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from unittest import TestCase, main
from numpy import array
from numpy.testing import assert_allclose, assert_array_equal
from cogent3.core.moltype import get_moltype
from cogent3.parse import cisbp, jaspar
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Gavin Huttley"]
__license__ = "BSD-3"
__version__ = "2023.2.12a1"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Alpha"
class TestPwmParsers(TestCase):
def test_jaspar(self):
"""correctly load jaspar formatted counts matrix"""
path = "data/sample.jaspar"
mid, pwm = jaspar.read(path)
assert mid == ["PSSMid", "HGNCsymbol"], "ID line wrong"
# note state indices are ordered by moltype
list(get_moltype("dna"))
expect = [
[35, 374, 30, 121, 6, 121, 33],
[0, 10, 0, 0, 3, 2, 44],
[352, 3, 354, 268, 360, 222, 155],
[2, 2, 5, 0, 10, 44, 157],
]
assert_array_equal(pwm.array, array(expect).T)
self.assertEqual(pwm[0, "A"], 352)
self.assertEqual(pwm[3, "T"], 121)
def test_cisbp(self):
"""correctly read a wights matrix"""
path = "data/M0926_1.02.txt"
pfm = cisbp.read(path)
expect = [
[0.37, 0.55, 0.17, 0.06, 0.64, 0.28, 0.18, 0.26, 0.35],
[0.24, 0.19, 0.07, 0.09, 0.15, 0.28, 0.08, 0.29, 0.28],
[0.2, 0.17, 0.53, 0.78, 0.11, 0.16, 0.26, 0.18, 0.19],
[0.18, 0.09, 0.24, 0.06, 0.1, 0.28, 0.48, 0.27, 0.18],
]
assert_allclose(pfm.array, array(expect).T, atol=1e-2)
assert_allclose(pfm[0, "A"], 0.199862209150251)
self.assertEqual(pfm[6, "C"], 0.0787969447816471)
if __name__ == "__main__":
main()
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