def test_venn_gchart_data_is_correct(): 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' labels = 'a,b,c' expected_data = {'chco': '00FF00,FF0000,0000FF', 'chd': 't:1.0,0.4,0.7167,0.0667,0.05,0.1833,0.0167', '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') for key in expected_data.keys(): e = expected_data[key] o = data[key] assert e == o
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_data_is_correct(): 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" labels = "a,b,c" expected_data = { "chco": "00FF00,FF0000,0000FF", "chd": "t:1.0,0.4,0.7167,0.0667,0.05,0.1833,0.0167", "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", ) for key in expected_data.keys(): e = expected_data[key] o = data[key] assert e == o
def test_venn_gchart_data_is_correct(): 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' labels = 'a,b,c' expected_data = {'chco': '00FF00,FF0000,0000FF', 'chd': 't:1.0,0.4,0.7167,0.0667,0.05,0.1833,0.0167', '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') for key in expected_data.keys(): e = expected_data[key] o = data[key] assert_equal(e, o, 'Key:{!r}\nExpected:{!r}\nObserved:{!r}\n'.format(key, e, o))
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)