def test_venn_gchart_png_is_saved_correctly():
here = os.path.dirname(__file__)
expected = open(os.path.join(here, "gchart-expected.png")).read()
original = pybedtools.example_bedtool(
"rmsk.hg18.chr21.small.bed").sort().merge()
a = pybedtools.BedTool(original[:300]).saveas()
b = (pybedtools.BedTool(original[:20]).saveas().cat(
pybedtools.BedTool(original[400:500]).saveas()))
c = (pybedtools.BedTool(original[15:30]).saveas().cat(
pybedtools.BedTool(original[450:650]).saveas()))
colors = "00FF00,FF0000,0000FF"
outfn = "gchart_out.png"
labels = "a,b,c"
data = venn_gchart.venn_gchart(
a=a.fn,
b=b.fn,
c=c.fn,
colors=colors.split(","),
labels=labels.split(","),
size="300x300",
)
venn_gchart.gchart(data, outfn)
assert_equal(open(outfn).read(), expected)
os.unlink(outfn)
def test_venn_gchart_png_is_saved_correctly():
from nose.plugins.skip import SkipTest
raise SkipTest('Small differences between fonts in PNG are sometimes produced and need to be accounted for')
here = os.path.dirname(__file__)
expected = open(os.path.join(here, 'gchart-expected.png')).read()
original = pybedtools.example_bedtool('rmsk.hg18.chr21.small.bed').sort().merge()
a = pybedtools.BedTool(original[:300]).saveas()
b = pybedtools.BedTool(original[:20]).saveas().cat(pybedtools.BedTool(original[400:500]).saveas())
c = pybedtools.BedTool(original[15:30]).saveas().cat(pybedtools.BedTool(original[450:650]).saveas())
colors='00FF00,FF0000,0000FF'
outfn = 'gchart_out.png'
labels = 'a,b,c'
data = venn_gchart.venn_gchart(a=a.fn,
b=b.fn,
c=c.fn,
colors=colors.split(','),
labels=labels.split(','),
size='300x300')
venn_gchart.gchart(data, outfn)
assert_equal(open(outfn).read(), expected)
os.unlink(outfn)
def test_venn_gchart_png_is_saved_correctly():
from nose.plugins.skip import SkipTest
raise SkipTest('Small differences between fonts in PDF are sometimes produced and need to be accounted for')
here = os.path.dirname(__file__)
expected = open(os.path.join(here, 'gchart-expected.png')).read()
original = pybedtools.example_bedtool('rmsk.hg18.chr21.small.bed').sort().merge()
a = pybedtools.BedTool(original[:300]).saveas()
b = pybedtools.BedTool(original[:20]).saveas().cat(pybedtools.BedTool(original[400:500]).saveas())
c = pybedtools.BedTool(original[15:30]).saveas().cat(pybedtools.BedTool(original[450:650]).saveas())
colors='00FF00,FF0000,0000FF'
outfn = 'gchart_out.png'
labels = 'a,b,c'
data = venn_gchart.venn_gchart(a=a.fn,
b=b.fn,
c=c.fn,
colors=colors.split(','),
labels=labels.split(','),
size='300x300')
venn_gchart.gchart(data, outfn)
assert_equal(open(outfn).read(), expected)
os.unlink(outfn)
def test_venn_gchart():
here = os.path.dirname(__file__)
expected = open(os.path.join(here, 'gchart-expected.png')).read()
original = pybedtools.example_bedtool(
'rmsk.hg18.chr21.small.bed').sort().merge()
a = pybedtools.BedTool(original[:300]).saveas()
b = pybedtools.BedTool(original[:20]).saveas().cat(
pybedtools.BedTool(original[400:500]).saveas())
c = pybedtools.BedTool(original[15:30]).saveas().cat(
pybedtools.BedTool(original[450:650]).saveas())
colors = '00FF00,FF0000,0000FF'
outfn = 'gchart_out.png'
labels = 'a,b,c'
expected_data = {
'chco': '00FF00,FF0000,0000FF',
'chd':
't:1.0,0.4,0.716666666667,0.0666666666667,0.05,0.183333333333,0.0166666666667',
'chs': '300x300',
'cht': 'v',
'chdl': 'a|b|c'
}
data = venn_gchart.venn_gchart(a=a.fn,
b=b.fn,
c=c.fn,
colors=colors.split(','),
labels=labels.split(','),
size='300x300')
print data
for key in expected_data.keys():
e = expected_data[key]
o = data[key]
print 'key:', key
print 'expected:', e
print 'observed:', o
assert e == o
venn_gchart.gchart(data, outfn)
assert open(outfn).read() == expected
os.unlink(outfn)
def test_venn_gchart():
here = os.path.dirname(__file__)
expected = open(os.path.join(here, 'gchart-expected.png')).read()
pybedtools.bedtool.random.seed(1)
a = pybedtools.example_bedtool('rmsk.hg18.chr21.small.bed')
b = a.random_subset(100).shuffle(genome='hg19', seed=1)
b = b.cat(a.random_subset(100, seed=1))
c = a.random_subset(200).shuffle(genome='hg19', seed=2)
c = c.cat(b.random_subset(100, seed=1))
colors='00FF00,FF0000,0000FF'
outfn = 'out.png'
labels = 'a,b,c'
expected_data = {'chco': '00FF00,FF0000,0000FF',
'chd': 't:1.0,0.2,0.3,0.104,0.048,0.1,0.048',
'chs': '300x300',
'cht': 'v',
'chdl': 'a|b|c'}
data = venn_gchart.venn_gchart(a=a.fn,
b=b.fn,
c=c.fn,
colors=colors.split(','),
labels=labels.split(','),
size='300x300')
print data
for key in expected_data.keys():
e = expected_data[key]
o = data[key]
print 'key:', key
print 'expected:', e
print 'observed:', o
assert e == o
venn_gchart.gchart(data, outfn)
assert open(outfn).read() == expected
os.unlink(outfn)
def test_venn_gchart():
here = os.path.dirname(__file__)
expected = open(os.path.join(here, 'gchart-expected.png')).read()
original = pybedtools.example_bedtool('rmsk.hg18.chr21.small.bed').sort().merge()
a = pybedtools.BedTool(original[:300]).saveas()
b = pybedtools.BedTool(original[:20]).saveas().cat(pybedtools.BedTool(original[400:500]).saveas())
c = pybedtools.BedTool(original[15:30]).saveas().cat(pybedtools.BedTool(original[450:650]).saveas())
colors='00FF00,FF0000,0000FF'
outfn = 'gchart_out.png'
labels = 'a,b,c'
expected_data = {'chco': '00FF00,FF0000,0000FF',
'chd': 't:1.0,0.4,0.716666666667,0.0666666666667,0.05,0.183333333333,0.0166666666667',
'chs': '300x300',
'cht': 'v',
'chdl': 'a|b|c'}
data = venn_gchart.venn_gchart(a=a.fn,
b=b.fn,
c=c.fn,
colors=colors.split(','),
labels=labels.split(','),
size='300x300')
print(data)
for key in list(expected_data.keys()):
e = expected_data[key]
o = data[key]
print('key:', key)
print('expected:', e)
print('observed:', o)
assert e == o
venn_gchart.gchart(data, outfn)
assert open(outfn).read() == expected
os.unlink(outfn)
def test_venn_gchart_png_is_saved_correctly():
here = os.path.dirname(__file__)
expected = open(os.path.join(here, 'gchart-expected.png')).read()
original = pybedtools.example_bedtool('rmsk.hg18.chr21.small.bed').sort().merge()
a = pybedtools.BedTool(original[:300]).saveas()
b = pybedtools.BedTool(original[:20]).saveas().cat(pybedtools.BedTool(original[400:500]).saveas())
c = pybedtools.BedTool(original[15:30]).saveas().cat(pybedtools.BedTool(original[450:650]).saveas())
colors='00FF00,FF0000,0000FF'
outfn = 'gchart_out.png'
labels = 'a,b,c'
data = venn_gchart.venn_gchart(a=a.fn,
b=b.fn,
c=c.fn,
colors=colors.split(','),
labels=labels.split(','),
size='300x300')
venn_gchart.gchart(data, outfn)
assert_equal(open(outfn).read(), expected)
os.unlink(outfn)
