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import sys
import os
basedir = os.path.dirname(__file__)
sys.path.insert(0, basedir + '/../src/')
import shutil
import unittest
import os
import numpy
from transit_test import *
import pytransit.norm_tools as norm_tools
import pytransit.tnseq_tools as tnseq_tools
from pytransit.analysis.gumbel import GumbelMethod
from pytransit.analysis.binomial import BinomialMethod
from pytransit.analysis.griffin import GriffinMethod
from pytransit.analysis.hmm import HMMMethod
from pytransit.analysis.resampling import ResamplingMethod
from pytransit.analysis.rankproduct import RankProductMethod
# RAW STATISTICS:
raw_ctrl_rep1 = (0.41855103545338784, 53.913866362844317, 128.81073464420675, 70.0, 3855.0, 4022244.0, 4.022213863266365, 33.02399374787363)
raw_ctrl_rep2 = (0.51571610481871188, 86.141009315729505, 167.03183885640027, 89.0, 5944.0, 6426550.0, 3.975522680364774, 33.45593924344892)
raw_exp_rep1 = (0.43946116212050129, 52.944722203605657, 120.47645336424084, 56.0, 47546.0, 3949941.0, 54.83729352080048, 4237.703504066973)
raw_exp_rep2 = (0.43891160109912203, 53.013082233094295, 120.78305084745763, 46.0, 217960.0, 3955041.0, 105.78284470780153, 14216.199240166581)
raw_exp_rep3 = (0.35898398230681589, 60.667260907445879, 168.99712493465759, 60.0, 102013.0, 4526081.0, 42.17620960361282, 2327.971405759911)
raw_means = [53.913866362844317, 86.141009315729505, 52.944722203605657, 53.013082233094295, 60.667260907445879]
class TestNormMethods(TransitTestCase):
def test_nonorm(self):
data,position = tnseq_tools.get_data(all_data_list)
norm_data,factors = norm_tools.normalize_data(data, "nonorm")
self.assertTrue((factors == numpy.array([ 1.])).all())
N = len(all_data_list)
for k in range(N):
self.assertEqual(numpy.mean(norm_data[k]), raw_means[k])
def test_TTR(self):
N = len(all_data_list)
data,position = tnseq_tools.get_data(all_data_list)
norm_data,factors = norm_tools.normalize_data(data, "TTR")
self.assertFalse((factors == numpy.ones(N)).all())
for k in range(N):
self.assertNotEqual(numpy.mean(norm_data[k]), raw_means[k])
# """
def test_resampling_nonorm(self):
args = [ctrl_rep1, ctrl_rep2, small_annotation, output, "-s", "1000", "-n", "nonorm"]
G = ResamplingMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
pvals, qvals = significant_pvals_qvals(output)
self.assertLessEqual(len(pvals), 5)
self.assertLessEqual(len(qvals), 1)
#
def test_resampling_TTR(self):
args = [ctrl_rep1, ctrl_rep2, small_annotation, output, "-s", "1000", "-n", "TTR"]
G = ResamplingMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
pvals, qvals = significant_pvals_qvals(output)
self.assertLessEqual(len(pvals), 1)
self.assertLessEqual(len(qvals), 1)
#
def test_resampling_NZMean(self):
args = [ctrl_rep1, ctrl_rep2, small_annotation, output, "-s", "1000", "-n", "nzmean"]
G = ResamplingMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
pvals, qvals = significant_pvals_qvals(output)
self.assertLessEqual(len(pvals), 5)
self.assertLessEqual(len(qvals), 1)
#
def test_resampling_TotReads(self):
args = [ctrl_rep1, ctrl_rep2, small_annotation, output, "-s", "1000", "-n", "totreads"]
G = ResamplingMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
pvals, qvals = significant_pvals_qvals(output)
self.assertLessEqual(len(pvals), 5)
self.assertLessEqual(len(qvals), 1)
#
def test_resampling_Quantile(self):
args = [ctrl_rep1, ctrl_rep2, small_annotation, output, "-s", "1000", "-n", "quantile"]
G = ResamplingMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
hits = count_hits(output)
pvals, qvals = significant_pvals_qvals(output)
self.assertLessEqual(len(pvals), 5)
self.assertLessEqual(len(qvals), 1)
#
def test_resampling_ZINFNB(self):
args = [ctrl_rep1, ctrl_rep2, small_annotation, output, "-s", "1000", "-n", "zinfnb"]
G = ResamplingMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
#
"""
def test_resampling_BGC(self):
args = [ctrl_data_txt, exp_data_txt, annotation, output, "-s", "1000", "-n", "betageom"]
G = ResamplingMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
hits = count_hits(output)
self.assertLessEqual(hits, 20)
"""
# """
#
"""
def test_resampling_aBGC(self):
args = [ctrl_data_txt, exp_data_txt, annotation, output, "-s", "1000", "-n", "aBGC"]
G = ResamplingMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
"""
if __name__ == '__main__':
unittest.main()
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