def testNoRename(self): read = MockRead('foo1') ngsutils.bam.renamepair.read_renamepair(read, '/') self.assertEqual(read.qname, 'foo1') assertNotIn(('ZN', '1'), read.tags)
def testNoRename(self): read = MockRead("foo1") ngsutils.bam.renamepair.read_renamepair(read, "/") self.assertEqual(read.qname, "foo1") assertNotIn(("ZN", "1"), read.tags)
def testCufflinksXS(self): read1 = MockRead('foo', tid=1, pos=1, is_reverse=True, tags=[('ZZ', 1)]) read2 = MockRead('bar', tid=1, pos=1, tags=[('ZZ', 1)]) read3 = MockRead('baz', tags=[('ZZ', 1)]) chain = _TestChain([ read1, read2, read3, ]) chain = ngsutils.bam.tag.CufflinksXS(chain) for r in chain.filter(): assertIn(('ZZ', 1), r.tags) if r.qname == 'foo': assertIn(('XS', '-'), r.tags) elif r.qname == 'bar': assertIn(('XS', '+'), r.tags) elif r.qname == 'baz': assertNotIn(('XS', '+'), r.tags) assertNotIn(('XS', '-'), r.tags)