def pair1():
p = (SimpleMapping(), SimpleMapping())
p[0].set_name("p1:read/1")
p[1].set_name("p1:read/2")
p[0].tid = "chr1"
p[1].tid = "chr1"
p[0].ref_id = 0
p[1].ref_id = 0
p[0].pos = 12345
p[1].pos = p[0].pos + 150
p[0].set_read1(True)
p[1].set_read2(True)
p[0].qual = 50
p[1].qual = 30
return p
def setUp(self):
self.monitor = StandardMonitor(SavingLogger())
self.filter = FilterLink(self.monitor)
self.receiver = self.filter.set_next(type(self).Receiver())
# create two mappings, m1, m2. We put them in self.pair
# m1 has:
# name = first
# tid = tid1
# m2 has:
# name = second
# tid = tid2
self.pair = [ SimpleMapping(), SimpleMapping() ]
self.m1, self.m2 = self.pair
self.m1.set_name("first") ; self.m2.set_name("second")
self.m1.tid = "tid1" ; self.m2.tid = "tid2"
self.m1.qual = 50 ; self.m2.qual = 30
def pair2():
# reversed reads such that r2 is at a lower position than r1
p = (SimpleMapping(), SimpleMapping())
p[0].set_name("p1:read/1")
p[1].set_name("p1:read/2")
p[0].tid = "chr1"
p[1].tid = "chr1"
p[0].ref_id = 0
p[1].ref_id = 0
p[0].pos = 12345 + 150
p[1].pos = p[0].pos - 150
p[0].set_read1(True)
p[1].set_read2(True)
p[0].qual = 50
p[1].qual = 30
return p
def setUp(self):
self.pair = (SimpleMapping(), SimpleMapping())
self.pair[0].set_read1(True)
self.pair[1].set_read2(True)
for m in self.pair:
m.set_paired(True)
m.set_name("CRESSIA_129:1:1:10605:12550#0")
m.tid = "chr21"
m.ref_id = 20
m.qual = 60
m.set_cigar([(100, "M")])
m.mtid = "chr21"
m.m_ref_id = 20
m1, m2 = self.pair
m1.pos = m2.mpos = 25839277
m2.pos = m1.mpos = 25839109
m1.isize = -268
m2.isize = 268
def setUp(self):
self.mapping = SimpleMapping()
self.f = SamFormatter()
class TestSamFormatter(unittest.TestCase):
def setUp(self):
self.mapping = SimpleMapping()
self.f = SamFormatter()
def test_default(self):
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_name(self):
self.mapping.set_name("my name")
self.assertEqual("\t".join( map(str, ["my name", 0, "*", 0, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_flag(self):
self.mapping.flag = 163
self.assertEqual("\t".join( map(str, ['', 163, "*", 0, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_reference(self):
self.mapping.tid = "chr21"
self.assertEqual("\t".join( map(str, ['', 0, "chr21", 0, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_mate_reference(self):
self.mapping.mtid = "chr21"
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "chr21", 0, 0, "", "" ])), self.__do_format())
self.mapping.mtid = "="
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "=", 0, 0, "", "" ])), self.__do_format())
def test_pos(self):
self.mapping.pos = 1234
self.assertEqual("\t".join( map(str, ['', 0, "*", 1234, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_mate_pos(self):
self.mapping.mpos = 1234
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 1234, 0, "", "" ])), self.__do_format())
def test_mapq(self):
self.mapping.qual = 55
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 55, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_cigar(self):
self.mapping.set_cigar([ (100, 'M') ])
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "100M", "*", 0, 0, "", "" ])), self.__do_format())
self.mapping.set_cigar([ (80, 'M'), (20, 'S') ])
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "80M20S", "*", 0, 0, "", "" ])), self.__do_format())
def test_isize(self):
self.mapping.isize = 273
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 273, "", "" ])), self.__do_format())
self.mapping.isize = -273
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, -273, "", "" ])), self.__do_format())
def test_seq(self):
self.mapping.set_seq_5("AGCTNN")
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 0, "AGCTNN", "" ])), self.__do_format())
def test_qual(self):
bq = array.array('B', [22, 33, 45])
self.mapping.set_base_qualities(bq)
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 0, "", "7BN" ])), self.__do_format())
def test_tags(self):
self.mapping.add_tag( ("XC", 'i', 18) )
self.mapping.add_tag( ("HI", 'Z', "llo") )
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 0, "", "", "XC:i:18", "HI:Z:llo" ])), self.__do_format())
def __do_format(self):
return self.f.format(self.mapping)
def setUp(self): self.mapping = SimpleMapping() self.f = SamFormatter()
class TestSamFormatter(unittest.TestCase):
def setUp(self):
self.mapping = SimpleMapping()
self.f = SamFormatter()
def test_default(self):
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_name(self):
self.mapping.set_name("my name")
self.assertEqual("\t".join( map(str, ["my name", 0, "*", 0, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_flag(self):
self.mapping.flag = 163
self.assertEqual("\t".join( map(str, ['', 163, "*", 0, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_reference(self):
self.mapping.tid = "chr21"
self.assertEqual("\t".join( map(str, ['', 0, "chr21", 0, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_mate_reference(self):
self.mapping.mtid = "chr21"
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "chr21", 0, 0, "", "" ])), self.__do_format())
self.mapping.mtid = "="
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "=", 0, 0, "", "" ])), self.__do_format())
def test_pos(self):
self.mapping.pos = 1234
self.assertEqual("\t".join( map(str, ['', 0, "*", 1234, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_mate_pos(self):
self.mapping.mpos = 1234
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 1234, 0, "", "" ])), self.__do_format())
def test_mapq(self):
self.mapping.qual = 55
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 55, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_cigar(self):
self.mapping.set_cigar([ (100, 'M') ])
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "100M", "*", 0, 0, "", "" ])), self.__do_format())
self.mapping.set_cigar([ (80, 'M'), (20, 'S') ])
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "80M20S", "*", 0, 0, "", "" ])), self.__do_format())
def test_isize(self):
self.mapping.isize = 273
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 273, "", "" ])), self.__do_format())
self.mapping.isize = -273
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, -273, "", "" ])), self.__do_format())
def test_seq(self):
self.mapping.set_seq_5("AGCTNN")
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 0, "AGCTNN", "" ])), self.__do_format())
def test_qual(self):
bq = array.array('B', [22, 33, 45])
self.mapping.set_base_qualities(bq)
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 0, "", "7BN" ])), self.__do_format())
def test_tags(self):
self.mapping.add_tag( ("XC", 'i', 18) )
self.mapping.add_tag( ("HI", 'Z', "llo") )
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 0, "", "", "XC:i:18", "HI:Z:llo" ])), self.__do_format())
def __do_format(self):
return self.f.format(self.mapping)
def setUp(self):
self.mapping = SimpleMapping()
class TestProtobufSeqMapping(TestProtobufSerialization):
def setUp(self):
self.mapping = SimpleMapping()
def test_simple(self):
self.__try_and_compare_maps(self.mapping)
def test_seq(self):
small_seq = "AGCTNN"
self.mapping.set_seq_5(small_seq)
self.mapping.set_base_qualities(array.array("B", [ i + 25 for i in range(len(small_seq)) ]))
self.__try_and_compare_maps(self.mapping)
def test_cigar(self):
self.mapping.set_cigar([ (100, "M") ])
self.__try_and_compare_maps(self.mapping)
self.mapping.set_cigar([ (80, "M"), (20, "S") ])
self.__try_and_compare_maps(self.mapping)
def test_flag(self):
self.mapping.flag = 0x04
self.__try_and_compare_maps(self.mapping)
def test_name(self):
self.mapping.set_name("CRESSIA_129:1:1:10029:122606#0/2")
self.__try_and_compare_maps(self.mapping)
def test_qual(self):
self.mapping.qual = 60
self.__try_and_compare_maps(self.mapping)
def test_tags(self):
self.mapping.add_tag( ("XC", 'i', 22) )
self.mapping.add_tag( ("R2", 'Z', "bla") )
self.__try_and_compare_maps(self.mapping)
def test_pos(self):
self.mapping.pos = 280781134
self.__try_and_compare_maps(self.mapping)
def test_tid(self):
self.mapping.tid = "chr19"
self.__try_and_compare_maps(self.mapping)
def test_ref_id(self):
self.mapping.ref_id = 12
self.__try_and_compare_maps(self.mapping)
self.mapping.ref_id = 0
self.__try_and_compare_maps(self.mapping)
def test_no_ref_id(self):
self.mapping.ref_id = None
self.__try_and_compare_maps(self.mapping)
def __try_and_compare_maps(self, mapping):
self.protected_compare_seq_maps(mapping, self.__pipe_map_through(mapping))
def __pipe_map_through(self, mapping):
message = io.serialize_seq(mapping)
return io.unserialize_seq(message)
def setUp(self):
self.mapping = SimpleMapping()
class TestProtobufSeqMapping(TestProtobufSerialization):
def setUp(self):
self.mapping = SimpleMapping()
def test_simple(self):
self.__try_and_compare_maps(self.mapping)
def test_seq(self):
small_seq = "AGCTNN"
self.mapping.set_seq_5(small_seq)
self.mapping.set_base_qualities(
array.array("B", [i + 25 for i in range(len(small_seq))]))
self.__try_and_compare_maps(self.mapping)
def test_cigar(self):
self.mapping.set_cigar([(100, "M")])
self.__try_and_compare_maps(self.mapping)
self.mapping.set_cigar([(80, "M"), (20, "S")])
self.__try_and_compare_maps(self.mapping)
def test_flag(self):
self.mapping.flag = 0x04
self.__try_and_compare_maps(self.mapping)
def test_name(self):
self.mapping.set_name("CRESSIA_129:1:1:10029:122606#0/2")
self.__try_and_compare_maps(self.mapping)
def test_qual(self):
self.mapping.qual = 60
self.__try_and_compare_maps(self.mapping)
def test_tags(self):
self.mapping.add_tag(("XC", 'i', 22))
self.mapping.add_tag(("R2", 'Z', "bla"))
self.__try_and_compare_maps(self.mapping)
def test_pos(self):
self.mapping.pos = 280781134
self.__try_and_compare_maps(self.mapping)
def test_tid(self):
self.mapping.tid = "chr19"
self.__try_and_compare_maps(self.mapping)
def test_ref_id(self):
self.mapping.ref_id = 12
self.__try_and_compare_maps(self.mapping)
self.mapping.ref_id = 0
self.__try_and_compare_maps(self.mapping)
def test_no_ref_id(self):
self.mapping.ref_id = None
self.__try_and_compare_maps(self.mapping)
def __try_and_compare_maps(self, mapping):
self.protected_compare_seq_maps(mapping,
self.__pipe_map_through(mapping))
def __pipe_map_through(self, mapping):
message = io.serialize_seq(mapping)
return io.unserialize_seq(message)
