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import matplotlib
matplotlib.use('Agg')
import sys
import os
basedir = os.path.dirname(__file__)
sys.path.insert(0, basedir + '/../src/')
import shutil
import unittest
from transit_test import *
import pytransit
from pytransit import norm_tools
from pytransit import tnseq_tools
# Single condition methods
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.anova import AnovaMethod
from pytransit.analysis.zinb import ZinbMethod
# Comparative methods
from pytransit.analysis.resampling import ResamplingMethod
from pytransit.analysis.rankproduct import RankProductMethod
from pytransit.analysis.utest import UTestMethod
# Genetic Interactions
from pytransit.analysis.gi import GIMethod
hasR = False
try:
import rpy2.robjects
hasR = True
except Exception as e:
hasR = False
class TestMethods(TransitTestCase):
def test_Gumbel(self):
args = [ctrl_data_txt, small_annotation, output, "-s", "1000", "-b", "100"]
G = GumbelMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
def test_Binomial(self):
args = [ctrl_data_txt, small_annotation, output, "-s", "1000", "-b", "100"]
G = BinomialMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
def test_Griffin(self):
args = [ctrl_data_txt, small_annotation, output, "-s", "1000", "-b", "100"]
G = GriffinMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
def test_HMM(self):
args = [mini_wig, small_annotation, output]
G = HMMMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output+".sites.txt"))
genes_path = output+".genes.txt"
self.assertTrue(os.path.exists(genes_path))
def test_resampling(self):
args = [ctrl_data_txt, exp_data_txt, small_annotation, output, "-l"]
G = ResamplingMethod.fromargs(args)
G.Run()
(sig_pvals, sig_qvals) = (significant_pvals_qvals(output, pcol=-2, qcol=-1))
self.assertLessEqual(
abs(len(sig_pvals) - 37),
2,
"sig_pvals expected in range: %s, actual: %d" % ("[35, 39]", len(sig_qvals)))
self.assertLessEqual(
abs(len(sig_qvals) - 35),
2,
"sig_qvals expected in range: %s, actual: %d" % ("[33, 37]", len(sig_qvals))) # maybe acceptable range should be expanded to 38
def test_resampling_combined_wig(self):
# The conditions in the args should be matched case-insensitively.
args = ["-c", combined_wig, samples_metadata, "Glycerol", "cholesterol", small_annotation, output, "-a"]
G = ResamplingMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
(sig_pvals, sig_qvals) = (significant_pvals_qvals(output, pcol=-2, qcol=-1))
print(len(sig_pvals))
print(len(sig_qvals))
self.assertLessEqual(
abs(len(sig_pvals) - 37),
2,
"sig_pvals expected in range: %s, actual: %d" % ("[35, 39]", len(sig_qvals)))
self.assertLessEqual(
abs(len(sig_qvals) - 35),
1,
"sig_qvals expected in range: %s, actual: %d" % ("[34, 36]", len(sig_qvals)))
def test_resampling_adaptive(self):
args = [ctrl_data_txt, exp_data_txt, small_annotation, output, "-a", "--ctrl_lib", "AA", "--exp_lib", "AAA"]
G = ResamplingMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
(sig_pvals, sig_qvals) = (significant_pvals_qvals(output, pcol=-2, qcol=-1))
self.assertLessEqual(
abs(len(sig_pvals) - 37),
2,
"sig_pvals expected in range: %s, actual: %d" % ("[35, 39]", len(sig_qvals)))
self.assertLessEqual(
abs(len(sig_qvals) - 35),
2,
"sig_qvals expected in range: %s, actual: %d" % ("[34, 36]", len(sig_qvals)))
def test_resampling_histogram(self):
args = [ctrl_data_txt, exp_data_txt, small_annotation, output, "-s", "1000", "-h"]
G = ResamplingMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
self.assertTrue(
os.path.isdir(hist_path),
"histpath expected: %s" % (hist_path))
def test_resampling_multistrain(self):
args = [ctrl_data_txt, exp_data_txt, ','.join([small_annotation, small_annotation]), output, "-h"]
G = ResamplingMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
self.assertTrue(
os.path.isdir(hist_path),
"histpath expected: %s" % (hist_path))
def test_anova(self):
args = [combined_wig, samples_metadata, small_annotation, output]
G = AnovaMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
(sig_pvals, sig_qvals) = (significant_pvals_qvals(output, pcol=-3, qcol=-2))
sig_qvals.sort()
self.assertEqual(
len(sig_pvals),
30,
"sig_pvals expected: %d, actual: %d" % (30, len(sig_pvals)))
self.assertEqual(
len(sig_qvals),
24,
"sig_qvals expected: %d, actual: %d" % (24, len(sig_qvals)))
@unittest.skipUnless(hasR, "requires R, rpy2")
def test_zinb(self):
args = [combined_wig, samples_metadata, small_annotation, output]
G = ZinbMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
(sig_pvals, sig_qvals) = (significant_pvals_qvals(output, pcol=-3, qcol=-2))
sig_qvals.sort()
self.assertEqual(
len(sig_pvals),
31,
"sig_pvals expected: %d, actual: %d" % (31, len(sig_pvals)))
self.assertEqual(
len(sig_qvals),
30,
"sig_qvals expected: %d, actual: %d" % (30, len(sig_qvals)))
@unittest.skipUnless(hasR, "requires R, rpy2")
def test_zinb_covariates(self):
args = [combined_wig, samples_metadata_covariates, small_annotation, output, "--covars", "batch", "--condition", "NewConditionCol"]
G = ZinbMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
(sig_pvals, sig_qvals) = (significant_pvals_qvals(output, pcol=-3, qcol=-2))
sig_qvals.sort()
self.assertEqual(
len(sig_pvals),
15,
"sig_pvals expected: %d, actual: %d" % (15, len(sig_pvals)))
self.assertEqual(
len(sig_qvals),
10,
"sig_qvals expected: %d, actual: %d" % (10, len(sig_qvals)))
@unittest.skipUnless(hasR, "requires R, rpy2")
def test_zinb_interactions(self):
args = [combined_wig, samples_metadata_interactions, small_annotation, output, "--covars", "batch", "--interactions", "atm"]
G = ZinbMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
(sig_pvals, sig_qvals) = (significant_pvals_qvals(output, pcol=-3, qcol=-2))
sig_qvals.sort()
self.assertEqual(
len(sig_pvals),
3,
"sig_pvals expected: %d, actual: %d" % (3, len(sig_pvals)))
self.assertEqual(
len(sig_qvals),
0,
"sig_qvals expected: %d, actual: %d" % (0, len(sig_qvals)))
def test_utest(self):
args = [ctrl_data_txt, exp_data_txt, small_annotation, output]
G = UTestMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
def test_GI(self):
args = [ctrl_data_txt, exp_data_txt, ctrl_data_txt, exp_data_txt, small_annotation, output,
"-s", "1000"]
G = GIMethod.fromargs(args)
G.Run()
self.assertTrue(os.path.exists(output))
if __name__ == '__main__':
unittest.main()
#suite = unittest.TestLoader().loadTestsFromTestCase(TestMethods)
#unittest.TextTestRunner(verbosity=2).run(suite)
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