def setUp(self):
self.cmpH5 = None
resourcesDir = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../kineticsTools/resources')
ref = self.getReference()
alnFile = self.getAlignments()
assert os.path.exists(alnFile) and os.path.exists(ref)
self.ds = AlignmentSet(alnFile, referenceFastaFname=ref)
self.contigs = ReferenceUtils.loadReferenceContigs(ref, self.ds)
self.ipdModel = IpdModel(self.contigs,
os.path.join(resourcesDir, "P6-C4.h5"))
# Create a functional KineticWorker object that can be poked at
self.kw = KineticWorker(self.ipdModel)
# Put in our cmp.h5 - this is normally supplied by the Worker
self.kw.caseCmpH5 = self.ds
self.kw.controlCmpH5 = None
self.kw.options = self.getOpts()
def setUp(self):
self.cmpH5 = None
resourcesDir = os.path.join(os.path.dirname(os.path.abspath(__file__)), '../kineticsTools/resources')
ref = self.getReference()
alnFile = self.getAlignments()
assert os.path.exists(alnFile) and os.path.exists(ref)
self.ds = AlignmentSet(alnFile, referenceFastaFname=ref)
self.contigs = ReferenceUtils.loadReferenceContigs(ref, self.ds)
self.ipdModel = IpdModel(self.contigs, os.path.join(resourcesDir, "P6-C4.h5"))
# Create a functional KineticWorker object that can be poked at
self.kw = KineticWorker(self.ipdModel)
# Put in our cmp.h5 - this is normally supplied by the Worker
self.kw.caseCmpH5 = self.ds
self.kw.controlCmpH5 = None
self.kw.options = self.getOpts()
def setUp(self):
# Load the lambda genome from our sample data
dataDir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data')
resourcesDir = os.path.join(os.path.dirname(os.path.abspath(__file__)), '../kineticsTools/resources')
ref = os.path.join(dataDir, 'lambda', 'sequence', 'lambda.fasta')
cmpFile = os.path.join(dataDir, "p4-c2-lambda-mod-decode.cmp.h5")
self.cmpH5 = AlignmentSet(cmpFile, referenceFastaFname=ref)
self.contigs = ReferenceUtils.loadReferenceContigs(ref, self.cmpH5)
self.ipdModel = IpdModel(self.contigs, os.path.join(resourcesDir, "P4-C2.h5"))
# Create a functional KineticWorker object that can be poked at manually.
self.kw = KineticWorker(self.ipdModel)
# Put in our cmp.h5 - this is normally supplied by the Worker superclass
self.kw.caseCmpH5 = self.cmpH5
self.kw.controlCmpH5 = None
self.kw.options = self.getOpts()
class _TestBase(object):
MAX_ALIGNMENTS = 1500
"""
Common test functionality. All input type tests should inherit from this,
and yield identical results.
"""
def getOpts(self):
"""Derived tests can override this to customize behaviour"""
return self.basicOpts()
def basicOpts(self):
"""Mock up some options for the kinetic worker"""
self_ = self
class opts:
def __init__(self):
self.mapQvThreshold = -1
self.cap_percentile = 99.0
self.minCoverage = 3
self.subread_norm = True
self.maxCoverage = 200
self.identify = True
self.methylFraction = False
self.pvalue = 0.01
self.modsToCall = ['H', 'J', 'K']
# Bug 23546: need to set values for these two new flags:
self.identifyMinCov = 5
self.methylMinCov = 10
self.useLDA = False
self.maxAlignments = self_.MAX_ALIGNMENTS
self.randomSeed = None
return opts()
def getAlignments(self):
raise NotImplementedError()
def getReference(self):
refDir = "/pbi/dept/secondary/siv/references"
return os.path.join(refDir, "Helicobacter_pylori_J99", "sequence",
"Helicobacter_pylori_J99.fasta")
def setUp(self):
self.cmpH5 = None
resourcesDir = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../kineticsTools/resources')
ref = self.getReference()
alnFile = self.getAlignments()
assert os.path.exists(alnFile) and os.path.exists(ref)
self.ds = AlignmentSet(alnFile, referenceFastaFname=ref)
self.contigs = ReferenceUtils.loadReferenceContigs(ref, self.ds)
self.ipdModel = IpdModel(self.contigs,
os.path.join(resourcesDir, "P6-C4.h5"))
# Create a functional KineticWorker object that can be poked at
self.kw = KineticWorker(self.ipdModel)
# Put in our cmp.h5 - this is normally supplied by the Worker
self.kw.caseCmpH5 = self.ds
self.kw.controlCmpH5 = None
self.kw.options = self.getOpts()
def test_private_api(self):
start = 50
end = 100
REF_GROUP_ID = "gi|12057207|gb|AE001439.1|"
referenceWindow = ReferenceWindow(0, REF_GROUP_ID, start, end)
bounds = (start, end)
rir = list(
self.kw.caseCmpH5.readsInRange(referenceWindow.refName,
referenceWindow.start,
referenceWindow.end))
self.assertEqual(len(rir), 301)
chunks = self.kw._fetchChunks(REF_GROUP_ID, (start, end),
self.kw.caseCmpH5)
factor = 1.0 / self.ds.readGroupTable[0].FrameRate
rawIpds = self.kw._loadRawIpds(rir, start, end, factor)
logging.critical(len(rawIpds))
# XXX note that this is very dependent on the exact order of reads
# found by readsInRange(), which may be altered by changes to the
# implementation of the dataset API. It should, however, remain
# consistent across equivalent input types.
# XXX 2015-08-28 disabling this for now because it will change if the
# dataset contains multiple .bam files
#self.assertEqual("%.4f" % rawIpds[0][2], "0.2665")
log.info(rawIpds)
chunks = self.kw._chunkRawIpds(rawIpds)
#log.critical(chunks)
def test_small_decode(self):
"""Test for known modifications near the start of H. pylori genome"""
# XXX should have mods on 60- (m4C), 89+ (m6A), 91- (m6A)
start = 50
end = 100
REF_GROUP_ID = "gi|12057207|gb|AE001439.1|"
referenceWindow = ReferenceWindow(0, REF_GROUP_ID, start, end)
bounds = (start, end)
self.kw._prepForReferenceWindow(referenceWindow)
kinetics = self.kw._summarizeReferenceRegion(bounds, False, True)
mods = self.kw._decodePositiveControl(kinetics, bounds)
log.info(mods)
# Verify that we detect m6A mods at 14982 and 14991
m6AMods = [
x for x in mods
if x['modification'] == 'm6A' and x['tpl'] in (88, 90)
]
self.assertEqual(len(m6AMods), 2)
m4CMods = [
x for x in mods
if x['modification'] == 'm4C' and x['tpl'] in (59, )
]
self.assertEqual(len(m4CMods), 1)
for x in mods:
if x['strand'] == 0:
self.assertEqual(x['tpl'], 88)
else:
self.assertTrue(x['tpl'] in [59, 90])
class _TestBase(object):
MAX_ALIGNMENTS = 1500
"""
Common test functionality. All input type tests should inherit from this,
and yield identical results.
"""
def getOpts(self):
"""Derived tests can override this to customize behaviour"""
return self.basicOpts()
def basicOpts(self):
"""Mock up some options for the kinetic worker"""
self_ = self
class opts:
def __init__(self):
self.mapQvThreshold = -1
self.cap_percentile = 99.0
self.minCoverage = 3
self.subread_norm = True
self.maxCoverage = 200
self.identify = True
self.methylFraction = False
self.pvalue = 0.01
self.modsToCall = ['H', 'J', 'K']
# Bug 23546: need to set values for these two new flags:
self.identifyMinCov = 5
self.methylMinCov = 10
self.useLDA = False
self.maxAlignments = self_.MAX_ALIGNMENTS
self.randomSeed = None
return opts()
def getAlignments (self):
raise NotImplementedError()
def getReference (self):
refDir = "/pbi/dept/secondary/siv/references"
return os.path.join(refDir, "Helicobacter_pylori_J99", "sequence",
"Helicobacter_pylori_J99.fasta")
def setUp(self):
self.cmpH5 = None
resourcesDir = os.path.join(os.path.dirname(os.path.abspath(__file__)), '../kineticsTools/resources')
ref = self.getReference()
alnFile = self.getAlignments()
assert os.path.exists(alnFile) and os.path.exists(ref)
self.ds = AlignmentSet(alnFile, referenceFastaFname=ref)
self.contigs = ReferenceUtils.loadReferenceContigs(ref, self.ds)
self.ipdModel = IpdModel(self.contigs, os.path.join(resourcesDir, "P6-C4.h5"))
# Create a functional KineticWorker object that can be poked at
self.kw = KineticWorker(self.ipdModel)
# Put in our cmp.h5 - this is normally supplied by the Worker
self.kw.caseCmpH5 = self.ds
self.kw.controlCmpH5 = None
self.kw.options = self.getOpts()
def test_private_api (self):
start = 50
end = 100
REF_GROUP_ID = "gi|12057207|gb|AE001439.1|"
referenceWindow = ReferenceWindow(0, REF_GROUP_ID, start, end)
bounds = (start, end)
rir = list(self.kw.caseCmpH5.readsInRange(referenceWindow.refName,
referenceWindow.start, referenceWindow.end))
self.assertEqual(len(rir), 301)
chunks = self.kw._fetchChunks(REF_GROUP_ID, (start, end),
self.kw.caseCmpH5)
factor = 1.0 / self.ds.readGroupTable[0].FrameRate
rawIpds = self.kw._loadRawIpds(rir, start, end, factor)
logging.critical(len(rawIpds))
# XXX note that this is very dependent on the exact order of reads
# found by readsInRange(), which may be altered by changes to the
# implementation of the dataset API. It should, however, remain
# consistent across equivalent input types.
# XXX 2015-08-28 disabling this for now because it will change if the
# dataset contains multiple .bam files
#self.assertEqual("%.4f" % rawIpds[0][2], "0.2665")
log.info(rawIpds)
chunks = self.kw._chunkRawIpds(rawIpds)
#log.critical(chunks)
def test_small_decode (self):
"""Test for known modifications near the start of H. pylori genome"""
# XXX should have mods on 60- (m4C), 89+ (m6A), 91- (m6A)
start = 50
end = 100
REF_GROUP_ID = "gi|12057207|gb|AE001439.1|"
referenceWindow = ReferenceWindow(0, REF_GROUP_ID, start, end)
bounds = (start, end)
self.kw._prepForReferenceWindow(referenceWindow)
kinetics = self.kw._summarizeReferenceRegion(bounds, False, True)
mods = self.kw._decodePositiveControl(kinetics, bounds)
log.info(mods)
# Verify that we detect m6A mods at 14982 and 14991
m6AMods = [x for x in mods if x['modification'] == 'm6A' and x['tpl'] in (88, 90) ]
self.assertEqual(len(m6AMods), 2)
m4CMods = [x for x in mods if x['modification'] == 'm4C' and x['tpl'] in (59,) ]
self.assertEqual(len(m4CMods), 1)
for x in mods:
if x['strand'] == 0:
self.assertEqual(x['tpl'], 88)
else:
self.assertTrue(x['tpl'] in [59,90])
