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()
