECORDS
dss = list(ds1.split(chunks=12, zmws=True))
assert len(dss) == 12
assert sum([len(ds_) for ds_ in dss]) == FILT_RECORDS
assert dss[0].zmwRanges == [
('m150404_101626_42267_c100807920800000001823174110291514_s1_p0',
7, 22073)]
assert dss[-1].zmwRanges == [
('m141115_075238_ethan_c100699872550000001823139203261572_s1_p0',
127695, 163468)]
@pytest.mark.internal_data
def test_multi_movie_split_zmws_existing_filters(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:
#assert sum(1 for _ in ds1) == N_RECORDS
assert len(ds1) == N_RECORDS
ds1.filters.addRequirement(
movie=[('=',
'm150404_101626_42267_c100807920800000001823174110291514_s1_p0'),
('=',
'm141115_075238_ethan_c100699872550000001823139203261572_s1_p0')],
zm=[('>', 10), ('>', 127900)])
ds1.filters.mapRequirement(
zm=[('<', 10000), ('<', 140000)])
FILT_RECORDS = 117776
assert len(ds1) == FILT_RECORDS
ds1._index = None
ds1.updateCounts()
assert len(ds1) == FILT_RECORDS
dss = list(ds1.split(chunks=1, zmws=True))
assert len(dss) == 1
assert len(dss[0]) == FILT_RECORDS
assert sum([len(ds_) for ds_ in dss]) == FILT_RECORDS
dss = list(ds1.split(chunks=12, zmws=True))
assert len(dss) == 12
assert sum([len(ds_) for ds_ in dss]) == FILT_RECORDS
assert dss[0].zmwRanges == [
('m150404_101626_42267_c100807920800000001823174110291514_s1_p0',
11, 1515)]
assert dss[-1].zmwRanges == [
('m141115_075238_ethan_c100699872550000001823139203261572_s1_p0',
137634, 139999)]
@pytest.mark.internal_data
def test_movie_split(self):
N_RECORDS = 1745161
N_RECORDS_1 = 959539
N_RECORDS_2 = 785622
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:
#assert sum(1 for _ in ds1) == N_RECORDS
assert len(ds1) == N_RECORDS
dss = list(ds1.split_movies(1))
assert len(dss) == 1
assert sum([len(ds_) for ds_ in dss]) == N_RECORDS
assert len(ds1) == N_RECORDS
assert not ds1.filters
dss = list(ds1.split_movies(12))
assert len(dss) == 2
assert sum([len(ds_) for ds_ in dss]) == N_RECORDS
assert len(set(dss[0].index.qId)) == 1
assert len(set(dss[-1].index.qId)) == 1
assert dss[0].qid2mov[list(set(dss[0].index.qId))[
0]] == 'm150404_101626_42267_c100807920800000001823174110291514_s1_p0'
assert len(dss[0]) == N_RECORDS_1
assert dss[-1].qid2mov[list(set(dss[-1].index.qId))[0]
] == 'm141115_075238_ethan_c100699872550000001823139203261572_s1_p0'
assert len(dss[-1]) == N_RECORDS_2
@pytest.mark.internal_data
def test_split_references(self):
test_file_1 = ('/pbi/dept/secondary/siv/testdata/SA3-RS/lambda/'
'2372215/0007_tiny/Alignment_Results/m150404_1016'
'26_42267_c100807920800000001823174110291514_s1_p'
'0.1.aligned.bam')
test_file_2 = ('/pbi/dept/secondary/siv/testdata/SA3-Sequel/ecoli/'
'315/3150204/r54049_20160508_152025/1_A01/Alignment'
'_Results/m54049_160508_155917.alignmentset.xml')
test_file_3 = ('/pbi/dept/secondary/siv/testdata/SA3-RS/ecoli/'
'tiny-multimovie/Alignment_Results/'
'combined.alignmentset.xml')
NREC1 = len(AlignmentSet(test_file_1))
NREC2 = len(AlignmentSet(test_file_2))
NREC3 = len(AlignmentSet(test_file_3))
NREC = NREC1 + NREC2 + NREC3
assert not NREC1 == 0
assert not NREC2 == 0
assert not NREC3 == 0
assert not NREC == 0
ds1 = AlignmentSet(test_file_1, test_file_2, test_file_3)
# used to get total:
#assert sum(1 for _ in ds1) == N_RECORDS
assert len(ds1) == NREC
dss = list(ds1.split_references(1))
assert len(dss) == 1
assert sum([len(ds_) for ds_ in dss]) == NREC
assert len(ds1) == NREC
assert not ds1.filters
dss = list(ds1.split_references(12))
assert len(dss) == 2
assert sum([len(ds_) for ds_ in dss]) == NREC
assert len(set(dss[0].index.tId)) == 1
assert len(set(dss[-1].index.tId)) == 1
assert dss[0].tid2rname[list(set(dss[0].index.tId))[
0]] == 'ecoliK12_pbi_March2013'
assert len(dss[0]) == NREC2 + NREC3
assert dss[-1].tid2rname[list(set(dss[-1].index.tId))
[0]] == 'lambda_NEB3011'
assert len(dss[-1]) == NREC1
@pytest.mark.internal_data
def test_multi_movie_split_zmws_with_existing_movie_filter(self):
# TODO: test with three movies and two chunks
N_RECORDS = 959539
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)
dss = list(ds1.split_movies(2))
assert len(dss) == 2
ds1 = dss[0]
# used to get total:
#assert sum(1 for _ in ds1) == N_RECORDS
assert len(ds1) == N_RECORDS
dss = list(ds1.split(chunks=1, zmws=True))
assert len(dss) == 1
assert sum([len(ds_) for ds_ in dss]) == N_RECORDS
dss = list(ds1.split(chunks=12, zmws=True))
assert len(dss) == 12
assert sum([len(ds_) for ds_ in dss]) == N_RECORDS
for ds in dss:
assert ds.zmwRanges[0][0] == 'm150404_101626_42267_c100807920800000001823174110291514_s1_p0'
@pytest.mark.skip(reason="broken")
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(14))
bams = ds2.externalResources.resourceIds
assert len(bams) == 2
refwindows = ds2.refWindows
assert 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
assert count(res1.readsInRange(*refwindows[0])) == 1409
assert count(res2.readsInRange(*refwindows[0])) == 1375
assert count(ds2.readsInRange(*refwindows[0])) == 2784
assert count(ds2.records) == 2784
ds2.disableFilters()
assert count(ds2.records) == 53552
assert 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 = list(ds3.split(contigs=True))
assert 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...
assert not refWindows == sorted(ds3.refWindows)
assert 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 = list(ds3.split(contigs=True, maxChunks=1))
assert len(dss) == 1
refWindows = sorted(reduce(lambda x, y: x + y,
[ds.refWindows for ds in dss]))
assert refWindows == old_refWindows
dss = list(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...
assert 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)
assert found
# test with maxchunks but no breaking contigs
dss = list(ds3.split(contigs=True, maxChunks=36))
assert 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
assert found
# test with maxchunks and breaking contigs is allowed (triggers
# targetsize, may result in fewer chunks)
dss = list(ds3.split(contigs=True, maxChunks=36, breakContigs=True))
assert 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
assert found
# test with previous setup and smaller targetSize, resulting in more
# chunks
dss = list(ds3.split(contigs=True, maxChunks=36, breakContigs=True,
targetSize=10))
assert 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
assert found
# test with byRecords and fewer chunks than atoms
dss = list(ds3.split(contigs=True, chunks=3, byRecords=True))
assert 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
assert 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 = list(ds3.split(contigs=True, chunks=16, byRecords=True))
assert 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
assert found
# test with byRecords and updateCounts
random_few = orf
dss = list(ds3.split(contigs=True, chunks=3, byRecords=True,
updateCounts=True))
assert len(dss) == 3
sizes = sorted([dset.numRecords for dset in dss])
assert 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
assert found
# test with byRefLength and updateCounts
random_few = orf
dss = list(ds3.split(contigs=True, chunks=3, updateCounts=True))
assert len(dss) == 3
sizes = sorted([dset.numRecords for dset in dss])
assert sizes == [28, 30, 34]
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
assert found
def test_split_by_contigs_with_split(self):
# test to make sure the refWindows work when chunks == # refs
ds3 = AlignmentSet(data.getBam())
dss = list(ds3.split(contigs=True))
assert 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...
assert not 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
assert found
old_refWindows = refWindows
dss = list(ds3.split(contigs=True, chunks=1))
assert len(dss) == 1
refWindows = sorted(reduce(lambda x, y: x + y,
[ds.refWindows for ds in dss]))
assert refWindows == old_refWindows
dss = list(ds3.split(contigs=True, chunks=24))
assert 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)
assert found
dss = list(ds3.split(contigs=True, chunks=36))
assert 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
assert found
def test_refWindows(self):
ds = AlignmentSet(data.getBam())
dss = list(ds.split(chunks=2, contigs=True))
assert len(dss) == 2
log.debug(dss[0].filters)
log.debug(dss[1].filters)
assert '( 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')])
assert str(ds.filters) == (
'( rname = E.faecalis.2 AND tstart '
'< 99 AND tend > 0 ) OR ( rname = '
'E.faecalis.2 AND tstart < 299 AND tend > 100 )')
assert ds.refWindows == [('E.faecalis.2', 0, 99),
('E.faecalis.2', 100, 299)]
@pytest.mark.skip(reason="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 = list(sset.split(zmws=True, maxChunks=5))
def test_subreadset_split_metadata_element_name(self):
fn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
log.debug(fn)
sset = SubreadSet(data.getXml(9),
data.getXml(12))
chunks = list(sset.split(chunks=5, zmws=False, ignoreSubDatasets=True))
assert len(chunks) == 2
chunks[0].write(fn)
def test_contigset_split(self):
ref = ReferenceSet(data.getXml(8))
exp_n_contigs = len(ref)
refs = ref.split(10)
assert len(refs) == 10
obs_n_contigs = 0
for r in refs:
obs_n_contigs += sum(1 for _ in r)
assert obs_n_contigs == exp_n_contigs
@pytest.mark.internal_data
@pytest.mark.constools
def test_isBarcoded(self):
empty = upstreamdata.getEmptyBam()
nonempty = ('/pbi/dept/secondary/siv/testdata/'
'pblaa-unittest/Sequel/Phi29/m54008_160219_003234'
'.tiny.subreadset.xml')
# One empty one non empty
sset = SubreadSet(nonempty, empty, skipMissing=True)
assert sset.isBarcoded
# Just nonempty
sset = SubreadSet(nonempty, skipMissing=True)
assert len(sset) == 15133
assert sset.isBarcoded
# Just empty
# This is crazy, the pbi must be out of date:
sset = SubreadSet(empty)
assert len(sset) == 0
assert sset.isBarcoded
# To confirm current behavior, I will regenerate the pbi with a
# current pbindex:
efn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
log.info("Copying to {}".format(efn))
sset.copyTo(efn)
sset.induceIndices(force=True)
assert not sset.isBarcoded
@pytest.mark.internal_data
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 = list(sset.split(chunks=3, barcodes=True))
assert [str(ss.filters) for ss in ssets] == [
"( bc = [0, 0] )",
"( bc = [1, 1] )",
"( bc = [2, 2] )"]
sset = SubreadSet(fn, skipMissing=True)
assert len(sset) == 15133
sset.filters = None
assert str(sset.filters) == ""
sset.updateCounts()
assert len(sset) == 2667562
sset.filters.addRequirement(bc=[('=', '[2, 2]')])
assert str(sset.filters) == "( bc = [2, 2] )"
sset.updateCounts()
assert len(sset) == 4710
sset.filters = None
assert str(sset.filters) == ""
sset.updateCounts()
assert len(sset) == 2667562
sset.filters.addRequirement(bc=[('=', '[2,2]')])
assert str(sset.filters) == "( bc = [2,2] )"
sset.updateCounts()
assert len(sset) == 4710
@pytest.mark.internal_data
def test_barcode_split_maxChunks(self):
fn = ('/pbi/dept/secondary/siv/testdata/'
'pblaa-unittest/Sequel/Phi29/m54008_160219_003234'
'.tiny.subreadset.xml')
sset = SubreadSet(fn, skipMissing=True)
ssets = list(sset.split(maxChunks=2, barcodes=True))
assert [str(ss.filters) for ss in ssets] == [
"( bc = [0, 0] )",
"( bc = [1, 1] ) OR ( bc = [2, 2] )"]
sset = SubreadSet(fn, skipMissing=True)
assert len(sset) == 15133
sset.filters = None
assert str(sset.filters) == ""
sset.updateCounts()
assert len(sset) == 2667562
sset.filters = ssets[0].filters
assert str(sset.filters) == "( bc = [0, 0] )"
sset.updateCounts()
assert len(sset) == 5370
sset.filters = None
assert str(sset.filters) == ""
sset.updateCounts()
assert len(sset) == 2667562
sset.filters = ssets[1].filters
assert str(sset.filters) == "( bc = [1, 1] ) OR ( bc = [2, 2] )"
sset.updateCounts()
assert len(sset) == 9763
@pytest.mark.internal_data
def test_split_read_groups(self):
fn = "/pbi/dept/secondary/siv/testdata/pbcore-unittest/data/combined.alignmentset.xml"
ds = AlignmentSet(fn)
assert len(ds) == 30
ds_rgs = ds._split_read_groups()
assert sorted([len(ds_rg) for ds_rg in ds_rgs]) == [9, 10, 11]
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