Exemple #1
0
    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)
Exemple #2
0
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)
Exemple #3
0
    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)