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from __future__ import print_function
import IsoSpecPy
from IsoSpecPy.Formulas import *
import math
try:
math.isclose
except AttributeError:
def isclose(a, b, rel_tol=1e-09, abs_tol=0.0):
return abs(a - b) <= max(rel_tol * max(abs(a), abs(b)), abs_tol)
math.isclose = isclose
glu = IsoSpecPy.IsoThreshold(0.0, formula=glucose)
ca = IsoSpecPy.IsoThreshold(0.0, formula=caffeine)
def test_wasserstein_distance():
print("Checking Wasserstein distance...", end=" ")
print(ca.wassersteinDistance(glu), end=" ")
assert math.isclose(ca.wassersteinDistance(glu), 14.03495145836358)
print("OK!")
def test_normalization():
print("Checking normalization... ", end="")
ubiq = IsoSpecPy.IsoTotalProb(0.9999, ubiquitin)
print(ubiq.total_prob(), end=" ")
assert math.isclose(ubiq.total_prob(), 0.9999, rel_tol=0.01)
ubiq = IsoSpecPy.IsoTotalProb(0.9999, ubiquitin)
ubiq.scale(0.5)
assert math.isclose(ubiq.total_prob(), 0.9999 * 0.5, rel_tol=0.01)
ubiq._recalculate_everything()
assert math.isclose(ubiq.total_prob(), 0.9999 * 0.5, rel_tol=0.01)
ubiq = IsoSpecPy.IsoTotalProb(0.9999, ubiquitin)
ubiq.scale(0.5)
ubiq.normalize()
assert math.isclose(ubiq.total_prob(), 1.0)
ubiq._recalculate_everything()
assert math.isclose(ubiq.total_prob(), 1.0)
print("OK!")
def test_addition():
print("Checking addition...", end=" ")
wa = IsoSpecPy.IsoThreshold(0.0, formula=water)
ox = IsoSpecPy.IsoThreshold(0.0, formula=oxygen)
s = wa + ox
assert math.isclose(s.total_prob(), 2.0)
assert len(list(s)) == len(list(wa)) + len(list(ox)) == 15
print("OK!")
def test_sorting():
print("Checking sorting...", end=" ")
ubiq = IsoSpecPy.IsoTotalProb(0.9999, ubiquitin)
ubiq.sort_by_mass()
assert list(ubiq.masses) == sorted(ubiq.masses)
ubiq.sort_by_prob()
assert list(ubiq.probs) == sorted(ubiq.probs)
print("OK!")
def test_binning():
print("Checking binning...", end=" ")
ubiq = IsoSpecPy.IsoTotalProb(0.999999, ubiquitin)
# ubiq.plot()
print(len(ubiq), end=" -> ")
bu = ubiq.binned()
ubiq._recalculate_everything()
print(len(bu), end=" ")
bu._recalculate_everything()
assert math.isclose(ubiq.total_prob(), bu.total_prob())
print("OK!")
def test_convolution():
print("Checking convolution...", end=" ")
o = IsoSpecPy.IsoThreshold(0.0, formula="H1")
sur = IsoSpecPy.IsoThreshold(0.0, formula=sucrose)
wa = IsoSpecPy.IsoThreshold(0.0, formula=water)
# (glu*glu).plot()
# (sur*wa).plot()
WSD = (sur * wa).wassersteinDistance(glu * glu)
print(WSD, end=" ")
assert math.isclose(WSD, 0.0, abs_tol=1e-7)
print("OK!")
def test_negative_formulas():
print("Checking negative formulas... ", end="")
try:
I = Iso(formula="C-10")
print("FAIL: exception not thrown")
raise AssertionError("Exception not thrown for negative formula")
except Exception as e:
print(
"""exception successfully obtained, message: "{}" -> OK!""".format((str(e)))
)
def test_fasta_negative_formulas():
print("Checking FASTA + negative formulas... ", end="")
try:
I = Iso(fasta="C", formula="C-5")
print("FAIL: exception not thrown")
except Exception as e:
print(
"""exception successfully obtained, message: "{}" -> OK!""".format((str(e)))
)
def test_fasta_modification():
print("Checking FASTA + modification... ", end="")
# Selenation of methionine
I = IsoSpecPy.IsoTotalProb(0.999, formula="C5H9N1O1Se1")
I2 = IsoSpecPy.IsoTotalProb(0.999, fasta="M", formula="S-1Se1")
WSD = I.wassersteinDistance(I2)
print(WSD, end="")
assert math.isclose(I.wassersteinDistance(I2), 0.0)
print(" -> OK!")
formulas = "C1 P1 H1 H100 P100 N100 O100 C100H100N100 C100O100".split()
def test_empiric_avg_mass():
print("Checking empiric avg mass... ", end="")
isos = [IsoSpecPy.Iso(formula) for formula in formulas]
dists = [IsoSpecPy.IsoThreshold(0.0, formula) for formula in formulas]
diffs = [
abs(i.getTheoreticalAverageMass() - d.empiric_average_mass())
for i, d in zip(isos, dists)
]
print(max(diffs), end="")
assert max(diffs) < 1e-6
print(" -> OK!")
def test_empiric_variance():
print("Checking empiric variance... ", end="")
isos = [IsoSpecPy.Iso(formula) for formula in formulas]
dists = [IsoSpecPy.IsoThreshold(0.0, formula) for formula in formulas]
diffs = [abs(i.variance() - d.empiric_variance()) for i, d in zip(isos, dists)]
print(max(diffs), end="")
assert max(diffs) < 1e-6
print(" -> OK!")
def test_empiric_stddev():
print("Checking empiric stddev... ", end="")
isos = [IsoSpecPy.Iso(formula) for formula in formulas]
dists = [IsoSpecPy.IsoThreshold(0.0, formula) for formula in formulas]
diffs = [abs(i.stddev() - d.empiric_stddev()) for i, d in zip(isos, dists)]
print(max(diffs), end="")
assert max(diffs) < 1e-6
print(" -> OK!")
def test_get_monoisotopic_mass():
print("Checking monoisotopic mass...", end=" ")
mol = IsoSpecPy.Iso(formula="C100H100N100O100Se100Sn100Pb100U100")
mono_mass = mol.getMonoisotopicPeakMass()
print(mono_mass, end=" ")
assert math.isclose(68885.198515667, mono_mass, rel_tol=1e-9)
print("OK!")
if __name__ == "__main__":
test_wasserstein_distance()
test_normalization()
test_addition()
test_sorting()
test_binning()
test_convolution()
test_negative_formulas()
test_fasta_negative_formulas()
test_fasta_modification()
test_empiric_avg_mass()
test_empiric_variance()
test_empiric_stddev()
test_get_monoisotopic_mass()
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