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from unittest import TestCase, main
from cogent3.draw.letter import get_character
from cogent3.draw.logo import _char_hts_as_lists, get_logo
from cogent3.util.dict_array import DictArrayTemplate
__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 LogoTests(TestCase):
"""testing utility functions"""
def test_get_logo(self):
"""returns Drawable"""
data = [
[0.1, 0.3, 0.5, 0.1],
[0.25, 0.25, 0.25, 0.25],
[0.05, 0.8, 0.05, 0.1],
[0.7, 0.1, 0.1, 0.1],
[0.6, 0.15, 0.05, 0.2],
]
data = DictArrayTemplate(5, "ACGT").wrap(data)
get_logo(data)
def test_get_logo_missing(self):
"""copes with positions with no values"""
data = [
[0.1, 0.3, 0.5, 0.1],
[0.05, 0.8, 0.05, 0.1],
[0, 0, 0, 0],
[0.7, 0.1, 0.1, 0.1],
[0.6, 0.15, 0.05, 0.2],
]
data = DictArrayTemplate(5, "ACGT").wrap(data)
get_logo(data)
def test_get_logo_alt_input_type(self):
"""copes with positions with no values"""
data = [
{"A": 0.1, "C": 0.3, "G": 0.5, "T": 0.1},
{"A": 0.05, "C": 0.8, "G": 0.05, "T": 0.1},
{"A": 0.0, "C": 0.0, "G": 0.0, "T": 0.0},
{"A": 0.7, "C": 0.1, "G": 0.1, "T": 0.1},
{"A": 0.6, "C": 0.15, "G": 0.05, "T": 0.2},
]
get_logo(data)
data[-2] = {}
get_logo(data)
def test_letter_methods(self):
"""exercising some Letter methods"""
# shift
l = get_character("G")
self.assertEqual(l.x, 0)
self.assertEqual(l.y, 0)
l.shift(2, 2)
self.assertEqual(l.x, 2)
self.assertEqual(l.y, 2)
# scale adjusts the scale attributes
orig_width = l.scale_x
orig_height = l.scale_y
l.scale(x=0.5, y=2)
self.assertEqual(l.scale_x, orig_width / 2)
self.assertEqual(l.scale_y, orig_height * 2)
# invert changes the degree attr
l.rotate(180)
self.assertEqual(l.degrees, 180)
def test_input_conversion(self):
"""correctly convert a series of dicts or a DictArray to lists"""
data = [dict(A=0.1, C=0.2), dict(A=0.1, C=0.2)]
base = [("A", 0.1), ("C", 0.2)]
expect = [base, base]
got = _char_hts_as_lists(data)
self.assertEqual(got, expect)
#
data = [dict(A=0.1, C=0.2), {}]
base = [("A", 0.1), ("C", 0.2)]
expect = [base, None]
got = _char_hts_as_lists(data)
self.assertEqual(got, expect)
data = [dict(A=0.1, C=0.2), None]
base = [("A", 0.1), ("C", 0.2)]
expect = [base, None]
got = _char_hts_as_lists(data)
self.assertEqual(got, expect)
if __name__ == "__main__":
main()
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