def testRename(self):
read = MockRead('foo/1')
ngsutils.bam.renamepair.read_renamepair(read, '/')
self.assertEqual(read.qname, 'foo') # update occurs in place
assertIn(('ZN', '1'), read.tags) # added tag
def testRename(self):
read = MockRead("foo/1")
ngsutils.bam.renamepair.read_renamepair(read, "/")
self.assertEqual(read.qname, "foo") # update occurs in place
assertIn(("ZN", "1"), read.tags) # added tag
def testNoClipping(self):
read = MockRead('foo', 'AAAATTTTCCCGGG', 'AAAABBBBBBBCCC', tags=[('XA', 1)], tid=1, pos=1, cigar='14M')
code = ngsutils.bam.removeclipping.read_removeclipping(read)
self.assertEqual(code, 0)
self.assertEqual(read.qname, 'foo') # update occurs in place
assertIn(('XA', 1), read.tags) # added tag
self.assertEqual(read.seq, 'AAAATTTTCCCGGG')
self.assertEqual(read.qual, 'AAAABBBBBBBCCC')
def testUnmapped(self):
read = MockRead('foo', 'AAAATTTTCCCGGG', 'AAAABBBBBBBCCC', tags=[('XA', 1)])
code = ngsutils.bam.removeclipping.read_removeclipping(read)
self.assertEqual(code, 1)
self.assertEqual(read.qname, 'foo') # update occurs in place
assertIn(('XA', 1), read.tags) # added tag
self.assertEqual(read.seq, 'AAAATTTTCCCGGG')
self.assertEqual(read.qual, 'AAAABBBBBBBCCC')
def testUnmapped(self):
read = MockRead('foo',
'AAAATTTTCCCGGG',
'AAAABBBBBBBCCC',
tags=[('XA', 1)])
code = ngsutils.bam.removeclipping.read_removeclipping(read)
self.assertEqual(code, 1)
self.assertEqual(read.qname, 'foo') # update occurs in place
assertIn(('XA', 1), read.tags) # added tag
self.assertEqual(read.seq, 'AAAATTTTCCCGGG')
self.assertEqual(read.qual, 'AAAABBBBBBBCCC')
def testNoClipping(self):
read = MockRead('foo',
'AAAATTTTCCCGGG',
'AAAABBBBBBBCCC',
tags=[('XA', 1)],
tid=1,
pos=1,
cigar='14M')
code = ngsutils.bam.removeclipping.read_removeclipping(read)
self.assertEqual(code, 0)
self.assertEqual(read.qname, 'foo') # update occurs in place
assertIn(('XA', 1), read.tags) # added tag
self.assertEqual(read.seq, 'AAAATTTTCCCGGG')
self.assertEqual(read.qual, 'AAAABBBBBBBCCC')
def testRemoveClipping(self):
read = MockRead('foo', 'AAAATTTTCCCGGG', 'AAAABBBBBBBCCC', tags=[('XA', 1)], tid=1, pos=1, cigar='4S7M3S')
code = ngsutils.bam.removeclipping.read_removeclipping(read)
self.assertEqual(code, 2)
self.assertEqual(read.qname, 'foo') # update occurs in place
assertIn(('XA', 1), read.tags) # added tag
assertIn(('ZA', 4), read.tags) # added tag
assertIn(('ZB', 3), read.tags) # added tag
assertIn(('ZC', 0.5), read.tags) # added tag
self.assertEqual(read.seq, 'TTTTCCC')
self.assertEqual(read.qual, 'BBBBBBB')
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)
def testRemoveClipping(self):
read = MockRead('foo',
'AAAATTTTCCCGGG',
'AAAABBBBBBBCCC',
tags=[('XA', 1)],
tid=1,
pos=1,
cigar='4S7M3S')
code = ngsutils.bam.removeclipping.read_removeclipping(read)
self.assertEqual(code, 2)
self.assertEqual(read.qname, 'foo') # update occurs in place
assertIn(('XA', 1), read.tags) # added tag
assertIn(('ZA', 4), read.tags) # added tag
assertIn(('ZB', 3), read.tags) # added tag
assertIn(('ZC', 0.5), read.tags) # added tag
self.assertEqual(read.seq, 'TTTTCCC')
self.assertEqual(read.qual, 'BBBBBBB')