Python Bedpe.info1 Examples

Example #1

File: bedpetovcfconverter_tests.py Project: MMesbahU/svtools

 def test_adjust_by_tag(self):
     entry1 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND;AF=0.2', 'SVTYPE=BND;AF=0.2' ]
     b1 = Bedpe(entry1)
     self.assertEqual(self.converter.adjust_by_tag(b1, 'CIPOS', '+', 200), 200)
     self.assertEqual(self.converter.adjust_by_tag(b1, 'CIPOS', '-', 200), 201)
     b1.info1 = 'SVTYPE=BND;AF=0.2;CIPOS=-2,3'
     self.assertEqual(self.converter.adjust_by_tag(b1, 'CIPOS', '-', 200), 203)
     self.assertEqual(self.converter.adjust_by_tag(b1, 'CIPOS', '+', 200), 202)

Example #2

File: bedpetovcfconverter_tests.py Project: jeldred/svtools

    def test_adjust_by_ciend(self):
        entry1 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', 'SVTYPE=BND;AF=0.2', 'SVTYPE=BND;AF=0.2' ]
        b1 = Bedpe(entry1)
        self.assertEqual(self.converter.adjust_by_ciend(b1), 301)
        b1.o2 = '+'
        self.assertEqual(self.converter.adjust_by_ciend(b1), 300)

        b1.info1 = 'SVTYPE=BND;AF=0.2;CIEND=-2,3'
        self.assertEqual(self.converter.adjust_by_ciend(b1), 302)
        b1.o2 = '-'
        self.assertEqual(self.converter.adjust_by_ciend(b1), 303)

Example #3

File: bedpetovcfconverter_tests.py Project: zyworship/svtools

 def test_adjust_by_tag(self):
     entry1 = [
         '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
         'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND;AF=0.2',
         'SVTYPE=BND;AF=0.2'
     ]
     b1 = Bedpe(entry1)
     self.assertEqual(self.converter.adjust_by_tag(b1, 'CIPOS', '+', 200),
                      200)
     self.assertEqual(self.converter.adjust_by_tag(b1, 'CIPOS', '-', 200),
                      201)
     b1.info1 = 'SVTYPE=BND;AF=0.2;CIPOS=-2,3'
     self.assertEqual(self.converter.adjust_by_tag(b1, 'CIPOS', '-', 200),
                      203)
     self.assertEqual(self.converter.adjust_by_tag(b1, 'CIPOS', '+', 200),
                      202)