def test_save_multiple_phasePlot2(self):
rseq2 = sequenceParameters.SequenceParameters(
testTools.generate_random_sequence(minLen=20, maxLen=500))
plots.save_multiple_phasePlot2(
[self.rseq, rseq2], 'tmpfiles/mult_PP', ['a', 'b'], 'TEST TITLE')
plots.save_multiple_phasePlot2(
[self.rseq, rseq2], 'tmpfiles/mult_PP_NO_LEGEND', ['a', 'b'], 'TEST TITLE', False)
plots.save_multiple_phasePlot2([self.rseq,
rseq2],
'tmpfiles/mult_PP_NO_LEGEND_xLim1.png',
['a',
'b'],
title='TEST TITLE',
legendOn=False,
xLim=1)
plots.save_multiple_phasePlot2([self.rseq,
rseq2],
'tmpfiles/mult_PP_NO_LEGEND_xlim2.png',
['a',
'b'],
title='TEST TITLE',
legendOn=False,
xLim=2)
plots.save_multiple_phasePlot2([self.rseq,
rseq2],
'tmpfiles/mult_PP_NO_LEGEND_xlim2_ylim2.png',
['a',
'b'],
title='TEST TITLE',
legendOn=False,
xLim=2,
yLim=2)
plots.save_multiple_phasePlot2([self.rseq,
rseq2],
'tmpfiles/mult_PP_NO_LEGEND_xlim2_ylim2_fs_20.png',
['a',
'b'],
title='TEST TITLE',
legendOn=False,
xLim=2,
yLim=2,
fontSize=20)
plots.save_multiple_phasePlot2([self.rseq,
rseq2],
'tmpfiles/mult_PP_NO_LEGEND_xlim2_ylim2_fs_20.pdf',
['a',
'b'],
title='TEST TITLE',
legendOn=False,
xLim=2,
yLim=2,
fontSize=20,
saveFormat='pdf')
def test_save_multiple_phasePlot(self):
rseq2 = sequenceParameters.SequenceParameters(testTools.generate_random_sequence(minLen=20, maxLen=500))
fp1 = self.rseq.get_fraction_positive()
fn1 = self.rseq.get_fraction_negative()
fp2 = rseq2.get_fraction_positive()
fn2 = rseq2.get_fraction_negative()
plots.save_multiple_phasePlot([fp1, fp2], [fn1, fn2], "tmpfiles/mult_PP", ["a", "b"], "TEST TITLE")
plots.save_multiple_phasePlot(
[fp1, fp2], [fn1, fn2], "tmpfiles/mult_PP_NO_LEGEND", ["a", "b"], title="TEST TITLE", legendOn=False
)
plots.save_multiple_phasePlot(
[fp1, fp2],
[fn1, fn2],
"tmpfiles/mult_PP_NO_LEGEND_xLim1",
["a", "b"],
title="TEST TITLE",
legendOn=False,
xLim=1,
)
plots.save_multiple_phasePlot(
[fp1, fp2],
[fn1, fn2],
"tmpfiles/mult_PP_NO_LEGEND_xlim2",
["a", "b"],
title="TEST TITLE",
legendOn=False,
xLim=2,
)
plots.save_multiple_phasePlot(
[fp1, fp2],
[fn1, fn2],
"tmpfiles/mult_PP_NO_LEGEND_xlim2_ylim2",
["a", "b"],
title="TEST TITLE",
legendOn=False,
xLim=2,
yLim=2,
)
plots.save_multiple_phasePlot(
[fp1, fp2],
[fn1, fn2],
"tmpfiles/mult_PP_NO_LEGEND_xlim2_ylim2_fs_20",
["a", "b"],
title="TEST TITLE",
legendOn=False,
xLim=2,
yLim=2,
fontSize=20,
)
def test_save_multiple_uverskyPlot(self):
rseq2 = sequenceParameters.SequenceParameters(testTools.generate_random_sequence(minLen=20, maxLen=500))
hy1 = self.rseq.get_uversky_hydropathy()
mnc1 = self.rseq.get_mean_net_charge()
hy2 = rseq2.get_uversky_hydropathy()
mnc2 = rseq2.get_mean_net_charge()
plots.save_multiple_uverskyPlot([hy1, hy2], [mnc1, mnc2], "tmpfiles/mult_UV", ["a", "b"], "TEST TITLE")
plots.save_multiple_uverskyPlot(
[hy1, hy2], [mnc1, mnc2], "tmpfiles/mult_UV_NO_LEGEND", ["a", "b"], title="TEST TITLE", legendOn=False
)
plots.save_multiple_uverskyPlot(
[hy1, hy2],
[mnc1, mnc2],
"tmpfiles/mult_UV_NO_LEGEND_xLim1",
["a", "b"],
title="TEST TITLE",
legendOn=False,
xLim=1,
)
plots.save_multiple_uverskyPlot(
[hy1, hy2],
[mnc1, mnc2],
"tmpfiles/mult_UV_NO_LEGEND_xlim2",
["a", "b"],
title="TEST TITLE",
legendOn=False,
xLim=2,
)
plots.save_multiple_uverskyPlot(
[hy1, hy2],
[mnc1, mnc2],
"tmpfiles/mult_UV_NO_LEGEND_xlim2_ylim2",
["a", "b"],
title="TEST TITLE",
legendOn=False,
xLim=2,
yLim=2,
)
plots.save_multiple_uverskyPlot(
[hy1, hy2],
[mnc1, mnc2],
"tmpfiles/mult_UV_NO_LEGEND_xlim2_ylim2_fs_20",
["a", "b"],
title="TEST TITLE",
legendOn=False,
xLim=2,
yLim=2,
fontSize=20,
)
def test_get_reduced_alphabet_sequence_predefined_alphabets(self):
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
# checks that a sequence with all 20 amino acids returns a reduced-alphabet sequence
# made up of i-residues which contains exactly i residues!
self.assertEqual(len(set(self.SP_60.get_reduced_alphabet_sequence(i)[0])),i)
random_seqs = testTools.generate_random_sequence(10)
for j in random_seqs:
# build obj
SP = SequenceParameters(j)
# check reduced alphabet sequence length matches
self.assertEqual(len(SP.get_reduced_alphabet_sequence(i)[0]), len(j))
def test_get_reduced_alphabet_sequence_predefined_alphabets(self):
for i in [2, 3, 4, 5, 6, 8, 10, 11, 12, 15, 18, 20]:
# checks that a sequence with all 20 amino acids returns a reduced-alphabet sequence
# made up of i-residues which contains exactly i residues!
self.assertEqual(
len(set(self.SP_60.get_reduced_alphabet_sequence(i)[0])), i)
random_seqs = testTools.generate_random_sequence(10)
for j in random_seqs:
# build obj
SP = SequenceParameters(j)
# check reduced alphabet sequence length matches
self.assertEqual(len(SP.get_reduced_alphabet_sequence(i)[0]),
len(j))
def test_save_multiple_phasePlot2(self):
rseq2 = sequenceParameters.SequenceParameters(testTools.generate_random_sequence(minLen=20, maxLen=500))
plots.save_multiple_phasePlot2([self.rseq, rseq2], "tmpfiles/mult_PP", ["a", "b"], "TEST TITLE")
plots.save_multiple_phasePlot2(
[self.rseq, rseq2], "tmpfiles/mult_PP_NO_LEGEND", ["a", "b"], "TEST TITLE", False
)
plots.save_multiple_phasePlot2(
[self.rseq, rseq2],
"tmpfiles/mult_PP_NO_LEGEND_xLim1",
["a", "b"],
title="TEST TITLE",
legendOn=False,
xLim=1,
)
plots.save_multiple_phasePlot2(
[self.rseq, rseq2],
"tmpfiles/mult_PP_NO_LEGEND_xlim2",
["a", "b"],
title="TEST TITLE",
legendOn=False,
xLim=2,
)
plots.save_multiple_phasePlot2(
[self.rseq, rseq2],
"tmpfiles/mult_PP_NO_LEGEND_xlim2_ylim2",
["a", "b"],
title="TEST TITLE",
legendOn=False,
xLim=2,
yLim=2,
)
plots.save_multiple_phasePlot2(
[self.rseq, rseq2],
"tmpfiles/mult_PP_NO_LEGEND_xlim2_ylim2_fs_20",
["a", "b"],
title="TEST TITLE",
legendOn=False,
xLim=2,
yLim=2,
fontSize=20,
)
def setUp(self):
self.rseq = sequenceParameters.SequenceParameters(testTools.generate_random_sequence(minLen=20, maxLen=500))
def test_save_multiple_phasePlot(self):
rseq2 = sequenceParameters.SequenceParameters(
testTools.generate_random_sequence(minLen=20, maxLen=500))
fp1 = self.rseq.get_fraction_positive()
fn1 = self.rseq.get_fraction_negative()
fp2 = rseq2.get_fraction_positive()
fn2 = rseq2.get_fraction_negative()
plots.save_multiple_phasePlot(
[fp1, fp2], [fn1, fn2], 'tmpfiles/mult_PP', ['a', 'b'], 'TEST TITLE')
plots.save_multiple_phasePlot([fp1,
fp2],
[fn1,
fn2],
'tmpfiles/mult_PP_NO_LEGEND.png',
['a',
'b'],
title='TEST TITLE',
legendOn=False)
plots.save_multiple_phasePlot([fp1,
fp2],
[fn1,
fn2],
'tmpfiles/mult_PP_NO_LEGEND_xLim1.png',
['a',
'b'],
title='TEST TITLE',
legendOn=False,
xLim=1)
plots.save_multiple_phasePlot([fp1,
fp2],
[fn1,
fn2],
'tmpfiles/mult_PP_NO_LEGEND_xlim2.png',
['a',
'b'],
title='TEST TITLE',
legendOn=False,
xLim=2)
plots.save_multiple_phasePlot([fp1,
fp2],
[fn1,
fn2],
'tmpfiles/mult_PP_NO_LEGEND_xlim2_ylim2.png',
['a',
'b'],
title='TEST TITLE',
legendOn=False,
xLim=2,
yLim=2)
plots.save_multiple_phasePlot([fp1,
fp2],
[fn1,
fn2],
'tmpfiles/mult_PP_NO_LEGEND_xlim2_ylim2_fs_20.png',
['a',
'b'],
title='TEST TITLE',
legendOn=False,
xLim=2,
yLim=2,
fontSize=20)
plots.save_multiple_phasePlot([fp1,
fp2],
[fn1,
fn2],
'tmpfiles/mult_PP_NO_LEGEND_xlim2_ylim2_fs_20.pdf',
['a',
'b'],
title='TEST TITLE',
legendOn=False,
xLim=2,
yLim=2,
fontSize=20,
saveFormat='pdf')
def setUp(self):
self.rseq = sequenceParameters.SequenceParameters(
testTools.generate_random_sequence(minLen=20, maxLen=500))
def test_save_multiple_uverskyPlot2(self):
rseq2 = sequenceParameters.SequenceParameters(
testTools.generate_random_sequence(minLen=20, maxLen=500))
hy1 = self.rseq.get_uversky_hydropathy()
mnc1 = self.rseq.get_mean_net_charge()
hy2 = rseq2.get_uversky_hydropathy()
mnc2 = rseq2.get_mean_net_charge()
plots.save_multiple_uverskyPlot2(
[self.rseq, rseq2], 'tmpfiles/mult_UV.png', ['a', 'b'], 'TEST TITLE')
plots.save_multiple_uverskyPlot2([self.rseq,
rseq2],
'tmpfiles/mult_UV2_NO_LEGEND.png',
['a',
'b'],
title='TEST TITLE',
legendOn=False)
plots.save_multiple_uverskyPlot2([self.rseq,
rseq2],
'tmpfiles/mult_UV2_NO_LEGEND_xLim1.png',
['a',
'b'],
title='TEST TITLE',
legendOn=False,
xLim=1)
plots.save_multiple_uverskyPlot2([self.rseq,
rseq2],
'tmpfiles/mult_UV2_NO_LEGEND_xlim2.png',
['a',
'b'],
title='TEST TITLE',
legendOn=False,
xLim=2)
plots.save_multiple_uverskyPlot2([self.rseq,
rseq2],
'tmpfiles/mult_UV2_NO_LEGEND_xlim2_ylim2.png',
['a',
'b'],
title='TEST TITLE',
legendOn=False,
xLim=2,
yLim=2)
plots.save_multiple_uverskyPlot2([self.rseq,
rseq2],
'tmpfiles/mult_UV2_NO_LEGEND_xlim2_ylim2_fs_20.png',
['a',
'b'],
title='TEST TITLE',
legendOn=False,
xLim=2,
yLim=2,
fontSize=20)
plots.save_multiple_uverskyPlot2([self.rseq,
rseq2],
'tmpfiles/mult_UV2_NO_LEGEND_xlim2_ylim2_fs_20.pdf',
['a',
'b'],
title='TEST TITLE',
legendOn=False,
xLim=2,
yLim=2,
fontSize=20,
saveFormat='pdf')