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()