def testUpdate(self):
'''check if updating fields affects other variable length data
'''
a = self.buildRead()
b = self.buildRead()
# check qname
b.query_name = "read_123"
checkFieldEqual(self, a, b, "query_name")
b.query_name = "read_12345678"
checkFieldEqual(self, a, b, "query_name")
b.query_name = "read_12345"
checkFieldEqual(self, a, b)
# check cigar
b.cigartuples = ((0, 10), )
checkFieldEqual(self, a, b, "cigartuples")
b.cigartuples = ((0, 10), (2, 1), (0, 10))
checkFieldEqual(self, a, b, "cigartuples")
b.cigartuples = ((0, 10), (2, 1), (0, 9), (1, 1), (0, 20))
checkFieldEqual(self, a, b)
# check seq
b.query_sequence = "ACGT"
checkFieldEqual(self,
a, b,
("query_sequence", "query_qualities", "query_length"))
b.query_sequence = "ACGT" * 3
checkFieldEqual(self,
a, b,
("query_sequence", "query_qualities", "query_length"))
b.query_sequence = "ACGT" * 10
checkFieldEqual(self, a, b, ("query_qualities",))
# reset qual
b = self.buildRead()
# check flags:
for x in (
"is_paired", "is_proper_pair",
"is_unmapped", "mate_is_unmapped",
"is_reverse", "mate_is_reverse",
"is_read1", "is_read2",
"is_secondary", "is_qcfail",
"is_duplicate", "is_supplementary"):
setattr(b, x, True)
self.assertEqual(getattr(b, x), True)
checkFieldEqual(self, a, b, ("flag", x,))
setattr(b, x, False)
self.assertEqual(getattr(b, x), False)
checkFieldEqual(self, a, b)
def testUpdate(self):
'''check if updating fields affects other variable length data
'''
a = self.buildRead()
b = self.buildRead()
# check qname
b.query_name = "read_123"
checkFieldEqual(self, a, b, "query_name")
b.query_name = "read_12345678"
checkFieldEqual(self, a, b, "query_name")
b.query_name = "read_12345"
checkFieldEqual(self, a, b)
# check cigar
b.cigartuples = ((0, 10), )
checkFieldEqual(self, a, b, "cigartuples")
b.cigartuples = ((0, 10), (2, 1), (0, 10))
checkFieldEqual(self, a, b, "cigartuples")
b.cigartuples = ((0, 10), (2, 1), (0, 9), (1, 1), (0, 20))
checkFieldEqual(self, a, b)
# check seq
b.query_sequence = "ACGT"
checkFieldEqual(self, a, b,
("query_sequence", "query_qualities", "query_length"))
b.query_sequence = "ACGT" * 3
checkFieldEqual(self, a, b,
("query_sequence", "query_qualities", "query_length"))
b.query_sequence = "ACGT" * 10
checkFieldEqual(self, a, b, ("query_qualities", ))
# reset qual
b = self.buildRead()
# check flags:
for x in ("is_paired", "is_proper_pair", "is_unmapped",
"mate_is_unmapped", "is_reverse", "mate_is_reverse",
"is_read1", "is_read2", "is_secondary", "is_qcfail",
"is_duplicate", "is_supplementary"):
setattr(b, x, True)
self.assertEqual(getattr(b, x), True)
checkFieldEqual(self, a, b, (
"flag",
x,
))
setattr(b, x, False)
self.assertEqual(getattr(b, x), False)
checkFieldEqual(self, a, b)