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import logging
import os
import platform
from pbcore.io import CmpH5Reader
from kineticsTools.ReferenceUtils import ReferenceWindow
from kineticsTools.KineticWorker import KineticWorker
from kineticsTools.ipdModel import IpdModel
from test import TestSetup
class TestDetectionMethylFraction(TestSetup):
# We inherit the setup method for test.py.
# If you need to customize your dataset, we should set up some different
# conventions
def getOpts(self):
opts = self.basicOpts()
opts.identify = False
opts.methylFraction = True
return opts
def testSmallDecode(self):
"""
Test modified fraction estimation in detection mode around a known modification in lambda
"""
# First methlyated A in lambda:
# strand motif onTarget seqid tpl
# 0 GCACNNNNNNGTT On 1 14983
start = 14900
end = 15100
referenceWindow = ReferenceWindow(1, "lambda_NEB3011", start, end)
bounds = (start, end)
self.kw._prepForReferenceWindow(referenceWindow)
kinetics = self.kw._summarizeReferenceRegion(bounds, True, False)
# Verify that we detect m6A mods at 14982 and 14991
m6AMods = [{'frac': x['frac'], 'fracLow': x['fracLow'], 'fracUp': x['fracUp'], 'tpl': x['tpl'], 'strand': x['strand']}
for x in kinetics if 'frac' in x and x['tpl'] in (14982, 14991)]
print(m6AMods)
for mod in m6AMods:
assert mod["frac"] > 0.5
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