def test_dict2xml_and_xml2dict(self):
d = {}
generated_xml = util.dict2xml(d, name='foo', pretty=False)
self.assertEqual(generated_xml, '<?xml version="1.0" ?><foo/>')
self.assertEqual(d, util.xml2dict(generated_xml))
d = {
'a': 1,
'b': 2,
'c': 3,
}
generated_xml = util.dict2xml(d, name='foobar', pretty=False)
desired_output = '<?xml version="1.0" ?><foobar><a>__int1</a><b>__int2</b><c>__int3</c></foobar>'
generated_d = util.xml2dict(generated_xml)
self.assertEqual(generated_xml, desired_output)
self.assertEqual(len(generated_d), 3)
self.assertEqual(generated_d, d)
d = {'a': {'aa': 1}}
desired_output = '<?xml version="1.0" ?><foo><a><aa>__int1</aa></a></foo>'
generated_xml = util.dict2xml(d, name='foo', pretty=False)
generated_d = util.xml2dict(generated_xml)
self.assertEqual(generated_xml, desired_output)
self.assertEqual(generated_d, d)
d = {
'a': {
'11': 1,
12: 1,
}
}
desired_output = '<?xml version="1.0" ?><foo><a><__int12>__int1</__int12><__num11>__int1</__num11></a></foo>'
generated_xml = util.dict2xml(d, name='foo', pretty=False)
generated_d = util.xml2dict(generated_xml)
self.assertEqual(generated_xml, desired_output)
self.assertEqual(generated_d, d)
d = {
'a': {
'aa': 1,
'ab': 1,
},
'b': {
'ba': 2,
'bb': 2,
},
}
desired_output = '<?xml version="1.0" ?><foo><a><aa>__int1</aa><ab>__int1</ab></a><b><ba>__int2</ba><bb>__int2</bb></b></foo>'
generated_xml = util.dict2xml(d, name='foo', pretty=False)
generated_d = util.xml2dict(generated_xml)
self.assertEqual(generated_xml, desired_output)
self.assertEqual(generated_d, d)
def main():
# Set up parameter options
ap = argparse.ArgumentParser(description=description)
ap.add_argument('bedfile',
help='Input bed format file',
nargs='?',
type=argparse.FileType('r'),
default=sys.stdin)
ap.add_argument('-o', '--out-format',
help='Output format',
choices=['xml','tsv', 'pkl'],
default='pkl')
params = ap.parse_args()
g2l = defaultdict(int)
with params.bedfile as f:
for line in f:
la = line.strip().split()
g2l[la[3]] += int(la[2]) - int(la[1])
# Output results
if params.out_format == 'tsv':
for g,l in g2l.iteritems():
sys.stdout.write('%s\t%s\n' % (g,l))
# Output in xml format
elif params.out_format == 'xml':
sys.stdout.write(util.dict2xml(g2l))
# Output in pickle format
else:
pickle.dump(g2l, sys.stdout, pickle.HIGHEST_PROTOCOL)
def test_dict2xml_and_xml2dict(self):
d = {}
generated_xml = util.dict2xml(d, name='foo', pretty=False)
self.assertEqual(generated_xml, '<?xml version="1.0" ?><foo/>')
self.assertEqual(d, util.xml2dict(generated_xml))
d = {'a': 1,
'b': 2,
'c': 3,}
generated_xml = util.dict2xml(d, name='foobar', pretty=False)
desired_output = '<?xml version="1.0" ?><foobar><a>__int1</a><b>__int2</b><c>__int3</c></foobar>'
generated_d = util.xml2dict(generated_xml)
self.assertEqual(generated_xml, desired_output)
self.assertEqual(len(generated_d), 3)
self.assertEqual(generated_d, d)
d = {'a': {'aa': 1}}
desired_output = '<?xml version="1.0" ?><foo><a><aa>__int1</aa></a></foo>'
generated_xml = util.dict2xml(d, name='foo', pretty=False)
generated_d = util.xml2dict(generated_xml)
self.assertEqual(generated_xml, desired_output)
self.assertEqual(generated_d, d)
d = {'a': {'11': 1,
12: 1,}}
desired_output = '<?xml version="1.0" ?><foo><a><__int12>__int1</__int12><__num11>__int1</__num11></a></foo>'
generated_xml = util.dict2xml(d, name='foo', pretty=False)
generated_d = util.xml2dict(generated_xml)
self.assertEqual(generated_xml, desired_output)
self.assertEqual(generated_d, d)
d = {'a': {'aa': 1,
'ab': 1,},
'b': {'ba': 2,
'bb': 2,},}
desired_output = '<?xml version="1.0" ?><foo><a><aa>__int1</aa><ab>__int1</ab></a><b><ba>__int2</ba><bb>__int2</bb></b></foo>'
generated_xml = util.dict2xml(d, name='foo', pretty=False)
generated_d = util.xml2dict(generated_xml)
self.assertEqual(generated_xml, desired_output)
self.assertEqual(generated_d, d)